Improve CLI usage instructions (#59)

* Improve CLI usage instructions

Expand upon the CLI instructions with an example and information
on where to find additional CLI applications. Adds an example data
file for ease of instruction.

Closes #43

Author: cswiercz

Java/README.md

@@ -102,18 +102,60 @@ mvn package -DexcludedGroups=functional
 
 ## Build Command-line (CLI) usage
 
-For some of the algorithms included in this package, there are CLI applications that can
-be used for experiments. These applications use `String::split` to read
-delimited data, and as such are **not intended for production use**. Instead,
-use these applications as example code and as a way to learn about the
-algorithms and their hyperparameters.
+> **Important.** The CLI applications use `String::split` to read delimited data
+> and as such are **not intended for production use**.
 
-After building the project (described in the previous section), you can invoke an example CLI application by adding the
-core jar file to your classpath. For example:
+For some of the algorithms included in this package there are CLI applications
+that can be used for experimentation as well as a way to learn about these
+algorithms and their hyperparameters. After building the project you can invoke
+an example CLI application by adding the core jar file to your classpath.
+
+In the example below we train and score a Random Cut Forest model on the
+three-dimensional data shown in Figure 3 in the original RCF paper.
+([PDF][rcf-paper]) These example data can be
+found at `../example-data/rcf-paper.csv`:
+
+```text
+$ tail data/example.csv
+-5.0074,-0.0038,-0.0237
+-5.0029,0.0170,-0.0057
+-4.9975,-0.0102,-0.0065
+4.9878,0.0136,-0.0087
+5.0118,0.0098,-0.0057
+0.0158,0.0061,0.0091
+5.0167,0.0041,0.0054
+-4.9947,0.0126,-0.0010
+-5.0209,0.0004,-0.0033
+4.9923,-0.0142,0.0030
+```
+
+(Note that there is one data point above that is not like the others.) The
+`AnomalyScoreRunner` application reads in each line of the input data as a
+vector data point, scores the data point, and then updates the model with this
+point. The program output appends a column of anomaly scores to the input:
 
 ```text
-% java -cp core/target/randomcutforest-core-1.0-alpha.jar com.amazon.randomcutforest.runner.AnomalyScoreRunner --help
-Usage: java -cp randomcutforest-core-1.0-alpha.jar com.amazon.randomcutforest.runner.AnomalyScoreRunner [options] < input_file > output_file
+$ java -cp core/target/randomcutforest-core-1.0.jar com.amazon.randomcutforest.runner.AnomalyScoreRunner < ../example-data/rcf-paper.csv > example_output.csv
+$ tail example_output.csv
+-5.0029,0.0170,-0.0057,0.8129401629464965
+-4.9975,-0.0102,-0.0065,0.6591046054520615
+4.9878,0.0136,-0.0087,0.8552217070518414
+5.0118,0.0098,-0.0057,0.7224686064066762
+0.0158,0.0061,0.0091,2.8299054033889814
+5.0167,0.0041,0.0054,0.7571453322237215
+-4.9947,0.0126,-0.0010,0.7259960347128676
+-5.0209,0.0004,-0.0033,0.9119498264685114
+4.9923,-0.0142,0.0030,0.7310102658466711
+Done.
+```
+
+(As you can see the anomalous data point was given large anomaly score.) You can
+read additional usage instructions, including options for setting model
+hyperparameters, using the `--help` flag:
+
+```text
+$ java -cp core/target/randomcutforest-core-1.0.jar com.amazon.randomcutforest.runner.AnomalyScoreRunner --help
+Usage: java -cp target/random-cut-forest-1.0.jar com.amazon.randomcutforest.runner.AnomalyScoreRunner [options] < input_file > output_file
 
 Compute scalar anomaly scores from the input rows and append them to the output rows.
 
@@ -130,6 +172,9 @@ Options:
         --help, -h: Print this help message and exit.
 ```
 
+Other CLI applications are available in the `com.amazon.randomcutforest.runner`
+package.
+
 ## Testing
 
 The core library test suite is divided into unit tests and "functional" tests. By "functional", we mean tests that 
@@ -181,3 +226,5 @@ benchmark methods will be executed.
 ```text
 % java -jar benchmark/target/randomcutforest-benchmark-1.0-jar-with-dependencies.jar RandomCutForestBenchmark\.updateAndGetAnomalyScore
 ```
+
+[rcf-paper]: http://proceedings.mlr.press/v48/guha16.pdf