the emacs org-mode · .tex/.pdf.html.odt... the emacs org-mode, andreas leha, 16 august 2011 14....

THE EMACS ORG-MODEReproducible Research and Beyond

Andreas Leha

Department for Medical StatisticsUniversity Medical Center Goumlttingen

Reproducible Research Existing Tools for Reproducible Research Org-mode Summary References

Outline

Reproducible Research

Existing Tools for Reproducible Research

Org-mode

Summary

The Emacs Org-mode Andreas Leha 16 August 2011 2


Orientation



Org-mode

Summary



What is Reproducible ResearchPossible Definition

a piece of reproducible research is an article that providesreaders with all the materials that are needed to produce thesame results as described in the publication

(Hothorn Held and Friede 2009)

+ code + parameters +

Bioinformatics (Vol26)(Hothorn and Leisch 2011)

I Better but similar results






A piece of reproducible research is usually notmethods section + published data


Nature Genetics (200506)(Ioannidis et al 2009)

not reproducible

56








A piece of reproducible research should ideally containmethods section + published data + code

+ parameters +

Biometrical Journal (Vol50)(Hothorn Held and Friede 2009)

potentially reproducible

89








A piece of reproducible research should ideally containmethods section + published data + code + parameters +



89





Why to use Reproducible Research

I Benefits for the researcher herselfIn the mid-1980s we realized that our laboratoryrsquosresearchers often had difficulty reproducing their owncomputations without considerable agony

(Schwab Karrenbach and Claerbout 2000)

I Benefits for othersI Precise lsquodescriptionrsquo of methodsI Easy re-use of applied methodsI No forensic bioinformatics

(Baggerly and Coombes 2009 Ioannidis et al 2009)



Barriers for Reproducible Research

(Banks 2011)

I Deliberate non-reproducibilityI Vagueness to cover potential mistakes

I External reasonsI Ownership of the dataI Collaboration partners

I Perception of effortI DisciplineI ResourcesI Change of work flow



Orientation



Org-mode

Summary




I ReDoc (Schwab Karrenbach and Claerbout 2000)GNU make rules synchronize code and output

I Sweave (Leisch 2002)interwoven R and LATEX by means of literate programming

I Compendium (Gentleman and Temple Lang 2007 Gentlemanet al 2005)scientific paper as R-package (including data code)based on Sweave

I Org-mode



Orientation



Org-mode

Summary



What is Org-mode

Org-mode is for keeping notes maintaining ToDo lists doingproject planning and authoring with a fast and effectiveplain-text system

httporgmodeorg

I Major mode of emacsI File formatI Created in 2003 by Carsten DominikI Current Version 77 maintainer Bastien GuerryI Very active development



Org-mode and Reproducible Research

I Through Org Babel a literate programming (Knuth 1984)system

I Written by Eric Schulte and Dan Davison

code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data

We first generate some data

a lt- rnorm (100 mean=00)b lt- rnorm (100 mean=08)

1radic2πσ2

eminus(xminusmicro)2

2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis

A t-test shows that the means are signifi-cantly different (p-value )

Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages

Example Commit Sizes in Org-mode v76 and v77

release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134

A Wilcoxon test shows lsquonosignificantrsquo difference (p-value0082)

Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



More Examples on Org Babel

I Website on uses of Org Babelhttporgmodeorgworgorg-contribbabeluseshtml

I Comparison to Sweave by demo (Eric Schulte)httporgmodeorgworgorg-contribbabeluseshtmlfoo

I Tutorial lsquoOrg-mode and Rrsquo by Erik Iversonhttpsgithubcomerikriversonorg-mode-R-tutorial

I Examples reproducible research papersI ldquoActive Document with Org-Moderdquo Schulte and Davison (2011)

on Org-mode itselfhttpsgithubcomeschulteCiSE

I ldquoA Model-based Age Estimate for Polynesian Colonization ofHawailsquoirdquo Dye (in press) with Setup for Org-modehttpsgithubcomtsdyehawaii-colonization



Org-mode for lsquobeyondrsquo

Some Highlights

I Note takingI Outlining FoldingI Rearrangement of whole branches

I ToDo lists OrganizerI AgendasI SchedulingI Mobile apps

I Tables Spreadsheet



Orientation



Org-mode

Summary



Summary

Using Org-mode for Research Can Give You

I Reproducibility

I Plain Text FilesI Visual User Experience

I Various Export Formats

I Various Programming Languages

I Intuitive Organizer

I

ButI Reproducibility is still limited by active development

I Less editing support than Sweave



Disclaimer

Claerboutrsquos principleAn article about computational science in a scientificpublication is not the scholarship itself it is merelyadvertising of the scholarship The actual scholarship is thecomplete software development environment and thecomplete set of instructions which generated the figures

(Buckheit and Donoho 1995)

CreditThis presentation about Org-mode is not the scholarshipitself it is merely advertising of the scholarship The actualscholarship is the complete software and all the credit goesto the developers



Disclaimer






Literature I

Baggerly Keith A and Kevin R Coombes (2009) ldquoDeriving chemosensitivity fromcell lines Forensic bioinformatics and reproducible research in high-throughputbiologyrdquo In Annals of Applied Statistics 3 (4) pp 1309ndash1334

Banks David (2011) ldquoReproducible Research A Range of Responserdquo InStatistics Politics and Policy 2 (1)

Buckheit Jonathan B and David L Donoho (1995) ldquoWaveLab and ReproducibleResearchrdquo In Wavelets and Statistics Ed by Anestis Antoniadis andGeorges Oppenheim Vol 103 Lecture notes in statistics Springer-Verlagpp 55ndash81

Dye Thomas S (in press) ldquoA Model-based Age Estimate for PolynesianColonization of Hawailsquoirdquo In Archaeology in Oceania

Gentleman Robert and Duncan Temple Lang (Mar 2007) ldquoStatistical Analysesand Reproducible Researchrdquo In Journal of Computational and GraphicalStatistics 161 pp 1ndash23

Gentleman Robert et al (2005) Bioinformatics and Computational BiologySolutions Using R and Bioconductor (Statistics for Biology and Health)Secaucus NJ USA Springer-Verlag New York Inc

Hothorn T L Held and T Friede (2009) ldquoBiometrical journal and reproducibleresearchrdquo In Biom J 514 pp 553ndash5



Literature II

Hothorn Torsten and Friedrich Leisch (2011) ldquoCase studies in reproducibilityrdquo InBriefings in Bioinformatics 123 pp 288ndash300

Ioannidis J P et al (2009) ldquoRepeatability of published microarray gene expressionanalysesrdquo In Nat Genet 412 pp 149ndash55

Knuth Donald E (1984) ldquoLiterate programmingrdquo In The Computer Journal 27pp 97ndash111

Leisch Friedrich (2002) ldquoSweave Dynamic Generation of Statistical ReportsUsing Literate Data Analysisrdquo In Compstat 2002 mdash Proceedings inComputational Statistics Ed by Wolfgang Haumlrdle and Bernd Roumlnz PhysicaVerlag Heidelberg pp 575ndash580

Schulte Eric and Dan Davison (2011) ldquoActive Document with Org-Moderdquo InComputing in Science Engineering 133 pp 66ndash73

Schwab M N Karrenbach and J Claerbout (2000) ldquoMaking scientificcomputations reproduciblerdquo In Computing in Science Engineering 26 pp 61ndash67



Thank you for your attention




Org-mode

Summary


Outline



Org-mode

Summary



Orientation



Org-mode

Summary

















not reproducible

56









+ parameters +



89











89













(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Orientation



Org-mode

Summary

















not reproducible

56









+ parameters +



89











89













(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary
















not reproducible

56









+ parameters +



89











89













(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary






+ parameters +



89











89













(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary








89













(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary










(Banks 2011)






Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Orientation



Org-mode

Summary







I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary






I Org-mode



Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Orientation



Org-mode

Summary



What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


What is Org-mode


httporgmodeorg







code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary





code

ltcodegt

+ org

lttextgt

document

tangle

weave



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


A Simple Example

The Data



1radic2πσ2


2σ2

Descriptive Values

mean sda -021 104b 071 092

Visualization

Analysis


Skip Screenshots



Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Export

code

ltcodegt

+ org

lttextgt

document

tangle

weavetexpdfhtmlodt



Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Export



Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Export



Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Various Languages

code

ltcodegt

+ org

lttextgt

document

tangle

weave

RPythonShellJava

texpdf

html

odt



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot



Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Various Languages


release

lines

100

101

102

103

104

v76 v77

lrr mean sdv76 1392 240196v77 4048 8134


Skip Screenshot













Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary












Some Highlights






Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Orientation



Org-mode

Summary



Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Summary


I Reproducibility





I





Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Disclaimer






Disclaimer






Literature I










Literature II













Org-mode

Summary


Disclaimer






Literature I










Literature II













Org-mode

Summary


Literature I










Literature II













Org-mode

Summary


Literature II













Org-mode

Summary






Org-mode

Summary

the emacs org-mode · .tex/.pdf.html.odt... the emacs org-mode, andreas leha, 16 august 2011 14....

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