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 [[SOCR_EduMaterials_AnalysesCommandLine | SOCR Analyses is available here]].
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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]].
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=== Introduction ===
=== Introduction ===
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These interactive analyses applets allow you to:
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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 command-line shell execution on local systems.
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* Enter data. Currently there are three ways available to obtain data:
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# Using the SOCR built-in example datasets by first clicking on the '''EXAMPLE''' and followed by the '''DATA''' button. They are from various commonly used college and graduate level statistics textbooks. Please see each Analysis Help pages for specific references.
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===General Usage===
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# Use random dataset generated by the SOCR Analyses '''RANDOM EXAMPLE''' button.
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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].
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# Copy from a text file with data or a spreadsheet.  
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* The command-line interface to SOCR Analyses generally uses '''EXAMPLE 1''' from the list of example data files for the corresponding analysis.
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* All Input files are ASCII (see examples within each of the specific analyses).
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* 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).
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* 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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* Calculate various statistics, critical values and p-values.
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===Analysis-specific Usage===
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# The '''MAPPING''' button must be clicked to map the variables, e.g. assigning variables to either the regressor or the response, in a simple linear regression.
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* [[SOCR_EduMaterials_AnalysesCommandLineAnovaOneWay]]
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# After all the above it set, the '''CALCULATE''' button generates statistical results.
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* [[SOCR_EduMaterials_AnalysesCommandLineAnovaTwoWay]]
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* Summarize the results.
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* [[SOCR_EduMaterials_AnalysesCommandLineChiSquareContingencyTable]]
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# The '''RESULT''' button leads to statistical results such as summary statistics and parameter estimates. The form and contents of the result depends on type of analyses.
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* [[SOCR_EduMaterials_AnalysesCommandLineChiSquareModelFit]]
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# The '''GRAPH''' button displays data scatter plots, regression diagnostics, etc.
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* [[SOCR_EduMaterials_AnalysesCommandLineDichotomousProportion]]
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* If you don't like something you did, or want to clear a previous example, use the '''CLEAR''' button. Note that this also clears out the data you entered earlier.
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* [[SOCR_EduMaterials_AnalysesCommandLineFisherExact]]
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<center>[[Image:SOCR_AnalysisHelp_ANOVA_Chu_042507_Fig1.jpg|590px]]</center>
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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]]
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=== Special User Interface for the Normal Power Analyses ===
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===Specific Volumetric Analyses===
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The Normal Power Analyses use a different set of buttons: '''SELECT PARAMETERS''' and '''COMPARE CURVES'''. More details are provided in the [[Power Analysis for Normal Distribution]] tutorials.
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* [[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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=== Tutorials ===
 
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Tutorials are available for the analyses of:
 
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* [[SOCR_EduMaterials_AnalysesActivities]]
 
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* [[Power Analysis for Normal Distribution]]
 
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===Command-Line Interfaces to SOCR Computational Statistics Libraries===
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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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In addition to accessing the SOCR analyses libraries via the [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] graphical user interface, SOCR users may access the computational SOCR Analyses libraries via shell-based command-line interface on their local machines. More information about these interfaces is available [[SOCR_EduMaterials_AnalysesCommandLine | at the command-line analyses interface pages]].
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===References===
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* 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.
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* 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.
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* 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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{{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}}

Current revision as of 21:21, 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

Specific Volumetric Analyses


References

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