Difference between revisions of "SOCR EduMaterials AnalysesCommandLine"
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===General Usage=== | ===General Usage=== | ||
| − | * Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/). | + | * 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. | * 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). | * All Input files are ASCII (see examples within each of the specific analyses). | ||
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* [[SOCR_EduMaterials_AnalysesCommandLineFDR_Correction]] | * [[SOCR_EduMaterials_AnalysesCommandLineFDR_Correction]] | ||
* [[SOCR_EduMaterials_AnalysesCommandLineVolumeKruskalWallis]] | * [[SOCR_EduMaterials_AnalysesCommandLineVolumeKruskalWallis]] | ||
| + | |||
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/SIGPNS_052109 Example uses of these tools as part of computational neuroimaging pipeline workflows]. | * [http://www.loni.ucla.edu/twiki/bin/view/CCB/SIGPNS_052109 Example uses of these tools as part of computational neuroimaging pipeline workflows]. | ||
| + | |||
| + | ===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. | ||
<hr> | <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.
Contents
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
- SOCR_EduMaterials_AnalysesCommandLineAnovaOneWay
- SOCR_EduMaterials_AnalysesCommandLineAnovaTwoWay
- SOCR_EduMaterials_AnalysesCommandLineChiSquareContingencyTable
- SOCR_EduMaterials_AnalysesCommandLineChiSquareModelFit
- SOCR_EduMaterials_AnalysesCommandLineDichotomousProportion
- SOCR_EduMaterials_AnalysesCommandLineFisherExact
- SOCR_EduMaterials_AnalysesCommandLineFlignerKilleen
- SOCR_EduMaterials_AnalysesCommandLineKolmogorovSmirnoff
- SOCR_EduMaterials_AnalysesCommandLineMultiRegression
- SOCR_EduMaterials_AnalysesCommandLineOneT
- SOCR_EduMaterials_AnalysesCommandLineTwoIndependentFriedman
- SOCR_EduMaterials_AnalysesCommandLineTwoIndependentKruskalWallis
- SOCR_EduMaterials_AnalysesCommandLineTwoIndependentTest
- SOCR_EduMaterials_AnalysesCommandLineTwoIndependentWilcoxon
- SOCR_EduMaterials_AnalysesCommandLineTwoPairedSignedTest
- SOCR_EduMaterials_AnalysesCommandLineTwoPairedT
- SOCR_EduMaterials_AnalysesCommandLineTwoPairSignedRank
- SOCR_EduMaterials_AnalysesCommandLineSimpleRegression
Specific Volumetric Analyses
- SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression
- SOCR_EduMaterials_AnalysesCommandLineVolume1Sample_T_test
- SOCR_EduMaterials_AnalysesCommandLineVolume2PairedSamples_Wilcoxon_RankSum
- SOCR_EduMaterials_AnalysesCommandLineVolume2Samples_T_test
- SOCR_EduMaterials_AnalysesCommandLineVolume2IndepSample_Wilcoxon_test
- SOCR_EduMaterials_AnalysesCommandLineFDR_Correction
- SOCR_EduMaterials_AnalysesCommandLineVolumeKruskalWallis
References
- Che, Annie, Cui, Jenny, and Dinov, Ivo (2009). 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) SOCR Analyses – an Instructional Java Web-based Statistical Analysis Toolkit, JOLT, 5(1), 1-19, March 2009.
- Dinov, ID. Statistics Online Computational Resource, Journal of Statistical Software, Vol. 16, No. 1, 1-16, October 2006.
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