Difference between revisions of "SOCR EduMaterials AnalysesCommandLine"

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This page includes the information on how to access the [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] libraries for statistical computing via shell-based command-line interface on local machines. More information about [[Help_pages_for_SOCR_Analyses | SOCR Analyses is available here]].
 
This page includes the information on how to access the [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] libraries for statistical computing via shell-based command-line interface on local machines. More information about [[Help_pages_for_SOCR_Analyses | SOCR Analyses is available here]].
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=== Introduction ===
 
=== Introduction ===
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In addition to the graphical user interfaces, via a web-browser, all [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] allow comman-line shell execution on local systems.
+
In addition to the graphical user interfaces, via a web-browser, all [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] allow command-line shell execution on local systems.
  
 
===General Usage===
 
===General Usage===
−
*  
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* Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/). You can also download the Complete [http://code.google.com/p/socr/downloads/detail?name=SOCR_CD.zip SOCR CD including all executables and HTML pages for offline invocation].
 +
* The command-line interface to SOCR Analyses generally uses '''EXAMPLE 1''' from the list of example data files for the corresponding analysis.
 +
* All Input files are ASCII (see examples within each of the specific analyses).
 +
* a '''-h''' flag at the end of the command-line indicates that the first row in all ASCII input data files is a '''HEADER''' row (so it's not interpreted as data).
 +
* When running large Java jobs on Grid architectures or when submitting jobs via ''qsub'', the following specification to request additional memory may be useful to avoid ''OutOfMemoryExceptions'': ''h_vmem=4.5G'':
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: <code>qsub -q short.q -t 1:12 -l h_vmem=4.5G,h_stack=10M VolumeMultipleRegression_FA.tcsh</code>
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===Analysis-specific Usage===
 +
* [[SOCR_EduMaterials_AnalysesCommandLineAnovaOneWay]]
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* [[SOCR_EduMaterials_AnalysesCommandLineAnovaTwoWay]]
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* [[SOCR_EduMaterials_AnalysesCommandLineChiSquareContingencyTable]]
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* [[SOCR_EduMaterials_AnalysesCommandLineChiSquareModelFit]]
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* [[SOCR_EduMaterials_AnalysesCommandLineDichotomousProportion]]
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* [[SOCR_EduMaterials_AnalysesCommandLineFisherExact]]
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* [[SOCR_EduMaterials_AnalysesCommandLineFlignerKilleen]]
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* [[SOCR_EduMaterials_AnalysesCommandLineKolmogorovSmirnoff]]
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* [[SOCR_EduMaterials_AnalysesCommandLineMultiRegression]]
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* [[SOCR_EduMaterials_AnalysesCommandLineOneT]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoIndependentFriedman]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoIndependentKruskalWallis]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoIndependentTest]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoIndependentWilcoxon]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoPairedSignedTest]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoPairedT]]
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* [[SOCR_EduMaterials_AnalysesCommandLineTwoPairSignedRank]]
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* [[SOCR_EduMaterials_AnalysesCommandLineSimpleRegression]]
 +
 
 +
===Specific Volumetric Analyses===
 +
* [[SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression]]
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* [[SOCR_EduMaterials_AnalysesCommandLineVolume1Sample_T_test]]
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* [[SOCR_EduMaterials_AnalysesCommandLineVolume2PairedSamples_Wilcoxon_RankSum]]
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* [[SOCR_EduMaterials_AnalysesCommandLineVolume2Samples_T_test]]
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* [[SOCR_EduMaterials_AnalysesCommandLineVolume2IndepSample_Wilcoxon_test]]
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* [[SOCR_EduMaterials_AnalysesCommandLineFDR_Correction]]
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* [[SOCR_EduMaterials_AnalysesCommandLineVolumeKruskalWallis]]
 +
 
  
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===Analysis-specific Usage==
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* [http://www.loni.ucla.edu/twiki/bin/view/CCB/SIGPNS_052109 Example uses of these tools as part of computational neuroimaging pipeline workflows].
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* ChiSquareModelFitCSV
 
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* TwoIndependentWilcoxonCSV
 
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* TwoPairSignedRankCSV
 
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* OneTCSV
 
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* TwoPairedSignedTestCSV
 
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* TwoPairedTCSV
 
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* TwoIndependentText
 
  
 +
===References===
 +
* Che, Annie, Cui, Jenny, and Dinov, Ivo (2009). [http://www.jstatsoft.org/v30/i03 SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit]. JSS, Vol. 30, Issue 3, Apr 2009.
 +
* Che, A, Cui, J, and Dinov, ID (2009) [http://jolt.merlot.org/vol5no1/dinov_0309.htm SOCR Analyses – an Instructional Java Web-based Statistical Analysis Toolkit], JOLT, 5(1), 1-19, March 2009.
 +
* Dinov, ID. [http://www.jstatsoft.org/v16/i11 Statistics Online Computational Resource], Journal of Statistical Software, Vol. 16, No. 1, 1-16, October 2006.
  
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<hr>
 
{{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLine}}
 
{{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLine}}

Latest revision as of 16:27, 27 August 2010

This page includes the information on how to access the SOCR Analyses libraries for statistical computing via shell-based command-line interface on local machines. More information about SOCR Analyses is available here.

Introduction

In addition to the graphical user interfaces, via a web-browser, all SOCR Analyses allow command-line shell execution on local systems.

General Usage

  • Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/). You can also download the Complete SOCR CD including all executables and HTML pages for offline invocation.
  • The command-line interface to SOCR Analyses generally uses EXAMPLE 1 from the list of example data files for the corresponding analysis.
  • All Input files are ASCII (see examples within each of the specific analyses).
  • a -h flag at the end of the command-line indicates that the first row in all ASCII input data files is a HEADER row (so it's not interpreted as data).
  • When running large Java jobs on Grid architectures or when submitting jobs via qsub, the following specification to request additional memory may be useful to avoid OutOfMemoryExceptions: h_vmem=4.5G:
qsub -q short.q -t 1:12 -l h_vmem=4.5G,h_stack=10M VolumeMultipleRegression_FA.tcsh

Analysis-specific Usage

Specific Volumetric Analyses


References

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