Merge pull request #9 from bd2kccd/v0.1.x

V0.1.x

README.md

@@ -1,4 +1,4 @@
-# causal-cmd v0.2.0
+# causal-cmd v0.1.1
 
 ## Introduction
 
@@ -22,13 +22,13 @@ In this example, we'll use download the [Retention.txt](http://www.ccd.pitt.edu/
 Keep in mind that causal-cmd has different switches for different algorithms. To start, type the following command in your terminal:
 
 ```
-java -jar causal-cmd-0.2.0-jar-with-dependencies.jar
+java -jar causal-cmd-0.1.1-jar-with-dependencies.jar
 ```
 
 And you'll see the following instructions:
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm <arg> | --simulate-data <arg>  [--version]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm <arg> | --simulate-data <arg>  [--version]
     --algorithm <arg>       FGESc, FGESd, GFCIc, GFCId
     --simulate-data <arg>   sem-rand-fwd, bayes-net-rand-fwd
     --version               Show software version.
@@ -38,7 +38,7 @@ usage: java -jar causal-cmd-0.2.0.jar --algorithm <arg> | --simulate-data <arg>
 In this example, we'll be running FGESc on this `Retention.txt`.
 
 ```
-java -jar causal-cmd-0.2.0-jar-with-dependencies.jar --algorithm FGESc --data Retention.txt
+java -jar causal-cmd-0.1.1-jar-with-dependencies.jar --algorithm FGESc --data Retention.txt
 ```
 
 This command will output the following messages in your terminal:
@@ -60,7 +60,7 @@ out = .
 output-prefix = FGESc_Retention.txt_1490193823839
 no-validation-output = false
 
-Running version 0.2.0 but unable to contact latest version server.  To disable checking use the skip-latest option.
+Running version 0.1.1 but unable to contact latest version server.  To disable checking use the skip-latest option.
 There are 170 cases and 8 variables.
 Wed, March 22, 2017 10:43:45 AM: Start reading in data file.
 Wed, March 22, 2017 10:43:45 AM: End reading in data file.
@@ -125,7 +125,7 @@ The GFCI algorithm has additional edge types:
 ## Complete Usage Guide
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm <arg> | --simulate-data <arg>  [--version]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm <arg> | --simulate-data <arg>  [--version]
     --algorithm <arg>       FGESc, FGESd, GFCIc, GFCId
     --simulate-data <arg>   sem-rand-fwd, bayes-net-rand-fwd
     --version               Show software version.
@@ -136,7 +136,7 @@ You can use the `--algorithm <arg>` parameter to see specific algorithm usage in
 ### FGESc
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm FGESc [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESc [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
  -f,--data <arg>                Data file.
@@ -160,7 +160,7 @@ usage: java -jar causal-cmd-0.2.0.jar --algorithm FGESc [-d <arg>] [--exclude-va
 ### FGESd
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm FGESd [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm FGESd [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
  -f,--data <arg>                Data file.
@@ -185,7 +185,7 @@ usage: java -jar causal-cmd-0.2.0.jar --algorithm FGESd [-d <arg>] [--exclude-va
 ### GFCIc
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm GFCIc [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm GFCIc [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--penalty-discount <arg>] [--skip-latest] [--skip-nonzero-variance] [--skip-unique-var-name] [--tetrad-graph-json] [--thread <arg>] [--verbose]
     --alpha <arg>               Cutoff for p values (alpha). Default is 0.01.
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.
@@ -210,7 +210,7 @@ usage: java -jar causal-cmd-0.2.0.jar --algorithm GFCIc [--alpha <arg>] [-d <arg
 ### GFCId
 
 ```
-usage: java -jar causal-cmd-0.2.0.jar --algorithm GFCId [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
+usage: java -jar causal-cmd-0.1.1.jar --algorithm GFCId [--alpha <arg>] [-d <arg>] [--exclude-variables <arg>] -f <arg> [--faithfulness-assumed] [--help] [--json] [--knowledge <arg>] [--max-degree <arg>] [--no-validation-output] [-o <arg>] [--output-prefix <arg>] [--sample-prior <arg>] [--skip-category-limit] [--skip-latest] [--skip-unique-var-name] [--structure-prior <arg>] [--tetrad-graph-json] [--thread <arg>] [--verbose]
     --alpha <arg>               Cutoff for p values (alpha). Default is 0.01.
  -d,--delimiter <arg>           Data delimiter either comma, semicolon, space, colon, or tab. Default: comma for *.csv, else tab.
     --exclude-variables <arg>   A file containing variables to exclude.

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>0.2.0-SNAPSHOT</version>
+    <version>0.1.1-SNAPSHOT</version>
     <packaging>jar</packaging>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -120,12 +120,12 @@
         <dependency>
             <groupId>edu.pitt.dbmi</groupId>
             <artifactId>data-reader</artifactId>
-            <version>0.1.3</version>
+            <version>0.1.4</version>
         </dependency>
         <dependency>
             <groupId>edu.cmu</groupId>
             <artifactId>tetrad-lib</artifactId>
-            <version>6.2.0-SNAPSHOT</version>
+            <version>6.0.1-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>