an introduction to r: get familiar with r guangxu liu bio7932

An introduction to R: get An introduction to R: get familiar with Rfamiliar with R

Guangxu LiuGuangxu Liu

Bio7932Bio7932

1. Download and installation of R1. Download and installation of R2. Get familiar with R2. Get familiar with R3. Input data and read data from file3. Input data and read data from file4. Commonly used R code 4. Commonly used R code 5. Something need to be aware5. Something need to be aware6. Reference for R6. Reference for R

Step by step proc.Step by step proc.

Outline

1.Downloading R 1.Downloading R official website: official website: www.R-project.orgwww.R-project.org

Where to download

R.

After we choose the correct server and computer system, After we choose the correct server and computer system, we will get something like below. we will get something like below.

What we want is here!

Choose again?!!Choose again?!!

Here it is!

Installation:Installation:

Proc: Proc: Simply use the download installation file.Simply use the download installation file.

Available options: Available options: Choose install directionChoose install direction language (English, simple Chinese only) ?language (English, simple Chinese only) ? Set up the methods for viewing help informatioSet up the methods for viewing help informatio

n(html, txt, chm)n(html, txt, chm) Select components, customize ….Select components, customize ….

2. Get familiar with R (Sorry about using chinese version)

File; Edit; Others; Package; Help function

Basic introduction of R, such as Version…

Working place, where we write code, see the verbal or numerial r

esults

3. Input data and read data from file3. Input data and read data from file

Basic proc:Basic proc: x<x<-function() -function() x=data name; <- assignment; function()=the mx=data name; <- assignment; function()=the m

ethods for reading dataethods for reading data

Function():Function(): c() for example, x<-c(1,2,3,4,5) c() for example, x<-c(1,2,3,4,5) read.table() read.table() scan()scan() Read data using Rcmdr packageRead data using Rcmdr package

Examples: Read data with Rcmdr package

Load package from package

option

Rcmdr

Rcmdr windows (right windows below)

Rcmdr-Data-Inport data (Thanks god, Rcmdr is in English!)

File can be read by Rcmdr includes txt,spss,mintab,stata,excel….

For example: open the excel file contains the data, select the data you want to input and copy it by right click and copy or ctl+c.

Then switch back to Rcmdr windows and choose data i

nput from txt & clipboard

Data name

1.Variable name in first line or not

2. NA

How the data are separated(Tabs here for

excel)

All setting looks fine

now

Read the data

The R code for what we did

Output window? Do not show graphic

results

General information of

the data

An example show how t-test results displayed in output windows

T test R code

Results form the t-test

Lot’s functions

here, such as make graph, load statistics

package

R code for box plot

If we make graph (box plot for example)

Graph result shows in R graphics window (right windows)

View data and edit

your data

View data window shows the data

View data and edit data after data input

Edit data in the data edit windows

4. Commonly used R code4. Commonly used R code ls()ls() show all the available data (objects) show all the available data (objects) in the work space or memoryin the work space or memory rm()rm() delete data, remove objects delete data, remove objects ? ? get online help about *** get online help about *** lm()lm() fit a simple regression and look at it fit a simple regression and look at it resid()resid() residuals from one model residuals from one model fitted()fitted() fits from one model fits from one model plot()plot() scatter plot scatter plot

5. Something needs to be kept in mind

Capital letter matters: v≠V

Data (Objects) are vector or matrix

Some examples

VCL and vcl are different dat

a objects

Commends: don’t use capital letter at all is a good idea

Use ls() show the data in workspac

e

Use “?ls” to learn more about ls() fuct

ion

Online help(don’t need

internet connection

in fact)

Use ?lm learn more about lm()

There are lot’s components in lm()

Details about all those components

A simple example (without data input part)A simple example (without data input part)

Step 1:Read and built

a new data with name f

Use f to view the data f in workspace

Data from fertilization data of Liu (2006), and we know there should have a simple linear relationship between ln and density.

Density=log(sperm/egg density) ln=log(fertilized egg/unfertilized egg).

So the model will be ln=a+b*density+error

Use fm<-lm(ln~density,data=f) to build up the linear model

fm<-lm(ln~density,data=f)

Assign fm as the linear model

Model is basedon ln and density,

use ln as dependentand density as variable

There ln and density come from

Use fm to view fm

Shows what’s

fm

Use summary(fm) to see more details

Details of fm, including df, SE, t value and P

Use plot(fitted(fm),resid(fm),xlab="fitted",ylab="residual",main="residual vs fUse plot(fitted(fm),resid(fm),xlab="fitted",ylab="residual",main="residual vs fits") check residual vs fits. Graph shown on the right side windowits") check residual vs fits. Graph shown on the right side window

Here xlab(),ylab(),main() are R codes to give x,y and the whole graph labels.

6.Reference for R (http://www.r-project.org)6.Reference for R (http://www.r-project.org)

This makes me change my presentation title to “An introduction to R: get familiar with R”

1.Free reference on R official website2. Practical Regression and Anova using R, Julian J. Faraway, 2002

ThanksThanks

Picture above from www.R-project.org