SOCR EduMaterials AnalysesCommandLineFisherExact

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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.
* 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).
-
* 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)
 
-
* Number of variables have to be indicated at the end (after '''-h''' flag). If no number of variables is included, 5 is set as defaul.
 
==Fisher Exact Test Usage==
==Fisher Exact Test Usage==
* Generic Setting:
* Generic Setting:
<code>
<code>
-
java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt -h [number_of_variables] 5
+
java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt
</code>
</code>
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<code>java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/
<code>java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/
-
ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/f.txt -h 5</code>
+
ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/f.txt</code>
<code>date</code>
<code>date</code>
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==Example Input data files==
==Example Input data files==
-
One test datafile is included with the SOCR analyses command-line distribution ('''f.txt'''). The ASCII content of each of these is included below. Note that the first lines in these files are column headers. This requires the "-h" flag at the end of the command line execution so that these first lines are interpreted as column headers.
+
One test datafile is included with the SOCR analyses command-line distribution ('''f.txt'''). The ASCII content of each of these is included below.
<center>
<center>
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|-
|-
! colspan=5 | f.txt
! colspan=5 | f.txt
-
|-
 
-
| A
 
-
| B
 
-
| C
 
-
| D
 
-
| E
 
|-
|-
| 5.0
| 5.0
| 4.0
| 4.0
-
| 7.0
 
-
| 10.0
 
-
| 12.0
 
|-
|-
| 1.0
| 1.0
| 3.0
| 3.0
-
| 1.0
 
-
| 0.0
 
-
| 2.0
 
-
|-
 
-
| 16.0
 
-
| 12.0
 
-
| 22.0
 
-
| 22.0
 
-
| 35.0
 
-
|-
 
-
| 5.0
 
-
| 4.0
 
-
| 3.0
 
-
| 5.0
 
-
| 4.0
 
-
|-
 
-
| 10.0
 
-
| 9.0
 
-
| 7.0
 
-
| 13.0
 
-
| 10.0
 
-
|-
 
-
| 19.0
 
-
| 18.0
 
-
| 18.0
 
-
| 37.0
 
-
| 58.0
 
-
|-
 
-
| 10.0
 
-
| 7.0
 
-
| 6.0
 
-
| 8.0
 
-
| 7.0
 
|}
|}
</center>
</center>
{{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFisherExact}}
{{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFisherExact}}

Current revision as of 01:01, 13 June 2009

This page includes the information on how to access the Fisher Exact Test library via shell-based command-line interface on local machines. More information about other SOCR Analyses command-line interfaces 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/).
  • 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).

Fisher Exact Test Usage

  • Generic Setting:

java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt

  • Example: Edit a new file (FisherExactCSV.csh) using any editor and paste this inside (make sure the file has executable permissions). Some operating systems/platforms may require variants of this (C-shell) script.

#!/bin/csh

date

java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/ ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/f.txt

date

exit

Example Input data files

One test datafile is included with the SOCR analyses command-line distribution (f.txt). The ASCII content of each of these is included below.

f.txt
5.0 4.0
1.0 3.0

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