TIBCO Spotfire S+® 8.2Function Guide

November 2010

TIBCO Software Inc.

IMPORTANT INFORMATION

SOME TIBCO SOFTWARE EMBEDS OR BUNDLES OTHER TIBCO SOFTWARE. USE OF SUCH EMBEDDED OR BUNDLED TIBCO SOFTWARE IS SOLELY TO ENABLE THE FUNCTIONALITY (OR PROVIDE LIMITED ADD-ON FUNCTIONALITY) OF THE LICENSED TIBCO SOFTWARE. THE EMBEDDED OR BUNDLED SOFTWARE IS NOT LICENSED TO BE USED OR ACCESSED BY ANY OTHER TIBCO SOFTWARE OR FOR ANY OTHER PURPOSE.

USE OF TIBCO SOFTWARE AND THIS DOCUMENT IS SUBJECT TO THE TERMS AND CONDITIONS OF A LICENSE AGREEMENT FOUND IN EITHER A SEPARATELY EXECUTED SOFTWARE LICENSE AGREEMENT, OR, IF THERE IS NO SUCH SEPARATE AGREEMENT, THE CLICKWRAP END USER LICENSE AGREEMENT WHICH IS DISPLAYED DURING DOWNLOAD OR INSTALLATION OF THE SOFTWARE (AND WHICH IS DUPLICATED IN TIBCO SPOTFIRE S+® LICENSES). USE OF THIS DOCUMENT IS SUBJECT TO THOSE TERMS AND CONDITIONS, AND YOUR USE HEREOF SHALL CONSTITUTE ACCEPTANCE OF AND AN AGREEMENT TO BE BOUND BY THE SAME.

This document contains confidential information that is subject to U.S. and international copyright laws and treaties. No part of this document may be reproduced in any form without the written authorization of TIBCO Software Inc.

TIBCO Software Inc., TIBCO, Spotfire, TIBCO Spotfire S+, Insightful, the Insightful logo, the tagline "the Knowledge to Act," Insightful Miner, S+, S-PLUS, TIBCO Spotfire Axum, S+ArrayAnalyzer, S+EnvironmentalStats, S+FinMetrics, S+NuOpt, S+SeqTrial, S+SpatialStats, S+Wavelets, S-PLUS Graphlets, Graphlet, Spotfire S+ FlexBayes, Spotfire S+ Resample, TIBCO Spotfire Miner, TIBCO Spotfire S+ Server, TIBCO Spotfire Statistics Services, and TIBCO Spotfire Clinical Graphics are either registered trademarks or trademarks of TIBCO Software Inc. and/or subsidiaries of TIBCO Software Inc. in the United States and/or other countries. All other product and company names and marks mentioned in this document are the property of their respective owners and are mentioned for identification purposes only. This

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software may be available on multiple operating systems. However, not all operating system platforms for a specific software version are released at the same time. Please see the readme.txt file for the availability of this software version on a specific operating system platform.

THIS DOCUMENT IS PROVIDED “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THIS DOCUMENT COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS. CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN; THESE CHANGES WILL BE INCORPORATED IN NEW EDITIONS OF THIS DOCUMENT. TIBCO SOFTWARE INC. MAY MAKE IMPROVEMENTS AND/OR CHANGES IN THE PRODUCT(S) AND/OR THE PROGRAM(S) DESCRIBED IN THIS DOCUMENT AT ANY TIME.

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Reference The correct bibliographic reference for this document is as follows:

TIBCO Spotfire S+® 8.2 Function Guide, TIBCO Software Inc.

Technical Support

For technical support, please visit http://spotfire.tibco.com/support and register for a support account.

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TIBCO SPOTFIRE S+ BOOKS

The TIBCO Spotfire S+® documentation includes books to address your focus and knowledge level. Review the following table to help you choose the Spotfire S+ book that meets your needs. These books are available in PDF format in the following locations:

• In your Spotfire S+ installation directory (SHOME\help on Windows, SHOME/doc on UNIX/Linux).

• In the Spotfire S+ Workbench, from the Help � Spotfire S+ Manuals menu item.

• In Microsoft® Windows®, in the Spotfire S+ GUI, from the Help � Online Manuals menu item.

Note about Naming

Throughout the documentation, we have attempted to distinguish between the language (S-PLUS) and the product (Spotfire S+).

• “S-PLUS” refers to the engine, the language, and its constituents (that is objects, functions, expressions, and so forth).

• “Spotfire S+” refers to all and any parts of the product beyond the language, including the product user interfaces, libraries, and documentation, as well as general product and language behavior.

Spotfire S+ documentation.

Information you need if you... See the...

Must install or configure your current installation of Spotfire S+; review system requirements.

Installtion and Administration Guide

Want to review the third-party products included in Spotfire S+, along with their legal notices and licenses.

Licenses

iv

Are new to the S language and the Spotfire S+ GUI, and you want an introduction to importing data, producing simple graphs, applying statistical

models, and viewing data in Microsoft Excel®.

Getting Started Guide

Are a new Spotfire S+ user and need how to use Spotfire S+, primarily through the GUI.

User’s Guide

Are familiar with the S language and Spotfire S+, and you want to use the Spotfire S+ plug-in, or customization, of the Eclipse Integrated Development Environment (IDE).

Spotfire S+ Workbench User’s Guide

Have used the S language and Spotfire S+, and you want to know how to write, debug, and program functions from the Commands window.

Programmer’s Guide

Are familiar with the S language and Spotfire S+, and you want to extend its functionality in your own application or within Spotfire S+.

Application Developer’s Guide

Are familiar with the S language and Spotfire S+, and you are looking for information about creating or editing graphics, either from a Commands window or the Windows GUI, or using Spotfire S+ supported graphics devices.

Guide to Graphics

Are familiar with the S language and Spotfire S+, and you want to use the Big Data library to import and manipulate very large data sets.

Big Data User’s Guide

Want to download or create Spotfire S+ packages for submission to the Comprehensive S-PLUS Archive Network (CSAN) site, and need to know the steps.

Guide to Packages

Spotfire S+ documentation. (Continued)

Information you need if you... See the...

v

Are looking for categorized information about individual S-PLUS functions.

Function Guide

If you are familiar with the S language and Spotfire S+, and you need a reference for the range of statistical modelling and analysis techniques in Spotfire S+. Volume 1 includes information on specifying models in Spotfire S+, on probability, on estimation and inference, on regression and smoothing, and on analysis of variance.

Guide to Statistics, Vol. 1

If you are familiar with the S language and Spotfire S+, and you need a reference for the range of statistical modelling and analysis techniques in Spotfire S+. Volume 2 includes information on multivariate techniques, time series analysis, survival analysis, resampling techniques, and mathematical computing in Spotfire S+.

Guide to Statistics, Vol. 2

Spotfire S+ documentation. (Continued)

Information you need if you... See the...

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Add to Existing Plot 1ANOVA Models 2Big Data Library 4Bootstrap Methods 7Categorical Data 8Character Data Operations 9Clustering 10Complex Numbers 12Computations Related to Plotting 13curl Library 15Data Attributes 15Data Directories 16Data Manipulation 17Data Sets 24Data Types 30Dates Objects 36Debugging Tools 38Deprecated Functions 39Documentation 39Dynamic Graphics 40Error Handling 40Genetics Related Functions 41Graphical Devices 41Hexagonal Binning 43High-Level Plots 43Input/Output-Files 46Interacting with Plots 49Interfaces to Other Languages 49Jackknife Methods 50Library of Correlated Data Methods 51Library of Missing Data Methods 52

CONTENTS

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Contents

Library of Robust Methods 58Linear Algebra 61Lists 64Loess Objects 65Logical Operators 65Looping and Iteration 67Mathematical Operations 69Matrices and Arrays 73Methods and Generic Functions 77Miscellaneous 80Missing Values 80Mixed Effects Models 80Multivariate Techniques 89nlme Library (version 3) 92Non-linear Regression 101Nonparametric Statistics 102Optimization 102Ordinary Differential Equations 103Package System 103Package Utils Library (adapted from R) 103Printing 103Probability Distributions and Random Numbers 105Programming 109Quality Control 114Regression 115Regression and Classification Trees 118Resampling (Bootstrap, Jackknife, and Permutations) 119Robust/Resistant Techniques 121Spotfire S+ Session Environment 123Smoothing Operations 124Statistical Inference 125Statistical Models 126Survival Analysis 137Time Series 140Trellis Displays 143Utilities 147

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Add to Existing Plot

CLASS OF FUNCTIONSThis guide contains the complete list of function available in S-PLUS, and is organized by class.

Add to Existing Plot abline Plot Line in Intercept-Slope Formabline.default Plot Line in Intercept-Slope Formarrows Plot Disconnected Line Segments or Arrowsaxes Plot Titling Information and/or Axis Labelsaxis Add an Axis to the Current Plotaxis.line.render Plotting - Internal Functionsaxis.render Low-level Axis Plotting Functionbox Add a Box Around a Plotboxes Boxplots at Specified Locationsbreaks.render Plotting - Internal Functionscontour Contour Plotcontour.old Contour Plotdouble.buffer Control double buffering of graphics window for dynamic

graphicsgrid.render Plotting: Low-Level Functionshex.legend Add a Legend Hexagonal Lattice Plothexagons Add Hexagonal Cells to Plot of "hexbin" Objecthloc.render Plotting: Low-Level Functionsidentify Identify Points on Plot - Generic Functionidentify.default Identify Points on Plot - Generic Functionidentify.hexbin Identify Points On a Hexagonal Binned Plotidentify.xyplot Identify Points on Trellis Xyplotimage Plot a Grayscale or Color Imageimage.legend Add a Legend to an Image Plotkey Put a Key or Legend on a Plotlabclust Label a Cluster Plotlabels Labels for Printing or Plotting - Generic functionlabels.default Labels for Printing or Plotting - Generic functionlabels.render Plotting - Internal Functionslegend Put a Legend on a Plotlines Add Lines or Points to Current Plotlines.render Plotting: Low-Level Functionsmatlines Plot Columns of Matrices

1

ANOVA Models

matplot Plot Columns of Matricesmatpoints Plot Columns of Matricesmtext Text in the Margins of a Plotmtext.no.overlap Low-Level Plotting Functionpanel.smooth Smoothing Scatterplots on Multipanel Displaysperspp Project Points onto Three-Dimensional Perspective Plotsplotlabels Labels for Printing or Plotting - Generic functionplotlabels.default Labels for Printing or Plotting - Generic functionpoints Add Lines or Points to Current Plotpolygon Shade in a Polygonal Figureqqline Produce a Line through a Normal QQ-Plotrect Draws and Shades Rectanglesrug Add a Rug to a Plotsegments Plot Disconnected Line Segments or Arrowsstackbar.render Plotting: Low-Level Functionsstamp Time Stamp Output, Graph, and Audit Filesubplot Add a Plot to an Existing Plotsymbols Draw Symbols on a Plottext Plot Texttext.default Plot Texttext.tree Place Text on a Dendrogramticks.render Plotting - Internal Functionstitle Plot Titling Information and/or Axis Labelstslines Plot Multiple Time Seriestsplot Plot Multiple Time Seriestspoints Plot Multiple Time Seriesusa United States Coastline and State Boundaries

ANOVA Models C Factor with Chosen Contrastsalias Aliases (Dependencies) in a Model - Generic functionalias.aovlist Alias Method for Multiple Strata Analysis of Variancealias.design Alias Method for Design Objectsanova Compute an Anova Table - Generic functionanova.discrim The ANOVA method for the discrim object.aov Fit an Analysis of Variance Modelaov.genyates Analysis of Variance for Balanced Designsaov.object Analysis of Variance Objects

2

ANOVA Models

aovlist.object Analysis of Variance Objectscontr.helmert Contrast or Dummy Variable Matrixcontr.poly Contrast or Dummy Variable Matrixcontr.sum Contrast or Dummy Variable Matrixcontr.treatment Contrast or Dummy Variable Matrixcontrasts Contrasts Attributecontrasts<- Contrasts Attributedesign Generate a Design Objectdesign.object Design Objectsdesign.table Arrange Response as a Arrayeff.aovlist Compute Efficiency Factors for aovlist Model Termsfac.design Generate Factorial Designsfactor.names Factor and Level Namesfactor.names<- Factor and Level Namesfractionate Produce a Fractional Factorial Designfriedman.test Friedman Rank Sum Testinteraction Compute the Interaction of Several Factorsinteraction.plot Two-Way Interaction Plotsis.random Random Factorskruskal.test Kruskal-Wallis Rank Sum Testmanova Fit a Multivariate Analysis of Variance Modelmaov.object Analysis of Variance Objectsmodel.tables Compute Tables of Estimates for Model Object - Generic

functionmodel.tables.aov Tables of Means and Effects for ANOVA Modelsmodel.tables.aovlist Tables of Means and Effects for ANOVA Modelsmulticomp Multiple Comparisonsmulticomp.default Multiple Comparisonsmulticomp.discrim The multiple comparisons method for the discrim object.multicomp.gls Multiple Comparisons For Generalized Least Squares

Modelsmulticomp.lm Multiple Comparisonsmulticomp.lme Multiple Comparisons For Linear Mixed Effects Modelsoa.design Generate an Orthogonal Array Designplot.design Plot a Function of Each Level of Factors or Termsplot.factor Summary Plots by Factorsplot.varcomp Plot of Random Componentsproj Projection Matrix

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Big Data Library

proj.default Projection Matrixqdunnett Quantiles for Dunnett's Comparisons with Controlqmvt Quantiles for the Equicorrelated Multivariate-t Distributionqmvt.sim Simulation-based Quantiles of the Multivariate-t

Distributionqqnorm.aov Normal or Half-Normal Plots of Effectsqqnorm.aovlist Normal or Half-Normal Plots of Effectsqqnorm.maov Normal or Half-Normal Plots of Effectsqtukey Quantiles of Tukey's Studentized Range Distributionrandomize Random Ordering for the Runs of a Designraov Random Effects Analysis of Variancereplications Number of Replications of Termsse.contrast Standard Errors for Contrasts among Model Terms - Generic

Functionse.contrast.aov Standard Errors for Contrasts between Meansse.contrast.aovlist Standard Errors for Contrasts between MeansssType3 Compute Type III Sum of Squares - Generic FunctionssType3.aovlist Compute Type III Sum of SquaresssType3.default Compute Type III Sum of SquaresssType3.formula Compute Type III Sum of SquaresssType3.lm Compute Type III Sum of Squaressummary.aov Summary of an Analysis of Variance Objectsummary.aovlist Summary of an Analysis of Variance Objectsummary.manova Create a Manova Tablevarcomp Variance Componentsvarcomp.object Variance Component Objects

Big Data Library ExpressionLanguage Expression Language[<-.bdFrame Subscript a bdFrame[<-.bdVector Subscript a bdVector[.bdFrame Subscript a bdFrame[.bdVector Subscript a bdVectoras.bdCharacter Big Data Character Vectoras.bdFactor Big Data Factorsas.bdFrame Convert big data objectsas.bdLogical Big Data Logical Vectorsas.bdNumeric Big Data Numeric Vectorsas.bdTimeDate Big Data Time Date Objects

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Big Data Library

as.bdVector Big Data Vectorsbd.assoc.rules Generate Association Rrulesbd.assoc.rules.get.item.counts Count Association Rule Items.

bd.assoc.rules.graph Create a Plot of a Set of Association Rulesbd.aggregate Column Aggregate Values Within Data Blocksbd.append Append data setsbd.bin Create Categoriesbd.block.apply Execute Spotfire S+ Script on Blocksbd.by.group Apply Function to Data Blocksbd.by.window Apply Function to Data Blocks Defined by a Moving

Windowbd.cache.cleanup Analyze BDO Cache Filesbd.cache.info Analyze BDO Cache Filesbd.cache.temp.dir Sets and Retrieves the Directory for Creating Temporary

Cache Filesbd.coerce Coerce To or From a Big Data Objectbd.cor Compute Correlations or Covariancesbd.create.columns Create New Columnsbd.crosstabs Create Crosstabulationbd.data.viewer Show Data Viewerbd.duplicated Find the Unique rows in a dataset.bd.filter.columns Remove Data Set Columnsbd.filter.rows Filter Rowsbd.join Join Multiple Inputsbd.modify.columns Modify Column Names and Typesbd.normalize Normalize Databd.object.info Extract Internal Information about a bdFrame or bdVector

Objectbd.options Big Data Processing Optionsbd.pack.object Packing Databd.partition Partition Databd.relational.difference Get the Relational Difference of 2 Data Setsbd.relational.divide Get the Relational Division of 2 Columnsbd.relational.intersection Get the Relational Intersection of 2 Data Setsbd.relational.join Get the Relational Join of 2 Data Setsbd.relational.product Get the Relational Product of 2 Data Setsbd.relational.project Remove Data Set Columnsbd.relational.restrict Select Rows Using a Relational Restriction

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Big Data Library

bd.relational.union Get the Relational Union of 2 Data Setsbd.remove.missing Handle Missing Valuesbd.reorder.columns Reorder Columnsbd.run.iminer.worksheet From TIBCO Spotfire Statistics Services, Runs an Insightful

Miner Worksheet in Batch Modebd.sample Sample Rowsbd.select.rows Select Columns and Rowsbd.shuffle Reorder Databd.sort Sort Rowsbd.split Split Rowsbd.split.by.group Divide Data into Blocksbd.split.by.window Divide Data into Blocks Defined by a Moving Windowbd.stack Stack Columnsbd.string.column.width Maximum Column String Widthbd.tally Measures Internal Big Data Operationsbd.transpose Transpose Databd.unique Find the Unique Rows in a Dataset.bd.univariate Calculate Univariate Statisticsbd.unpack.object Packing Databd.unstack Unstack a ColumnbdCharacter Big Data Character VectorbdCharacter.object Big Data ObjectsbdCluster Big Data K-Means ClusteringbdFactor Big Data FactorsbdFactor.object Big Data ObjectsbdFrame Construct a bdFrame ObjectbdFrame.object Big Data ObjectsbdGlm Big Data Generalized Linear ModelbdLm Big Data Linear ModelsbdLogical Big Data Logical VectorsbdNumeric Big Data Numeric VectorsbdNumeric.object Big Data ObjectsbdObject.object Big Data ObjectsbdPackedObject Packing DatabdPrincomp Big Data Principal Component AnalysisbdSignalSeries Constructor Function For bdSignalSeries ObjectsbdTimeDate Big Data Time Date ObjectsbdTimeDate.object Big Data Objects

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Bootstrap Methods

bdTimeSeries Constructor Function for bdTimeSeries ClassbdTimeSpan Constructor Function For bdTimeSpan ClassbdVector.object Big Data Objectsclass.bdCharacter Big Data Objectsclass.bdFactor Big Data Objectsclass.bdFrame Big Data Objectsclass.bdNumeric Big Data Objectsclass.bdObject Big Data Objectsclass.bdTimeDate Big Data Objectsclass.bdVector Big Data Objectsfitted.bdCluster Big Data Predict Cluster Membershipfitted.bdPrincomp Big Data Principal Component Scoresis.bdCharacter Big Data Character Vectoris.bdFactor Big Data Factorsis.bdLogical Big Data Logical Vectorsis.bdNumeric Big Data Numeric Vectorsis.bdTimeDate Big Data Time Date Objectsis.bdVector Big Data Vectorsnames.bdFrame Column Namesplot.bdSignalSeries Big-Data Signal Plotplot.bdTimeSeries Big-Data Calendar Time Series Plotpredict.bdCluster Big Data Predict Cluster Membershippredict.bdPrincomp Big Data Principal Component Scoresshow.bdInternalCache Print bdInternalCache Objectsummary.bdFrame Summarize bdFrame Object

Bootstrap Methods addSamples Add New Replicates to Bootstrap Objectbootstats Calculate Bootstrap Statisticsbootstrap General Nonparametric Bootstrappingjack.after.bootstrap Perform Jackknife-After-Bootstraplimits.bca Calculate BCa Confidence Limitslimits.emp Calculate Empirical Percentiles of Replicatesplot.jack.after.bootstrap Influence Plot Using Jackknife-After-Bootstrapplot.resamp Plot Method for Resample Objectsprint.jack.after.bootstrap Print a Jackknife-After-Bootstrap Objectprint.resamp Print a Resample Objectprint.summary.bootstrap Print a Summary of Bootstrap Object

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Categorical Data

print.summary.resamp Print a Summary of Resample Objectqqnorm.resamp Quantile-Quantile Plots for Resample Objectsresamp.get.dimnames Support for Bootstrap and Jackkniferesamp.get.fit.func Support for Bootstrap and Jackkniferesamp.get.indices Support for Bootstrap and Jackknifesamp.boot.bal Construct Matrix of Resamplessamp.boot.mc Construct Matrix of Resamplessamp.permute Construct Matrix of Resamplessummary.bootstrap Summary Method for Bootstrap Objectssummary.resamp Summary Method for Resample Objectsupdate.bootstrap Add New Replicates to Bootstrap Object

Categorical Data Ops.data.frame Ops Group Method for Data Frame ObjectsOps.factor Ops Group Method for Factors and Ordered FactorsOps.ordered Ops Group Method for Factors and Ordered FactorsSubscript.factor Subscript a Factor Object[.factor Subscript a Factor Object[<-.factor Subscript a Factor Objectaggregate Compute Summary Statistics of Subsets of Dataaggregate.data.frame Compute Column-by-Column Summaries of Groups of

Observationsaggregate.default Compute Summary Statistics of Subsets of Dataas.factor Create Factor Objectas.ordered Create or Modify Ordered Factorsby Split a Dataset by Factors and Apply a Function to the Partsby.data.frame Split a Dataset by Factors and Apply a Function to the Partsby.default Split a Dataset by Factors and Apply a Function to the Partscodes Codes of an Ordered Factorcrosstabs Create a Contingency Table from Factor Datacut Create Category by Cutting Continuous Datacut.dates Create a Factor from a Dates Objectcut.default Create Category by Cutting Continuous Datafactor Create Factor Objectis.factor Create Factor Objectis.ordered Create or Modify Ordered Factorslevels Levels Attribute

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Character Data Operations

levels.factor Levels Attribute for Factor Objects.levels<-.factor Levels Attribute for Factor Objects.loglin Contingency Table Analysismerge.levels Merge the Levels of a Factornlevels Number of Levels of a Factorordered Create or Modify Ordered Factorsordered<- Create or Modify Ordered Factorsordered<-.default Create or Modify Ordered Factorsprint.crosstabs Print Output of crosstabs Functionrowsum Row Sums of a Matrix, Based on a Grouping Variable.split Split Data by Groupssplit.default Split Data by Groupstable Create Contingency Table from Categoriestabulate Count Entries in Binstapply Apply a Function to a Ragged Array

Character Data Operations AsciiToInt Convert ASCII Characters to Decimal Representationas.character Character Objectsascii Ascii character codesbasename Manipulate File Pathscasefold Convert Case of Character Stringscharacter Character Objectscharmatch Partial Matching of Character StringsdQuote Quote TextdelimMatch Delimited Pattern Matchingdirname Manipulate File Pathsformat Formatted Character Dataformat.char Formatting Using C-style Formatsformat.default Format Atomic DataformatC Formatting Using C-style Formatsgettext Translate Text Messagesgettextf C-style formatted outputgrep Search for Pattern in Textgsub Replace part of a character string.is.all.white Test for White Spaceis.character Character Objectsmake.unique Make Character Strings Unique

9

Clustering

match Match Items against a Table - Generic functionnchar Lengths of Character Stringsngettext Translate Text MessagesoldGrep Search for Pattern in Textpaste Concatenate Data to Make Character Datapmatch Partial Matching of Character Items in a Vectorprint.char.matrix Print a char.matrix Object to Make a Formatted TableregMatch Match Strings to Regular Expression Patterns.regexpr Pattern Matching in Stringsrle Run Length EncodingsQuote Quote Textsort Sort into Ascending Numeric or Alphabetic or Time

(Position) Ordersprintf C-style formatted outputstring.bounding.box Bounding Boxes of Multiline Stringsstring.break.line Change Strings with Line Breaks into Multiple Stringsstrip.blanks Strip Spaces from Stringsstrsplit Split strings into pieces based on regular expressionsubstituteString Replace part of a character string.substring Extract or Replace Portions of Character Stringstempdir Returns a Vector of Character Strings that are Virtually

Certain to be Unique Filenamestempfile Create Unique Names for Filestolower Convert Case of Character Stringstoupper Convert Case of Character Strings

Clustering agnes Agglomerative Clusteringagnes.object Agglomerative Nesting ObjectbdCluster Big Data K-Means Clusteringclara Clustering Large Datasetsclara.object Clustering Large Applications Objectclorder Re-Order Leaves of a Cluster Treeclusplot Clusplot - Generic Functionclusplot.default Bivariate clusplotclusplot.partition Bivariate Clusplot of a Partitioning Objectcluster Identify Clusterscutree Create Groups from Hierarchical Clusteringdaisy Dissimilarity Matrix Calculation

10

Clustering

diana Divisive Cluster Analysisdiana.object Divisive Analysis Objectdissimilarity.object Dissimilarity Matrix Objectdist Distance Matrix Calculationfanny Fuzzy Cluster Analysisfanny.object Fuzzy Analysis Objecthclust Hierarchical Clusteringhierarchical.object Hierarchical Clustering Objectkmeans Hartigan's K-Means Clusteringlabclust Label a Cluster Plotmclass Classification Produced By mclust mclust Model-based Hierarchical Clusteringmona Monothetic Cluster Analysismona.object Monothetic Analysis Objectmreloc Iterative Relocation For mclust / mclass pam Clustering Around Medoidspam.object Partitioning Around Medoids Objectpartition.object Partitioning Objectplclust Plot Trees From Hierarchical Clusteringplot.agnes Plots of an Agglomerative Hierarchical Clusteringplot.diana Plots of a Divisive Hierarchical Clusteringplot.mona Banner of Monothetic Divisive Hierarchical Clusteringsplot.partition Plot of a Partition of the Data Setpltree Clustering Trees - Generic Functionpltree.agnes Clustering Tree Of Agglomerative Hierarchical Clusteringspltree.diana Clustering Tree Of Divisive Hierarchical Clusteringspltree.hierarchical Clustering Tree of an Agglomerative or a Divisive

Hierarchical Clusteringprint.agnes Use print() on an agnes objectprint.clara Use print() on a clara objectprint.diana Use print() on a diana objectprint.dissimilarity Use print() on a dissimilarity objectprint.fanny Use print() on a fanny objectprint.mona Use print() on a mona objectprint.pam Use print() on a pam objectprint.summary.agnes Use print() on a summary.agnes objectprint.summary.clara Use print() on a summary.clara objectprint.summary.diana Use print() on a summary.diana object

11

Complex Numbers

print.summary.fanny Use print() on a summary.fanny objectprint.summary.mona Use print() on a summary.mona objectprint.summary.pam Use print() on a summary.pam objectsubtree Extract Part of a Cluster Treesummary.agnes Summary method for agnes objectssummary.clara Summary method for clara objectssummary.diana Summary method for diana objectssummary.fanny Summary Method for fanny Objectssummary.mona Summary Method for mona Objectssummary.pam Summary Method for pam Objects

Complex Numbers %% Arithmetic Operators%/% Arithmetic Operators+ Arithmetic Operators.Uminus Arithmetic OperatorsArg Basic Complex Number ManipulationArithmetic Arithmetic OperatorsComplex Basic Complex Number ManipulationConj Basic Complex Number ManipulationIm Basic Complex Number ManipulationMod Basic Complex Number ManipulationRe Basic Complex Number Manipulation^ Arithmetic Operatorsacos Inverse Trigonometric Functionsacosh Inverse Hyperbolic Trigonometric Functionsas.complex Complex Valued Objectsasin Inverse Trigonometric Functionsasinh Inverse Hyperbolic Trigonometric Functionsatan Inverse Trigonometric Functionsatanh Inverse Hyperbolic Trigonometric Functionscomplex Complex Valued Objectscos Trigonometric Functionscosh Hyperbolic Trigonometric Functionsexp Exponential Functionsfft Fast Fourier Transformgamma Gamma Function (and its Natural Logarithm)is.complex Complex Valued Objects

12

Computations Related to Plotting

lgamma Gamma Function (and its Natural Logarithm)log Exponential Functionslog2 Exponential Functionslog10 Exponential Functionslogb Exponential Functionspolyroot Find the Roots of a Polynomialsin Trigonometric Functionssinh Hyperbolic Trigonometric Functionssqrt Exponential Functionstan Trigonometric Functionstanh Hyperbolic Trigonometric Functions

Computations Related to Plotting AsciiToInt Convert ASCII Characters to Decimal Representationacf Estimate Autocovariance, Autocorrelation or Partial

Autocorrelationadd.color.values Modify the Table of Named Colorsapprox Linear Interpolation of Pointsas.trellis.data.frame.series Internal Plotting Functionas.trellis.data.frame.signal Internal Plotting Functionaxis.compute.time.breaks Compute Market Open and Close Times for Axis Breaksaxis.numeric Axis for Numeric Dataaxis.time Time Axis for Time Series Plotaxis.time.breaks Internal Calculations for Time Series Plottingaxis.time.build Compute Time Series Axisaxis.time.grid Internal Calculations for Time Series Plottingaxis.time.label.format Format Label for Time Axisaxis.time.labels Internal Calculations for Time Series Plottingaxis.time.scale Internal Calculations for Time Series Plottingaxis.time.ticks Internal Calculations for Time Series Plottingbandwidth.bcv Biased Cross-Validation for Bandwidth Selectionbandwidth.hb Histogram Bin Based Bandwidth Selectionbandwidth.nrd Normal Reference Density Bandwidth Selectionbandwidth.sj Bandwidth Selection by Pilot Estimation of Derivativesbandwidth.ucv Unbiased Cross-Validation for Bandwidth Selectionboxplot Boxplotschull Convex Hull of a Planar Set of Pointscm.colors Create Color Sets Suitable for Image Palettes

13

Computations Related to Plotting

co.intervals Conditioning Intervalscol2rgb Convert Color Specified to RGB Integer Tripletcolor.values Get Color Names and Valuescolors Get Color Names and Valuesdensity Estimate Probability Density Functiongood.layout Calculate Layout for Trellisgraphsheet.options Options for graphsheet Graphics Devicegray Generate Shades of Gray at Different Levelsgray.colors Generate Gamma-Corrected Shades of Graygrey Generate Shades of Gray at Different Levelsgrey.colors Generate Gamma-Corrected Shades of Grayheat.colors Create Color Sets Suitable for Image Paletteshist Plot a Histogramhist.factor Plot a Histogramhist2d Calculate Two-Dimensional Histogramhsl Convert HSL Color Specification to RGBhsv Convert HSV Color Specification to RGBimage.palette Set or Get Default Palette and Image Palette RGB Valuesinterp Bivariate Interpolation for Irregular Dataksmooth Densities or Regressions Using Kernel Smootherslowess Scatter Plot Smoothingmstree Minimal Spanning Tree and Multivariate Planingnclass.fd Freedman-Diaconis Method for Histogram Bin Countsnclass.scott Scott Method for Histogram Bin Countsnclass.sturges Sturges Method for Histogram Bin Countspalette Set or Get Default Palette and Image Palette RGB Valuespar Graphical Parameterspersp.setup Line Styles for Perspective Plotsplclust Plot Trees From Hierarchical Clusteringplot.loess Display of Fitted LOESS Models by Coplotsplot.size.scale Low-Level Plotting Functionppoints Plotting Points for QQplotspreplot Precompute a Plotting Object - Generic Functionpreplot.loess Display of Fitted LOESS Models by Coplotspretty Vector of Prettied Valuespretty.log Vector of Prettied Log Valuesqqnorm Quantile-Quantile Plots - Generic Functionqqnorm.default Quantile-Quantile Plots - Generic Function

14

curl Library

qqplot Quantile-Quantile Plots - Generic Functionquickvu Make Simple Vu-Graphsrange Range of Datarainbow Create a Color Set Based on Sequence in HSV Color Spacergb Create RGB Value from Numeric RGB Intensitiesrgb2hsl Create HSL Value from Numeric RGB Intensitiesrgb2hsv Create HSV Value from Numeric RGB Intensitiesspline Cubic Spline Approximationterrain.values Create Color Sets Suitable for Image Palettestopo.colors Create Color Sets Suitable for Image Palettesuse.device.palette Use Device-Specific Palette or Global Paletteuse.legacy.graphics Use Legacy Graphics Internal Codeuser.to.plot Low-Level Plotting Functionxysort Rearrange x-y Data for Fast Plotting

curl Library download.file Download a File from the Internet

Data Attributes attr Attribute of an Objectattributes All Attributes of an Objectcol Column and Row Identification in a Matrixdim Dim Attribute of an Objectdim<- Dim Attribute of an Objectdimnames Dimnames Attribute of an Objectlength Length of a Vector or Listlevels Levels Attributemode Data Mode of the Values in a Vectornames Names Attribute of an Objectnames<- Names Attribute of an Objectncol Extents of a Matrixnlevels Number of Levels of a Factornrow Extents of a Matrixrow Column and Row Identification in a Matrixslice.index Slice Identification in an Arraystorage.mode Data Mode of the Values in a Vectorstructure An Object with Given Attributestsp Tsp Attribute of a Time Series Object

15

Data Directories

Data Directories «- Assign a Name to an Object<- Assign a Name to an Object-> Assign a Name to an Object.First.lib Shared Functions and Data Sets.Last.lib Shared Functions and Data SetsAssignment Assign a Name to an ObjectNLSstClosestX Inverse InterpolationNLSstLfAsymptote Horizontal Asymptote on the Left SideNLSstRtAsymptote Horizontal Asymptote on the Right Side_ Assign a Name to an Objectas.variable Make Factor or Numeric Variable out of VectorasTable Convert groupedData to a matrixassign Assign Object to Database or Frameattach Attach a Chapter or Database to the Search Listattach.data.frame Attach Method for Data Frame Objectsattach.pframe Attach Method for Data Frame ObjectsbalancedGrouped Create a groupedData object from a matrixcbind.data.frame Build Data Frame from Columnsconflicts Report on Conflicts Among Databasesdata.dump Produce Text Representations of S-PLUS Objectsdata.restore Bring Back Data-Dumped Objectsdatabase.attr Utilities for Use with Spotfire S+ Databasesdatabase.object Utilities for Use with Spotfire S+ Databasesdatabase.status Utilities for Use with Spotfire S+ Databasesdatabase.type Utilities for Use with Spotfire S+ Databasesdetach Detach Data from the Search Listdget Write a Text Representation of a S-PLUS Objectdput Write a Text Representation of a S-PLUS Objectdump Produce Text Representations of S-PLUS Objectsexists Search for a S-PLUS Objectfind Find the Database that Contains an Objectfix Fix a Function.gapply Apply a Function by Groupsget Search for a S-PLUS ObjectgetInitial Get Initial Parameter EstimatesisBalanced Check a Design for Balance

16

Data Manipulation

library Shared Functions and Data Setsmake.fields Convert Fixed Format Data to Fieldsmasked Report Masked S-PLUS Objectsmodule Access Add-On Modulenew.database Make a New Directory Databaseobjcopy Assign Copies of Objects to a Databaseobjdiff Differences Between S-PLUS Objectsobjects Find S-PLUS Object Namesobjects.summary Summary Information about S-PLUS Objectsprint.objects.summary Summary Information about S-PLUS Objectsrbind.data.frame Create a Data Frame from RowsreadMapped Read and Write Raw (Binary) DatareadRaw Read and Write Raw (Binary) Dataremove Remove Objects from a Databaserestore Bring Back Dumped Objectsrm Remove by Namesearch View the Search List.setDBStatus Set Read/Write Permission on a Spotfire S+ DatabasesortedXyData Create a sortedXyData objecttrue.file.name Map Object Name into File NameupdateChapter Update Revised Version of a ChapterwriteRaw Read and Write Raw (Binary) Data

Data Manipulation $ Extract or Replace Parts of an Object - Generic Operators%in% Tell if items are in a set.%w/o% Find the Unique Values of a Set«- Assign a Name to an Object<- Assign a Name to an Object-> Assign a Name to an Object: Sequences of Numbers@ Extract or Replace Slot in S-PLUS ObjectAssignment Assign a Name to an ObjectEdit Edit function using Spotfire S+ script windowEdit (Script window) Edit function using Spotfire S+ script windowEdit.data Edit a datasetgroupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an Array

17

Data Manipulation

groupAlls.data.frame Computes Group Sums, Means, Variances, Standard Deviations for a Vector or Columns of an Array

groupAlls.default Computes Group Sums, Means, Variances, Standard Deviations for a Vector or Columns of an Array

groupAnys Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

ArraygroupMeans.data.frame Computes Group Means for a Vector or Columns of an

ArraygroupMeans.default Computes Group Means for a Vector or Columns of an

ArraygroupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an ArraygroupProds Computes Group Products for a Vector or Columns of an

ArraygroupProds.data.frame Computes Group Products for a Vector or Columns of an

ArraygroupProds.default Computes Group Products for a Vector or Columns of an

ArraygroupRanges Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.data.frame Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.default Computes Group Ranges for a Vector or Columns of an

ArraygroupStdevs Computes Group Standard Deviations for a Vector or

Columns of an Array.groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

Array

18

Data Manipulation

groupVars.data.frame Computes Group Variances for a Vector or Columns of an Array

groupVars.default Computes Group Variances for a Vector or Columns of an Array

NCOL Uniform Rectangular Data FunctionsNLSstClosestX Inverse InterpolationNLSstLfAsymptote Horizontal Asymptote on the Left SideNLSstRtAsymptote Horizontal Asymptote on the Right SideNROW Uniform Rectangular Data FunctionsRows Select Rows of a Data Frame or ListSubscript Extract or Replace Parts of an Object - Generic OperatorsSubscript.data.frame Subscript a Data FrameSubscript.factor Subscript a Factor ObjectSubscript.tree Subscript a Tree Object[ Extract or Replace Parts of an Object - Generic Operators[<- Extract or Replace Parts of an Object - Generic Operators[<-.bdFrame Subscript a bdFrame[<-.bdVector Subscript a bdVector[<-.data.frame Subscript a Data Frame[.bdFrame Subscript a bdFrame[.bdVector Subscript a bdVector[.cts Subscript a Time Series Object[.data.frame Subscript a Data Frame[.factor Subscript a Factor Object[.its Subscript a Time Series Object[.rts Subscript a Time Series Object[.tree Subscript a Tree Object[<-.factor Subscript a Factor Object[[ Extract or Replace Parts of an Object - Generic Operators[[<-.data.frame Subscript a Data Frame[[«- Extract or Replace Parts of an Object - Generic Operators[[.data.frame Subscript a Data Frame_ Assign a Name to an Objectabbreviate Generate Abbreviationsappend Insert or Merge Dataas.bdFrame Convert big data objectsas.char.rect Uniform Rectangular Data Functionsas.rectangular Uniform Rectangular Data Functions

19

Data Manipulation

bd.aggregate Column Aggregate Values Within Data Blocksbd.append Append data setsbd.block.apply Execute Spotfire S+ Script on Blocksbd.by.group Apply Function to Data Blocksbd.by.window Apply Function to Data Blocks Defined by a Moving

Windowbd.coerce Coerce To or From a Big Data Objectbd.create.columns Create New Columnsbd.duplicated Find the Unique rows in a dataset.bd.filter.columns Remove Data Set Columnsbd.filter.rows Filter Rowsbd.relational.difference Get the Relational Difference of 2 Data Setsbd.relational.divide Get the Relational Division of 2 Columnsbd.relational.intersection Get the Relational Intersection of 2 Data Setsbd.relational.join Get the Relational Join of 2 Data Setsbd.relational.product Get the Relational Product of 2 Data Setsbd.relational.project Remove Data Set Columnsbd.relational.restrict Select Rows Using a Relational Restrictionbd.relational.union Get the Relational Union of 2 Data Setsbd.reorder.columns Reorder Columnsbd.sample Sample Rowsbd.select.rows Select Columns and Rowsbd.sort Sort Rowsbd.split Split Rowsbd.split.by.group Divide Data into Blocksbd.split.by.window Divide Data into Blocks Defined by a Moving Windowbd.stack Stack Columnsbd.string.column.width Maximum Column String Widthbd.unique Find the Unique Rows in a Dataset.bd.unstack Unstack a ColumnbdCharacter.object Big Data ObjectsbdFactor.object Big Data ObjectsbdFrame Construct a bdFrame ObjectbdFrame.object Big Data ObjectsbdNumeric.object Big Data ObjectsbdObject.object Big Data ObjectsbdTimeDate.object Big Data ObjectsbdVector.object Big Data Objects

20

Data Manipulation

c Combine Values into a Vector or Listcasefold Convert Case of Character Stringscbind Build Matrix from Columns or Rowscharmatch Partial Matching of Character Stringsclass.bdCharacter Big Data Objectsclass.bdFactor Big Data Objectsclass.bdFrame Big Data Objectsclass.bdNumeric Big Data Objectsclass.bdObject Big Data Objectsclass.bdTimeDate Big Data Objectsclass.bdVector Big Data ObjectscolIds Uniform Rectangular Data FunctionscolMaxs Row and Column Summaries - min, max, and rangecolMeans Row and Column SummariescolMedians Compute medians columnwisecolMins Row and Column Summaries - min, max, and rangecolProds Columnwise ProductscolQuantiles Compute quantiles columnwisecolRanges Row and Column Summaries - min, max, and rangecolStdevs Row and Column SummariescolSums Row and Column SummariescolVars Row and Column Summariescolnames Uniform Rectangular Data Functionscolnames <- Uniform Rectangular Data Functionsconcat Vector Concatenationconcat.two Vector ConcatenationdQuote Quote TextdelimMatch Delimited Pattern Matchingduplicated Unique or Duplicated Valuesduplicated.data.frame Unique or Duplicated Rows in a Data Frame, or unique

combinations of multiple variablesduplicatedList Match and duplicated for simple listsed Invoke ed Text Editoredit Text Editoredit (Text Editor) Text Editoremacs Invoke emacs Text Editorfix Fix a Function.grep Search for Pattern in Text

21

Data Manipulation

groupedData Construct a groupedData Objectgsub Replace part of a character string.gsummary Summarize by Groupshead Get the First or Last Part of an Objectifelse Conditional Data Selectionindex.rowcol Find Indices into 1 or 2-dim Datasetintersect Find the Intersection of Multiple Setsis.element Tell if items are in a set.is.monthend The End of Month Day Informationis.na Test For Missing Values - Generic functionis.rectangular Uniform Rectangular Data Functionsjitter Separate Data Points by Jitteringlength Length of a Vector or Listmatch Match Items against a Table - Generic functionmatch.data.frame Match rows of a data frame in another data frame, or match

"rows" of listsmatchList Match and duplicated for simple listsmerge Merge Two Datasets and Match Columnsmerge.data.frame Merge Two Datasets and Match Columnsmerge.default Merge Two Datasets and Match Columnsna.exclude Filter Missing Values From a Data Framena.fail Filter Missing Values From a Data Framena.include Replace NA's in a Factor with a New Levelna.omit Filter Missing Values From a Data Framenafitted Adjust for Missing Valuesnafitted.default Adjust for Missing Valuesnafitted.exclude Adjust for Missing Valuesnames.bdFrame Column Namesnapredict Adjust for Missing Valuesnapredict.default Adjust for Missing Valuesnapredict.exclude Adjust for Missing Valuesnaprint Print Missing Value Informationnaprint.default Print Missing Value Informationnaprint.exclude Print Missing Value Informationnaprint.omit Print Missing Value Informationnaresid Adjust for Missing Valuesnaresid.default Adjust for Missing Valuesnaresid.exclude Adjust for Missing Values

22

Data Manipulation

notSorted Determine if a vector is sorted.numCols Uniform Rectangular Data FunctionsnumRows Uniform Rectangular Data FunctionsoldGrep Search for Pattern in Textorder Ordering to Create Sorted Datapaste Concatenate Data to Make Character Datapmatch Partial Matching of Character Items in a Vectorrbind Build Matrix from Columns or RowsregMatch Match Strings to Regular Expression Patterns.regexpr Pattern Matching in Stringsrep Replicate Data Valuesrep.int Replicate Integer Vectorreplace Insert or Merge Datarev Reverse the Order of a Vector or Listrle Run Length Encodingrow.names Row Names Attributerow.names<- Row Names AttributerowIds Uniform Rectangular Data FunctionsrowMaxs Row and Column Summaries - min, max, and rangerowMeans Row and Column SummariesrowMins Row and Column Summaries - min, max, and rangerowRanges Row and Column Summaries - min, max, and rangerowStdevs Row and Column SummariesrowSums Row and Column SummariesrowVars Row and Column Summariesrownames Uniform Rectangular Data Functionsrownames <- Uniform Rectangular Data Functionsrowsum Row Sums of a Matrix, Based on a Grouping Variable.sQuote Quote Textsd Row and Column Summariesseq Sequences of Numbersseq.default Sequences of NumbersseriesLag Time Series Lag/Lead FunctionseriesLength The Length of a "signalSeries" ("bdSignalSeries") or

"timeSeries" ("bdTimeSeries") objectsetdiff Find the Unique Values of a Setsort Sort into Ascending Numeric or Alphabetic or Time

(Position) Order

23

Data Sets

sort.list Vector of Indices that Sort Datasplit Split Data by Groupssplit.default Split Data by Groupsstrip.blanks Strip Spaces from Stringsstrsplit Split strings into pieces based on regular expressionstructure An Object with Given Attributessub Uniform Rectangular Data Functionssubscript2d Uniform Rectangular Data Functionssubscript2d<- Uniform Rectangular Data FunctionssubstituteString Replace part of a character string.substring Extract or Replace Portions of Character StringssubtractMeans Subtract Group Means from Each Entry for a Vector or

Columns of an Arraytail Get the First or Last Part of an Objecttolower Convert Case of Character Stringstoupper Convert Case of Character Stringsunion Find the Union of Multiple Setsunique Unique or Duplicated Valuesunique.data.frame Unique or Duplicated Rows in a Data Frame, or unique

combinations of multiple variablesunlist Simplify the Structure of a Listunname Remove "names" or "dimnames"unpaste Split a Character String into Fieldsvi Invoke vi Text Editorwhich Find TRUE values in logical vectorzapsmall Coerce Small Numbers to Zero for Printing

Data Sets .Last.value Keep the Value of the Last Un-assigned S Expression.Machine Machine Arithmetic Constants.Random.seed Seeds for Random Number Generators.Temporary.file.list List of Auto-Created Files to be Removed at Session End.laenv Tuning Parameters for gebra ComputationsLETTERS The AlphabetPuromycin Biochemical Reactions of Cells Treated with Puromycinair New York Ozone Concentrationakima Waveform Distortion Data for Bivariate Interpolationakima.x Waveform Distortion Data for Bivariate Interpolationakima.y Waveform Distortion Data for Bivariate Interpolation

24

Data Sets

akima.z Waveform Distortion Data for Bivariate Interpolationanimals Sample Data Sets For Cluster Analysisauthor Character Counts for Books by Various Authorsauthor.count Character Counts for Books by Various Authorsauto Statistics of Automobile Modelsauto.stats Statistics of Automobile Modelsaxis.break.table Time Series Axis Style Tablesaxis.label.table Time Series Axis Style Tablesaxis.tick.table Time Series Axis Style Tablesbar.old Style List for Barplotsbar.splus Style List for Barplotsbarley Sample Data Sets for Trellis Graphicsbarley.disease Barley Disease Databarley.exposed Barley Disease Databicoal Bituminous Coal Production in USAbicoal.tons Bituminous Coal Production in USAbladder Sample Data Sets For Survival Analysisbonds Daily Yields of Six AT&T Bondsbonds.coupon Daily Yields of Six AT&T Bondsbonds.yield Daily Yields of Six AT&T Bondsbxp.att Style List for Boxplotsbxp.old Style List for Boxplotsbxp.splus Style List for Boxplotscapacitor Sample Data Sets For Survival Analysiscar Fuel Consumption Datacar.all Automobile Data from Consumer Reportscar.gals Fuel Consumption Datacar.miles Fuel Consumption Datacar.test.frame Automobile Data from Consumer Reportscar.time Fuel Consumption Datacatalyst Comparing the Yield of Two Catalystscereal Consumer Attitudes Towards Breakfast Cerealscereal.attitude Consumer Attitudes Towards Breakfast Cerealschernoff2 Mineral Contents Data (used by Chernoff)city Names and Locations of Selected U.S. Citiescity.name Names and Locations of Selected U.S. Citiescity.state Names and Locations of Selected U.S. Citiescity.x Names and Locations of Selected U.S. Cities

25

Data Sets

city.y Names and Locations of Selected U.S. Citiesclaims Cost of Automobile Insurance Claimscluster.datasets Sample Data Sets For Cluster Analysisco2 Mauna Loa Carbon Dioxide Concentrationcorn Corn Yields and Rainfallcorn.rain Corn Yields and Rainfallcorn.yield Corn Yields and Rainfallcss.colors CSS Named Colorscu.dimensions Automobile Data from Consumer Reportscu.specs Automobile Data from Consumer Reportscu.summary Automobile Data from Consumer Reportsdating Sample Data Sets for Trellis Graphicsdjia Dow Jones Industrial Averagedrug.mult Drug Study Data for Repeated Measuresenvironmental Sample Data Sets for Trellis Graphicsethanol Measurement of Exhaust from Burning Ethanoleuro Sample Data Sets For Cluster Analysisevap Soil Evaporation Dataevap.x Soil Evaporation Dataevap.y Soil Evaporation Dataexch.rate Foreign Exchange Ratesfed.rate Federal Reserve Interest Ratesfont Vector Drawn Fontsformat.timeDate Sample Formatsformat.timeSpan Sample Formatsfreeny Revenue Datafreeny.x Revenue Datafreeny.y Revenue Datafuel.frame Automobile Data from Consumer Reportsfusion.time Sample Data Sets for Trellis Graphicsgalaxy Radial Velocity of Galaxy NGC7531ganglion Sample Data Sets for Trellis Graphicsgas Measurement of Exhaust from Burning Ethanolgeyser Old Faithful Geyser Datagr.pars Names of Graphical Parameters guayule Rate of Germination of Treated Guayule Seedsgun Speed of Firing Naval Gunshalibut Halibut Data

26

Data Sets

hamster Sample Data Sets for Trellis Graphicsheart Sample Data Sets For Survival Analysishstart US Housing Startsiris Fisher's Iris Datairis.df Fisher's Iris Datakyphosis Spinal Disease in Children Dataletters The Alphabetleukemia Sample Data Sets For Survival Analysisliver Carcinogeneity Studies of Rat Liversliver.cells Carcinogeneity Studies of Rat Liversliver.exper Carcinogeneity Studies of Rat Liversliver.gt Carcinogeneity Studies of Rat Liversliver.section Carcinogeneity Studies of Rat Liverslongley Longley's Regression Datalongley.x Longley's Regression Datalongley.y Longley's Regression Datalottery New Jersey Pick-It Lottery Data (First Set)lottery.number New Jersey Pick-It Lottery Data (First Set)lottery.payoff New Jersey Pick-It Lottery Data (First Set)lottery2 New Jersey Pick-It Lottery Data (Second Set)lottery2.number New Jersey Pick-It Lottery Data (Second Set)lottery2.payoff New Jersey Pick-It Lottery Data (Second Set)lottery3 New Jersey Pick-It Lottery Data (Third Set)lottery3.number New Jersey Pick-It Lottery Data (Third Set)lottery3.payoff New Jersey Pick-It Lottery Data (Third Set)lung Sample Data Sets For Survival Analysislynx Canadian Lynx Trappingsmarket.survey AT&T Telemarketing Datamelanoma Sample Data Sets for Trellis Graphicsmonth Month Names and Abbreviationsmonth.abb Month Names and Abbreviationsmonth.name Month Names and Abbreviationsnet.packet Network Packet Trafficoa.12.2p11 Standard Orthogonal Array Designsoa.16.2p15 Standard Orthogonal Array Designsoa.18.2p1x3p7 Standard Orthogonal Array Designsoa.20.2p19 Standard Orthogonal Array Designsoa.24.2p23 Standard Orthogonal Array Designs

27

Data Sets

oa.24.3p1x2p4 Standard Orthogonal Array Designsoa.27.3p13 Standard Orthogonal Array Designsoa.32.2p31 Standard Orthogonal Array Designsoa.36.2p3x3p4 Standard Orthogonal Array Designsoa.4.2p3 Standard Orthogonal Array Designsoa.8.2p7 Standard Orthogonal Array Designsoa.9.3p4 Standard Orthogonal Array Designsoa.Matrices Standard Orthogonal Array Designsoilcity Monthly Excess Returns of Oil City Petroleum, Inc. Stocks

and the Marketovarian Sample Data Sets For Survival Analysisozone Ozone Concentrations in the Northeast U.S.ozone.city Ozone Concentrations in the Northeast U.S.ozone.median Ozone Concentrations in the Northeast U.S.ozone.quartile Ozone Concentrations in the Northeast U.S.ozone.xy Ozone Concentrations in the Northeast U.S.pi Fundamental Constant: pipigment Moisture Content of Pigments Experimentpingpong US Table Tennis Association Datapolarization Sample Data Sets for Trellis Graphicsprim Particle Physics Dataprim4 Particle Physics Dataprim9 Particle Physics Dataps.colors.rgb Colors for PostScript driverps.paper.regions Imageable Regions for PostScript Printersps.setcolor.hsb PostScript Procedures for Setting Colorsps.setcolor.rgb PostScript Procedures for Setting Colorsps.setfont.latin1 PostScript Procedures for Font Selectionps.setfont.std PostScript Procedures for Font Selectionquakes.bay Bay Area Earthquakesr.default.colors R Default Palette Colorsr.default.image.colors R Default Image Colorsrain New York City Precipitationrain.nyc1 New York City Precipitationrain.nyc2 New York City Precipitationrubber Sample Data Sets for Trellis Graphicsruspini Sample Data Sets For Cluster Analysissaving Savings Rates for Countries

28

Data Sets

saving.x Savings Rates for Countriessay.wavelet Speech Signalsensors Responses of eight sensors to a gasship Manufacturing Shipmentssinger Sample Data Sets for Trellis Graphicssliced.ball 3D Ball with Slice Removedsolder AT&T Solder Experimentsolder.balance AT&T Solder Experimentsolder2 AT&T Solder Experimentsplus.default.colors Spotfire S+ Default Palette Colorssplus.default.image.colors Spotfire S+ Default Image Colorsstack Stack-loss Datastack.loss Stack-loss Datastack.x Stack-loss Datastate States of the U.S.state.abb States of the U.S.state.center States of the U.S.state.division States of the U.S.state.name States of the U.S.state.region States of the U.S.state.x77 States of the U.S.steam Steam Usage Datasteam.x Steam Usage Datasteam.y Steam Usage Datastore.co.helmert Stored Contrastsstore.co.mean Stored Contrastsstore.co.poly Stored Contrastssunspots Monthly Mean Relative Sunspot Numberssurvival.datasets Sample Data Sets For Survival Analysisswiss Fertility Data for Switzerland in 1888swiss.fertility Fertility Data for Switzerland in 1888swiss.x Fertility Data for Switzerland in 1888switzerland Heights of Switzerland on 12 by 12 Gridtbauc.1y Treasury Bill Auction Ratestbauc.3m Treasury Bill Auction Ratestbauc.6m Treasury Bill Auction Ratestbond Treasury Bond Futures Trading Datatcm.curve Treasury Constant Maturity Curve

29

Data Types

telsam Interviewer Response Datatelsam.response Interviewer Response Datatestscores Scores from Mathematics Qualifying Examstone Bricker's Tone-Ringer Preference Datatone.appeal Bricker's Tone-Ringer Preference Datatrellis.datasets Sample Data Sets for Trellis Graphicsutil Earnings and Market/Book Ratio for Utilitiesutil.earn Earnings and Market/Book Ratio for Utilitiesutil.mktbook Earnings and Market/Book Ratio for Utilitiesversion Spotfire S+ Version Information.voice Voice Spectrogram Datavoice.five Voice Spectrogram Datavotes Votes for Republican Candidate in Presidential Electionsvotes.repub Votes for Republican Candidate in Presidential Electionsvotes.year Votes for Republican Candidate in Presidential Electionswafer AT&T Wafer Experimentx11.colors X11 Named Colors

Data Types Gamma Generate a Family ObjectNextMethod Methods Invoked from S-PLUS FunctionsUseMethod Methods Invoked from S-PLUS Functionsaov.object Analysis of Variance Objectsaovlist.object Analysis of Variance Objectsarima.object ARIMA Model Objectarray Multi-Way Arraysas.array Multi-Way Arraysas.bdCharacter Big Data Character Vectoras.bdFactor Big Data Factorsas.bdLogical Big Data Logical Vectorsas.bdNumeric Big Data Numeric Vectorsas.bdVector Big Data Vectorsas.character Character Objectsas.complex Complex Valued Objectsas.double Double Precision Objectsas.factor Create Factor Objectas.function Function Objectsas.integer Integer Objects

30

Data Types

as.list List Objectsas.logical Logical Objectsas.matrix Matrix Objectsas.name Name Objectsas.null Null Objectsas.numeric Numeric Objectsas.single Single Precision Objectsas.ts Time Series Objectsas.vector Vectors (Simple Objects)bdCharacter Big Data Character VectorbdCharacter.object Big Data ObjectsbdFactor Big Data FactorsbdFactor.object Big Data ObjectsbdFrame.object Big Data ObjectsbdLogical Big Data Logical VectorsbdNumeric Big Data Numeric VectorsbdNumeric.object Big Data ObjectsbdObject.object Big Data ObjectsbdTimeDate.object Big Data ObjectsbdVector.object Big Data Objectsbinomial Generate a Family ObjectcallGeneric Call the Current Generic Functioncharacter Character Objectsclass Class Attribute of an Objectclass.«- Class &lt;&lt;-class.<- Class &lt;-class.()<- Class ()&lt;-class.ANY Class ANYclass.CLASS Class CLASSclass.GENERIC Class GENERICclass.NULL Class NULLclass.UNKNOWN Class UNKNOWNclass.UNSET Class UNSETclass.VIRTUAL Class VIRTUALclass.array Class arrayclass.atomic Class atomicclass.attached Class attachedclass.bdCharacter Big Data Objects

31

Data Types

class.bdFactor Big Data Objectsclass.bdFrame Big Data Objectsclass.bdNumeric Big Data Objectsclass.bdObject Big Data Objectsclass.bdTimeDate Big Data Objectsclass.bdVector Big Data Objectsclass.break Class breakclass.call Class callclass.call... Class call...class.character Class characterclass.classRepresentation Class classRepresentationclass.classVersions Class classVersionsclass.comment Class commentclass.comment.expression Class comment.expressionclass.complex Class complexclass.connection Class connectionclass.controlSemantics Class controlSemanticsclass.database Class databaseclass.device Class deviceclass.directory Class directoryclass.docStyle Class docStyleclass.documentsGeneric Class documentsGenericclass.expression Class expressionclass.fifo Class fifoclass.file Class fileclass.for Class forclass.function Class functionclass.groupGeneric Class groupGenericclass.groupVec Group Vector Classclass.groupVecVirtual Group Vector Classclass.if Class ifclass.indexLookup Class indexLookupclass.integer Class integerclass.interface Class interfaceclass.internal Class internalclass.iterateState Class iterateStateclass.language Class languageclass.levelsLookup Class levelsLookup

32

Data Types

class.list Class listclass.logical Class logicalclass.matrix Class matrixclass.methodDef Class methodDefclass.methodsGeneric Class methodsGenericclass.missing Class missingclass.named Class namedclass.next Class nextclass.numeric Class numericclass.numericSequence Numeric Sequence Classclass.parse Class parseclass.pipe Class pipeclass.positions Virtual Classes for Time-Related Objectsclass.positionsCalendar Virtual Classes for Time-Related Objectsclass.positionsNumeric Virtual Classes for Time-Related Objectsclass.raw Class rawclass.recursive Class recursiveclass.repeat Class repeatclass.return Class returnclass.semanticAssertion Class semanticAssertionclass.semanticMethod Class semanticMethodclass.semanticState Class semanticStateclass.sequence Class sequenceclass.series Base Class for Time Series and Signalsclass.seriesVirtual Base Class for Time Series and Signalsclass.signalSeries signalSeries Classclass.single Class singleclass.string Class stringclass.stringFactor Class stringFactorclass.stringOrdered Class stringOrderedclass.structure Class structureclass.terminal Class terminalclass.text Class textclass.textConnection Class textConnectionclass.timeDate Time and Date Classclass.timeEvent Event Classclass.timeInterval Virtual Classes for Time-Related Objectsclass.timeRelative Relative Time Class

33

Data Types

class.timeSequence Time Sequence Classclass.timeSeries Calendar Time Series Classclass.timeSpan Time Span Classclass.timeZone Time Zone Classesclass.timeZoneC Time Zone Classesclass.timeZoneS Time Zone Classesclass.vector Class vectorclass.while Class whilecomplex Complex Valued Objectscoxph.object Proportional Hazards Regression Objectcusum.object Cusum Quality Control Chart Objectdata.class Class of an Objectdata.frame.object Data Frame Objectsdesign.object Design Objectsdouble Double Precision Objectsextends Test Relations Between Classesfactanal.object Factor Analysis Objectsfactor Create Factor Objectfamily Generate a Family Objectfamily.default Generate a Family Objectfamily.object A Family of GLM Modelsformula.object Model Formula Objectsgam.object Generalized Additive Model Objectgaussian Generate a Family ObjectgetClass Get the Definition of a ClassgetClassDef Get the Definition of a ClassgetClassVersions Get Version Information for a ClassgetClasses Get the Classes Defined on a ChaptergetObjectClass Get Object ClassesgetSlots The Names, Classes of the Slots for an Objectglm.object Generalized Linear Model Objecthtest.object Hypotheses Testing Objectsinherits Test Inheritance of an Objectinteger Integer Objectsinverse.gaussian Generate a Family Objectis Test Relations Between Classesis.array Multi-Way Arraysis.atomic Test for Recursive or Atomic Objects

34

Data Types

is.bdCharacter Big Data Character Vectoris.bdFactor Big Data Factorsis.bdLogical Big Data Logical Vectorsis.bdNumeric Big Data Numeric Vectorsis.bdVector Big Data Vectorsis.character Character Objectsis.complex Complex Valued Objectsis.double Double Precision Objectsis.factor Create Factor Objectis.function Function Objectsis.integer Integer Objectsis.language Test for Recursive or Atomic Objectsis.list List Objectsis.logical Logical Objectsis.matrix Matrix Objectsis.name Name Objectsis.null Null Objectsis.numeric Numeric Objectsis.recursive Test for Recursive or Atomic Objectsis.single Single Precision Objectsis.symbol Name Objectsis.ts Time Series Objectsis.vector Vectors (Simple Objects)isClass Test for a Classlist List Objectslm.object Linear Least Squares Model Objectlms.object Least Median of Squares Objectloadings.object Loadings Matrix Objectsloess.object Loess Model Objectlogical Logical Objectslts.object Least Trimmed Squares Objectmaov.object Analysis of Variance Objectsmatrix Matrix Objectsmcd.object Minimum Covariance Determinant Objectmethods List Methods of Old-Style (SV3) Generic Functionsmlm Linear Least Squares Model Objectmlm.object Linear Least Squares Model Objectmve.object Minimum Volume Ellipsoid Object

35

Dates Objects

new Generate a New Objectnull Null Objectsnumeric Numeric ObjectsnumericSequence Constructor For numericSequence ClassoldMethods Version 3 Methods for S Functionspframe Construct a Parameterized Data Frame Objectpframe.object Parametrized Data Frame Objectspoisson Generate a Family Objectprincomp.object Principal Component Objectsqcc.object Quality Control Chart Objectquasi Generate a Family ObjectsetClass Define or Re-Define a Class of ObjectssetGeneric Create Generic FunctionsetGroupGeneric Create a Group Generic Functionshewhart.object Shewhart Quality Control Chart Objectsingle Single Precision Objectsslot Extract or Replace Data in Objects With SlotsslotNames The Names, Classes of the Slots for an Objectterms.object Class of Objects for Terms in a Modeltree.object Regression or Classification Tree Objecttree.sequence.object Regression or Classification Tree Objectts Time Series Objectsunclass Class Attribute of an Objectvarcomp.object Variance Component Objectsvector Vectors (Simple Objects)~ Model Formula Objects

Dates Objects as.bdTimeDate Big Data Time Date ObjectsbdTimeDate Big Data Time Date ObjectsbdTimeSpan Constructor Function For bdTimeSpan Classchron Create a Chronological Objectclass.positions Virtual Classes for Time-Related Objectsclass.positionsCalendar Virtual Classes for Time-Related Objectsclass.positionsNumeric Virtual Classes for Time-Related Objectsclass.timeDate Time and Date Classclass.timeEvent Event Classclass.timeInterval Virtual Classes for Time-Related Objects

36

Dates Objects

class.timeRelative Relative Time Classclass.timeSpan Time Span Classclass.timeZone Time Zone Classesclass.timeZoneC Time Zone Classesclass.timeZoneS Time Zone Classescts Regular Calendar Time Series Objectscut.dates Create a Factor from a Dates Objectdates Generate Datesday.of.week Convert between Julian and Calendar Datesdays Return Various Periods from a Time or Date Objectformat.dates Support for Function dates .hms Return Various Periods from a Time Vectorholiday.AllSaints Holiday Generating Functionsholiday.Anzac Holiday Generating Functionsholiday.Australia Holiday Generating Functionsholiday.Bastille Holiday Generating Functionsholiday.Canada Holiday Generating Functionsholiday.Christmas Holiday Generating Functionsholiday.Columbus Holiday Generating Functionsholiday.Easter Holiday Generating Functionsholiday.GoodFriday Holiday Generating Functionsholiday.Independence Holiday Generating Functionsholiday.Labor Holiday Generating Functionsholiday.MLK Holiday Generating Functionsholiday.May Holiday Generating Functionsholiday.Memorial Holiday Generating Functionsholiday.NYSE Holiday Generating Functionsholiday.NewYears Holiday Generating Functionsholiday.Presidents Holiday Generating Functionsholiday.Remembrance Holiday Generating Functionsholiday.StPatricks Holiday Generating Functionsholiday.Thanksgiving Holiday Generating Functionsholiday.Thanksgiving.Canada Holiday Generating Functionsholiday.USFederal Holiday Generating Functionsholiday.VE Holiday Generating Functionsholiday.Veterans Holiday Generating Functionsholiday.Victoria Holiday Generating Functionsholiday.fixed Holiday Generating Functions

37

Debugging Tools

holiday.nearest.weekday Holiday Generating Functionsholiday.weekday.number Holiday Generating Functionsholidays Holiday Generating Functionhours Return Various Periods from a Time Vectoris.bdTimeDate Big Data Time Date Objectsis.cts Regular Calendar Time Series Objectsjulian Convert between Julian and Calendar Datesleap.year Convert between Julian and Calendar Datesmdy Return Various Periods from a Time Vectorminutes Return Various Periods from a Time Vectormonth.day.year Convert between Julian and Calendar Datesmonths Return Various Periods from a Time or Date Objectorigin Generate Datesquarters Return Various Periods from a Time or Date Objectseconds Return Various Periods from a Time Vectorseq.dates Sequences of DatestimeAlign Alignment of TimestimeCalendar Constructor Function For timeDate ObjectstimeConvert Convert from one time zone to another.timeDate Constructor Function for timeDate ObjectstimeDefaults Time Class Internal FunctionstimeEvent Constructor Function For timeEvent ObjectstimeRelative Constructor Function for timeRelative ClasstimeSeq Sequences of TimestimeSequence Create a Time Sequence ObjecttimeSpan Constructor Function For timeSpan ClasstimeZoneC Constructor Function for timeZoneC ClasstimeZoneConvert Convert Time ZonestimeZoneList Time Zone ListtimeZoneS Constructor Function for timeZoneS Classwdydy Return Various Periods from a Time Vectorweekdays Return Various Periods from a Time or Date Objectyeardays Return Various Periods from a Time Vectoryears Return Various Periods from a Time or Date Object

Debugging Tools recover Interaction after Error

38

Deprecated Functions

Deprecated Functions Deprecated Deprecated Functionsdbdetach Database Manipulation Routines - Generic functionsdbexists Database Manipulation Routines - Generic functionsdbobjects Database Manipulation Routines - Generic functionsdbobjects.default Database Manipulation Routines - Generic functionsdbread Database Manipulation Routines - Generic functionsdbremove Database Manipulation Routines - Generic functionsdbwrite Database Manipulation Routines - Generic functionsgraphics Create a Graphics Objecthpgl Hewlett-Packard HP-GL Plottershplj Graphics Device for Hewlett-Packard LaserJet Printersls List of Datasets in Data Directoryprint.graphics Display a Graphics Objectsas.fget Indirectly Load SAS Data into Spotfire S+sas.get Convert a SAS Dataset to an Spotfire S+ Datasetstepfun Compute a Step Functionsurvreg Regression for a Parametric Survival Modelvu Create Vu-Graphs (Slides)win.graph Deprecated Graphics Device: Use graphsheet Insteadwin.printer Deprecated Graphics Device: Use graphsheet Insteadwin3 Execute a Windows Application

Documentation ? Online Information on All Sorts of ObjectsJavaHelp Online DocumentationQuestion.mark Online Information on All Sorts of ObjectsRelease.Notes Spotfire S+ for Windows Release NotesTRUNC_AUDIT Truncate the Audit Fileagain Display, Edit, Re-evaluate and Save Past Spotfire S+

Expressionsargs Display the Argument List of a Functionaudit.file Name of the File Used for the Auditfind.doc Find Help File Containing a Specific Help Topic.help Online Documentationhelp.findsum Help Systemhelp.off Help System

39

Dynamic Graphics

help.on.help Online Documentationhelp.running Help Systemhelp.start Help Systemhistory Display, Edit, Re-evaluate and Save Past S-PLUS

Expressionsprompt Construct Documentation for Function or Dataprompt.data.frame Construct Documentation for Function or Dataprompt.default Construct Documentation for Function or DatapromptHtml Construct HTML Documentation for a Function or DatareadDoc Read a Documentation Fileslynx Online Documentationstamp Time Stamp Output, Graph, and Audit Filetopic List Functions and Datasets Related to a Phraseversion.number Spotfire S+ Version Information.

Dynamic Graphics brush Brush a Matrix of Scatter Plotsdouble.buffer Control double buffering of graphics window for dynamic

graphicsspin Display Rotating Three Dimensional Scatterplots

Error Handling Command.edit Command Line Editing in Spotfire S+DBLEPR Printing from a Fortran RoutineINTPR Printing from a Fortran RoutineREALPR Printing from a Fortran RoutineXERROR Error Output and Termination for Fortran RoutinesXERRWV Error Output and Termination for Fortran Routinesbrowser Browse an Object - Generic functionbrowser.default Browse Interactively in a Function's Framedebugger Computational State at the Time of an Errordump.calls Save All Calls or Frames on Errorsdump.frames Save All Calls or Frames on Errorserror.level Return or Modify the Current Error LevelgetOption Set or Return Optionsinfo Information on the Current Spotfire S+inspect Diagnostic Evaluation Under Interactive Controlmasked Report Masked S-PLUS Objectson.exit Exit Expression For a Function

40

Genetics Related Functions

options Set or Return Optionsproblem.summary Report the number of warnings and errors so far in the

current session.restart Take Over Error Handlingsend.self Send a Signal to the S Processstd.trace Control over Tracingstd.xtrace Control over Tracingstop Error and Warning Messagesstopifnot Stop if not All Truesys.trace Control over Tracingtprint Trace Calls to Functionstrace Trace Calls to Functionstrace.on Control over Tracingtraceback Return Call Stacktry Continue after errorsuntrace Trace Calls to Functionswarning Error and Warning Messageswarnings Print Warning Messagesxerror Error Message Handling and Control for Fortran Routinesxerror.clear Error Message Handling and Control for Fortran Routinesxerror.maxpr Error Message Handling and Control for Fortran Routinesxerror.setfile Error Message Handling and Control for Fortran Routinesxerror.summary Error Message Handling and Control for Fortran Routines

Genetics Related Functions align.pedigree Generate Plotting Information for a Pedigreeautohint Align a pedigree to print wellbesthint Create a hints matrix for a pedigree.familycheck Error Check for a Family Classificationkinship Compute a kinship matrixlmekin Mixed Effects Model Using a Kinship Matrix.makefamid Identify family groupsmakekinship Create a sparse kinship matrixpedigree Create Pedigree Structureplot.pedigree Plot Pedigrees

Graphical Devices .Device Control Multiple Graphics Devices

41

Graphical Devices

.Devices Control Multiple Graphics DevicesDevice.Default Initialize Graphics DeviceDevices List of Graphical Devicesclose.screen Split a Graphics Display and Control Multiple Screensdev.ask Pause between Plotsdev.control Copy Graphics Between Graphics Devicesdev.copy Copy Graphics Between Graphics Devicesdev.cur Control Multiple Graphics Devicesdev.list Control Multiple Graphics Devicesdev.next Control Multiple Graphics Devicesdev.off Control Multiple Graphics Devicesdev.prev Control Multiple Graphics Devicesdev.print Copy Graphics Between Graphics Devicesdev.set Control Multiple Graphics Devicesdev.start Control Multiple Graphics Devicesemf.graph Enhanced Metafile Graphics Deviceerase.screen Split a Graphics Display and Control Multiple Screensgraphics.off Turn Off All Graphics Devicesgraphsheet Graphics Device for Windows/NTgraphsheet.options Options for graphsheet Graphics Devicejava.graph Graphics Device for Java-Enabled Spotfire S+motif Graphics Device for the X11 Window Systempdf.graph Graphics Device to Produce Adobe Portable Document

Formatpostscript Graphics Device for PostScript Printersprinter Graphics Device for Any Terminalprompt.screen Split a Graphics Display and Control Multiple Screensps.colors.rgb Colors for PostScript driverps.hsb2rgb Convert PostScript Color Specificationsps.options Set or Return PostScript Optionsps.options.send Send PostScript Optionsps.paper.regions Imageable Regions for PostScript Printersps.rgb2hsb Convert PostScript Color Specificationsps.setcolor.hsb PostScript Procedures for Setting Colorsps.setcolor.rgb PostScript Procedures for Setting Colorsps.setfont.latin1 PostScript Procedures for Font Selectionps.setfont.std PostScript Procedures for Font Selectionpscript Graphics Device for PostScript Printers

42

Hexagonal Binning

rgb2matrix Convert X11 rgb.txt file to matrixscreen Split a Graphics Display and Control Multiple Screenssplit.screen Split a Graphics Display and Control Multiple Screenstek14 Tektronix Graphics Devicestek14q Tektronix Graphics Devicestree.screens Partition the Graphics Area for Tree Plotswin.colorscheme Set the Color Scheme Used By graphsheet .wmf.graph Windows Metafiles Graphics Devicexgetrgb Inquire current color settings

Hexagonal Binning cell2xy Compute x , y Coordinates From Hexagon Cell Idserode.hexbin Erode a Hexagonally Binned Imagehex.legend Add a Legend Hexagonal Lattice Plothexagons Add Hexagonal Cells to Plot of "hexbin" Objecthexbin Bivariate Binning into Hexagonal Cellsidentify.hexbin Identify Points On a Hexagonal Binned Plotpanel.hexbin Panel Function for Hexbins panel.hexbin.lmline Panel Function for Hexbins panel.hexbin.loess Panel Function for Hexbins panel.hexbin.smooth.spline Panel Function for Hexbins plot.hexbin Plot A Hexagonal Latticerayplot Adds Rays with Optional Confidence Arcs (Sectors)smooth.hexbin Hexagonal Bin Smoothingsummary.hexbin Summary Method for a Hexagonally Binned Objectxy2cell Compute Hexagon Cell Ids From x and y

High-Level Plots acf.plot Plot Autocovariance or Autocorrelationarima.diag.plot Plot Diagnostics for ARIMA Modelbarplot Bar Graphbd.crosstabs Create Crosstabulationbiplot Biplot of Multivariate Databiplot.default Biplot of Multivariate Databiplot.factanal Biplots for Principal Components and Factor Analysis

Modelsbiplot.princomp Biplots for Principal Components and Factor Analysis

Modelsboxplot Boxplots

43

High-Level Plots

bxp Boxplots From Processed Dataclusplot Clusplot - Generic Functionclusplot.default Bivariate clusplotclusplot.partition Bivariate Clusplot of a Partitioning Objectcontour Contour Plotcontour.old Contour Plotcoplot Conditioning Plotdotchart Draw a Dot Charterror.bar Plot Pointwise Error Barsfaces Plot Symbolic Facesgraphsheet.options Options for graphsheet Graphics Devicehist Plot a Histogramhist.factor Plot a Histogramimage Plot a Grayscale or Color Imageinteraction.plot Two-Way Interaction Plotslag.plot Plot Lagged Scatter Plotsmonthplot Seasonal Subseries Plotmulbar Multiple Bar Plotnclass.fd Freedman-Diaconis Method for Histogram Bin Countsnclass.scott Scott Method for Histogram Bin Countsnclass.sturges Sturges Method for Histogram Bin Countspairs Produce All Pairwise Scatter Plots - Generic Functionpairs.data.frame Produce a Scatterplot Matrix for a Data Framepairs.default Produce a Scatterplot Matrixpar Graphical Parameterspartition.tree Plot a Low-Dimensional Tree Objectpersp Three-Dimensional Perspective Plotspie Pie Chartsplclust Plot Trees From Hierarchical Clusteringplot Plots - Generic functionplot.aareg Plot an aareg Objectplot.agnes Plots of an Agglomerative Hierarchical Clusteringplot.bdPrincomp Plot of the Variances of Derived Variablesplot.bdSignalSeries Big-Data Signal Plotplot.bdTimeSeries Big-Data Calendar Time Series Plotplot.compare.fits Comparison Plots for Linear Modelsplot.data.frame Distributional Plots of Variables in a Data Frameplot.default Scatter Plots

44

High-Level Plots

plot.design Plot a Function of Each Level of Factors or Termsplot.diana Plots of a Divisive Hierarchical Clusteringplot.factor Summary Plots by Factorsplot.gam Plot Components of a GAM Objectplot.glm Generate Diagnostic Plots for a GLM Objectplot.hexbin Plot A Hexagonal Latticeplot.kaplanMeier Plot Method for kaplanMeier plot.lmRobMM Generate Diagnostic Plots for a Robust LM Objectplot.lme Plot an lme Objectplot.lms Diagnostic Plots for an "lms" Objectplot.loadings Plot Loadingsplot.loess Display of Fitted LOESS Models by Coplotsplot.lts Diagnostic Plots for an "lts" Objectplot.mcd Diagnostic Plots for an "mcd" Objectplot.mlm Plot a Multiresponse Linear Modelplot.mona Banner of Monothetic Divisive Hierarchical Clusteringsplot.multicomp Confidence Bound Plotsplot.mve Diagnostic Plots for an "mve" Objectplot.partition Plot of a Partition of the Data Setplot.pedigree Plot Pedigreesplot.preplot.gam Plot Components of a GAM Objectplot.preplot.loess Display Local Regression Surfaceplot.princomp Plot of the Variances of Derived Variablesplot.signalSeries Signal Plotplot.survfit Plot Method for survfit plot.timeSeries Calendar Time Series Plotplot.times Plot Method for Dates or Times Objectsplot.tree Plot a Tree Objectplot.varcomp Plot of Random ComponentsplotTimeDate Plot a timeDate Objectplotfit Plot of a Two-Way Fitpltree Clustering Trees - Generic Functionpltree.agnes Clustering Tree Of Agglomerative Hierarchical Clusteringspltree.diana Clustering Tree Of Divisive Hierarchical Clusteringspltree.hierarchical Clustering Tree of an Agglomerative or a Divisive

Hierarchical Clusteringpreplot.loess Display of Fitted LOESS Models by Coplotsqqnorm Quantile-Quantile Plots - Generic Function

45

Input/Output-Files

qqnorm.default Quantile-Quantile Plots - Generic Functionqqplot Quantile-Quantile Plots - Generic Functionrayplot Adds Rays with Optional Confidence Arcs (Sectors)sablplot Plot a Sabl Decompositionscatter.smooth Scatter Plot with a Smooth Curvescreeplot Plot of the Variances of Derived Variablesscreeplot.bdPrincomp Plot of the Variances of Derived Variablesscreeplot.princomp Plot of the Variances of Derived Variablessmatrix Symbolic Matrix for Multivariate Dataspec.pgram Estimate Spectrum with Smoothed Periodogramspec.plot Plot Spectraspectrum Estimate Spectrum of Time Seriesstars Star Plots of Multivariate Datastarsymb Plot a Single Star Symbolstem Stem and Leaf Displaysymbols Draw Symbols on a Plottslines Plot Multiple Time Seriestsplot Plot Multiple Time Seriestspoints Plot Multiple Time Seriesusa United States Coastline and State Boundaries

Input/Output-Files .System Execute a UNIX CommandcontentsData Gets the Names of All Data Sets, Sheets, or Tables in a

Specified Data File or DatabaseSys.getenv Get Environment VariablesSys.getlocale Set or get locale-specific informationSys.getpid Get Process IDSys.localeconv Set or get locale-specific informationSys.putenv Set Environment VariablesSys.setlocale Set or get locale-specific informationSys.setenv Sets Environment Variables for Use by Other Processes

Called from Spotfire S+Sys.withlocale Set or get locale-specific informationagain Display, Edit, Re-evaluate and Save Past S-PLUS

Expressionsbasename Manipulate File Pathscat General Printingclose Connection Objects

46

Input/Output-Files

closeDBConnection Closes open connection to an ODBC data sourcecloseData Close A Data Handlecount.fields Count the Number of Fields per Linedata.dump Produce Text Representations of S-PLUS Objectsdata.restore Bring Back Data-Dumped Objectsdget Write a Text Representation of an S-PLUS Objectdir Manipulate File Pathsdir.create File and Directory Manipulationdirname Manipulate File Pathsdos Execute a DOS Commanddput Write a Text Representation of an S-PLUS Objectdump Produce Text Representations of S-PLUS ObjectsdumpChapter Dump Objects in Specified ChapterexecuteSQL Execute SQL QueriesexecuteSql Execute SQL QueriesexportData Export Datafifo Connection Objectsfile Connection Objectsfile.append File and Directory Manipulationfile.copy File and Directory Manipulationfile.create File and Directory Manipulationfile.exists Check if a File Existsfile.info File and Directory Manipulationfile.realpath Absolute path name for a file.file.remove Absolute path name for a file.file.rename Absolute path name for a file.file.show Display Filesfile.splitpath Split a File Pathfiles.in.dir Files in a DirectorygetDataInfo Information on Data File Via a Data Handlegetenv Get Environment Variableshistory Display, Edit, Re-evaluate and Save Past S-PLUS

Expressionshtml.table Generate HTML Table of DataimportData Import DataimportObjToDF Create a Data Frame From an Import ObjectinitSybaseConnection Utility functions for importData and exportDatainputWaiting Check Connection.

47

Input/Output-Files

is.dir Check if a Directory Existsis.symlink Check if a Directory ExistsisDatabaseType Utility functions for importData and exportData isDirectDatabaseType Utility functions for importData and exportData isOpen Check Connection.list.files List the Files in a Directorymkdir Make a Directorynew.database Make a New Directory Databaseopen Connection ObjectsopenDBConnection Maintains open connection to an ODBC data source

between callsopenData Open an External Data FileopenOrImportData Open and/or Import Datapath.expand Expand ~ in File Pathspipe Connection Objectsprintgraph Print the Current Plotread.dcf Read and Write Data in DCF Formatread.from.clipboard Read Text from the Windows Clipboardread.table Create a Data Frame by Reading a TablereadNextDataRows Read Next Block of Rows from External Filereadline Read a Line from the Terminalrmdir Remove a Directoryscan Input Data from a File or Connectionsink Send Spotfire S+ Output to a Filesink.number Send Spotfire S+ Output to a Filesource Parse and Evaluate Spotfire S+ Expressions from a Filestderr Connection Objectsstdin Connection Objectsstdout Connection Objectssystemfile Find Names of Spotfire S+ System FilestextConnection Connection Objectsunix Execute a UNIX Commandunix.shell Execute a UNIX Commandunlink Remove a Filewrite Write Data to ASCII Filewrite.dcf Reads and Writes Data in Dcf Formatwrite.table Write Matrix of Data to a Filewrite.to.clipboard Copy Text to the Windows Clipboard

48

Interacting with Plots

writeNextDataRows Write a Data Frame to an External File

Interacting with Plots dev.ask Pause between Plotsframe Advance Graphics Device to Next Frame or Figuregraphicsmode Redraw Graphics and Change Graphics Terminal Stateidentify Identify Points on Plot - Generic Functionidentify.cusum Identify Points On a Cusum Quality Control Chart.identify.default Identify Points on Plot - Generic Functionidentify.hexbin Identify Points On a Hexagonal Binned Plotidentify.shewhart Identify Points On a Shewhart Quality Control Chart.identify.tree Identify Observations in Tree Nodesidentify.xyplot Identify Points on Trellis Xyplotlocator Get Coordinates from Plotlocator.2dtrellis Get Coordinates from Trellis Plotmenu Menu Interaction Functionpath.tree Follow Paths to Selected Nodes of a Treeprintgraph Print the Current Plotredraw Redraw Graphics and Change Graphics Terminal Statetextmode Redraw Graphics and Change Graphics Terminal Statexgetrgb Inquire current color settings

Interfaces to Other Languages .C Call a Fortran or C Routine.First.lib Shared Functions and Data Sets.Fortran Call a Fortran or C Routine.Internal Call Internal C Code.Last.lib Shared Functions and Data Sets.System Execute a UNIX CommandcontentsData Gets the Names of All Data Sets, Sheets, or Tables in a

Specified Data File or DatabaseDBLEPR Printing from a Fortran RoutineINTPR Printing from a Fortran RoutineNM Display Symbol Table of Compiled CodeREALPR Printing from a Fortran RoutineS_alloc Storage Allocation in CXERROR Error Output and Termination for Fortran RoutinesXERRWV Error Output and Termination for Fortran Routines

49

Jackknife Methods

as.double Double Precision Objectsas.single Single Precision Objectscall_S Call Spotfire S+ from a C Routinedos Execute a DOS Commanddouble Double Precision ObjectsexecuteSQL Execute SQL QueriesexecuteSql Execute SQL QueriesexportData Export DataimportData Import Datainteractive Test For Interactive Execution of Sis.double Double Precision Objectsis.loaded Code Availabilityis.single Single Precision Objectslibrary Shared Functions and Data Setsmodule Access Add-On ModuleopenData Open an External Data FileopenOrImportData Open and/or Import Dataperl Call Perl from within Spotfire S+sas.contents List the Variables in a SAS Datasetsas.datasets List SAS Datasets Stored in a Directorysingle Single Precision Objectssymbol.C Code Availabilitysymbol.For Code Availabilitysymbol.S Code Availabilityunix Execute a UNIX Commandunix.shell Execute a UNIX Commandxerror Error Message Handling and Control for Fortran Routinesxerror.clear Error Message Handling and Control for Fortran Routinesxerror.maxpr Error Message Handling and Control for Fortran Routinesxerror.setfile Error Message Handling and Control for Fortran Routinesxerror.summary Error Message Handling and Control for Fortran Routines

Jackknife Methods jackknife General Nonparametric Jackknifejackstats Calculate Jackknife Statisticsplot.resamp Plot Method for Resample Objectsprint.resamp Print a Resample Objectprint.summary.resamp Print a Summary of Resample Object

50

Library of Correlated Data Methods

qqnorm.resamp Quantile-Quantile Plots for Resample Objectsresamp.get.dimnames Support for Bootstrap and Jackkniferesamp.get.fit.func Support for Bootstrap and Jackkniferesamp.get.indices Support for Bootstrap and Jackknifesummary.resamp Summary Method for Resample Objects

Library of Correlated Data Methods ACF.glme Autocorrelation Function for glme ResidualsProstate Prostate cancer data of American men from a subset of

SEER DataSeizure Effect of progabide on frequency of seizures.Socatt British Social Attitudes Survey - 1983SpruceGrpd Growth of sitka spruce trees over three growing seasons.Terat.Binary Teratological Data on RatsVariogram.glme Calculate Semi-variogram for Residuals from a glme ObjectWheeze Data on Health Effects of Air Pollutioncgeefit Function to call C++ Cgeefit Functioncoef.gee Extracts coefficients from gee ObjectscorDesign Create a Multiblock or a Multilayer Correlation DesigncorDesign.object Multiblock or Multilayer Correlation Design Objectfitted.gee Compute fitted values for for gee Objectsfitted.glmList Extract glmList Fitted Valuesfitted.glme Extract glme Fitted Valuesfitted.glmeStruct Calculate glmeStruct Fitted Valuesgee Fit a Generalized Estimation Equation Modelgee.fit Fit a Generalized Estimation Equation Model with

Structured Covariancegee.fit.object Generalized Estimating Equation Objectgee.object Generalized Estimating Equation ObjectgeeControl Set Control Parameters for Generalized Estimation Equation

ModelsgeeDesign Design a Generalized Estimation Equation ModelgeeDesign.object Generalized Estimating Equation Design ObjectglmList List of glm Objects with a Common ModelglmList.groupedData glmList Fit from a groupedData Objectglme Generalized Linear Mixed-Effects Modelsglme.glmList GLME fit from glmList Objectglme.groupedData GLME fit from groupedData ObjectglmeStruct Generalized Linear Mixed-Effects Structure

51

Library of Missing Data Methods

initialize.glmeStruct Initialize a glmeStruct Objectintervals.glme Confidence Intervals on glme Parameterspredict.glmList Predictions from a glmList Objectpredict.glme Predictions from an glme Objectprint.glmList Print a glmList Objectprint.glme Print a glme Objectprint.summary.glmList Print a summary.glmList Objectprint.summary.glme Print a summary.glme ObjectranDesign Specify a Mixed Models to be fit with Generalized

Estimating EquationsrecordDesign Sort a Data Frame by Specified Variables and Provide

Record IDsresiduals.gee Computes residuals for gee Objectsresiduals.glmList Extract glmList Residualsresiduals.glme Extract glme Residualsresiduals.glmeStruct Calculate glmeStruct Residualssummary.glmList Summarize a glmList Objectsummary.glme Summarize a glme Objectsummary.recordDesign Summary Method for recordDesign Objectsupdate.glmList Update a glmList Objectupdate.glme Update a glme ObjectvarDesign Create a Variance Design for a Generalized Estimating

Equation ModelvarDesign.object Variance Design Objectxglm Fit Extended Generalized Linear Model

Library of Missing Data Methods Gauss Multivariate Normal Model ObjectGauss.object Multivariate Normal Model ObjectGauss.start Initial Values for Gauss functionsGauss.start.default Initial Values for Gauss functionsGauss.start.preGauss Initial Values for Gauss functionsGaussNames Parameter Names For Multivariate Normal ModelsLoglin Log-Linear Model ObjectLoglin.get.x Compute the Model MatrixLoglin.object Log-Linear Model ObjectLoglinNames Cell Names For Log-Linear Models[.Gauss Extract or Replace Parts of an Object[.Loglin Extract or Replace Parts of an Object

52

Library of Missing Data Methods

[.cgm Extract or Replace Parts of an Object[.miVariable Subscript an miVariable Objectalgorithm Model Algorithmall.names.assigned Find Names in an Expresionall.names.used Find Names in an Expresionas.miList Create "miList" Objectas.miVariable Create "miVariable" Objectbelt Seatbelt use in Injury Accidentscgm Conditional Multivariate Gaussian Model Objectcgm.object Conditional Multivariate Gaussian Model Objectcgm.start Starting Values in Conditional Multivariate Gaussian

ModelscgmDesign Get Design Matrix in Conditional Gaussian ModelscgmLmCoef Linear Model Coefficient in Conditional Gaussian ModelscgmNames Parameter Names For Conditional Multivariate Gaussian

Modelscheck.Cgm.prior Check Log-linear component of the CGM Prior.check.Gauss.prior Check an normal Inverse Wishart Priorcheck.Loglin.prior Parameters in a Log-linear Model Prior.chi.Loglin chi-squared statistic for incomplete categorical datacholesterol Example data frames for missing data librarycholesterolImpExample Example data frames for missing data librarycompleteCgm Conditional Gaussian Model for Complete DatacompleteGauss Multivariate Normal Models for Complete DatacompleteLoglin Log-Linear Models for Complete DataconvertLoglin Contingency table to data framecrime Categorical Crime DatacrimeImpExample Categorical Crime Datada.object "da" ObjectdaAcfPlot ACF Plots for missmodel objectsdaCgm Data Augmentation for Conditional Gaussian ModelsdaCgm.control Set Control Parameters for daCgm daCgm.default Data Augmentation for Conditional Gaussian ModelsdaCgm.methods Data Augmentation for Conditional Gaussian ModelsdaCgm.missmodel Data Augmentation for Conditional Gaussian ModelsdaCgm.preCgm Data Augmentation for Conditional Gaussian ModelsdaGauss Data Augmentation for Multivariate Normal ModelsdaGauss.control Set Control Parameters for daGauss

53

Library of Missing Data Methods

daGauss.default Data Augmentation for Multivariate Normal ModelsdaGauss.methods Data Augmentation for Multivariate Normal ModelsdaGauss.missmodel Data Augmentation for Multivariate Normal ModelsdaGauss.preGauss Data Augmentation for Multivariate Normal ModelsdaLoglin Data Augmentation for Log-Linear ModelsdaLoglin.compute Data Augmentation for Log-Linear ModelsdaLoglin.control Set Control Parameters for daLoglin daLoglin.default Data Augmentation for Log-Linear ModelsdaLoglin.methods Data Augmentation for Log-Linear ModelsdaLoglin.missmodel Data Augmentation for Log-Linear ModelsdaLoglin.preLoglin Data Augmentation for Log-Linear ModelsdataDepPrior Data Dependent Priors.dataDepPrior.preCgm Data Dependent Prior for CGMdataDepPrior.preGauss Data Dependent Prior; Gaussian ModeldataDepPrior.preLoglin Data Dependent Prior; Log-linear Modelem.object "em" ObjectemCgm EM Algorithm for Conditional Gaussian ModelsemCgm.control Set Control Parameters for emCgm emCgm.default EM Algorithm for Conditional Gaussian ModelsemCgm.methods EM Algorithm for Conditional Gaussian ModelsemCgm.missmodel EM Algorithm for Conditional Gaussian ModelsemCgm.preCgm EM Algorithm for Conditional Gaussian ModelsemGauss EM Algorithm for Multivariate Normal ModelsemGauss.control Set Control Parameters for emGauss emGauss.default EM Algorithm for Multivariate Normal ModelsemGauss.degenerate Estimates in Multivariate Normal ModelsemGauss.methods EM Algorithm for Multivariate Normal ModelsemGauss.missmodel EM Algorithm for Multivariate Normal ModelsemGauss.preGauss EM Algorithm for Multivariate Normal ModelsemLoglin EM Algorithm for Log-Linear ModelsemLoglin.compute EM Algorithm for Log-Linear ModelsemLoglin.control Set Control Parameters for emLoglin emLoglin.default EM Algorithm for Log-Linear ModelsemLoglin.methods EM Algorithm for Log-Linear ModelsemLoglin.missmodel EM Algorithm for Log-Linear ModelsemLoglin.preLoglin EM Algorithm for Log-Linear Modelsget.margins.Loglin Computes Marginal ModelsimpCgm Impute Both Factor and Numeric Data

54

Library of Missing Data Methods

impCgm.default Impute Data under CGMimpCgm.methods Impute Data under CGMimpCgm.missmodel Impute Data under CGMimpCgm.preCgm Impute Data under CGMimpGauss Impute Multivariate Normal DataimpGauss.default Impute Multivariate Normal DataimpGauss.methods Impute Multivariate Normal DataimpGauss.missmodel Impute Multivariate Normal DataimpGauss.preGauss Impute Multivariate Normal DataimpLoglin Impute Factor DataimpLoglin.default Impute Factor DataimpLoglin.methods Impute Factor DataimpLoglin.missmodel Impute Factor DataimpLoglin.preLoglin Impute Factor Datais.mi Presence of Multiple Imputationsis.miList Presence of Multiple Imputationsis.miVariable Presence of Multiple Imputationsis.missmodel "missmodel" Objectsis.preCgm "preCgm" Objectsis.preGauss "preGauss" Objectsis.preLoglin "preLoglin" Objectslanguage Foreign Language Attitude Scale datalanguageImpExample Foreign Language Attitude Scale datalength.miVariable Length of an miVariable object.length<-.miVariable Length of an miVariable object.logpost Compute Log-Posterior Modelogpost.Gauss Log-posterior Density for Multivariate Normal Modelslogpost.Gauss.compute Mode of Log-posterior Distributionlogpost.Loglin Log-Posterior Density for Incomplete Factor Datalogpost.cgm Log-posterior Density for Conditional Gaussian Modelsmarijuana Changes in Heart Rate due to Marijuana Usemcar Diagnostics for "Missing Completely At Random"mdCgm Estimates for Conditional Gaussian ModelsmdGauss Estimates for Multivariate Normal ModelsmdLoglin Estimates for Loglinear Modelsmi.object Multiple imputations objectmiAnova Compute an Anova Table for a Multiple Imputations Object

- Generic function

55

Library of Missing Data Methods

miAnovaAux Compute an Anova Table for a Multiple Imputations Object - Generic function

miApply Apply a Function to Multiple ImputationsmiChiSquareTest Combine Multiple Imputation InferencesmiDiscard Discard Multiple ImputationsmiEval Evaluate an Expression in Parallel for Multiple ImputationsmiEvalA Evaluate an Expression in Parallel for Multiple ImputationsmiFTest Combine Multiple Imputation InferencesmiLikelihoodTest Combine Multiple Imputation InferencesmiList Create "miList" ObjectmiList.object Multiple imputations objectmiMean Compute Means or Variances Across ImputationsmiMeanSE Combine Multiple Imputation InferencesmiMeanSEAux Combine Multiple Imputation InferencesmiMeanSEAux.lm Combine Multiple Imputation InferencesmiMeanSEDefault Combine Multiple Imputation InferencesmiMeanSEList Combine Multiple Imputation InferencesmiMeanSEMatrix Combine Multiple Imputation InferencesmiModifyExpr Modify an Expression for Multiple Imputation EvaluationmiNames Names of Multiple ImputationsmiPrint Print an object containing multiple imputationsmiReps Number of Multiple ImputationsmiSubscript Extract or assign a single multiple imputation setmiSubscript<- Extract or assign a single multiple imputation setmiSummary Summary for Multiple Imputations Objects - Generic

FunctionmiSummaryAux Summary for Multiple Imputations Objects - Generic

FunctionmiSummaryAux.default Summary for Multiple Imputations Objects - Generic

FunctionmiSummaryAux.lm Summary Method for Multiple Imputation Linear ModelsmiTrim Reorganize a Multiple Imputations ObjectmiTrimAux Reorganize a Multiple Imputations ObjectmiVar Compute Means or Variances Across ImputationsmiVariable Create "miVariable" ObjectmiVariable.object Multiple imputations objectmiss Describe Missing Data Patternsmissmodel.object "missmodel" ObjectparamIter Extract Parameters from a missmodel Object

56

Library of Missing Data Methods

paramIter.Gauss Extract Parameters from a missmodel ObjectparamIter.Loglin Extract Parameters from a missmodel ObjectparamIter.cgm Extract Parameters from a missmodel ObjectparamIter.missmodel Extract Parameters from a missmodel Objectplot.mcar Plot diagnostics for "Missing Completely at Random"

(MCAR)plot.miss Graphically displays pattern of missing dataplot.missmodel Plots a "missmodel" object produced by data augmentationpreCgm Preprocessor for Conditional Gaussian Model RoutinespreCgm.object Class "preCgm" preGauss Preprocessor for Multivariate Normal Model RoutinespreGauss.object Class "preGauss" preLoglin Preprocessor for Log-Linear Models RoutinespreLoglin.object Class "preLoglin" print.Gauss Print a Class "Gauss" Objectprint.Loglin Print a Class "Loglin" Objectprint.cgm Print a Class "cgm" Objectprint.da Print a Class "da" Objectprint.em Print a Class "em" Objectprint.mcar Print tests for "Missing Completely at Random" (MCAR)print.miSummary.lm Use print on an miSummary.lm objectprint.miss Print information about missing value patterns.print.missmodel Print a Class "missmodel" Objectprint.preCgm Print a Class "preCgm" Objectprint.preGauss Print a Class "preGauss" Objectprint.preLoglin Print a Class "preLoglin" ObjectpriorGauss Prior Parameters in Multivariate Normal ModelpriorLoglin Prior Parameters in Log-linear Modelprot.dat Protective Service DataredundantList Check list for redundancyshow.miVariable Print an miVariable objectstlouis3 St. Louis Risk Research Projectsummary.miVariable Summarize an miVariable objectsummary.miss Print information about missing value patterns.worstFraction Worst Fraction of Missing InformationworstFraction.Gauss Worst Fraction of Missing InformationworstFraction.Loglin Worst Fraction of Missing InformationworstFraction.cgm Worst Fraction of Missing Information

57

Library of Robust Methods

worstFraction.methods Worst Fraction of Missing InformationworstLinFun Calculate "worst linear function of the parameters"

Library of Robust Methods RCp A Robust Version of Mallows' Cpadd1.lmRob Add Terms to a Robust Linear Model Objectanova.lmRob Use anova() on an lmRob objectaovRob Fit a Robust Analysis of Variance Modelchi.weight Chi (Weight) Functioncor.lmRob Robust Correlation Matrixcov.lmRob Robust Covariance MatrixcovRob Robust Covariance/Correlation Matrix EstimationcovRob.control Control Parameters for Robust Covariance Estimationcrossvalidate.discRob Crossvalidation Method for class discRob deviance.lmRob Use deviance() on an lmRob objectdiscRob Robust Discriminant Analysisdrop1.lmRob Compute an Anova Object by Dropping Termsfit.models Model ComparisongammaMLE Maximum Likelihood Parameter Estimates for Asymmetric

DistributionsgammaMLE.control Control for MLE Estimate of a Gamma DistributiongammaRob Robust Asymmetric Distribution Parameter EstimatesgammaRob.control Control for the Robust Gamma Parameter EstimatorglmRob Fit a Robust Generalized Linear ModelglmRob.cubif.control Control for Bounded Influence Robust GLM EstimatorglmRob.mallows.control Control for Mallows-type Robust GLM EstimatorglmRob.misclass.control Control for Misclassification Robust GLM EstimatorglmRob.object Robust Generalized Linear Model Objectsidentify.cov Identify a cell in a Correlation Image Displayimage.cov Correlation Image Displayimport.dat Monthly Imports and Import Taxes of Argentinalawson.dat Lawson and Gold Data SetlmRob High Breakdown and High Efficiency Robust Linear

RegressionlmRob.RFPE Robust Final Prediction ErrorslmRob.effvy Constant for the Optimal Loss (Weight) FunctionlmRob.fit.compute Fit a Robust Linear ModellmRob.genetic.control Control for Robust Linear Regression with Genetic

Algorithm

58

Library of Robust Methods

lmRob.object Robust Linear Model ObjectslmRob.robust.control Control Parameters for Robust Linear RegressionlmRobBI Bounded Influence Robust RegressionlmRobBI.bRobust Utility Functions for Bounded Influence Robust RegressionlmRobBI.control Control Parameters for Bounded Influence Robust

RegressionlmRobBI.cov0 Utility Functions for Bounded Influence Robust RegressionlmRobBI.cov1 Utility Functions for Bounded Influence Robust RegressionlmRobBI.eff Tuning Constant for Bounded Influence EstimatorlmRobBI.fit.S Utility Functions for Bounded Influence Robust RegressionlmRobBI.object Robust Linear Model Objects - Bounded Influence

EstimatorlmRobBI.ts1 Utility Functions for Bounded Influence Robust RegressionlognormMLE Maximum Likelihood Parameter Estimates for Asymmetric

DistributionslognormRob Robust Asymmetric Distribution Parameter EstimateslognormRob.control Control Parameters for the Robust Lognormal Parameter

Estimatorsnewtaxes.dat Monthly Import Taxes of Argentinaplot.RCp Create an RCp Plotplot.aovRob Plots for Robust Analysis of Variance Modelsplot.aovfm Comparison Plots for Analysis of Variance Modelsplot.asymfm Comparison Plots for Fitted Asymmetric Distributionsplot.asymmetric.dstn Diagnostic Plots for Asymmetric Distribution Modelsplot.covRob Plot Method for Objects of Class "covRob"plot.covfm Comparison Plots for Covariance/Correlation Modelsplot.fit.models Plot Dispatch for fit.models Objectsplot.gammaMLE Diagnostic Plots for Asymmetric Distribution Modelsplot.gammaRob Diagnostic Plots for Asymmetric Distribution Modelsplot.glmRob Diagnostic Plots for Robustly Fitted Generalized Linear

Modelsplot.glmfm Comparison Plots for Generalized Linear Modelsplot.lmRob Diagnostic Plots for Robustly Fitted Linear Modelsplot.lmRobBI Plot an lmRobBI Objectplot.lmfm Comparison Plots for Linear Regression Modelsplot.lognormMLE Diagnostic Plots for Asymmetric Distribution Modelsplot.lognormRob Diagnostic Plots for Asymmetric Distribution Modelsplot.pcompfm Comparison Plots for Principal Components Modelsplot.princompRob Plot Method for Robust Principal Components Objects

59

Library of Robust Methods

plot.table.rq Plot Table of Quantile Regression Resultsplot.weibullMLE Diagnostic Plots for Asymmetric Distribution Modelsplot.weibullRob Diagnostic Plots for Asymmetric Distribution Modelspredict.discRob Prediction Method for class discRob predict.lmRob Use predict() on an lmRob ObjectprincompRob Robust Principal Component Analysisprint.lmRobBI Print Method for an lmRobBI Objectprint.lmRobMM Use print() on an lmRobMM objectprint.summary.lmRobBI Print Method for a summary.lmRobBIprint.summary.lmRobMM Print Method for a summary.lmRobMM Objectpsi.weight Psi (Weight) Functionpsp.weight Psp (Weight) Functionranks Quantile Regression Ranksresiduals.glmRob Use residuals() on a glmRob objectresiduals.lmRob Use residuals() on an lmRob Objectresiduals.lmRobBI Compute Residuals from an lmRobBI Objectrho.weight Rho (Weight) Functionrq Quantile Regressionrq.fit.br Quantile Regression Fitting by Exterior Point Methodsrq.fit.fn Quantile Regression Fitting via Interior Point Methodsrq.object Linear Quantile Regression Process Objectrrs.test Quantile Regression Rankscore Testrsquared.lmRob Robust R-Squaredscale.lmRob Robust Scale Estimatesmooth.splineRob summary.RCp Summary Method for RCp class objectssummary.aovRob Summary Method for class "aovRob"summary.aovfm Summary Method for Analysis of Variance Modelssummary.asymfm Summary Method for Asymmetric Distribution Modelssummary.asymmetric.dstn Summary Method for Asymmetric Distribution Modelssummary.covRob Summary Method for Objects of Class "covRob"summary.covfm Summary Method for Covariance/Correlation Modelssummary.discRob Summary method for class discRob summary.discfm Summary Method for Discriminant Analysis Modelssummary.fit.models Summary Dispatch for fit.models Objectssummary.gammaMLE Summary Method for Asymmetric Distribution Modelssummary.gammaRob Summary Method for Asymmetric Distribution Modelssummary.glmRob Summary Method for Generalized Linear Model Objects

60

Linear Algebra

summary.glmfm Summary Method for Generalized Linear Modelssummary.lmRob Summary Method for class "lmRob" summary.lmRobBI Summary Method for class "lmRobBI" summary.lmfm Summary Method for Linear Modelssummary.lognormMLE Summary Method for Asymmetric Distribution Modelssummary.lognormRob Summary Method for Asymmetric Distribution Modelssummary.pcompfm Summary Method for Principal Components Modelssummary.princompRob Summary Method for Robust Principal Components

Objectssummary.weibullMLE Summary Method for Asymmetric Distribution Modelssummary.weibullRob Summary Method for Asymmetric Distribution Modelstable.rq Table of Quantile Regression Resultstest.lmRob Various Tests of Robust Regression Estimatesupdate.lmRob Use update() on an lmRob ObjectweibullMLE Maximum Likelihood Parameter Estimates for Asymmetric

DistributionsweibullMLE.control Control for the MLE of a Weibull DistributionweibullRob Robust Asymmetric Distribution Parameter EstimatesweibullRob.control Control for the Robust Weibull Parameter Estimatorweights.lmRob Robust Weight Vectorweights.lmRobBI Robust Weight Vector for Bounded Influence Estimateswww.weight Optimal Weight Functionxyellipse xyellipse

Linear Algebra %*% Matrix Multiplication Operator%c% Matrix Cross Product%o% Generalized Outer Products.laenv Tuning Parameters for Linear Algebra ComputationsMatrix-product Matrix Multiplication Operatoraperm Array Permutationsaperm.default Array Permutationsapply Apply a Function to Sections of an Arrayas.qr QR Matrix Decompositionbacksolve Backsolve Upper-Triangular Equationschol Choleski Decomposition of Symmetric MatrixcolMaxs Row and Column Summaries - min, max, and rangecolMeans Row and Column SummariescolMedians Compute medians columnwise

61

Linear Algebra

colMins Row and Column Summaries - min, max, and rangecolProds Columnwise ProductscolQuantiles Compute quantiles columnwisecolRanges Row and Column Summaries - min, max, and rangecolStdevs Row and Column SummariescolSums Row and Column SummariescolVars Row and Column Summariescrossprod Matrix Cross Productdet Determinant of a Matrixdeterminant Determinant of a Matrixdiag Diagonal Matriceseigen Eigenvalues and Eigenvectors of a Matrixeigen.default Eigenvalues and Eigenvectors of a Matrixgchol Generalized Cholesky Decompositionginverse Generalized Inverse of a MatrixgroupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.data.frame Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.default Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAnys Computes Group Sums, Means, Variances, Standard

Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

ArraygroupMeans.data.frame Computes Group Means for a Vector or Columns of an

ArraygroupMeans.default Computes Group Means for a Vector or Columns of an

ArraygroupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an Array

62

Linear Algebra

groupProds Computes Group Products for a Vector or Columns of an Array

groupProds.data.frame Computes Group Products for a Vector or Columns of an Array

groupProds.default Computes Group Products for a Vector or Columns of an Array

groupRanges Computes Group Ranges for a Vector or Columns of an Array

groupRanges.data.frame Computes Group Ranges for a Vector or Columns of an Array

groupRanges.default Computes Group Ranges for a Vector or Columns of an Array

groupStdevs Computes group standard deviations for a vector or columns of an array.

groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

ArraygroupVars.data.frame Computes Group Variances for a Vector or Columns of an

ArraygroupVars.default Computes Group Variances for a Vector or Columns of an

Arrayis.qr QR Matrix Decompositionla.env Set Tuning Parameters for Linear Algebra Computationsouter Generalized Outer Productsprcomp Principal Components Analysisqr QR Matrix Decompositionqr.Q Reconstruct the Q, R, or X Matrices from a QR Objectqr.R Reconstruct the Q, R, or X Matrices from a QR Objectqr.X Reconstruct the Q, R, or X Matrices from a QR Objectqr.coef Use a QR Matrix Decompositionqr.default QR Matrix Decompositionqr.fitted Use a QR Matrix Decompositionqr.qty Use a QR Matrix Decompositionqr.qy Use a QR Matrix Decompositionqr.resid Use a QR Matrix DecompositionrowMaxs Row and Column Summaries - min, max, and rangerowMeans Row and Column SummariesrowMins Row and Column Summaries - min, max, and rangerowRanges Row and Column Summaries - min, max, and range

63

Lists

rowStdevs Row and Column SummariesrowSums Row and Column SummariesrowVars Row and Column Summariesscale Scale Columns of a Matrixsd Row and Column Summariessolve Solve Linear Equations and Invert Matrices - Generic

Functionsolve.bdsmatrix Solve Matrix Equations with Generalized Cholesky

Decompositionsolve.default Solve Linear Equations and Invert Matrices - Generic

Functionsolve.gchol Solve Matrix Equations With Generalized Cholesky

DecompositionsubtractMeans Subtract group means from each entry for a vector or

columns of an array.svd Singular Value Decomposition of a Matrixsvd.default Singular Value Decomposition of a Matrixt Matrix Transposet.default Matrix Transposevecnorm p-norm of a Vector

Lists $ Extract or Replace Parts of an Object - Generic OperatorsSubscript Extract or Replace Parts of an Object - Generic OperatorsSubscript.data.frame Subscript a Data Frame[ Extract or Replace Parts of an Object - Generic Operators[<- Extract or Replace Parts of an Object - Generic Operators[<-.data.frame Subscript a Data Frame[.data.frame Subscript a Data Frame[[ Extract or Replace Parts of an Object - Generic Operators[[<-.data.frame Subscript a Data Frame[[«- Extract or Replace Parts of an Object - Generic Operators[[.data.frame Subscript a Data Frameas.list List Objectsc Combine Values into a Vector or Listis.list List Objectslapply Apply a Function to Components of a List or Vectorlength Length of a Vector or Listlist List Objectsnames Names Attribute of an Object

64

Loess Objects

names<- Names Attribute of an Objectprint.list Print a Listrev Reverse the Order of a Vector or Listsapply Apply a Function to Components of a List or Vectorsplit Split Data by Groupssplit.default Split Data by Groupsunlist Simplify the Structure of a List

Loess Objects anova.loess Anova Method for Loess Objectscoplot Conditioning Plotexpand.grid Create Data Frame from Marginal Gridlo Specify a Loess Fit in a GAM Formulaloess Fit a Local Regression Modelloess.control Computational Options for Loess Fittingloess.dfit Local Regression Fitting (Direct)loess.dfitse Local Regression Fitting and Standard Errors (Direct)loess.ifit Local Regression Fitting (Interpolations by k-d Tree)loess.ise Local Regression Fitting Standard Errorsloess.object Loess Model Objectloess.raw Local Regression Fittingloess.smooth Smooth Loess Curveplot.loess Display of Fitted LOESS Models by Coplotsplot.preplot.loess Display Local Regression Surfacepredict.loess Evaluation of Local Regression Surfacespreplot.loess Display of Fitted LOESS Models by Coplotsprint.loess Print Method for a LOESS Object or its Summaryprint.summary.loess Print Method for a LOESS Object or its Summaryspecs.loess Specifications of Local Regression Modelsummary.loess Summary Method for Local Regression Models

Logical Operators ! Logical Operators!= Comparison Operators< Comparison Operators<= Comparison Operators== Comparison OperatorsComparison Comparison Operators

65

Logical Operators

Logic Logical Operatorsall Logical Sum and Productall.equal Test Two Objects for Full Equality - Generic functionall.equal.numeric Test Two Numeric Objects for Full Equalityany Logical Sum and Productas.logical Logical Objectscompare Signum Function and Comparisoncomplete.cases Find Complete Cases of Observationselse Conditional Expressions and Operatorsidentical Test for Complete Equalityif Conditional Expressions and Operatorsifelse Conditional Data SelectionigroupAlls Compute Summary Statistics by GroupigroupAnys Compute Summary Statistics by GroupigroupMaxs Compute Summary Statistics by GroupigroupMeans Compute Summary Statistics by GroupigroupMins Compute Summary Statistics by GroupigroupProds Compute Summary Statistics by GroupigroupRanges Compute Summary Statistics by GroupigroupSums Compute Summary Statistics by GroupisTRUE Test for Logical Object of Length One with Value Trueis.finite Check IEEE Arithmetic Valuesis.inf Check IEEE Arithmetic Valuesis.infinite Check IEEE Arithmetic Valuesis.logical Logical Objectsis.na Test For Missing Values - Generic functionis.nan Check IEEE Arithmetic Valuesis.number Check IEEE Arithmetic Valueslogical Logical Objectssign Signum Function and Comparisonwhich Find TRUE values in logical vectorwhich.inf Determine Which Values are Missing Values or IEEE

Special Valueswhich.max Index of the minimum or maximum valuewhich.min Index of the minimum or maximum valuewhich.na Determine Which Values are Missing Values or IEEE

Special Valueswhich.nan Determine Which Values are Missing Values or IEEE

Special Values

66

Looping and Iteration

xor Logical Operators| Logical Operators|| Conditional Expressions and Operators

Looping and Iteration For Manage Compute-Intensive IterationSyntax The Structure of Spotfire S+ Expressionsaggregate Compute Summary Statistics of Subsets of Dataaggregate.data.frame Compute Column-by-Column Summaries of Groups of

Observationsaggregate.default Compute Summary Statistics of Subsets of Dataapply Apply a Function to Sections of an Arrayby Split a Dataset by Factors and Apply a Function to the Partsby.data.frame Split a Dataset by Factors and Apply a Function to the Partsby.default Split a Dataset by Factors and Apply a Function to the PartscolMeans Row and Column SummariescolStdevs Row and Column SummariescolSums Row and Column SummariescolVars Row and Column SummariescomponentsApply Apply a function to components of an objectfunction The Structure of Spotfire S+ ExpressionsgroupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.data.frame Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.default Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAnys Computes Group Sums, Means, Variances, Standard

Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

Array

67

Looping and Iteration

groupMeans.data.frame Computes Group Means for a Vector or Columns of an Array

groupMeans.default Computes Group Means for a Vector or Columns of an Array

groupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an ArraygroupProds Computes Group Products for a Vector or Columns of an

ArraygroupProds.data.frame Computes Group Products for a Vector or Columns of an

ArraygroupProds.default Computes Group Products for a Vector or Columns of an

ArraygroupRanges Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.data.frame Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.default Computes Group Ranges for a Vector or Columns of an

ArraygroupStdevs Computes group standard deviations for a vector or

columns of an array.groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

ArraygroupVars.data.frame Computes Group Variances for a Vector or Columns of an

ArraygroupVars.default Computes Group Variances for a Vector or Columns of an

Arraylapply Apply a Function to Components of a List or VectorrecursiveApply Apply a function to an object and its components,

recursively.return The Structure of Spotfire S+ ExpressionsrowMeans Row and Column SummariesrowStdevs Row and Column SummariesrowSums Row and Column SummariesrowVars Row and Column Summariesrowsum Row Sums of a Matrix, Based on a Grouping Variable.sapply Apply a Function to Components of a List or Vectorsd Row and Column SummariessubtractMeans Subtract group means from each entry for a vector or

columns of an array.

68

Mathematical Operations

sweep Sweep Out Array Summariestapply Apply a Function to a Ragged Array{ The Structure of Spotfire S+ Expressions

Mathematical Operations != Comparison Operators%% Arithmetic Operators%/% Arithmetic Operators%w/o% Find the Unique Values of a Set%in% Tell if items are in a set.+ Arithmetic Operators.Uminus Arithmetic Operators< Comparison Operators<= Comparison Operators== Comparison OperatorsArg Basic Complex Number ManipulationArithmetic Arithmetic OperatorsComparison Comparison OperatorsComplex Basic Complex Number ManipulationConj Basic Complex Number ManipulationIm Basic Complex Number ManipulationMath Mathematical Function Groups and Group GenericsMath.data.frame Math Group Method for Data Frame ObjectsMath2 Mathematical Function Groups and Group GenericsMod Basic Complex Number ManipulationRe Basic Complex Number ManipulationSummary.data.frame Summary Group Method for Data Frame Objects^ Arithmetic Operatorsabs Absolute Valueacos Inverse Trigonometric Functionsacosh Inverse Hyperbolic Trigonometric Functionsapprox Linear Interpolation of Pointsasin Inverse Trigonometric Functionsasinh Inverse Hyperbolic Trigonometric Functionsatan Inverse Trigonometric Functionsatanh Inverse Hyperbolic Trigonometric Functionsbits.per.integer Return the Number of Bits in a Spotfire S+ Integerceiling Integer Values

69

Mathematical Operations

choose Factorial, Combinations, Permutationschoose.multinomial Factorial, Combinations, Permutationschull Convex Hull of a Planar Set of PointscolMaxs Row and Column Summaries - min, max, and rangecolMeans Row and Column SummariescolMedians Compute medians columnwisecolMins Row and Column Summaries - min, max, and rangecolProds Columnwise ProductscolQuantiles Compute quantiles columnwisecolRanges Row and Column Summaries - min, max, and rangecolStdevs Row and Column SummariescolSums Row and Column SummariescolVars Row and Column Summariescombinations Returns All Combinations or Permutations of Size K

Elements out of Ncombn Generates Combinations of M Elements out of Xcor Variance, Covariance, and Correlationcos Trigonometric Functionscosh Hyperbolic Trigonometric Functionscov2cor Variance, Covariance, and Correlationcummax Cumulative Maxima and Minimacummin Cumulative Maxima and Minimacumprod Cumulative Sums and Productscumsum Cumulative Sums and Productsderiv Symbolic Partial Derivatives of Expressionsderiv.default Symbolic Partial Derivatives of Expressionsdiff Create an Object of Differencesdigamma Evaluate the Digamma Functionexp Exponential Functionsexpm1 Exponential Functionsfactorial Factorial, Combinations, Permutationsfloor Integer Valuesgamma Gamma Function (and its Natural Logarithm)groupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.data.frame Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.default Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an Array

70

Mathematical Operations

groupAnys Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

ArraygroupMeans.data.frame Computes Group Means for a Vector or Columns of an

ArraygroupMeans.default Computes Group Means for a Vector or Columns of an

ArraygroupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an ArraygroupProds Computes Group Products for a Vector or Columns of an

ArraygroupProds.data.frame Computes Group Products for a Vector or Columns of an

ArraygroupProds.default Computes Group Products for a Vector or Columns of an

ArraygroupRanges Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.data.frame Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.default Computes Group Ranges for a Vector or Columns of an

ArraygroupStdevs Computes group standard deviations for a vector or

columns of an array.groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

ArraygroupVars.data.frame Computes Group Variances for a Vector or Columns of an

ArraygroupVars.default Computes Group Variances for a Vector or Columns of an

Array

71

Mathematical Operations

igroupAlls Compute Summary Statistics by GroupigroupAnys Compute Summary Statistics by GroupigroupMaxs Compute Summary Statistics by GroupigroupMeans Compute Summary Statistics by GroupigroupMins Compute Summary Statistics by GroupigroupProds Compute Summary Statistics by GroupigroupRanges Compute Summary Statistics by GroupigroupSums Compute Summary Statistics by Groupintersect Find the Intersection of Multiple Setsis.element Tell if items are in a set.is.finite Check IEEE Arithmetic Valuesis.inf Check IEEE Arithmetic Valuesis.infinite Check IEEE Arithmetic Valuesis.nan Check IEEE Arithmetic Valuesis.number Check IEEE Arithmetic Valuesjitter Separate Data Points by Jitteringkurtosis Compute Skewness and Kurtosislgamma Gamma Function (and its Natural Logarithm)location.lms Univariate Location and Scale Estimation.log Exponential Functionslog2 Exponential Functionslog10 Exponential Functionslog1p Exponential Functionslogb Exponential Functionsmax Extremesmean Mean Value (Arithmetic Average)median Medianmin Extremesmstree Minimal Spanning Tree and Multivariate Planingpeaks Find Local Maximapermutations Returns All Combinations or Permutations of Size K

Elements out of Npmax Parallel Maximum or Minimumpmin Parallel Maximum or Minimumpolyroot Find the Roots of a Polynomialprod Sums and Productsquantile Empirical Quantilesrange Range of Data

72

Matrices and Arrays

rank Ranks of Dataround Rounding FunctionsrowMaxs Row and Column Summaries - min, max, and rangerowMeans Row and Column SummariesrowMins Row and Column Summaries - min, max, and rangerowRanges Row and Column Summaries - min, max, and rangerowStdevs Row and Column SummariesrowSums Row and Column SummariesrowVars Row and Column Summariessd Row and Column Summariessetdiff Find the Unique Values of a Setsignif Rounding Functionssin Trigonometric Functionssinh Hyperbolic Trigonometric Functionsskewness Compute Skewness and Kurtosisspline Cubic Spline Approximationsqrt Exponential Functionsstd.tolerance Tolerances for Numeric Comparisonsstdev Standard DeviationsubtractMeans Subtract group means from each entry for a vector or

columns of an array.sum Sums and Productstan Trigonometric Functionstanh Hyperbolic Trigonometric Functionstrigamma Trigamma Functiontrunc Integer Valuesunion Find the Union of Multiple Setsvar Variance, Covariance, and Correlationwhich.inf Determine Which Values are Missing Values or IEEE

Special Valueswhich.max Index of the minimum or maximum valuewhich.min Index of the minimum or maximum valuewhich.na Determine Which Values are Missing Values or IEEE

Special Valueswhich.nan Determine Which Values are Missing Values or IEEE

Special Valueszapsmall Coerce Small Numbers to Zero for Printing

Matrices and Arrays

73

Matrices and Arrays

$ Extract or Replace Parts of an Object - Generic Operators%*% Matrix Multiplication Operator%c% Matrix Cross ProductMatrix-product Matrix Multiplication OperatorSubscript Extract or Replace Parts of an Object - Generic Operators[ Extract or Replace Parts of an Object - Generic Operators[<- Extract or Replace Parts of an Object - Generic Operators[[ Extract or Replace Parts of an Object - Generic Operators[[«- Extract or Replace Parts of an Object - Generic Operatorsaggregate Compute Summary Statistics of Subsets of Dataaggregate.data.frame Compute Column-by-Column Summaries of Groups of

Observationsaggregate.default Compute Summary Statistics of Subsets of Dataaperm Array Permutationsaperm.default Array Permutationsapply Apply a Function to Sections of an Arrayarray Multi-Way Arraysas.array Multi-Way Arraysas.matrix Matrix Objectsbacksolve Backsolve Upper-Triangular EquationsbdsBlock Sparse Block Diagonal MatricesbdsI Sparse Identity Matricesbdsmatrix Create a Sparse Symmetric Block Diagonal Matrixbdsmatrix.ibd Create a bdsmatrix From a Listby Split a Dataset by Factors and Apply a Function to the Partsby.data.frame Split a Dataset by Factors and Apply a Function to the Partsby.default Split a Dataset by Factors and Apply a Function to the Partscbind Build Matrix from Columns or Rowschol Choleski Decomposition of Symmetric Matrixcol Column and Row Identification in a MatrixcolMeans Row and Column SummariescolStdevs Row and Column SummariescolSums Row and Column SummariescolVars Row and Column Summariescrossprod Matrix Cross Productdiag Diagonal Matricesdim Dim Attribute of an Objectdim<- Dim Attribute of an Object

74

Matrices and Arrays

dimnames Dimnames Attribute of an Objectdrop Drop Length One Dimensions of an Arrayeigen Eigenvalues and Eigenvectors of a Matrixeigen.default Eigenvalues and Eigenvectors of a Matrixgchol Generalized Cholesky Decompositionginverse Generalized Inverse of a MatrixgroupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.data.frame Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.default Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAnys Computes Group Sums, Means, Variances, Standard

Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

ArraygroupMeans.data.frame Computes Group Means for a Vector or Columns of an

ArraygroupMeans.default Computes Group Means for a Vector or Columns of an

ArraygroupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an ArraygroupProds Computes Group Products for a Vector or Columns of an

ArraygroupProds.data.frame Computes Group Products for a Vector or Columns of an

ArraygroupProds.default Computes Group Products for a Vector or Columns of an

ArraygroupRanges Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.data.frame Computes Group Ranges for a Vector or Columns of an

Array

75

Matrices and Arrays

groupRanges.default Computes Group Ranges for a Vector or Columns of an Array

groupStdevs Computes group standard deviations for a vector or columns of an array.

groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

ArraygroupVars.data.frame Computes Group Variances for a Vector or Columns of an

ArraygroupVars.default Computes Group Variances for a Vector or Columns of an

Arrayis.array Multi-Way Arraysis.matrix Matrix Objectskronecker Kronecker Productslower.tri Logical Matrix Giving the Lower Trianglematlines Plot Columns of Matricesmatplot Plot Columns of Matricesmatpoints Plot Columns of Matricesmatrix Matrix Objectsmerge Merge Two Datasets and Match Columnsmerge.data.frame Merge Two Datasets and Match Columnsmerge.default Merge Two Datasets and Match Columnsncol Extents of a Matrixnrow Extents of a Matrixprint.array Print a Multi-Dimensional Arrayrbind Build Matrix from Columns or Rowsrow Column and Row Identification in a MatrixrowMeans Row and Column SummariesrowStdevs Row and Column SummariesrowSums Row and Column SummariesrowVars Row and Column Summariesscale Scale Columns of a Matrixsd Row and Column Summariesslice.index Slice Identification in an Arraysolve Solve Linear Equations and Invert Matrices - Generic

Functionsolve.default Solve Linear Equations and Invert Matrices - Generic

Function

76

Methods and Generic Functions

solve.gchol Solve Matrix Equations With Generalized Cholesky Decomposition

subtractMeans Subtract group means from each entry for a vector or columns of an array.

svd Singular Value Decomposition of a Matrixsvd.default Singular Value Decomposition of a Matrixsweep Sweep Out Array Summariest Matrix Transposet.default Matrix Transposetapply Apply a Function to a Ragged Arraytsmatrix Create Matrix with Time Series as Columnsupper.tri Logical Matrix Giving the Lower or Upper Triangle

Methods and Generic Functions ! Logical Operators$ Extract or Replace Parts of an Object - Generic OperatorsArith Arithmetic operations with two operands.Compare Equality and inequality comparisons of two operands.Groups Function Groups and Group GenericsLogic Logical OperatorsMath Mathematical Function Groups and Group GenericsMath2 Mathematical Function Groups and Group GenericsMethods Object-Oriented MethodsNextMethod Methods Invoked from Spotfire S+ FunctionsOps Operators for Arithmetic, Comparison, and LogicSubscript Extract or Replace Parts of an Object - Generic OperatorsSubscript.data.frame Subscript a Data FrameSummary Summary is a group generic function.UseMethod Methods Invoked from Spotfire S+ Functions[ Extract or Replace Parts of an Object - Generic Operators[<- Extract or Replace Parts of an Object - Generic Operators[<-.data.frame Subscript a Data Frame[.data.frame Subscript a Data Frame[[ Extract or Replace Parts of an Object - Generic Operators[[<-.data.frame Subscript a Data Frame[[«- Extract or Replace Parts of an Object - Generic Operators[[.data.frame Subscript a Data Frameaov.object Analysis of Variance Objectsaovlist.object Analysis of Variance Objects

77

Methods and Generic Functions

arima.object ARIMA Model Objectas.formula Define or Extract a Model Formula - Generic Functioncheck.factor Check for a Legitimate Factor Objectcov.mcd Minimum Covariance Determinant Estimation - Generic

Function cov.mve Minimum Volume Ellipsoid Covariance Estimationcoxph.object Proportional Hazards Regression Objectcusum.object Cusum Quality Control Chart Objectdata.frame.object Data Frame Objectsdesign.object Design Objectsdeviance Deviance of a Fitted Model - Generic FunctionexistsMethod Search for a Method for a Generic Functionfactanal.object Factor Analysis Objectsfamily.object A Family of GLM ModelsfindMethod Find a Method for a Generic Functionformula Define or Extract a Model Formula - Generic Functionformula.default Define or Extract a Model Formula - Generic Functionformula.object Model Formula Objectsgam.object Generalized Additive Model ObjectgetGroupMembers Find All the Functions Sharing a Particular GroupgetMethod Get a Method for a Generic Functionglm.object Generalized Linear Model ObjectgroupVec groupVec ConstructorgroupVecClasses groupVec Class Data AccessgroupVecClasses<- groupVec Class Data AccessgroupVecColumn groupVec Class - Data AccessgroupVecColumn<- groupVec Class - Data AccessgroupVecData groupVec Class Data AccessgroupVecData<- groupVec Class Data AccessgroupVecExtValid groupVec Extended Class ValidationgroupVecNames groupVec Class Data AccessgroupVecNames<- groupVec Class Data AccessgroupVecNonVec groupVec Extended Class ValidationgroupVecValid groupVec Object ValidationhasMethod Search for a Method for a Generic Functionhtest.object Hypotheses Testing ObjectsigroupAlls Compute Summary Statistics by GroupigroupAnys Compute Summary Statistics by Group

78

Methods and Generic Functions

igroupMaxs Compute Summary Statistics by GroupigroupMeans Compute Summary Statistics by GroupigroupMins Compute Summary Statistics by GroupigroupProds Compute Summary Statistics by GroupigroupRanges Compute Summary Statistics by GroupigroupSums Compute Summary Statistics by GroupisGeneric Determine Whether a Function is a Genericlm.object Linear Least Squares Model ObjectlmRobMM.object Robust Linear Model Objectslms.object Least Median of Squares Objectlmsreg Least Median of Squares Robust Regressionloadings.object Loadings Matrix Objectsloess.object Loess Model Objectlts.object Least Trimmed Squares Objectltsreg Least Trimmed Squares Robust Regressionmaov.object Analysis of Variance Objectsmcd.object Minimum Covariance Determinant Objectmethods List Methods of Old-Style (SV3) Generic Functionsmlm Linear Least Squares Model Objectmlm.object Linear Least Squares Model Objectmve.object Minimum Volume Ellipsoid Objectpframe Construct a Parameterized Data Frame Objectpframe.object Parametrized Data Frame Objectspredict.arima Use predict() on a arima Class Objectprincomp.object Principal Component Objectsqcc.object Quality Control Chart ObjectselectMethod Get a Method for a Generic FunctionsetMethod Define a Method for a Generic Functionshewhart.object Shewhart Quality Control Chart Objectspecs Specifications of a Model - Generic Functionstep Build a Model in a Stepwise Fashion - Generic Functionsummary Summarize an Object - Generic Functionterms.object Class of Objects for Terms in a ModeltraceMethod Trace a Methodtree.object Regression or Classification Tree Objecttree.sequence.object Regression or Classification Tree Objectxor Logical Operators| Logical Operators

79

Miscellaneous

~ Model Formula Objects

Miscellaneous bd.data.viewer Show Data Viewerbd.options Big Data Processing Optionsbd.pack.object Packing Databd.unpack.object Packing DatabdPackedObject Packing Datadate Today's Date and Timeodometer Multi Radix Counter

Missing Values anyMissing Test For Missing Values - Generic functionis.missing Check of Length 0 or MissingnumberMissing Count Number of Missing Values - Generic function

Mixed Effects Models ACF.lme Autocorrelation Function for lme ResidualsAIC Akaike Information CriterionAIC.logLik AIC of a logLik ObjectBIC Bayesian Information CriterionBIC.logLik BIC of a logLik ObjectDim Extract Dimensions from an ObjectDim.corSpatial Dimensions of a corSpatial ObjectDim.corStruct Dimensions of a corStruct ObjectDim.pdMat Dimensions of a pdMat ObjectNLSstClosestX Inverse InterpolationNLSstLfAsymptote Horizontal Asymptote on the Left SideNLSstRtAsymptote Horizontal Asymptote on the Right SideNames Names Associated with an ObjectNames.formula Extract Names from a formulaNames.pdBlocked Names of a pdBlocked ObjectNames.pdMat Names of a pdMat ObjectNames.reStruct Names of an reStruct ObjectSSasymp Asymptotic regression modelSSasympOff Asymptotic Regression Model with an OffsetSSasympOrig Asymptotic Regression Model through the OriginSSbiexp Biexponential model

80

Mixed Effects Models

SSfol First-order Compartment ModelSSfpl Four-parameter Logistic ModelSSlogis Logistic modelSSmicmen Michaelis-Menten modelVariogram Calculate Semi-VariogramVariogram.corExp Calculate Semi-Variogram for a corExp ObjectVariogram.corGaus Calculate Semi-Variogram for a corGaus ObjectVariogram.corLin Calculate Semi-Variogram for a corLin ObjectVariogram.corRatio Calculate Semi-Variogram for a corRatio ObjectVariogram.corSpatial Calculate Semi-Variogram for a corSpatial ObjectVariogram.corSpher Calculate Semi-Variogram for a corSpher ObjectVariogram.default Calculate Semi-VariogramVariogram.gls Calculate Semi-Variogram for Residuals from a gls ObjectVariogram.lme Calculate Semi-Variogram for Residuals from an lme Object[.pdMat Subscript a pdMat ObjectallCoef Extract Coefficients from a Set of Objectsanova.gls Compare Likelihoods of Fitted Objectsanova.lme Compare Likelihoods of Fitted Objectsas.matrix.corStruct Matrix of a corStruct Objectas.matrix.pdMat Matrix of a pdMat Objectas.matrix.reStruct Matrices of an reStruct ObjectasNatural Convert to Natural ParameterizationasNatural.corBand Convert corBand Object to Natural ParameterizationasNatural.corStruct Convert corStruct Object to Natural ParameterizationasNatural.corSymm Convert corSymm Object to Natural ParameterizationasNatural.pdBand Convert pdBand Object to Natural ParameterizationasNatural.pdMat Convert pdMat Object to Natural ParameterizationasNatural.pdSymm Convert pdSymm Object to Natural ParameterizationasNatural.varFunc Convert varFunc Object to Natural ParameterizationasOneFormula Combine Formulas of a Set of ObjectsasOneSidedFormula Convert to One-Sided FormulaasTable Convert groupedData to a matrixaugPred Augmented PredictionsbalancedGrouped Create a groupedData object from a matrixcoef.corStruct Coefficients of a corStruct Objectcoef.gls Extract gls Coefficientscoef.gnls Extract gnls Coefficientscoef.lmList Extract lmList Coefficients

81

Mixed Effects Models

coef.lme Extract lme Coefficientscoef.modelStruct Extract modelStruct Object Coefficientscoef.pdCompSymm pdCompSymm Object Coefficientscoef.pdDiag pdDiag Object Coefficientscoef.pdIdent pdIdent Object Coefficientscoef.pdMat pdMat Object Coefficientscoef.reStruct reStruct Object Coefficientscoef.varFunc varFunc Object Coefficientscoef<- Assign Values to Coefficientscollapse Collapse According to Groupscollapse.groupedData Collapse a groupedData ObjectcompareFits Compare Fitted ObjectscomparePred Compare PredictionscorAR1 AR(1) Correlation StructurecorARMA ARMA(p,q) Correlation StructurecorBand Banded Correlation StructurecorBandNat Banded Correlation in Natural ParameterizationcorCAR1 Continuous AR(1) Correlation StructurecorClasses Correlation Structure ClassescorCompSymm Compound Symmetry Correlation StructurecorExp Exponential Correlation StructurecorFactor Factor of a Correlation MatrixcorFactor.corStruct Factor of a corStruct Object MatrixcorGaus Gaussian Correlation StructurecorLin Linear Correlation StructurecorMatrix Extract Correlation MatrixcorMatrix.corStruct Matrix of a corStruct ObjectcorMatrix.pdMat Extract Correlation Matrix from a pdMat ObjectcorMatrix.reStruct Extract Correlation Matrix from Components of an reStruct

ObjectcorRatio Rational Quadratic Correlation StructurecorSpatial Spatial Correlation StructurecorSpher Spherical Correlation StructurecorStrat Stratified Correlation StructurecorSymm General Correlation StructurecorSymmNat General Correlation in Natural Parameterizationcovariate<- Assign Covariate Valuescovariate<-.varFunc Assign varFunc Covariate

82

Mixed Effects Models

fitted.gls Extract gls Fitted Valuesfitted.glsStruct Calculate glsStruct Fitted Valuesfitted.gnls Extract gnls Fitted Valuesfitted.gnlsStruct Calculate gnlsStruct Fitted Valuesfitted.lmList Extract lmList Fitted Valuesfitted.lme Extract lme Fitted Valuesfitted.lmeStruct Calculate lmeStruct Fitted Valuesfitted.nlmeStruct Calculate nlmeStruct Fitted Valuesfixed.effects Extract Fixed Effectsfixed.effects.lmList Extract lmList Fixed Effectsfixed.effects.lme Extract lme Fixed Effectsfixef Extract Fixed Effectsfixef.lmList Extract lmList Fixed Effectsfixef.lme Extract lme Fixed Effectsformula.corStruct Extract corStruct Object Formulaformula.gls Extract gls Object Formulaformula.gnls Extract gnls Object Formulaformula.groupedData Extract groupedData Formulaformula.lmList Extract lmList Object Formulaformula.lme Extract lme Object Formulaformula.modelStruct Extract modelStruct Object Formulaformula.nlme Extract nlme Object Formulaformula.nls Extract Model Formula from nls Objectformula.nlsList Extract nlsList Object Formulaformula.pdBlocked Extract pdBlocked Formulaformula.pdMat Extract pdMat Formulaformula.reStruct Extract reStruct Object Formulaformula.varFunc Extract varFunc Formulagapply Apply a Function by GroupsgetCovariate Extract Covariate from an ObjectgetCovariate.corStruct Extract corStruct Object CovariategetCovariate.data.frame Extract Data Frame CovariategetCovariate.varFunc Extract varFunc CovariategetCovariateFormula Extract Covariates FormulagetData Extract Data from an ObjectgetData.gls Extract gls Object DatagetData.lmList Extract lmList Object DatagetData.lme Extract lme Object Data

83

Mixed Effects Models

getGroups Extract Grouping Factors from an ObjectgetGroups.corStruct Extract corStruct GroupsgetGroups.data.frame Extract Groups from a Data FramegetGroups.gls Extract gls Object GroupsgetGroups.lmList Extract lmList Object GroupsgetGroups.lme Extract lme Object GroupsgetGroups.varFunc Extract varFunc GroupsgetGroupsFormula Extract Grouping FormulagetGroupsFormula.gls Extract gls Object Grouping FormulagetGroupsFormula.lmList Extract lmList Object Grouping FormulagetGroupsFormula.lme Extract lme Object Grouping FormulagetGroupsFormula.reStruct Extract reStruct Grouping FormulagetInitial Get Initial Parameter EstimatesgetResponse Extract Response Variable from an ObjectgetResponse.data.frame Extract Response from a Data FramegetResponse.gls Extract gls Object ResponsegetResponse.lmList Extract lmList Object ResponsegetResponse.lme Extract lme Object ResponsegetResponseFormula Extract Formula Specifying Response VariablegetStrata Extract Stratification VariablegetStrata.data.frame Extract Strata from a Data FramegetStrataFormula Extract Stratification Formulagls Fit Linear Model Using Generalized Least SquaresglsControl Control Values for gls FitglsObject Fitted gls ObjectglsStruct Generalized Least Squares Structuregnls Fit Nonlinear Model Using Generalized Least SquaresgnlsControl Control Values for gnls FitgnlsObject Fitted gnls ObjectgnlsStruct Generalized Nonlinear Least Squares StructuregroupedData Construct a groupedData Objectgsummary Summarize by Groupsinitialize Initialize Objectinitialize.corStruct Initialize corStruct Objectinitialize.glsStruct Initialize a glsStruct Objectinitialize.lmeStruct Initialize an lmeStruct Objectinitialize.reStruct Initialize reStruct Objectinitialize.varFunc Initialize varFunc Object

84

Mixed Effects Models

intervals Confidence Intervals on Coefficientsintervals.gls Confidence Intervals on gls Parametersintervals.lmList Confidence Intervals on lmList Coefficientsintervals.lme Confidence Intervals on lme ParametersisBalanced Check a Design for BalanceisInitialized Check if Object is InitializedisInitialized.reStruct Check if an reStruct Object is InitializedisInitialized<- Set Initialization StatuslmList List of lm Objects with a Common ModellmList.groupedData lmList Fit from a groupedData Objectlme Linear Mixed-Effects Modelslme.groupedData LME fit from groupedData Objectlme.lmList LME fit from lmList ObjectlmeControl Control Values for lme FitlmeObject Fitted lme ObjectlmeScale Scale for lme OptimizationlmeStruct Linear Mixed-Effects Structurelmekin Mixed Effects Model Using a Kinship Matrix.logDet Extract the Logarithm of the DeterminantlogDet.corStruct Extract corStruct Log-DeterminantlogDet.pdMat Extract Log-Determinant from a pdMat ObjectlogDet.reStruct Extract reStruct Log-DeterminantslogLik Extract Log-LikelihoodlogLik.corStruct Extract corStruct Log-LikelihoodlogLik.gls Log-Likelihood of a gls ObjectlogLik.glsStruct Log-Likelihood of a glsStruct ObjectlogLik.gnls Log-Likelihood of a gnls ObjectlogLik.gnlsStruct Log-Likelihood of a gnlsStruct ObjectlogLik.lm Extract Log-Likelihood from an lm ObjectlogLik.lmList Log-Likelihood of an lmList ObjectlogLik.lme Log-Likelihood of an lme ObjectlogLik.lmeStruct Log-Likelihood of an lmeStruct ObjectlogLik.reStruct Calculate reStruct Log-LikelihoodlogLik.varFunc Extract varFunc logLikmatrix<- Assign Matrix Valuesmatrix<-.pdKron Assign Matrix to a pdKron Objectmatrix<-.pdMat Assign Matrix to a pdMat Objectmatrix<-.reStruct Assign reStruct Matrices

85

Mixed Effects Models

model.matrix.reStruct reStruct Model MatrixneedUpdate Check if Update is NeededneedUpdate.modelStruct Check if a modelStruct Object Needs Updatingnlme Nonlinear Mixed-Effects Modelsnlme.nlsList NLME fit from nlsList ObjectnlmeControl Control Values for nlme FitnlmeObject Fitted nlme ObjectnlmeStruct Nonlinear Mixed-Effects StructurenlsList List of nls Objects with a Common ModelnlsList.selfStart nlsList Fit from a selfStart Functionpairs.compareFits Pairs Plot of compareFits Objectpairs.lmList Pairs Plot of an lmList Objectpairs.lme Pairs Plot of an lme ObjectpdBand Banded Positive-Definite MatrixpdBandNat Banded Positive-Definite Matrix in Natural ParameterizationpdBlocked Positive-Definite Block Diagonal MatrixpdClasses Positive-Definite Matrix ClassespdCompSymm Positive-Definite Matrix with Compound Symmetry

StructurepdConstruct Construct pdMat ObjectspdConstruct.pdBlocked Construct pdBlocked ObjectspdDiag Diagonal Positive-Definite MatrixpdFactor Square-Root Factor of a Positive-Definite MatrixpdFactor.reStruct Extract Square-Root Factor from Components of an reStruct

ObjectpdIdent Multiple of the Identity Positive-Definite MatrixpdKron Kronecker-Product Positive-Definite MatrixpdMat Positive-Definite MatrixpdMatrix Extract Matrix or Square-Root Factor from a pdMat ObjectpdMatrix.reStruct Extract Matrix or Square-Root Factor from an reStruct

ObjectpdNatural General Positive-Definite Matrix in Natural ParametrizationpdStrat Stratified Positive-Definite MatrixpdSymm General Positive-Definite MatrixpdSymmNat General Positive-Definite Matrix in Natural

Parameterizationplot.ACF Plot an ACF Objectplot.Variogram Plot a Variogram Objectplot.augPred Plot an augPred Object

86

Mixed Effects Models

plot.compareFits Plot a compareFits Objectplot.gls Plot a gls Objectplot.intervals.lmList Plot lmList Confidence Intervalsplot.lmList Plot an lmList Objectplot.lme Plot an lme Objectplot.nffGroupedData Plot an nffGroupedData Objectplot.nfnGroupedData Plot an nfnGroupedData Objectplot.nmGroupedData Plot an nmGroupedData Objectplot.ranef.lmList Plot a ranef.lmList Objectplot.ranef.lme Plot a ranef.lme ObjectpooledSD Extract Pooled Standard Deviationpredict.gls Predictions from a gls Objectpredict.gnls Predictions from a gnls Objectpredict.lmList Predictions from an lmList Objectpredict.lme Predictions from an lme Objectpredict.nlme Predictions from an nlme Objectprint.anova.lme Print an anova.lme Objectprint.corStruct Print a corStruct Objectprint.gls Print a gls Objectprint.groupedData Print a groupedData Objectprint.intervals.gls Print an intervals.gls Objectprint.intervals.lme Print an intervals.lme Objectprint.lmList Print an lmList Objectprint.lme Print an lme Objectprint.modelStruct Print a modelStruct Objectprint.pdMat Print a pdMat Objectprint.reStruct Print an reStruct Objectprint.summary.corStruct Print a summary.corStruct Objectprint.summary.gls Print a summary.gls Objectprint.summary.lmList Print a summary.lmList Objectprint.summary.lme Print a summary.lme Objectprint.summary.modelStruct Print a summary.modelStruct Objectprint.summary.pdMat Print a summary.pdMat Objectprint.summary.varFunc Print a summary.varFunc Objectprint.varFunc Print a varFunc ObjectpruneLevels Prune Factor Levelsqqnorm.gls Normal Plot of Residuals from a gls Object

87

Mixed Effects Models

qqnorm.lme Normal Plot of Residuals or Random Effects from an lme Object

random.effects Extract Random Effectsrandom.effects.lmList Extract lmList Random Effectsrandom.effects.lme Extract lme Random Effectsranef Extract Random Effectsranef.lmList Extract lmList Random Effectsranef.lme Extract lme Random EffectsreStruct Random Effects Structurerecalc Recalculate Condensed Linear Model Objectrecalc.corStruct Recalculate for corStruct Objectrecalc.modelStruct Recalculate for a modelStruct Objectrecalc.reStruct Recalculate for an reStruct Objectrecalc.varFunc Recalculate for varFunc Objectresiduals.gls Extract gls Residualsresiduals.glsStruct Calculate glsStruct Residualsresiduals.gnls Extract gnls Residualsresiduals.gnlsStruct Calculate gnlsStruct Residualsresiduals.lmList Extract lmList Residualsresiduals.lme Extract lme Residualsresiduals.lmeStruct Calculate lmeStruct Residualsresiduals.nlmeStruct Calculate nlmeStruct ResidualsselfStart Construct Self-starting Nonlinear ModelsselfStart.default Construct Self-starting Nonlinear ModelsselfStart.formula Construct Self-starting Nonlinear Modelssimulate.lme simulate lme modelssolve.pdMat Calculate Inverse of a Positive-Definite Matrixsolve.reStruct Apply Solve to an reStruct ObjectsortedXyData Create a sortedXyData objectsplitFormula Split a Formulasummary.corStruct Summarize a corStruct Objectsummary.gls Summarize a gls Objectsummary.lmList Summarize an lmList Objectsummary.lme Summarize an lme Objectsummary.modelStruct Summarize a modelStruct Objectsummary.nlsList Summarize an nlsList Objectsummary.pdMat Summarize a pdMat Objectsummary.varFunc Summarize varFunc Object

88

Multivariate Techniques

update.gls Update a gls Objectupdate.gnls Update a gnls Objectupdate.groupedData Update a groupedData Objectupdate.lmList Update an lmList Objectupdate.lme Update an lme Objectupdate.modelStruct Update a modelStruct Objectupdate.nlme Update an nlme Objectupdate.nlsList Update an nlsList Objectupdate.varFunc Update varFunc ObjectvarClasses Variance Function ClassesvarComb Combination of Variance FunctionsvarConstPower Constant Plus Power Variance FunctionvarExp Exponential Variance FunctionvarFixed Fixed Variance FunctionvarFunc Variance Function StructurevarIdent Constant Variance FunctionvarPower Power Variance FunctionvarWeights Extract Variance Function WeightsvarWeights.glsStruct Variance Weights for glsStruct ObjectvarWeights.lmeStruct Variance Weights for lmeStruct Object

Multivariate Techniques MVNormal Multivariate Normal (Gaussian) Distributionanova.discrim The ANOVA method for the discrim object.bdCluster Big Data K-Means ClusteringbdPrincomp Big Data Principal Component Analysisbiplot Biplot of Multivariate Databiplot.default Biplot of Multivariate Databiplot.factanal Biplots for Principal Components and Factor Analysis

Modelsbiplot.princomp Biplots for Principal Components and Factor Analysis

Modelsbrush Brush a Matrix of Scatter Plotscancor Canonical Correlation Analysiscmdscale Classical Metric Multi-Dimensional Scalingcontour Contour Plotcontour.old Contour Plotcor Variance, Covariance, and Correlation

89

Multivariate Techniques

cov.mcd Minimum Covariance Determinant Estimation - Generic Function

cov.mcd.default Use cov.mcd on a Vector, Matrix, or Data Framecov.mcd.formula Use cov.mcd with a formula Objectcov.mve Minimum Volume Ellipsoid Covariance Estimationcov.mve.default Use cov.mve on a Vector, Matrix, or Data Framecov.mve.formula Use cov.mve with a formula Objectcov.wt Weighted Covariance Estimationcrosstabs Create a Contingency Table from Factor Datacrossvalidate.discrim Crossvaliation Method for a discrim Objectcutree Create Groups from Hierarchical Clusteringdiscr Multiple Discriminant Analysisdiscrim Estimate a Discriminant Functiondist Distance Matrix Calculationdmvnorm Multivariate Normal (Gaussian) Distributionfaces Plot Symbolic Facesfactanal Estimate a Factor Analysis Modelfactanal.fit.mle Maximum Likelihood Estimate of Factor Analysis Modelfactanal.fit.principal Factor Analysis via Principal Factorsfactanal.mle.control Control MLE Factor Analysis Algorithmfactanal.object Factor Analysis Objectsfactanal.start.mle Starting Values for MLE Factor Analysisfft Fast Fourier Transformfitted.bdCluster Big Data Predict Cluster Membershipfitted.bdPrincomp Big Data Principal Component Scoresfitted.factanal Extract Fitted Correlation Matrix or Residualshclust Hierarchical Clusteringhist2d Calculate Two-Dimensional Histogramkmeans Hartigan's K-Means Clusteringloadings Extract Loadings from an Objectloadings.default Extract Loadings from an Objectloadings.object Loadings Matrix Objectsloglin Contingency Table Analysismahalanobis Mahalanobis Distancemanova Fit a Multivariate Analysis of Variance Modelmstree Minimal Spanning Tree and Multivariate Planingmulbar Multiple Bar Plotmulticomp.discrim The multiple comparisons method for the discrim object.

90

Multivariate Techniques

obliquemin Oblimin Rotations of Loadings Matrixorthomax Orthomax Rotations of Orthogonal Matricespairs Produce All Pairwise Scatter Plots - Generic Functionpairs.data.frame Produce a Scatterplot Matrix for a Data Framepairs.default Produce a Scatterplot Matrixpersp Three-Dimensional Perspective Plotsperspp Project Points onto Three-Dimensional Perspective Plotsplot.bdPrincomp Plot of the Variances of Derived Variablesplot.loadings Plot Loadingsplot.mlm Plot a Multiresponse Linear Modelplot.princomp Plot of the Variances of Derived Variablespmvnorm Multivariate Normal (Gaussian) Distributionprcomp Principal Components Analysispredict.bdCluster Big Data Predict Cluster Membershippredict.bdPrincomp Big Data Principal Component Scorespredict.discrim Prediction Method for a discrim Objectpredict.factanal Factor Analysis Scorespredict.princomp Principal Component Scoresprincomp Principal Components Analysisprincomp.object Principal Component Objectsprint.factanal Print a Factor Analysis Objectprint.loadings Print a Loadings Matrixprint.princomp Print a Principal Components Objectprint.summary.princomp Print a Principal Component Summaryprocrustes Procrustes Rotationsresiduals.factanal Extract Fitted Correlation Matrix or Residualsrmvnorm Multivariate Normal (Gaussian) Distributionrotate Perform Rotationsrotate.default Perform Rotationsrotate.factanal Rotate Factor Analysis Objectrotate.princomp Rotate Factor Analysis Objectscreeplot Plot of the Variances of Derived Variablesscreeplot.bdPrincomp Plot of the Variances of Derived Variablesscreeplot.princomp Plot of the Variances of Derived Variablessmatrix Symbolic Matrix for Multivariate Dataspin Display Rotating Three Dimensional Scatterplotsstars Star Plots of Multivariate Datastarsymb Plot a Single Star Symbol

91

nlme Library (version 3)

subtree Extract Part of a Cluster Treesummary.bdPrincomp Summary of a Principal Components Objectsummary.discrim The summary method for the discrim object.summary.factanal Summary for a Factor Analysis Objectsummary.manova Create a Manova Tablesummary.princomp Summary of a Principal Components Objecttwoway Fit of a Two-Way Tablevar Variance, Covariance, and Correlation

nlme Library (version 3) ACF Autocorrelation FunctionACF.gls Autocorrelation Function for gls ResidualsACF.lme Autocorrelation Function for lme ResidualsAIC Akaike Information CriterionAIC.logLik AIC of a logLik ObjectBIC Bayesian Information CriterionBIC.logLik BIC of a logLik ObjectDim Extract Dimensions from an ObjectDim.corSpatial Dimensions of a corSpatial ObjectDim.corStruct Dimensions of a corStruct ObjectDim.pdMat Dimensions of a pdMat ObjectNLSstClosestX Inverse InterpolationNLSstLfAsymptote Horizontal Asymptote on the Left SideNLSstRtAsymptote Horizontal Asymptote on the Right SideNames Names Associated with an ObjectNames.formula Extract Names from a formulaNames.pdBlocked Names of a pdBlocked ObjectNames.pdMat Names of a pdMat ObjectNames.reStruct Names of an reStruct ObjectSSasymp Asymptotic regression modelSSasympOff Asymptotic Regression Model with an OffsetSSasympOrig Asymptotic Regression Model through the OriginSSbiexp Biexponential modelSSfol First-order Compartment ModelSSfpl Four-parameter Logistic ModelSSlogis Logistic modelSSmicmen Michaelis-Menten modelVarCorr Extract variance and correlation components

92

nlme Library (version 3)

Variogram Calculate Semi-VariogramVariogram.corExp Calculate Semi-Variogram for a corExp ObjectVariogram.corGaus Calculate Semi-Variogram for a corGaus ObjectVariogram.corLin Calculate Semi-Variogram for a corLin ObjectVariogram.corRatio Calculate Semi-Variogram for a corRatio ObjectVariogram.corSpatial Calculate Semi-Variogram for a corSpatial ObjectVariogram.corSpher Calculate Semi-Variogram for a corSpher ObjectVariogram.default Calculate Semi-VariogramVariogram.gls Calculate Semi-Variogram for Residuals from a gls ObjectVariogram.lme Calculate Semi-Variogram for Residuals from an lme Object[.pdMat Subscript a pdMat ObjectallCoef Extract Coefficients from a Set of Objectsanova.gls Compare Likelihoods of Fitted Objectsanova.lme Compare Likelihoods of Fitted Objectsas.matrix.corStruct Matrix of a corStruct Objectas.matrix.pdMat Matrix of a pdMat Objectas.matrix.reStruct Matrices of an reStruct ObjectasNatural Convert to Natural ParameterizationasNatural.corBand Convert corBand Object to Natural ParameterizationasNatural.corStruct Convert corStruct Object to Natural ParameterizationasNatural.corSymm Convert corSymm Object to Natural ParameterizationasNatural.pdBand Convert pdBand Object to Natural ParameterizationasNatural.pdMat Convert pdMat Object to Natural ParameterizationasNatural.pdSymm Convert pdSymm Object to Natural ParameterizationasNatural.varFunc Convert varFunc Object to Natural ParameterizationasOneFormula Combine Formulas of a Set of ObjectsasOneSidedFormula Convert to One-Sided FormulaasTable Convert groupedData to a matrixaugPred Augmented PredictionsbalancedGrouped Create a groupedData object from a matrixcoef.corStruct Coefficients of a corStruct Objectcoef.gls Extract gls Coefficientscoef.gnls Extract gnls Coefficientscoef.lmList Extract lmList Coefficientscoef.lme Extract lme Coefficientscoef.modelStruct Extract modelStruct Object Coefficientscoef.pdCompSymm pdCompSymm Object Coefficientscoef.pdDiag pdDiag Object Coefficients

93

nlme Library (version 3)

coef.pdIdent pdIdent Object Coefficientscoef.pdMat pdMat Object Coefficientscoef.reStruct reStruct Object Coefficientscoef.varFunc varFunc Object Coefficientscoef<- Assign Values to Coefficientscollapse Collapse According to Groupscollapse.groupedData Collapse a groupedData ObjectcompareFits Compare Fitted ObjectscomparePred Compare PredictionscorAR1 AR(1) Correlation StructurecorARMA ARMA(p,q) Correlation StructurecorBand Banded Correlation StructurecorBandNat Banded Correlation in Natural ParameterizationcorCAR1 Continuous AR(1) Correlation StructurecorClasses Correlation Structure ClassescorCompSymm Compound Symmetry Correlation StructurecorExp Exponential Correlation StructurecorFactor Factor of a Correlation MatrixcorFactor.corStruct Factor of a corStruct Object MatrixcorGaus Gaussian Correlation StructurecorLin Linear Correlation StructurecorMatrix Extract Correlation MatrixcorMatrix.corStruct Matrix of a corStruct ObjectcorMatrix.pdMat Extract Correlation Matrix from a pdMat ObjectcorMatrix.reStruct Extract Correlation Matrix from Components of an reStruct

ObjectcorRatio Rational Quadratic Correlation StructurecorSpatial Spatial Correlation StructurecorSpher Spherical Correlation StructurecorStrat Stratified Correlation StructurecorSymm General Correlation StructurecorSymmNat General Correlation in Natural Parameterizationcovariate<- Assign Covariate Valuescovariate<-.varFunc Assign varFunc Covariatefitted.gls Extract gls Fitted Valuesfitted.glsStruct Calculate glsStruct Fitted Valuesfitted.gnls Extract gnls Fitted Valuesfitted.gnlsStruct Calculate gnlsStruct Fitted Values

94

nlme Library (version 3)

fitted.lmList Extract lmList Fitted Valuesfitted.lme Extract lme Fitted Valuesfitted.lmeStruct Calculate lmeStruct Fitted Valuesfitted.nlmeStruct Calculate nlmeStruct Fitted Valuesfixed.effects Extract Fixed Effectsfixed.effects.lmList Extract lmList Fixed Effectsfixed.effects.lme Extract lme Fixed Effectsfixef Extract Fixed Effectsfixef.lmList Extract lmList Fixed Effectsfixef.lme Extract lme Fixed Effectsformula.corStruct Extract corStruct Object Formulaformula.gls Extract gls Object Formulaformula.gnls Extract gnls Object Formulaformula.groupedData Extract groupedData Formulaformula.lmList Extract lmList Object Formulaformula.lme Extract lme Object Formulaformula.modelStruct Extract modelStruct Object Formulaformula.nlme Extract nlme Object Formulaformula.nls Extract Model Formula from nls Objectformula.nlsList Extract nlsList Object Formulaformula.pdBlocked Extract pdBlocked Formulaformula.pdMat Extract pdMat Formulaformula.reStruct Extract reStruct Object Formulaformula.varFunc Extract varFunc Formulagapply Apply a Function by GroupsgetCovariate Extract Covariate from an ObjectgetCovariate.corStruct Extract corStruct Object CovariategetCovariate.data.frame Extract Data Frame CovariategetCovariate.varFunc Extract varFunc CovariategetCovariateFormula Extract Covariates FormulagetData Extract Data from an ObjectgetData.gls Extract gls Object DatagetData.lmList Extract lmList Object DatagetData.lme Extract lme Object DatagetGroups Extract Grouping Factors from an ObjectgetGroups.corStruct Extract corStruct GroupsgetGroups.data.frame Extract Groups from a Data FramegetGroups.gls Extract gls Object Groups

95

nlme Library (version 3)

getGroups.lmList Extract lmList Object GroupsgetGroups.lme Extract lme Object GroupsgetGroups.varFunc Extract varFunc GroupsgetGroupsFormula Extract Grouping FormulagetGroupsFormula.gls Extract gls Object Grouping FormulagetGroupsFormula.lmList Extract lmList Object Grouping FormulagetGroupsFormula.lme Extract lme Object Grouping FormulagetGroupsFormula.reStruct Extract reStruct Grouping FormulagetInitial Get Initial Parameter EstimatesgetResponse Extract Response Variable from an ObjectgetResponse.data.frame Extract Response from a Data FramegetResponse.gls Extract gls Object ResponsegetResponse.lmList Extract lmList Object ResponsegetResponse.lme Extract lme Object ResponsegetResponseFormula Extract Formula Specifying Response VariablegetStrata Extract Stratification VariablegetStrata.data.frame Extract Strata from a Data FramegetStrataFormula Extract Stratification Formulagls Fit Linear Model Using Generalized Least SquaresglsControl Control Values for gls FitglsObject Fitted gls ObjectglsStruct Generalized Least Squares Structuregnls Fit Nonlinear Model Using Generalized Least SquaresgnlsControl Control Values for gnls FitgnlsObject Fitted gnls ObjectgnlsStruct Generalized Nonlinear Least Squares StructuregroupedData Construct a groupedData Objectgsummary Summarize by Groupsinitialize Initialize Objectinitialize.corStruct Initialize corStruct Objectinitialize.glsStruct Initialize a glsStruct Objectinitialize.lmeStruct Initialize an lmeStruct Objectinitialize.reStruct Initialize reStruct Objectinitialize.varFunc Initialize varFunc Objectintervals Confidence Intervals on Coefficientsintervals.gls Confidence Intervals on gls Parametersintervals.lmList Confidence Intervals on lmList Coefficientsintervals.lme Confidence Intervals on lme Parameters

96

nlme Library (version 3)

isBalanced Check a Design for BalanceisInitialized Check if Object is InitializedisInitialized.reStruct Check if an reStruct Object is InitializedisInitialized<- Set Initialization StatuslmList List of lm Objects with a Common ModellmList.groupedData lmList Fit from a groupedData Objectlme Linear Mixed-Effects Modelslme.groupedData LME fit from groupedData Objectlme.lmList LME fit from lmList ObjectlmeControl Control Values for lme FitlmeObject Fitted lme ObjectlmeScale Scale for lme OptimizationlmeStruct Linear Mixed-Effects StructurelogDet Extract the Logarithm of the DeterminantlogDet.corStruct Extract corStruct Log-DeterminantlogDet.pdMat Extract Log-Determinant from a pdMat ObjectlogDet.reStruct Extract reStruct Log-DeterminantslogLik Extract Log-LikelihoodlogLik.corStruct Extract corStruct Log-LikelihoodlogLik.gls Log-Likelihood of a gls ObjectlogLik.glsStruct Log-Likelihood of a glsStruct ObjectlogLik.gnls Log-Likelihood of a gnls ObjectlogLik.gnlsStruct Log-Likelihood of a gnlsStruct ObjectlogLik.lm Extract Log-Likelihood from an lm ObjectlogLik.lmList Log-Likelihood of an lmList ObjectlogLik.lme Log-Likelihood of an lme ObjectlogLik.lmeStruct Log-Likelihood of an lmeStruct ObjectlogLik.reStruct Calculate reStruct Log-LikelihoodlogLik.varFunc Extract varFunc logLikmatrix<- Assign Matrix Valuesmatrix<-.pdKron Assign Matrix to a pdKron Objectmatrix<-.pdMat Assign Matrix to a pdMat Objectmatrix<-.reStruct Assign reStruct Matricesmodel.matrix.reStruct reStruct Model MatrixneedUpdate Check if Update is NeededneedUpdate.modelStruct Check if a modelStruct Object Needs Updatingnlme Nonlinear Mixed-Effects Modelsnlme.nlsList NLME fit from nlsList Object

97

nlme Library (version 3)

nlmeControl Control Values for nlme FitnlmeObject Fitted nlme ObjectnlmeStruct Nonlinear Mixed-Effects StructurenlsList List of nls Objects with a Common ModelnlsList.selfStart nlsList Fit from a selfStart Functionpairs.compareFits Pairs Plot of compareFits Objectpairs.lmList Pairs Plot of an lmList Objectpairs.lme Pairs Plot of an lme ObjectpdBand Banded Positive-Definite MatrixpdBandNat Banded Positive-Definite Matrix in Natural ParameterizationpdBlocked Positive-Definite Block Diagonal MatrixpdClasses Positive-Definite Matrix ClassespdCompSymm Positive-Definite Matrix with Compound Symmetry

StructurepdConstruct Construct pdMat ObjectspdConstruct.pdBlocked Construct pdBlocked ObjectspdDiag Diagonal Positive-Definite MatrixpdFactor Square-Root Factor of a Positive-Definite MatrixpdFactor.reStruct Extract Square-Root Factor from Components of an reStruct

ObjectpdIdent Multiple of the Identity Positive-Definite MatrixpdKron Kronecker-Product Positive-Definite MatrixpdMat Positive-Definite MatrixpdMatrix Extract Matrix or Square-Root Factor from a pdMat ObjectpdMatrix.reStruct Extract Matrix or Square-Root Factor from an reStruct

ObjectpdNatural General Positive-Definite Matrix in Natural ParametrizationpdStrat Stratified Positive-Definite MatrixpdSymm General Positive-Definite MatrixpdSymmNat General Positive-Definite Matrix in Natural

Parameterizationplot.ACF Plot an ACF Objectplot.Variogram Plot a Variogram Objectplot.augPred Plot an augPred Objectplot.compareFits Plot a compareFits Objectplot.gls Plot a gls Objectplot.intervals.lmList Plot lmList Confidence Intervalsplot.lmList Plot an lmList Objectplot.lme Plot an lme Object

98

nlme Library (version 3)

plot.nffGroupedData Plot an nffGroupedData Objectplot.nfnGroupedData Plot an nfnGroupedData Objectplot.nmGroupedData Plot an nmGroupedData Objectplot.ranef.lmList Plot a ranef.lmList Objectplot.ranef.lme Plot a ranef.lme ObjectpooledSD Extract Pooled Standard Deviationpredict.gls Predictions from a gls Objectpredict.gnls Predictions from a gnls Objectpredict.lmList Predictions from an lmList Objectpredict.lme Predictions from an lme Objectpredict.nlme Predictions from an nlme Objectprint.anova.lme Print an anova.lme Objectprint.corStruct Print a corStruct Objectprint.gls Print a gls Objectprint.groupedData Print a groupedData Objectprint.intervals.gls Print an intervals.gls Objectprint.intervals.lme Print an intervals.lme Objectprint.lmList Print an lmList Objectprint.lme Print an lme Objectprint.modelStruct Print a modelStruct Objectprint.pdMat Print a pdMat Objectprint.reStruct Print an reStruct Objectprint.summary.corStruct Print a summary.corStruct Objectprint.summary.gls Print a summary.gls Objectprint.summary.lmList Print a summary.lmList Objectprint.summary.lme Print a summary.lme Objectprint.summary.modelStruct Print a summary.modelStruct Objectprint.summary.pdMat Print a summary.pdMat Objectprint.summary.varFunc Print a summary.varFunc Objectprint.varFunc Print a varFunc ObjectpruneLevels Prune Factor Levelsqqnorm.gls Normal Plot of Residuals from a gls Objectqqnorm.lme Normal Plot of Residuals or Random Effects from an lme

Objectrandom.effects Extract Random Effectsrandom.effects.lmList Extract lmList Random Effectsrandom.effects.lme Extract lme Random Effectsranef Extract Random Effects

99

nlme Library (version 3)

ranef.lmList Extract lmList Random Effectsranef.lme Extract lme Random EffectsreStruct Random Effects Structurerecalc Recalculate Condensed Linear Model Objectrecalc.corStruct Recalculate for corStruct Objectrecalc.modelStruct Recalculate for a modelStruct Objectrecalc.reStruct Recalculate for an reStruct Objectrecalc.varFunc Recalculate for varFunc Objectresiduals.gls Extract gls Residualsresiduals.glsStruct Calculate glsStruct Residualsresiduals.gnls Extract gnls Residualsresiduals.gnlsStruct Calculate gnlsStruct Residualsresiduals.lmList Extract lmList Residualsresiduals.lme Extract lme Residualsresiduals.lmeStruct Calculate lmeStruct Residualsresiduals.nlmeStruct Calculate nlmeStruct ResidualsselfStart Construct Self-starting Nonlinear ModelsselfStart.default Construct Self-starting Nonlinear ModelsselfStart.formula Construct Self-starting Nonlinear Modelssimulate.lme simulate lme modelssolve.pdMat Calculate Inverse of a Positive-Definite Matrixsolve.reStruct Apply Solve to an reStruct ObjectsortedXyData Create a sortedXyData objectsplitFormula Split a Formulasummary.corStruct Summarize a corStruct Objectsummary.gls Summarize a gls Objectsummary.lmList Summarize an lmList Objectsummary.lme Summarize an lme Objectsummary.modelStruct Summarize a modelStruct Objectsummary.nlsList Summarize an nlsList Objectsummary.pdMat Summarize a pdMat Objectsummary.varFunc Summarize varFunc Objectupdate.gls Update a gls Objectupdate.gnls Update a gnls Objectupdate.groupedData Update a groupedData Objectupdate.lmList Update an lmList Objectupdate.lme Update an lme Objectupdate.modelStruct Update a modelStruct Object

100

Non-linear Regression

update.nlme Update an nlme Objectupdate.nlsList Update an nlsList Objectupdate.varFunc Update varFunc ObjectvarClasses Variance Function ClassesvarComb Combination of Variance FunctionsvarConstPower Constant Plus Power Variance FunctionvarExp Exponential Variance FunctionvarFixed Fixed Variance FunctionvarFunc Variance Function StructurevarIdent Constant Variance FunctionvarPower Power Variance FunctionvarWeights Extract Variance Function WeightsvarWeights.glsStruct Variance Weights for glsStruct ObjectvarWeights.lmeStruct Variance Weights for lmeStruct Object

Non-linear Regression TBS Transform Both Sides of a Nonlinear Regression Modelbrowser.ms Interactive browser for Tracing Minimizationderiv Symbolic Partial Derivatives of Expressionsderiv.default Symbolic Partial Derivatives of ExpressionsgetInitial Get Initial Parameter Estimatesintegrate Integral of a Real-valued Function over an Interval.ms Fit a Nonlinear Model by Minimum Sumsms.control Control of minimization in ms ms.object Nonlinear Fitting Objectnlminb Nonlinear Minimization subject to Box Constraintsnlminb.control Controls User Options for nlminb nlregb Nonlinear Least Squares Subject to Box Constraintsnlregb.control User Options to Control nlregb nls Nonlinear Least Squares Regressionnls.control Control the Iteration in nls() nls.object Nonlinear Least Squares Objectoptim General-purpose Optimizationoptimize Univariate Optimization of a Continuous Function.param Parameters in a Parametrized Data Frameparam<- Parameters in a Parametrized Data Frameparameters Parameters in a Parametrized Data Frameparameters<- Parameters in a Parametrized Data Frame

101

Nonparametric Statistics

pframe Construct a Parameterized Data Frame Objectpframe.object Parametrized Data Frame Objectsprofile Profile a Nonlinear Model - Generic Functionprofile.ms Profile Method for MS Objectssummary.ms Summary of an ms Modeluniroot Root Finder for Continuous Univariate Functions.

Nonparametric Statistics Wilcoxon Distribution of Wilcoxon Rank Sum Statisticace Regression Model Linearizationavas Additivity and Variance Stabilization for Regressionbs Generate a Basis for Polynomial Splinescor.test Test for Zero Correlationdwilcox Distribution of Wilcoxon Rank Sum Statisticfriedman.test Friedman Rank Sum Testgam Fit a Generalized Additive Modelgam.control Set Control Parameters for gam gam.object Generalized Additive Model Objectgam.scope Generate a Scope Argument for Stepwise GAMkruskal.test Kruskal-Wallis Rank Sum Testks.gof Kolmogorov-Smirnov Goodness-of-Fit Testlo Specify a Loess Fit in a GAM Formulana.gam.replace A Missing Data Filterns Generate a Basis Matrix for Natural Cubic Splinesplot.gam Plot Components of a GAM Objectplot.glm Generate Diagnostic Plots for a GLM Objectplot.preplot.gam Plot Components of a GAM Objectppreg Projection Pursuit Regressionpredict.gam Make Predictions from a Fitted GAM Objectpredict.smooth.spline Smoothing Spline at New Datapwilcox Distribution of Wilcoxon Rank Sum Statisticqwilcox Distribution of Wilcoxon Rank Sum Statisticrwilcox Distribution of Wilcoxon Rank Sum Statistics Specify a Smoothing Spline Fit in a GAM Formulastep.gam Build a GAM Model in a Step-Wise Fashionwilcox.test Wilcoxon Rank Sum and Signed Rank Sum Tests

Optimization

102

Ordinary Differential Equations

napsack Solve Knapsack Problemsnlmin Find Local Minimum of a Nonlinear Functionnlminb Nonlinear Minimization subject to Box Constraintsnlregb Nonlinear Least Squares Subject to Box Constraintsnls Nonlinear Least Squares Regressionnnls.fit Nonnegative Least Squaresoptim General-purpose Optimizationoptimize Univariate Optimization of a Continuous Function

Ordinary Differential Equations ivp.ab Initial Value Solver for Systems of Ordinary Differential

Equations

Package System getSversion Spotfire S+ Version Numberinstall.pkgutils Download and install the pkgutils library section from

CSANinstallFromDataFiles Install from Spotfire S+ Source Files into a PackageinstallFromSFiles Install from Spotfire S+ Source Files into a PackagepackageDescription Gets the Description of the Specified Packagerequire Load a Packagesystem.file Find Names of Spotfire S+ System FilesunresolvedGlobalReferences Find Undefined Functions and Data

Package Utils Library (adapted from R) install.pkgutils Download and install the pkgutils library section from

CSANpackageDescription Gets the Description of the Specified Packageread.dcf Read and Write Data in DCF Format

Printing cat General PrintingdQuote Quote Textdeparse Turn Parsed Expression into Character Formdget Write a Text Representation of a Spotfire S+ Objectfile.show Display Filesdput Write a Text Representation of a Spotfire S+ Objectformat Formatted Character Dataformat.char Formatting Using C-style Formatsformat.default Format Atomic Data

103

Printing

formatC Formatting Using C-style Formatshead Get the First or Last Part of an Objectlabels Labels for Printing or Plotting - Generic functionlabels.default Labels for Printing or Plotting - Generic functionlogcat Add note to log file and/or standard outputlpr Print a Spotfire S+ object on a printer.ls.print Print a Regression Summaryobjprint Print a Spotfire S+ object on a printer.page Page Through Dataplotlabels Labels for Printing or Plotting - Generic functionplotlabels.default Labels for Printing or Plotting - Generic functionpostscript Graphics Device for PostScript Printersprint Print Data - Generic functionprint.aareg Print an aareg Objectprint.agnes Use print() on an agnes objectprint.array Print a Multi-Dimensional Arrayprint.atomic Print Data with Atomic Modesprint.by Use print() on a by objectprint.char.matrix Print a char.matrix Object to Make a Formatted Tableprint.clara Use print() on a clara objectprint.connection Print Information about Connection Objectprint.crosstabs Print Output of crosstabs Functionprint.cts Print a Calendar Time Seriesprint.default Print Dataprint.diana Use print() on a diana objectprint.dissimilarity Use print() on a dissimilarity objectprint.factanal Print a Factor Analysis Objectprint.fanny Use print() on a fanny objectprint.gls Print a gls Objectprint.its Print Method for Irregular Time Seriesprint.list Print a Listprint.lmRobMM Use print() on an lmRobMM objectprint.loadings Print a Loadings Matrixprint.loess Print Method for a LOESS Object or its Summaryprint.manova Print a Manova Objectprint.matrix Print a Matrixprint.mona Use print() on a mona objectprint.pam Use print() on a pam object

104

Probability Distributions and Random Numbers

print.princomp Print a Principal Components Objectprint.rts Print Method for Regular Time Seriesprint.structure Print an Object with Attributesprint.summary.agnes Use print() on a summary.agnes objectprint.summary.clara Use print() on a summary.clara objectprint.summary.diana Use print() on a summary.diana objectprint.summary.factanal Print a Factor Analysis Summaryprint.summary.fanny Use print() on a summary.fanny objectprint.summary.lmRobMM Use print() on a summary.lmRobMM objectprint.summary.loess Print Method for a LOESS Object or its Summaryprint.summary.manova Print Manova Summaryprint.summary.mona Use print() on a summary.mona objectprint.summary.pam Use print() on a summary.pam objectprint.summary.princomp Print a Principal Component Summaryprint.summary.survfit Print Survfit Summaryprint.tree Print a Tree Objectprint.trellis Plot (!) a Trellis Objectprint.ts Print a Time Seriesps.colors.rgb Colors for PostScript driverps.hsb2rgb Convert PostScript Color Specificationsps.options Set or Return PostScript Optionsps.options.send Send PostScript Optionsps.rgb2hsb Convert PostScript Color Specificationsps.setfont.latin1 PostScript Procedures for Font Selectionps.setfont.std PostScript Procedures for Font Selectionpscript Graphics Device for PostScript Printersquickvu Make Simple Vu-Graphsread.dcf Read and Write Data in DCF Formatrgb2matrix Convert X11 rgb.txt file to matrixsQuote Quote Textsummary.default Default Summary Methodtail Get the First or Last Part of an Objectwrite.dcf Reads and Writes Data in Dcf Formatwrite.table Write Matrix of Data to a Filezapsmall Coerce Small Numbers to Zero for Printing

Probability Distributions and Random Numbers Beta Beta Distribution

105

Probability Distributions and Random Numbers

Binomial Binomial DistributionCauchy Cauchy DistributionChisquare Chi-Square DistributionExponential Exponential DistributionF F DistributionGAMMA Gamma DistributionGeometric Geometric DistributionHypergeometric Hypergeometric DistributionLogistic Logistic DistributionLognormal Lognormal DistributionMVNormal Multivariate Normal (Gaussian) DistributionNegBinomial Negative Binomial DistributionNormal Normal (Gaussian) DistributionPoisson Poisson DistributionRNGKind Sets and Inspects the State of the Random Number

GeneratorStable Stable Family of DistributionsT Student's t-DistributionUniform Uniform DistributionWeibull Weibull DistributionWilcoxon Distribution of Wilcoxon Rank Sum Statisticdbeta Beta Distributiondbinom Binomial Distributiondcauchy Cauchy Distributiondchisq Chi-Square Distributionddiscrete Gets the Density for a Discrete Distributiondensity Estimate Probability Density Functiondexp Exponential Distributiondf F Distributiondgamma Gamma Distributiondgeom Geometric Distributiondhyper Hypergeometric Distributiondlnorm Lognormal Distributiondlogis Logistic Distributiondmvnorm Multivariate Normal (Gaussian) Distributiondnbinom Negative Binomial Distributiondnorm Normal (Gaussian) Distributiondnrange Distribution of the Range of Standard Normals

106

Probability Distributions and Random Numbers

dpois Poisson DistributiondsurvReg Distributions available in survReg .dt Student's t-Distributiondunif Uniform Distributiondweibull Weibull Distributiondwilcox Distribution of Wilcoxon Rank Sum Statisticpbeta Beta Distributionpbinom Binomial Distributionpcauchy Cauchy Distributionpchisq Chi-Square Distributionpexp Exponential Distributionpdiscrete Gets the Cumulative Probability for a Discrete Distributionpf F Distributionpgamma Gamma Distributionpgeom Geometric Distributionphyper Hypergeometric Distributionplnorm Lognormal Distributionplogis Logistic Distributionpmvnorm Multivariate Normal (Gaussian) Distributionpnbinom Negative Binomial Distributionpnorm Normal (Gaussian) Distributionpnrange Distribution of the Range of Standard Normalsppoints Plotting Points for QQplotsppois Poisson DistributionpsurvReg Distributions available in survReg .pt Student's t-Distributionpunif Uniform Distributionpweibull Weibull Distributionpwilcox Distribution of Wilcoxon Rank Sum Statisticqbeta Beta Distributionqbinom Binomial Distributionqcauchy Cauchy Distributionqchisq Chi-Square Distributionqdiscrete Gets the Quantiles for a Discrete Distributionqdunnett Quantiles for Dunnett's Comparisons with Controlqexp Exponential Distributionqf F Distributionqgamma Gamma Distribution

107

Probability Distributions and Random Numbers

qgeom Geometric Distributionqhyper Hypergeometric Distributionqlnorm Lognormal Distributionqlogis Logistic Distributionqmvt Quantiles for the Equicorrelated Multivariate-t Distributionqmvt.sim Simulation-based Quantiles of the Multivariate-t

Distributionqnbinom Negative Binomial Distributionqnorm Normal (Gaussian) Distributionqnrange Distribution of the Range of Standard Normalsqpois Poisson Distributionqqnorm Quantile-Quantile Plots - Generic Functionqqnorm.default Quantile-Quantile Plots - Generic Functionqqplot Quantile-Quantile Plots - Generic FunctionqsurvReg Distributions available in survReg .qt Student's t-Distributionqtukey Quantiles of Tukey's Studentized Range Distributionquantile Empirical Quantilesqunif Uniform Distributionqweibull Weibull Distributionqwilcox Distribution of Wilcoxon Rank Sum Statisticrbeta Beta Distributionrbinom Binomial Distributionrcauchy Cauchy Distributionrchisq Chi-Square Distributionrdiscrete Gets the Random Generation for a Discrete Distributionrexp Exponential Distributionrf F Distributionrgamma Gamma Distributionrgeom Geometric Distributionrhyper Hypergeometric Distributionrlnorm Lognormal Distributionrlogis Logistic Distributionrmvnorm Multivariate Normal (Gaussian) Distributionrnbinom Negative Binomial Distributionrnorm Normal (Gaussian) Distributionrnrange Distribution of the Range of Standard Normalsrpois Poisson Distribution

108

Programming

rstab Stable Family of Distributionsrt Student's t-Distributionrunif Uniform Distributionrweibull Weibull Distributionrwilcox Distribution of Wilcoxon Rank Sum Statisticsample Generate Random Samples or Permutations of Dataset.seed Set Seed for Random Number Generatorsstem Stem and Leaf Display

Programming .Call Manipulate Spotfire S+ Objects from C.First Startup and Wrapup Actions.First.local Startup and Wrapup Actions.JavaField Call a Java Method or Get a Java Field Value ( Java-enabled

Spotfire S+ only).JavaMethod Call a Java Method or Get a Java Field Value ( Java-enabled

Spotfire S+ only).Last Startup and Wrapup Actions.S.init Startup and Wrapup ActionsCAP_For Manage Compute-Intensive IterationDBLEPR Printing from a Fortran RoutineFor Manage Compute-Intensive IterationINTPR Printing from a Fortran RoutineNextMethod Methods Invoked from Spotfire S+ FunctionsQuote Return an Unevaluated ExpressionREALPR Printing from a Fortran RoutineRecall Recursive Call of the Current FunctionS.init Startup and Wrapup ActionsS_alloc Storage Allocation in CSyntax The Structure of Spotfire S+ ExpressionsSys,sleep Sleep for a Specified PeriodUseMethod Methods Invoked from Spotfire S+ FunctionsXERROR Error Output and Termination for Fortran RoutinesXERRWV Error Output and Termination for Fortran Routinesaccess Check for file existence, readability, or writabilityagain Display, Edit, Re-evaluate and Save Past Spotfire S+

Expressionsall.names Find All Names in an Expressionall.vars Find All Variables Used in an Expression

109

Programming

allTrue Test for all inputs returning TRUE .allocated Memory Allocated in Spotfire S+ Framesamatch Argument Matchingas Generic Coercion Functionas.call Function Callsas.double Double Precision Objectsas.expression Expression Objectsas.function Function Objectsas.integer Integer Objectsas.name Name Objectsas.null Null Objectsassign Assign Object to Database or Framebreak Controlling Flow of Evaluationbrowser Browse an Object - Generic functionbrowser.default Browse Interactively in a Function's Framecall Function CallscallGeneric Call the Current Generic Functioncall_S Call Spotfire S+ from a C Routinecharmatch Partial Matching of Character Stringscleanup_call_S Call S from a C Routineclear.frame Move or Clear a Created FramecolMaxs Row and Column Summaries - min, max, and rangecolMedians Compute medians columnwisecolMins Row and Column Summaries - min, max, and rangecolProds Columnwise ProductscolQuantiles Compute quantiles columnwisecolRanges Row and Column Summaries - min, max, and rangecreateChapter Create a chapterdir List the Files in a Directorydataset.date Time Dataset was Last Changeddeparse Turn Parsed Expression into Character Formdo.call Execute a Function Calldo.test Test Spotfire S+ Functions and Expressionsdouble Double Precision Objectsdyn.close Open or Close a Shared Librarydyn.open Open or Close a Shared Libraryelse Conditional Expressions and Operatorserror.level Return or Modify the Current Error Level

110

Programming

eval Evaluate an Expressionfile.access Check for file existence, readability, or writabilityexpression Expression Objectsfile.exists Check if a File Existsfile.realpath Absolute path name for a file.files.in.dir Files in a Directoryfind.calls Find Calls to a Functionfix Fix a Function.for Controlling Flow of Evaluationframe.attr Attributes of the Current Evaluation Frameframe.attributes Attributes of the Current Evaluation Framefunction The Structure of Spotfire S+ ExpressionsfunctionComments Extract or Replace Function CommentshasArg Check for Argument Nameshistory Display, Edit, Re-evaluate and Save Past Spotfire S+

Expressionsif Conditional Expressions and Operatorsinspect Diagnostic Evaluation Under Interactive ControlinstallFromDataFiles Install from Spotfire S+ Source Files into a PackageinstallFromSFiles Install from Spotfire S+ Source Files into a Packageinteger Integer Objectsinteractive Test For Interactive Execution of Spotfire S+invisible Mark Function as Non-Printingis.R Test If Running Under Ris.atomic Test for Recursive or Atomic Objectsis.call Function Callsis.dir Check if a Directory Existsis.double Double Precision Objectsis.expression Expression Objectsis.function Function Objectsis.integer Integer Objectsis.language Test for Recursive or Atomic Objectsis.monthend The End of Month Day Informationis.name Name Objectsis.null Null Objectsis.recursive Test for Recursive or Atomic Objectsis.symlink Check if a Directory Existslist.files List the Files in a Directory

111

Programming

is.symbol Name Objectsjava.new.plot.action Java Graphics Action on a New Plot (spjava Package)make.names Make Character Strings into Legal Spotfire S+ NamesmakeChapter Make a chapter DLLmatch.arg Argument Verification Using Partial Matchingmatch.call Argument Matchingmatch.path Match Paths or Stringsmissing Check for Missing Argumentsmkdir Make a Directorymmap.control Control Size Threshold at which Objects Are Memory-

Mappedmode Data Mode of the Values in a Vectormove.frame Move or Clear a Created FramenDotArgs Number of Arguments to Functionnargs Number of Arguments to Functionnew.frame Create Explicit Frames in the Evaluatornext Controlling Flow of Evaluationnull Null Objectsobjcopy Assign Copies of Objects to a Databaseobjdiff Differences Between Spotfire S+ Objectson.exit Exit Expression For a Functionparse Parse Expressionsparse.test Check if String is a Valid Spotfire S+ ExpressionparseClass Parsing User Input InteractivelyparseSome Parsing User Input Interactivelyquote Return an Unevaluated ExpressionrawFromAscii Generate Class Raw Objects from StringsrawFromHex Generate Class Raw Objects from Stringsreadline Read a Line from the Terminalrepeat Controlling Flow of Evaluationrestart Take Over Error Handlingreturn The Structure of Spotfire S+ Expressionsrmdir Remove a DirectoryrowMaxs Row and Column Summaries - min, max, and rangerowMins Row and Column Summaries - min, max, and rangerowRanges Row and Column Summaries - min, max, and rangeseriesLag Time Series Lag/Lead Function

112

Programming

seriesLength The Length of a "signalSeries" ("bdSignalSeries") or "timeSeries" ("bdTimeSeries") object

set.parse.mode Parse ExpressionssetMonitor Asynchronous Task and Event ManagementsetReader Asynchronous Task and Event ManagementsetSubEvents Control Monitoring of Sub-eventssilent.startup Silent startup.sleep Sleep for a Specified PeriodsourceChapter Source Spotfire S+ code for chapterstd.trace Control over Tracingstd.xtrace Control over Tracingstop Error and Warning Messagesstopifnot Stop if not All Truestorage Show Memory Usagestorage.mode Data Mode of the Values in a Vectorsubstitute Substitute in an Expressionswitch Evaluate One of Several Expressionssynchronize Synchronize Datasetssys.call System Evaluator Statesys.calls System Evaluator Statesys.frame System Evaluator Statesys.frames System Evaluator Statesys.function System Evaluator Statesys.nframe System Evaluator Statesys.on.exit System Evaluator Statesys.parent System Evaluator Statesys.parents System Evaluator Statesys.status System Evaluator Statesys.trace Control over Tracingsystem Execute a Windows Applicationtempdir Returns a Vector of Character Strings that are Virtually

Certain to be Unique Filenamestempfile Create Unique Names for Filestprint Trace Calls to Functionstrace Trace Calls to Functionstrace.on Control over Tracingtraceback Return Call Stacktry Continue after errors

113

Quality Control

unlink Remove a FileunresolvedGlobalReferences Find Undefined Functions and Datauntrace Trace Calls to Functionswarning Error and Warning Messageswhile Controlling Flow of Evaluationxerror Error Message Handling and Control for Fortran Routinesxerror.clear Error Message Handling and Control for Fortran Routinesxerror.maxpr Error Message Handling and Control for Fortran Routinesxerror.setfile Error Message Handling and Control for Fortran Routinesxerror.summary Error Message Handling and Control for Fortran Routines{ The Structure of Spotfire S+ Expressions|| Conditional Expressions and Operators

Quality Control beyond.limits Indices of Points Beyond Control Limits in Shewhart Chartcusum Plot a Cumulative Sum Quality Control Chartcusum.object Cusum Quality Control Chart Objectdnrange Distribution of the Range of Standard Normalsidentify.cusum Identify Points On a Cusum Quality Control Chart.identify.shewhart Identify Points On a Shewhart Quality Control Chart.limits.R Shewhart Quality Control Limitslimits.c Shewhart Quality Control Limitslimits.np Shewhart Quality Control Limitslimits.p Shewhart Quality Control Limitslimits.s Shewhart Quality Control Limitslimits.u Shewhart Quality Control Limitslimits.xbar Shewhart Quality Control Limitsmoving.range Moving Standard Deviation and Range Estimation for

Control Chartsmoving.sigma Moving Standard Deviation and Range Estimation for

Control Chartspnrange Distribution of the Range of Standard Normalspointwise Pointwise Confidence Limits for Predictionsqcc Create a Quality Control Chart Objectqnrange Distribution of the Range of Standard Normalsrnrange Distribution of the Range of Standard Normalsruns.target Determine Indices of Points Violating the Runs Rule.sd.R Within Group Standard Deviation for Control Chartssd.c Within Group Standard Deviation for Control Charts

114

Regression

sd.ewma Within Group Standard Deviation for Control Chartssd.mR Within Group Standard Deviation for Control Chartssd.ma Within Group Standard Deviation for Control Chartssd.ms Within Group Standard Deviation for Control Chartssd.np Within Group Standard Deviation for Control Chartssd.p Within Group Standard Deviation for Control Chartssd.s Within Group Standard Deviation for Control Chartssd.u Within Group Standard Deviation for Control Chartssd.xbar Within Group Standard Deviation for Control Chartsshewhart Plot a Shewhart Quality Control Chartshewhart.object Shewhart Quality Control Chart Objectshewhart.rules Apply Default Rules Functions to a Shewhart Control Chart.stats.R Summary Statistics for Control Chartsstats.c Summary Statistics for Control Chartsstats.ewma Summary Statistics for Control Chartsstats.mR Summary Statistics for Control Chartsstats.ma Summary Statistics for Control Chartsstats.ms Summary Statistics for Control Chartsstats.np Summary Statistics for Control Chartsstats.p Summary Statistics for Control Chartsstats.s Summary Statistics for Control Chartsstats.u Summary Statistics for Control Chartsstats.xbar Summary Statistics for Control Charts

Regression ace Regression Model Linearizationadd1.lm Add Terms to a Linear Model Objectadd1.lmRobMM Add Terms to a Robust Linear Model Objectalias.lm Alias Pattern for Linear Regression Model Objectsalias.mlm Alias Pattern for Linear Regression Model Objectsarima.object ARIMA Model Objectavas Additivity and Variance Stabilization for Regressionbs Generate a Basis for Polynomial SplinescensorReg.object Parametric Censored Regression Model Objectcompare.fits Statistics for Comparing Linear Modelscor.lmRobMM Robust Correlation Matrixcov.lmRobMM Robust Covariance Matrixcoxph Fit Proportional Hazards Regression Model

115

Regression

drop1.lm Compute an Anova Object by Dropping Termsdrop1.lmRobMM Compute an Anova Object by Dropping Termsdummy.coef Extract Original Coefficients from a Linear Model - Generic

FunctiondurbinWatson The Durbin-Watson StatisticdurbinWatson.default The Durbin-Watson StatisticdurbinWatson.lm The Durbin-Watson Statisticeffects Single Degree of Freedom Effects from Fitted Modeleffects.lm Single Degree-of-freedom Effects for an lm Objectglm Fit a Generalized Linear Modelglm.control Set Control Parameters for Generalized Linear Modelglm.fit Fit a GLM without Computing the Model Matrixglm.links Family Support Objectsglm.object Generalized Linear Model Objectglm.variances Family Support Objectsglm.weights Family Support Objectshat Hat Diagonal Regression Diagnostickappa Estimate the Condition Numberkappa.default Estimate the Condition Numberkappa.lm Estimate the Condition Numberkappa.upper Estimate the Condition Numberksmooth Densities or Regressions Using Kernel Smoothersl1fit Minimum Absolute Residual (L1) Regressionleaps All-Subset Regressions by Leaps and Bounds lm Fit Linear Regression Modellm.fit General Fitting for Linear Modelslm.fit.chol Fit a Linear Modellm.fit.qr Fit a Linear Modellm.fit.svd Fit a Linear Modellm.influence Influence of Observations on Linear Modellm.object Linear Least Squares Model ObjectlmRobMM High Breakdown and High Efficiency Robust RegressionlmRobMM.genetic.control Control Parameters for MM Robust Regression with

Genetic AlgorithmlmRobMM.object Robust Linear Model ObjectslmRobMM.robust.control Control Parameters for MM Robust RegressionlmRobMM.ucovcoef Unscaled Covariance Matrix of Coefficient Estimateslms.object Least Median of Squares Object

116

Regression

lmsreg Least Median of Squares Robust Regressionlmsreg.default Use lmsreg on a Vector, Matrix, or Data Framelmsreg.formula Use lmsreg with a formula Objectlowess Scatter Plot Smoothingls.diag Compute Regression Diagnosticsls.print Print a Regression Summaryls.summary Compute Regression Diagnosticslsfit Linear Least-Squares Fitlts.object Least Trimmed Squares Objectltsreg Least Trimmed Squares Robust Regressionltsreg.default Use ltsreg on a Vector, Matrix, or Data Frameltsreg.formula Use ltsreg with a formula Objectmlm Linear Least Squares Model Objectmlm.object Linear Least Squares Model Objectns Generate a Basis Matrix for Natural Cubic Splinesplot.compare.fits Comparison Plots for Linear Modelsplot.lm Generate Diagnostic Plots for an LM Objectplot.lmRobMM Generate Diagnostic Plots for a Robust LM Objectplot.lms Diagnostic Plots for an "lms" Objectplot.lts Diagnostic Plots for an "lts" Objectpoly Generate a Basis for Polynomial Regressionpoly.transform Transform Coefficients from Orthogonal Polynomial Formppreg Projection Pursuit Regressionprint.compare.fits Print Method for class "compare.fits" proj Projection Matrixproj.default Projection Matrixrbiwt Robust Simple Regression by Biweightrreg M-Estimates of Regressionrsquared.lmRobMM Robust R-Squaredscale.lmRobMM Robust Scale EstimatessType3 Compute Type III Sum of Squares - Generic FunctionssType3.aovlist Compute Type III Sum of SquaresssType3.default Compute Type III Sum of SquaresssType3.formula Compute Type III Sum of SquaresssType3.lm Compute Type III Sum of Squaresstep.glm Build a GLM Model in a Step-Wise Fashionstepwise Stepwise Subset Selection for Multiple Regressionsummary.arima Summary Method for an ARIMA model fit

117

Regression and Classification Trees

summary.compare.fits Summary Method for class "compare.fits" summary.glm Summary Method for Fitted Generalized Linear Modelssummary.lm Summary Method for Linear Modelssummary.lmRobMM Summary Method for class "lmRobMM" survReg.object Parametric Survival Model Objectsurvreg.object Parametric Survival Model Objectweights.lmRobMM Robust Weight Vectorwt.andrews M-Estimates of Regressionwt.bisquare M-Estimates of Regressionwt.cauchy M-Estimates of Regressionwt.default M-Estimates of Regressionwt.fair M-Estimates of Regressionwt.hampel M-Estimates of Regressionwt.huber M-Estimates of Regressionwt.logistic M-Estimates of Regressionwt.median M-Estimates of Regressionwt.talworth M-Estimates of Regressionwt.welsch M-Estimates of Regression

Regression and Classification Trees Subscript.tree Subscript a Tree Object[.tree Subscript a Tree Objectbasis.tree Compute Orthogonal Basis for a Tree Objectbrowser.tree Return Contents of Selected Nodes of a Tree Objectburl.tree View Splits for Nodes of a Tree Objectcv.tree Cross Validation of a Tree Sequencedata.tree Return Data Used To Grow a Treedeviance.tree Deviance of a Tree Objectedit.tree Change Node Splits in a Binary Treegraft.tree Graft a Subtree onto the Original Treehist.tree Histograms of Predictors at Tree Nodesidentify.tree Identify Observations in Tree Nodesmeanvar.tree Mean-Variance Plot for a Tree Objectmisclass.tree Misclassification Errors for a Classification Treena.tree.replace Replace NA's in Predictor Variablesna.tree.replace.all Replace NA's in Predictor Variablesorder.tree Reorder Terminal Nodes of a Binary Tree.partition.tree Plot a Low-Dimensional Tree Object

118

Resampling (Bootstrap, Jackknife, and Permutations)

path.tree Follow Paths to Selected Nodes of a Treeplot.tree Plot a Tree Objectplot.tree.sequence Plot a Tree Sequencepost.tree PostScript Presentation Plot of a Tree Objectpred.tree Predicted Terminal Node from a Fitted Tree Objectpredict.tree Predictions from a Fitted Tree Objectprint.tree Print a Tree Objectprune.misclass Cost-complexity Pruning of Tree Objectprune.tree Cost-complexity Pruning of Tree Objectresiduals.tree Residuals From a Fitted Tree Objectrug.tree Augment a Dendrogram with a Rugselect.tree Select Subtrees of a Tree Objectshrink.tree Optimal Recursive Shrinking of Tree Objectssnip.tree Snip Subtrees of a Tree Objectsummary.tree Summarize a Fitted Tree Objecttext.tree Place Text on a Dendrogramtile.tree Augment a Dendrogram with Tilestree Fit a Regression or Classification Treetree.control Control For Tree Growingtree.object Regression or Classification Tree Objecttree.screens Partition the Graphics Area for Tree Plotstree.sequence.object Regression or Classification Tree ObjectRelease.Notes Spotfire S+ for Windows Release Notes

Resampling (Bootstrap, Jackknife, and Permutations) addSamples Add New Replicates to Bootstrap Objectbootstats Calculate Bootstrap Statisticsbootstrap General Nonparametric BootstrappinggroupAlls Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.data.frame Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAlls.default Computes Group Sums, Means, Variances, Standard

Deviations for a Vector or Columns of an ArraygroupAnys Computes Group Sums, Means, Variances, Standard

Deviations, or Other Summaries for a Vector or Columns of an Array

groupAnys.data.frame Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

119

Resampling (Bootstrap, Jackknife, and Permutations)

groupAnys.default Computes Group Sums, Means, Variances, Standard Deviations, or Other Summaries for a Vector or Columns of an Array

groupMaxs Computes Group Max for a Vector or Columns of an ArraygroupMaxs.data.frame Computes Group Max for a Vector or Columns of an ArraygroupMaxs.default Computes Group Max for a Vector or Columns of an ArraygroupMeans Computes Group Means for a Vector or Columns of an

ArraygroupMeans.data.frame Computes Group Means for a Vector or Columns of an

ArraygroupMeans.default Computes Group Means for a Vector or Columns of an

ArraygroupMins Computes Group Mins for a Vector or Columns of an ArraygroupMins.data.frame Computes Group Mins for a Vector or Columns of an ArraygroupMins.default Computes Group Mins for a Vector or Columns of an ArraygroupProds Computes Group Products for a Vector or Columns of an

ArraygroupProds.data.frame Computes Group Products for a Vector or Columns of an

ArraygroupProds.default Computes Group Products for a Vector or Columns of an

ArraygroupRanges Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.data.frame Computes Group Ranges for a Vector or Columns of an

ArraygroupRanges.default Computes Group Ranges for a Vector or Columns of an

ArraygroupStdevs Computes group standard deviations for a vector or

columns of an array.groupSums Computes Group Sums for a Vector or Columns of an ArraygroupSums.data.frame Computes Group Sums for a Vector or Columns of an ArraygroupSums.default Computes Group Sums for a Vector or Columns of an ArraygroupVars Computes Group Variances for a Vector or Columns of an

ArraygroupVars.data.frame Computes Group Variances for a Vector or Columns of an

ArraygroupVars.default Computes Group Variances for a Vector or Columns of an

Arrayjack.after.bootstrap Perform Jackknife-After-Bootstrapjackknife General Nonparametric Jackknifejackstats Calculate Jackknife Statisticslimits.bca Calculate BCa Confidence Limitslimits.emp Calculate Empirical Percentiles of Replicates

120

Robust/Resistant Techniques

plot.jack.after.bootstrap Influence Plot Using Jackknife-After-Bootstrapplot.resamp Plot Method for Resample Objectsprint.jack.after.bootstrap Print a Jackknife-After-Bootstrap Objectprint.resamp Print a Resample Objectprint.summary.bootstrap Print a Summary of Bootstrap Objectprint.summary.resamp Print a Summary of Resample Objectqqnorm.resamp Quantile-Quantile Plots for Resample Objectsresamp.get.dimnames Support for Bootstrap and Jackkniferesamp.get.fit.func Support for Bootstrap and Jackkniferesamp.get.indices Support for Bootstrap and Jackknifesamp.boot.bal Construct Matrix of Resamplessamp.boot.mc Construct Matrix of Resamplessamp.permute Construct Matrix of ResamplessubtractMeans Subtract group means from each entry for a vector or

columns of an array.summary.bootstrap Summary Method for Bootstrap Objectssummary.resamp Summary Method for Resample Objectsupdate.bootstrap Add New Replicates to Bootstrap Object

Robust/Resistant Techniques acm.ave Two Filter Robust Smootheracm.filt Approximate Conditional Mean Robust Filteracm.smo Approximate Conditional Mean Robust Smootheradd1.lmRobMM Add Terms to a Robust Linear Model Objectanova.lmRobMM Use anova() on an lmRobMM objectar.gm Fit Autoregression Using Robust GM-Estimateschb Constants for Huber and Bisquare Psichi.weight Chi (Weight) Functioncompare.fits Statistics for Comparing Linear Modelscor.lmRobMM Robust Correlation Matrixcov.lmRobMM Robust Covariance Matrixcov.mcd Minimum Covariance Determinant Estimation - Generic

Function cov.mcd.default Use cov.mcd on a Vector, Matrix, or Data Framecov.mcd.formula Use cov.mcd with a formula Objectcov.mve Minimum Volume Ellipsoid Covariance Estimationcov.mve.default Use cov.mve on a Vector, Matrix, or Data Framecov.mve.formula Use cov.mve with a formula Objectdrop1.lmRobMM Compute an Anova Object by Dropping Terms

121

Robust/Resistant Techniques

l1fit Minimum Absolute Residual (L1) RegressionlmRobMM High Breakdown and High Efficiency Robust RegressionlmRobMM.effvy Constant for the Optimal Loss (Weight) FunctionlmRobMM.genetic.control Control Parameters for MM Robust Regression with

Genetic AlgorithmlmRobMM.object Robust Linear Model ObjectslmRobMM.robust.control Control Parameters for MM Robust RegressionlmRobMM.ucovcoef Unscaled Covariance Matrix of Coefficient Estimateslms.object Least Median of Squares Objectlmsreg Least Median of Squares Robust Regressionlmsreg.default Use lmsreg on a Vector, Matrix, or Data Framelmsreg.formula Use lmsreg with a formula Objectlocation.lms Univariate Location and Scale Estimation.location.lts Univariate Location and Scale Estimationlocation.m Robust M-estimates of Locationlowess Scatter Plot Smoothinglts.object Least Trimmed Squares Objectltsreg Least Trimmed Squares Robust Regressionltsreg.default Use ltsreg on a Vector, Matrix, or Data Frameltsreg.formula Use ltsreg with a formula Objectmad Robust Estimates of Scalemcd.object Minimum Covariance Determinant Objectmean Mean Value (Arithmetic Average)median Medianmve.object Minimum Volume Ellipsoid Objectplot.compare.fits Comparison Plots for Linear Modelsplot.lmRobMM Generate Diagnostic Plots for a Robust LM Objectplot.lms Diagnostic Plots for an "lms" Objectplot.lts Diagnostic Plots for an "lts" Objectplot.mcd Diagnostic Plots for an "mcd" Objectplot.mve Diagnostic Plots for an "mve" Objectprint.compare.fits Print Method for class "compare.fits" psi.weight Psi (Weight) Functionpsp.weight Psp (Weight) Functionrbiwt Robust Simple Regression by Biweightrho.weight Rho (Weight) Functionrobust Generate a Robust Family Objectrreg M-Estimates of Regression

122

Spotfire S+ Session Environment

rsquared.lmRobMM Robust R-Squaredsabl Seasonal Decompositionscale.a Robust Estimates of Scalescale.lmRobMM Robust Scale Estimatescale.tau Robust Estimates of Scalesmooth Nonlinear Smoothing Using Running Medianssummary.compare.fits Summary Method for class "compare.fits" summary.lmRobMM Summary Method for class "lmRobMM" twoway Fit of a Two-Way Tablevarcomp Variance Componentsvarcomp.object Variance Component Objectsweights.lmRobMM Robust Weight Vectorwt.andrews M-Estimates of Regressionwt.bisquare M-Estimates of Regressionwt.cauchy M-Estimates of Regressionwt.default M-Estimates of Regressionwt.fair M-Estimates of Regressionwt.hampel M-Estimates of Regressionwt.huber M-Estimates of Regressionwt.logistic M-Estimates of Regressionwt.median M-Estimates of Regressionwt.talworth M-Estimates of Regressionwt.welsch M-Estimates of Regression

Spotfire S+ Session Environment Command.edit Command Line Editing in Spotfire S+Sys.getenv Get Environment VariablesSys.getpid Get Process IDSys.putenv Set Environment VariablesSys.setenv Sets Environment Variables for Use by Other Processes

Called from Spotfire S+allocated Memory Allocated in Spotfire S+ Framesdos.time Execution Timesexit Quit the Spotfire S+ Sessiongetenv Get Environment Variablesgethostname Get the name of the computer Spotfire S+ is running ongetOption Set or Return OptionsgetSversion Spotfire S+ Version Number

123

Smoothing Operations

getwd Get current directory.info Information on the Current Spotfire S+log.import Utility functions for verbose logging.log.searchPaths Utility functions for verbose logging.mem.tally.report Measure Memory Usagemem.tally.reset Measure Memory Usagememory.size Total Memory Used by Running Spotfire S+object.size Internal Size of an Objectoptions Set or Return Optionspar Graphical Parameterspath.expand Expand ~ in File Pathsplatform Spotfire S+ Platform Information.print.mem.tally Measure Memory Usageproc.time Running Time of Spotfire S+q Quit From Spotfire S+setwd Get or set current directorystorage Show Memory Usagesys.call System Evaluator Statesys.calls System Evaluator Statesys.frame System Evaluator Statesys.frames System Evaluator Statesys.function System Evaluator Statesys.nframe System Evaluator Statesys.on.exit System Evaluator Statesys.parent System Evaluator Statesys.parents System Evaluator Statesys.status System Evaluator Statesys.time System and clock time of Spotfire S+system Execute a Windows Applicationsystem.stat System Informationunix.time Execution Timesverbose Tell if we are logging details of session.version Spotfire S+ Version Information.whoami Get User Name

Smoothing Operations ace Regression Model Linearizationacm.ave Two Filter Robust Smoother

124

Statistical Inference

acm.filt Approximate Conditional Mean Robust Filteracm.smo Approximate Conditional Mean Robust Smootheravas Additivity and Variance Stabilization for Regressiondensity Estimate Probability Density Functionksmooth Densities or Regressions Using Kernel Smootherslowess Scatter Plot Smoothingppreg Projection Pursuit Regressionpredict.smooth.spline Smoothing Spline at New Datas Specify a Smoothing Spline Fit in a GAM Formulascatter.smooth Scatter Plot with a Smooth Curvesmooth Nonlinear Smoothing Using Running Medianssmooth.spline Fit a Smoothing Splinespec.pgram Estimate Spectrum with Smoothed Periodogramspec.smo Perform Modified Daniell (Rectangular) Smoothingspectrum Estimate Spectrum of Time Seriessupsmu Scatter Plot Smoothing Using Super Smoother

Statistical Inference binom.test Exact Binomial Testbinomial.sample.size Power and Sample Sizecdf.compare Graphs Two Cumulative Distribution Functions.chisq.gof Chi square Goodness-of-Fit Testchisq.test Pearson's Chi-square Test for Count Datacor.test Test for Zero Correlationfisher.test Fisher's Exact Test for Count Datafriedman.test Friedman Rank Sum Testhtest.object Hypotheses Testing Objectskruskal.test Kruskal-Wallis Rank Sum Testks.gof Kolmogorov-Smirnov Goodness-of-Fit Testmantelhaen.test Mantel-Haenszel Chi-Square Test for Count Datamcnemar.test McNemar's Chi-Square Test for Count Datanormal.sample.size Power and Sample Sizeprop.test Proportions Testsshapiro.test Shapiro-Wilk Test for NormalityssType3 Compute Type III Sum of Squares - Generic FunctionssType3.aovlist Compute Type III Sum of SquaresssType3.default Compute Type III Sum of SquaresssType3.formula Compute Type III Sum of Squares

125

Statistical Models

ssType3.lm Compute Type III Sum of Squarest.test Student's t-Testsvar.test F Test to Compare Two Varianceswilcox.test Wilcoxon Rank Sum and Signed Rank Sum Tests

Statistical Models ACF Autocorrelation FunctionACF.gls Autocorrelation Function for gls ResidualsACF.lme Autocorrelation Function for lme ResidualsAIC Akaike Information CriterionAIC.logLik AIC of a logLik ObjectBIC Bayesian Information CriterionBIC.logLik BIC of a logLik ObjectDim Extract Dimensions from an ObjectDim.corSpatial Dimensions of a corSpatial ObjectDim.corStruct Dimensions of a corStruct ObjectDim.pdMat Dimensions of a pdMat ObjectNames Names Associated with an ObjectNames.formula Extract Names from a formulaNames.pdBlocked Names of a pdBlocked ObjectNames.pdMat Names of a pdMat ObjectNames.reStruct Names of an reStruct ObjectSSasymp Asymptotic regression modelSSasympOff Asymptotic Regression Model with an OffsetSSasympOrig Asymptotic Regression Model through the OriginSSbiexp Biexponential modelSSfol First-order Compartment ModelSSfpl Four-parameter Logistic ModelSSlogis Logistic modelSSmicmen Michaelis-Menten modelVarCorr Extract variance and correlation componentsVariogram Calculate Semi-VariogramVariogram.corExp Calculate Semi-Variogram for a corExp ObjectVariogram.corGaus Calculate Semi-Variogram for a corGaus ObjectVariogram.corLin Calculate Semi-Variogram for a corLin ObjectVariogram.corRatio Calculate Semi-Variogram for a corRatio ObjectVariogram.corSpatial Calculate Semi-Variogram for a corSpatial ObjectVariogram.corSpher Calculate Semi-Variogram for a corSpher Object

126

Statistical Models

Variogram.default Calculate Semi-VariogramVariogram.gls Calculate Semi-Variogram for Residuals from a gls ObjectVariogram.lme Calculate Semi-Variogram for Residuals from an lme Object[.pdMat Subscript a pdMat Objectace Regression Model Linearizationadd.scope Resolve Scopes for Formulasadd1 Compute Models by Adding One Term - Generic Functionadd1.lmRobMM Add Terms to a Robust Linear Model ObjectallCoef Extract Coefficients from a Set of Objectsanova Compute an Anova Table - Generic functionanova.gam ANOVA Table for a GAM Objectanova.gls Compare Likelihoods of Fitted Objectsanova.lmRobMM Use anova() on an lmRobMM objectanova.lme Compare Likelihoods of Fitted Objectsaov Fit an Analysis of Variance Modelar Fit Univariate or Multivariate Autoregressive Modelarima.mle ARIMA Modeling via Gaussian Maximum Likelihoodarima.object ARIMA Model Objectas.data.frame Construct a Data Frame Objectas.data.frame.data.frame Construct a Data Frame Objectas.matrix.corStruct Matrix of a corStruct Objectas.matrix.pdMat Matrix of a pdMat Objectas.matrix.reStruct Matrices of an reStruct ObjectasNatural Convert to Natural ParameterizationasNatural.corBand Convert corBand Object to Natural ParameterizationasNatural.corStruct Convert corStruct Object to Natural ParameterizationasNatural.corSymm Convert corSymm Object to Natural ParameterizationasNatural.pdBand Convert pdBand Object to Natural ParameterizationasNatural.pdMat Convert pdMat Object to Natural ParameterizationasNatural.pdSymm Convert pdSymm Object to Natural ParameterizationasNatural.varFunc Convert varFunc Object to Natural ParameterizationasOneFormula Combine Formulas of a Set of ObjectsasOneSidedFormula Convert to One-Sided FormulaaugPred Augmented Predictionsavas Additivity and Variance Stabilization for RegressionbdFrame Construct a bdFrame ObjectbdGlm Big Data Generalized Linear ModelbdPrincomp Big Data Principal Component Analysis

127

Statistical Models

cmdscale Classical Metric Multi-Dimensional Scalingcoef Extract Coefficients, etc. from a Modelcoef.corStruct Coefficients of a corStruct Objectcoef.default Extract Coefficients, etc. from a Modelcoef.gls Extract gls Coefficientscoef.gnls Extract gnls Coefficientscoef.lmList Extract lmList Coefficientscoef.lme Extract lme Coefficientscoef.modelStruct Extract modelStruct Object Coefficientscoef.pdCompSymm pdCompSymm Object Coefficientscoef.pdDiag pdDiag Object Coefficientscoef.pdIdent pdIdent Object Coefficientscoef.pdMat pdMat Object Coefficientscoef.reStruct reStruct Object Coefficientscoef.varFunc varFunc Object Coefficientscoef<- Assign Values to Coefficientscoefficients Extract Coefficients, etc. from a Modelcollapse Collapse According to Groupscollapse.groupedData Collapse a groupedData Objectcompare.fits Statistics for Comparing Linear ModelscompareFits Compare Fitted ObjectscomparePred Compare PredictionscorAR1 AR(1) Correlation StructurecorARMA ARMA(p,q) Correlation StructurecorBand Banded Correlation StructurecorBandNat Banded Correlation in Natural ParameterizationcorCAR1 Continuous AR(1) Correlation StructurecorClasses Correlation Structure ClassescorCompSymm Compound Symmetry Correlation StructurecorExp Exponential Correlation StructurecorFactor Factor of a Correlation MatrixcorFactor.corStruct Factor of a corStruct Object MatrixcorGaus Gaussian Correlation StructurecorLin Linear Correlation StructurecorMatrix Extract Correlation MatrixcorMatrix.corStruct Matrix of a corStruct ObjectcorMatrix.pdMat Extract Correlation Matrix from a pdMat Object

128

Statistical Models

corMatrix.reStruct Extract Correlation Matrix from Components of an reStruct Object

corRatio Rational Quadratic Correlation StructurecorSpatial Spatial Correlation StructurecorSpher Spherical Correlation StructurecorStrat Stratified Correlation StructurecorSymm General Correlation StructurecorSymmNat General Correlation in Natural Parameterizationcovariate<- Assign Covariate Valuescovariate<-.varFunc Assign varFunc Covariatecoxme Fit a Mixed-Effects Cox Modelcoxph Fit Proportional Hazards Regression Modelcrossvalidate.discrim Crossvaliation Method for a discrim Objectdata.frame Construct a Data Frame Objectdata.frameAux Construct a Data Frame Objectdrop.scope Resolve Scopes for Formulasdrop1 Compute Models by Dropping Terms - Generic functiondrop1.lmRobMM Compute an Anova Object by Dropping Termsdummy.coef Extract Original Coefficients from a Linear Model - Generic

Functionfactanal Estimate a Factor Analysis Modelfactor.scope Resolve Scopes for Formulasfitted Extract Coefficients, etc. from a Modelfitted.default Extract Coefficients, etc. from a Modelfitted.gls Extract gls Fitted Valuesfitted.glsStruct Calculate glsStruct Fitted Valuesfitted.gnls Extract gnls Fitted Valuesfitted.gnlsStruct Calculate gnlsStruct Fitted Valuesfitted.lmList Extract lmList Fitted Valuesfitted.lme Extract lme Fitted Valuesfitted.lmeStruct Calculate lmeStruct Fitted Valuesfitted.nlmeStruct Calculate nlmeStruct Fitted Valuesfitted.values Extract Coefficients, etc. from a Modelfixed.effects Extract Fixed Effectsfixed.effects.lmList Extract lmList Fixed Effectsfixed.effects.lme Extract lme Fixed Effectsfixef Extract Fixed Effectsfixef.lmList Extract lmList Fixed Effects

129

Statistical Models

fixef.lme Extract lme Fixed Effectsformula.corStruct Extract corStruct Object Formulaformula.gls Extract gls Object Formulaformula.gnls Extract gnls Object Formulaformula.groupedData Extract groupedData Formulaformula.lmList Extract lmList Object Formulaformula.lme Extract lme Object Formulaformula.modelStruct Extract modelStruct Object Formulaformula.nlme Extract nlme Object Formulaformula.nls Extract Model Formula from nls Objectformula.nlsList Extract nlsList Object Formulaformula.pdBlocked Extract pdBlocked Formulaformula.pdMat Extract pdMat Formulaformula.reStruct Extract reStruct Object Formulaformula.varFunc Extract varFunc Formulagam Fit a Generalized Additive ModelgetCovariate Extract Covariate from an ObjectgetCovariate.corStruct Extract corStruct Object CovariategetCovariate.data.frame Extract Data Frame CovariategetCovariate.varFunc Extract varFunc CovariategetCovariateFormula Extract Covariates FormulagetData Extract Data from an ObjectgetData.gls Extract gls Object DatagetData.lmList Extract lmList Object DatagetData.lme Extract lme Object DatagetGroups Extract Grouping Factors from an ObjectgetGroups.corStruct Extract corStruct GroupsgetGroups.data.frame Extract Groups from a Data FramegetGroups.gls Extract gls Object GroupsgetGroups.lmList Extract lmList Object GroupsgetGroups.lme Extract lme Object GroupsgetGroups.varFunc Extract varFunc GroupsgetGroupsFormula Extract Grouping FormulagetGroupsFormula.gls Extract gls Object Grouping FormulagetGroupsFormula.lmList Extract lmList Object Grouping FormulagetGroupsFormula.lme Extract lme Object Grouping FormulagetGroupsFormula.reStruct Extract reStruct Grouping FormulagetInitial Get Initial Parameter Estimates

130

Statistical Models

getResponse Extract Response Variable from an ObjectgetResponse.data.frame Extract Response from a Data FramegetResponse.gls Extract gls Object ResponsegetResponse.lmList Extract lmList Object ResponsegetResponse.lme Extract lme Object ResponsegetResponseFormula Extract Formula Specifying Response VariablegetStrata Extract Stratification VariablegetStrata.data.frame Extract Strata from a Data FramegetStrataFormula Extract Stratification Formulaglm Fit a Generalized Linear Modelgls Fit Linear Model Using Generalized Least SquaresglsControl Control Values for gls FitglsObject Fitted gls ObjectglsStruct Generalized Least Squares Structuregnls Fit Nonlinear Model Using Generalized Least SquaresgnlsControl Control Values for gnls FitgnlsObject Fitted gnls ObjectgnlsStruct Generalized Nonlinear Least Squares Structureinitialize Initialize Objectinitialize.corStruct Initialize corStruct Objectinitialize.glsStruct Initialize a glsStruct Objectinitialize.lmeStruct Initialize an lmeStruct Objectinitialize.reStruct Initialize reStruct Objectinitialize.varFunc Initialize varFunc Objectintervals Confidence Intervals on Coefficientsintervals.gls Confidence Intervals on gls Parametersintervals.lmList Confidence Intervals on lmList Coefficientsintervals.lme Confidence Intervals on lme Parametersis.data.frame Construct a Data Frame ObjectisInitialized Check if Object is InitializedisInitialized.reStruct Check if an reStruct Object is InitializedisInitialized<- Set Initialization Statusl1fit Minimum Absolute Residual (L1) Regressionleaps All-Subset Regressions by Leaps and Bounds lm Fit Linear Regression ModellmList List of lm Objects with a Common ModellmList.groupedData lmList Fit from a groupedData ObjectlmRobMM High Breakdown and High Efficiency Robust Regression

131

Statistical Models

lmRobMM.object Robust Linear Model Objectslme Linear Mixed-Effects Modelslme.groupedData LME fit from groupedData Objectlme.lmList LME fit from lmList ObjectlmeControl Control Values for lme FitlmeObject Fitted lme ObjectlmeScale Scale for lme OptimizationlmeStruct Linear Mixed-Effects Structurelmekin Mixed Effects Model Using a Kinship Matrix.loess Fit a Local Regression ModellogDet Extract the Logarithm of the DeterminantlogDet.corStruct Extract corStruct Log-DeterminantlogDet.pdMat Extract Log-Determinant from a pdMat ObjectlogDet.reStruct Extract reStruct Log-DeterminantslogLik Extract Log-LikelihoodlogLik.corStruct Extract corStruct Log-LikelihoodlogLik.gls Log-Likelihood of a gls ObjectlogLik.glsStruct Log-Likelihood of a glsStruct ObjectlogLik.gnls Log-Likelihood of a gnls ObjectlogLik.gnlsStruct Log-Likelihood of a gnlsStruct ObjectlogLik.lm Extract Log-Likelihood from an lm ObjectlogLik.lmList Log-Likelihood of an lmList ObjectlogLik.lme Log-Likelihood of an lme ObjectlogLik.lmeStruct Log-Likelihood of an lmeStruct ObjectlogLik.reStruct Calculate reStruct Log-LikelihoodlogLik.varFunc Extract varFunc logLikloglin Contingency Table Analysislsfit Linear Least-Squares Fitmanova Fit a Multivariate Analysis of Variance Modelmatrix<- Assign Matrix Valuesmatrix<-.pdKron Assign Matrix to a pdKron Objectmatrix<-.pdMat Assign Matrix to a pdMat Objectmatrix<-.reStruct Assign reStruct Matricesmodel.matrix.reStruct reStruct Model Matrixms Fit a Nonlinear Model by Minimum Sumsmstree Minimal Spanning Tree and Multivariate PlaningneedUpdate Check if Update is NeededneedUpdate.modelStruct Check if a modelStruct Object Needs Updating

132

Statistical Models

nlme Nonlinear Mixed-Effects Modelsnlme.nlsList NLME fit from nlsList ObjectnlmeControl Control Values for nlme FitnlmeObject Fitted nlme ObjectnlmeStruct Nonlinear Mixed-Effects Structurenlregb Nonlinear Least Squares Subject to Box Constraintsnls Nonlinear Least Squares RegressionnlsList List of nls Objects with a Common ModelnlsList.selfStart nlsList Fit from a selfStart Functiononeway Fits a One-way Model to Univariate Data Grouped by a

Factorpairs.compareFits Pairs Plot of compareFits Objectpairs.lmList Pairs Plot of an lmList Objectpairs.lme Pairs Plot of an lme ObjectpdBand Banded Positive-Definite MatrixpdBandNat Banded Positive-Definite Matrix in Natural ParameterizationpdBlocked Positive-Definite Block Diagonal MatrixpdClasses Positive-Definite Matrix ClassespdCompSymm Positive-Definite Matrix with Compound Symmetry

StructurepdConstruct Construct pdMat ObjectspdConstruct.pdBlocked Construct pdBlocked ObjectspdDiag Diagonal Positive-Definite MatrixpdFactor Square-Root Factor of a Positive-Definite MatrixpdFactor.reStruct Extract Square-Root Factor from Components of an reStruct

ObjectpdIdent Multiple of the Identity Positive-Definite MatrixpdKron Kronecker-Product Positive-Definite MatrixpdMat Positive-Definite MatrixpdMatrix Extract Matrix or Square-Root Factor from a pdMat ObjectpdMatrix.reStruct Extract Matrix or Square-Root Factor from an reStruct

ObjectpdNatural General Positive-Definite Matrix in Natural ParametrizationpdStrat Stratified Positive-Definite MatrixpdSymm General Positive-Definite MatrixpdSymmNat General Positive-Definite Matrix in Natural

Parameterizationplot.ACF Plot an ACF Objectplot.Variogram Plot a Variogram Object

133

Statistical Models

plot.augPred Plot an augPred Objectplot.compare.fits Comparison Plots for Linear Modelsplot.compareFits Plot a compareFits Objectplot.gls Plot a gls Objectplot.intervals.lmList Plot lmList Confidence Intervalsplot.lm Generate Diagnostic Plots for an LM Objectplot.lmList Plot an lmList Objectplot.lmRobMM Generate Diagnostic Plots for a Robust LM Objectplot.lme Plot an lme Objectplot.nffGroupedData Plot an nffGroupedData Objectplot.nfnGroupedData Plot an nfnGroupedData Objectplot.nmGroupedData Plot an nmGroupedData Objectplot.ranef.lmList Plot a ranef.lmList Objectplot.ranef.lme Plot a ranef.lme ObjectpooledSD Extract Pooled Standard Deviationppreg Projection Pursuit Regressionpredict Make Predictions from a Fitted Model Objectpredict.arima Use predict() on a arima Class Objectpredict.discrim Prediction Method for a discrim Objectpredict.gls Predictions from a gls Objectpredict.gnls Predictions from a gnls Objectpredict.lmList Predictions from an lmList Objectpredict.lme Predictions from an lme Objectpredict.nlme Predictions from an nlme Objectprincomp Principal Components Analysisprint.anova.lme Print an anova.lme Objectprint.compare.fits Print Method for class "compare.fits" print.corStruct Print a corStruct Objectprint.gls Print a gls Objectprint.groupedData Print a groupedData Objectprint.intervals.gls Print an intervals.gls Objectprint.intervals.lme Print an intervals.lme Objectprint.lmList Print an lmList Objectprint.lme Print an lme Objectprint.modelStruct Print a modelStruct Objectprint.pdMat Print a pdMat Objectprint.reStruct Print an reStruct Objectprint.summary.corStruct Print a summary.corStruct Object

134

Statistical Models

print.summary.gls Print a summary.gls Objectprint.summary.lmList Print a summary.lmList Objectprint.summary.lme Print a summary.lme Objectprint.summary.modelStruct Print a summary.modelStruct Objectprint.summary.pdMat Print a summary.pdMat Objectprint.summary.varFunc Print a summary.varFunc Objectprint.varFunc Print a varFunc ObjectpruneLevels Prune Factor Levelsqqnorm.gls Normal Plot of Residuals from a gls Objectqqnorm.lme Normal Plot of Residuals or Random Effects from an lme

Objectrandom Include a Random Effects Term in an Additive Modelrandom.effects Extract Random Effectsrandom.effects.lmList Extract lmList Random Effectsrandom.effects.lme Extract lme Random Effectsranef Extract Random Effectsranef.lmList Extract lmList Random Effectsranef.lme Extract lme Random EffectsreStruct Random Effects Structurerecalc Recalculate Condensed Linear Model Objectrecalc.corStruct Recalculate for corStruct Objectrecalc.modelStruct Recalculate for a modelStruct Objectrecalc.reStruct Recalculate for an reStruct Objectrecalc.varFunc Recalculate for varFunc Objectresid Extract Coefficients, etc. from a Modelresiduals Extract Coefficients, etc. from a Modelresiduals.default Extract Coefficients, etc. from a Modelresiduals.gls Extract gls Residualsresiduals.glsStruct Calculate glsStruct Residualsresiduals.gnls Extract gnls Residualsresiduals.gnlsStruct Calculate gnlsStruct Residualsresiduals.lmList Extract lmList Residualsresiduals.lme Extract lme Residualsresiduals.lmeStruct Calculate lmeStruct Residualsresiduals.nlmeStruct Calculate nlmeStruct Residualsrreg M-Estimates of RegressionselfStart Construct Self-starting Nonlinear ModelsselfStart.default Construct Self-starting Nonlinear Models

135

Statistical Models

selfStart.formula Construct Self-starting Nonlinear Modelssimulate.lme simulate lme modelssolve.pdMat Calculate Inverse of a Positive-Definite Matrixsolve.reStruct Apply Solve to an reStruct Objectspectrum Estimate Spectrum of Time SeriessplitFormula Split a Formulastep Build a Model in a Stepwise Fashion - Generic Functionstepwise Stepwise Subset Selection for Multiple Regressionsummary.compare.fits Summary Method for class "compare.fits" summary.corStruct Summarize a corStruct Objectsummary.discrim The summary method for the discrim object.summary.gls Summarize a gls Objectsummary.lmList Summarize an lmList Objectsummary.lme Summarize an lme Objectsummary.modelStruct Summarize a modelStruct Objectsummary.nlsList Summarize an nlsList Objectsummary.pdMat Summarize a pdMat Objectsummary.varFunc Summarize varFunc Objecttree Fit a Regression or Classification Treeupdate Update a Fitted Model Objectupdate.default Update a Fitted Model Objectupdate.formula Update a Fitted Model Objectupdate.gls Update a gls Objectupdate.gnls Update a gnls Objectupdate.groupedData Update a groupedData Objectupdate.lmList Update an lmList Objectupdate.lme Update an lme Objectupdate.modelStruct Update a modelStruct Objectupdate.nlme Update an nlme Objectupdate.nlsList Update an nlsList Objectupdate.varFunc Update varFunc ObjectvarClasses Variance Function ClassesvarComb Combination of Variance FunctionsvarConstPower Constant Plus Power Variance FunctionvarExp Exponential Variance FunctionvarFixed Fixed Variance FunctionvarFunc Variance Function StructurevarIdent Constant Variance Function

136

Survival Analysis

varPower Power Variance FunctionvarWeights Extract Variance Function WeightsvarWeights.glsStruct Variance Weights for glsStruct ObjectvarWeights.lmeStruct Variance Weights for lmeStruct Objectvarcomp Variance Componentswt.andrews M-Estimates of Regressionwt.bisquare M-Estimates of Regressionwt.cauchy M-Estimates of Regressionwt.default M-Estimates of Regressionwt.fair M-Estimates of Regressionwt.hampel M-Estimates of Regressionwt.huber M-Estimates of Regressionwt.logistic M-Estimates of Regressionwt.median M-Estimates of Regressionwt.talworth M-Estimates of Regressionwt.welsch M-Estimates of Regression

Survival Analysis Surv Create a Survival Objectaareg Aalen's Additive Regression Model for Censored Dataanova.censorReg ANOVA Table for a class "censorReg" objectanova.censorReg.list ANOVA Table for a multiple class "censorReg" objectsanova.censorRegList ANOVA Table for a class "censorRegList" objectas.censor Create an object of class "censor" bladder Sample Data Sets For Survival Analysiscapacitor Sample Data Sets For Survival Analysiscensor Create an object of class "censor" censorReg Regression Model for Censored DatacensorReg.check.code Check truncation valuescensorReg.control Control values for routine censorRegcensorReg.distribution Table of numbers for parametric survival distributionscensorReg.good.data Checks for enough observationscensorReg.make.Y Transform the responsecensorReg.mlest Compute MLE for Censored Regression ModelscensorReg.object Parametric Censored Regression Model ObjectcensorReg.quantiles Quantiles for parametric survival distributionscensorReg.wfit Weighted least squares fit in parametric survival modelscluster Identify Clusters

137

Survival Analysis

cox.zph Test the Proportional Hazards Assumptioncoxme Fit a Mixed-Effects Cox Modelcoxme.control Control Parameters for coxmecoxph Fit Proportional Hazards Regression Modelcoxph.detail Details of a Cox Model Fitcoxph.object Proportional Hazards Regression ObjectdsurvReg Distributions available in survReg .f.phibf Failure probabilities for parametric survival modelsf.phis Density for parametric survival distributionf.phisl Log density for parametric survival distributionformula.censorRegList Use formula() on a censorRegList objectfrailty Fit a Penalized Factor Variablefrailty.gamma Random Effect Term for a Survival Modelfrailty.gaussian Random Effect Term for a Survival Modelfrailty.t Random Effect for a Survival Modelheart Sample Data Sets For Survival Analysisis.Surv Create a Survival Objectis.censor Create an object of class "censor" is.ratetable Verify that an object is of class ratetable .kaplanMeier Compute Nonparametric Survival EstimateskaplanMeier.fit Compute failure probability estimatesleukemia Sample Data Sets For Survival Analysislines.survfit Add Lines to a Survival Plotlung Sample Data Sets For Survival Analysisovarian Sample Data Sets For Survival Analysisplot.aareg Plot an aareg Objectplot.cox.zph Graphical Test of Proportional Hazardsplot.survfit Plot Method for survfit predict.coxph Predictions from a coxph Object.predict.survReg Predicted Values for a survReg Objectpredict.survreg Predicted Values for a survreg Objectprint.aareg Print an aareg Objectprint.censorReg Prints a class "censorReg" objectprint.censorRegList Print "censorRegList" objectprint.summary.censorReg Use print() on a summary.censorReg object"print.survfit Print a Short Summary of a Survival Curveprobplot Probability Plot - Generic Functionprobplot.censor Create Probability Plot for "censor" Object.

138

Survival Analysis

probplot.censorReg Create A Probability Plot for a Parametric Survival Modelprobplot6.censorReg Comparative probability plots for parametric survival

modelspspline Fit a Smoothing SplinepsurvReg Distributions available in survReg .pyears Person Yearsqftdist Quantiles for Parametric Survival/Censored Distributionsqftdist.dist Compute parametric failure distribution distancesqkaplanMeier Quantiles for Kaplan-Meier estimatesqqplot.censorReg.plot.quantiles Failure Distribution Plotqqplot.censorReg.setup Parametric Survival Probability Plot SetupqsurvReg Distributions available in survReg .ratetable Specify Variables to Match in Rate Tableresiduals.censorReg Compute Residuals for a Parametric Censored Regression

Modelresiduals.coxph Calculate Residuals for a Cox Regressionresiduals.survReg Compute Residuals for survReg Objectsresiduals.survreg Compute Residuals for survreg Objectsstrata Identify Strata Variablesstressplot Stress Plot - Generic Functionstressplot.censorReg Stress plot for parametric survival distributions.summary.aareg Summarize an aareg Fitsummary.censorReg Summary for censorReg objectsummary.censorRegList Summary for "censorRegList" objectsummary.survReg Summary for survReg Objectssummary.survfit Summary of a Survival Curvesummary.survreg Summary for survreg ObjectssurvReg Regression for a Parametric Survival ModelsurvReg.object Parametric Survival Model Objectsurvdiff Test Survival Curve Differencessurvexp Compute Expected Survivalsurvexp.az Census Data Sets for the Expected Survival and Person

Years Functionssurvexp.azr Census Data Sets for the Expected Survival and Person

Years Functionssurvexp.fit Compute Expected Survivalsurvexp.fl Census Data Sets for the Expected Survival and Person

Years Functionssurvexp.flr Census Data Sets for the Expected Survival and Person

Years Functions

139

Time Series

survexp.mn Census Data Sets for the Expected Survival and Person Years Functions

survexp.mnwhite Census Data Sets for the Expected Survival and Person Years Functions

survexp.us Census Data Sets for the Expected Survival and Person Years Functions

survexp.usr Census Data Sets for the Expected Survival and Person Years Functions

survexp.uswhite Census Data Sets for the Expected Survival and Person Years Functions

survfit Compute a Survival Curve for Censored Datasurvfit.object Survival Curve Objectsurvival.datasets Sample Data Sets For Survival Analysissurvreg.control Set Control Parameters for survreg survreg.object Parametric Survival Model Objecttcut Create Categories From Time Based Datauntangle.specials Process the specials Argument of the Terms Function

Time Series [.cts Subscript a Time Series Object[.its Subscript a Time Series Object[.rts Subscript a Time Series Objectacf Estimate Autocovariance, Autocorrelation or Partial

Autocorrelationacf.plot Plot Autocovariance or Autocorrelationacm.ave Two Filter Robust Smootheracm.filt Approximate Conditional Mean Robust Filteracm.smo Approximate Conditional Mean Robust Smootheraggregate Compute Summary Statistics of Subsets of Dataaggregate.cts Decrease Periodicity of Time Series by Aggregationaggregate.default Compute Summary Statistics of Subsets of Dataaggregate.rts Decrease Periodicity of Time Series by AggregationaggregateSeries Time Series and Signal Aggregationalign Time Series and Signal Interpolation and Alignmentar Fit Univariate or Multivariate Autoregressive Modelar.burg Fit Autoregression Using Burg's Algorithmar.gm Fit Autoregression Using Robust GM-Estimatesar.yw Fit Autoregression Using the Yule-Walker Equationsarima.diag Compute Diagnostics for ARIMA Modelarima.diag.plot Plot Diagnostics for ARIMA Model

140

Time Series

arima.filt Apply an ARIMA Filter to a Time Seriesarima.forecast Forecast a Time Series Using an ARIMA Modelarima.fracdiff Fractionally-Differenced ARIMA Modeling via Gaussian

MLEarima.fracdiff.sim Simulate Long-memory Time-series Dataarima.fracdiff.var Recompute Covariance Estimate for arima.fracdiffarima.mle ARIMA Modeling via Gaussian Maximum Likelihoodarima.sim Simulate a Univariate ARIMA Seriesarima.td Coefficients for Trading Day Regressionas.rts Regular Time Series Objectsas.trellis.data.frame.series Internal Plotting Functionas.trellis.data.frame.signal Internal Plotting Functionas.ts Time Series Objectsaxis.compute.time.breaks Compute Market Open and Close Times for Axis Breaksaxis.time Time Axis for Time Series Plotaxis.time.breaks Internal Calculations for Time Series Plottingaxis.time.build Compute Time Series Axisaxis.time.grid Internal Calculations for Time Series Plottingaxis.time.label.format Format Label for Time Axisaxis.time.labels Internal Calculations for Time Series Plottingaxis.time.scale Internal Calculations for Time Series Plottingaxis.time.ticks Internal Calculations for Time Series PlottingbdSignalSeries Constructor Function For bdSignalSeries ObjectsbdTimeSeries Constructor Function for bdTimeSeries Classchb Constants for Huber and Bisquare Psiclass.positions Virtual Classes for Time-Related Objectsclass.positionsCalendar Virtual Classes for Time-Related Objectsclass.positionsNumeric Virtual Classes for Time-Related Objectsclass.series Base Class for Time Series and Signalsclass.seriesVirtual Base Class for Time Series and Signalsclass.signalSeries signalSeries Classclass.timeInterval Virtual Classes for Time-Related Objectsclass.timeSeries Calendar Time Series Classcts Regular Calendar Time Series Objectscycle Create Time Vector or Index of Frequency.deltat Sampling Frequency of a Time Seriesdemod Complex Demodulation with Least Squares Lowpass Filterdiff Create an Object of Differences

141

Time Series

end Starting and Ending Times for Time Seriesfft Fast Fourier Transformfilter Apply a Filter to a Time Seriesfrequency Sampling Frequency of a Time Serieshloc High, Low, Open, and Close Calculationis.cts Regular Calendar Time Series Objectsis.its Irregular Time Series Objectis.rts Regular Time Series Objectsis.ts Time Series Objectsits Irregular Time Series Objectlag Create a Lagged Time Serieslag.plot Plot Lagged Scatter Plotsmonthplot Seasonal Subseries Plotnearby Futures Nearby Creation Functionpanel.hloc Trellis Panel Functions for Series Plottingpanel.signalSeries Trellis Panel Functions for Series Plottingpanel.stackbar Trellis Panel Functions for Series Plottingpanel.timeSeries Trellis Panel Functions for Series Plottingpeaks Find Local Maximaplot.bdSignalSeries Big-Data Signal Plotplot.bdTimeSeries Big-Data Calendar Time Series Plotplot.signalSeries Signal Plotplot.stl Plot an STL Objectplot.timeSeries Calendar Time Series Plotplot.times Plot Method for Dates or Times ObjectsplotTimeDate Plot a timeDate Objectpositions Positions Of series Objectspredict.arima Use predict() on a arima Class Objectprint.cts Print a Calendar Time Seriesprint.its Print Method for Irregular Time Seriesprint.rts Print Method for Regular Time Seriesprint.ts Print a Time Seriesrts Regular Time Series Objectssabl Seasonal Decompositionsablplot Plot a Sabl DecompositionseriesData Access Data Of series ObjectsseriesMerge Merging for Time Series and SignalsseriesValid Validation For series Objects

142

Trellis Displays

shift Create a Shifted Time SeriessignalSeries Constructor Function For signalSeries Objectsspec.ar Compute Autoregressive Spectrumspec.pgram Estimate Spectrum with Smoothed Periodogramspec.plot Plot Spectraspec.smo Perform Modified Daniell (Rectangular) Smoothingspec.taper Apply Split Cosine Bell Taper to a Time Seriesspectrum Estimate Spectrum of Time Seriesstart Starting and Ending Times for Time Seriesstl Seasonal Decomposition of a Time Seriesstl.control Computational Options for STLsummary.cts Summary Method for a Calendar Time Seriessummary.its Summary Method for an Irregularly Spaced Time Seriessummary.rts Summary Method for a Regular Time Seriestime Create Time Vector or Index of Frequency.timeSeries Constructor Function for timeSeries ClasstrellisPlot Trellis Plot of a Signal or Time SeriestrellisPlot.signalSeries Trellis Plot of a SignaltrellisPlot.timeSeries Trellis Plot of a Time Seriests Time Series Objectsts.intersect Intersection of Time Seriests.lines Plot Multiple Time Seriests.plot Plot Multiple Time Seriests.points Plot Multiple Time Seriests.union Union of Time Seriests.update Update Old ts Objectstslines Plot Multiple Time Seriestsmatrix Create Matrix with Time Series as Columnstsp Tsp Attribute of a Time Series Objecttspar Time Parameters of a Time Series Objecttsplot Plot Multiple Time Seriestspoints Plot Multiple Time SeriesunionPositions Positions Object Union With Toleranceunits Time Units of a Time Serieswindow Window a Time Series

Trellis Displays as.shingle Create a Shingle Object

143

Trellis Displays

banking Aspect Ratio Computations for Bankingbarchart Bar Graphbwplot Box and Whisker Plot (Box Plot)bwps.trellis Device Colormaps for Trellis Graphicscloud 3-D Point Cloudcolor.key Put a Color Key on a Plotcolorps.trellis Device Colormaps for Trellis Graphicscontourplot Produce a Contour Plot or Level Plotdensityplot Probability Density Plotsdotplot Multi-way Dot Plotequal.count Create Shingle of Conditioning Intervalsexample.bwplot Example Functions For Trellis Displaysexample.calendar Example Functions For Trellis Displaysexample.cloud Example Functions For Trellis Displaysexample.contour Example Functions For Trellis Displaysexample.coplot.fit Example Functions For Trellis Displaysexample.coplot.one Example Functions For Trellis Displaysexample.coplot.three Example Functions For Trellis Displaysexample.coplot.two Example Functions For Trellis Displaysexample.coplot2.fit Example Functions For Trellis Displaysexample.density Example Functions For Trellis Displaysexample.difscale Example Functions For Trellis Displaysexample.dotplot Example Functions For Trellis Displaysexample.draping Example Functions For Trellis Displaysexample.draping2 Example Functions For Trellis Displaysexample.ecount Example Functions For Trellis Displaysexample.frames2 Example Functions For Trellis Displaysexample.given Example Functions For Trellis Displaysexample.histo Example Functions For Trellis Displaysexample.level Example Functions For Trellis Displaysexample.level.fit Example Functions For Trellis Displaysexample.levelplot Example Functions For Trellis Displaysexample.normal.qq Example Functions For Trellis Displaysexample.oneway Example Functions For Trellis Displaysexample.overplot Example Functions For Trellis Displaysexample.pages Example Functions For Trellis Displaysexample.parallel Example Functions For Trellis Displaysexample.qqplot Example Functions For Trellis Displays

144

Trellis Displays

example.qqpool Example Functions For Trellis Displaysexample.quantile Example Functions For Trellis Displaysexample.reorder Example Functions For Trellis Displaysexample.rfs Example Functions For Trellis Displaysexample.robust Example Functions For Trellis Displaysexample.shingle Example Functions For Trellis Displaysexample.sl Example Functions For Trellis Displaysexample.slice.box Example Functions For Trellis Displaysexample.smooth Example Functions For Trellis Displaysexample.splom Example Functions For Trellis Displaysexample.splom2 Example Functions For Trellis Displaysexample.splom3 Example Functions For Trellis Displaysexample.strip Example Functions For Trellis Displaysexample.tmd Example Functions For Trellis Displaysexample.units.cm Example Functions For Trellis Displaysexample.wire Example Functions For Trellis Displaysexample.wire2 Example Functions For Trellis Displayshistogram Histogram of a Distributionidentify.xyplot Identify Points on Trellis Xyplotiris.trellis Device Colormaps for Trellis Graphicsis.shingle Create a Shingle Objectlevelplot Produce a Contour Plot or Level Plotlocator.2dtrellis Get Coordinates from Trellis Plotpanel.abline Add Lines to a Panelpanel.barchart Panel Function for Barchartspanel.bwplot Panel Function for Box and Whisker Plots (Box Plots)panel.cloud Panel Function for 3D Point Cloudpanel.contourplot Panel Function for Contour Plots and Level Plotspanel.densityplot Panel Function for Density Plotspanel.dotplot Panel Function for Dotplotspanel.fill Fill in a Panelpanel.grid Add Reference Grid to Panelspanel.hexbin Panel Function for Hexbins panel.hexbin.lmline Panel Function for Hexbins panel.hexbin.loess Panel Function for Hexbins panel.hexbin.smooth.spline Panel Function for Hexbins panel.histogram Panel Function for Histogramspanel.hloc Trellis Panel Functions for Series Plotting

145

Trellis Displays

panel.levelplot Panel Function for Contour Plots and Level Plotspanel.lmline Add Linear Regression Line to Panelpanel.loess Add Smooth Loess Curve to Panelpanel.parallel Panel Function for Parallel Coordinates Plotspanel.piechart Panel Function for Pie Chartspanel.plot.shingle Panel Function for plot.shingle panel.qq Panel Function for Scatterplotspanel.qqmath Panel Function for Scatterplotspanel.qqmathline Fit Line to QQ-Plot in Panelpanel.signalSeries Trellis Panel Functions for Series Plottingpanel.splom Panel Function for Scatterplotspanel.stackbar Trellis Panel Functions for Series Plottingpanel.stripplot Panel Function for 1-D Strip Plotpanel.superpose Panel Function for Superpositionpanel.timeSeries Trellis Panel Functions for Series Plottingpanel.tmd Panel Function for Tukey Mean-Difference Displayspanel.wireframe Panel Function for Wireframe Surfacepanel.xyplot Panel Function for Scatterplotsparallel Parallel Coordinate Plotspiechart Pie Chartsplot.shingle Plot Method for Shinglesprepanel.lmline Preliminary Computations to Add Linear Regression Lineprepanel.loess Preliminary Computations to Add Smooth Loess Curveprepanel.qqmathline Preliminary Computations to Fit Line to QQ-Plotprint.trellis Plot (!) a Trellis Objectqq Quantile-Quantile Plots for Comparing Multiple

Distributionsqqmath Q-Q Plot Using a Theoretical or Empirical Distributionreorder.factor Reorder the Levels of a Factorrfs Residual and Fit Spread Plotsshingle Create a Shingle Objectshow.settings Show the Trellis Customization Settingssplom Multi-Panel Scatterplot Matricesstrip.default Generate Strip Labelsstripplot One-Dimensional Scatter Plottmd Tukey Mean-Difference Plottrellis.device Starts Display Device For Trellis Functionstrellis.examples Example Functions For Trellis Displays

146

Utilities

trellis.par.get Get and Set Trellis Parameterstrellis.par.set Get and Set Trellis Parameterstrellis.settings Device Customization Settings For Trellis Displaystrellis.settings.bw Device Customization Settings For Trellis Displaystrellis.settings.bwps Device Customization Settings For Trellis Displaystrellis.settings.color Device Customization Settings For Trellis Displaystrellis.settings.colorps Device Customization Settings For Trellis Displaystrellis.settings.motif Device Customization Settings For Trellis Displaystrellis.settings.winbwps Device Customization Settings For Trellis Displaystrellis.settings.wincolorps Device Customization Settings For Trellis Displaystrellis.settings.wingraph Device Customization Settings For Trellis Displaystrellis.settings.winpcl Device Customization Settings For Trellis DisplaystrellisPlot Trellis Plot of a Signal or Time SeriestrellisPlot.signalSeries Trellis Plot of a SignaltrellisPlot.timeSeries Trellis Plot of a Time Serieswireframe 3-D Wireframe Surfacexyplot Conditioning Plots/Scatter Plots

Utilities BATCH Batch (Non-Interactive) Execution of Spotfire S+BUILD_JHELP Create JavaHelp Help Set for Installed Help FilesCHAPTER Initialize a Spotfire S+ Chapter and Create a Makefile for

User CodeCONVERTOLDSCRIPTS Convert SV3 Function Files to SV4CSH Start a subshell with the environment of Spotfire S+.Command.edit Command Line Editing in Spotfire S+EXEC Execute a ProgramHINSTALL Install Spotfire S+ Help FilesLICENSE Manage network licensing for Spotfire S+MODINSTALL Install Add-On ModduleNM Display Symbol Table of Compiled CodeTRUNC_AUDIT Truncate the Audit Filebd.cache.cleanup Analyze BDO Cache Filesbd.cache.info Analyze BDO Cache FilesconvertOldDoc Convert Nroff/Troff Style Help to SGMLconvertOldLibrary Convert Spotfire S+ 4.x and Earlier Objects to Spotfire S+

Version 5.x/6.xdoc_to_S Convert Nroff/Troff Style Help to SGMLmasked Report Masked Spotfire S+ Objects

147

Utilities

strwrap Wraps Character Strings for Paragraph Formattingvalidate Validation Tests

148