Add additional documentation on using the code

1 files changed, 72 insertions, 0 deletions

diff --git a/execs/R/utils.R b/execs/R/utils.R
index 504b5373..a170a1c0 100644
--- a/execs/R/utils.R
+++ b/execs/R/utils.R
@@ -10,6 +10,16 @@ library(RJSONIO)
 
 printf <- function(...) invisible(cat(sprintf(...)));
 
+#' Load a TCPDBench dataset
+#'
+#' This function reads in a JSON dataset in TCPDBench format (see TCPD 
+#' repository for schema) and creates a matrix representation of the dataset.  
+#' The dataset is scaled in the process.
+#'
+#' @param filename Path to the JSON file
+#' @return List object with the raw data in the \code{original} field, the time 
+#' index in the \code{time} field, and the data matrix in the \code{mat} field.
+#'
 load.dataset <- function(filename)
 {
     data <- fromJSON(filename)
@@ -48,6 +58,28 @@ load.dataset <- function(filename)
     return(out)
 }
 
+#' Prepare the experiment output
+#'
+#' This function creates a list of the necessary output data. This includes the 
+#' exact command that was run, dataset and script information, the hostname, 
+#' output status, any errors if present, and the detected change point location 
+#' and runtime.
+#'
+#' @param data the raw data loaded from the JSON file
+#' @param data.filename the path to the dataset filename
+#' @param status the output status code of the experiment. Currently in use are 
+#' 'SUCCESS' for when an experiment exited successfully, 'TIMEOUT' if the 
+#' experiment exceeded a limit on runtime, 'SKIP' if the method was supplied 
+#' with improper hyperparameters, and 'FAIL' if an error occurred.
+#' @param error a description of the error, if one occurred
+#' @param params input parameters (including defaults) to the method
+#' @param locations detected change point locations (important: these locations 
+#' are 0-based, whereas R array indices are 1-based. It is important to convert 
+#' them accordingly. Change point locations should be integers on the interval 
+#' [0, T-1], including both endpoints).
+#' @param runtime the runtime of the method.
+#'
+#' @return list with all the necessary output fields.
 prepare.result <- function(data, data.filename, status, error,
                            params, locations, runtime) {
     out <- list(error=NULL)
@@ -94,6 +126,13 @@ prepare.result <- function(data, data.filename, status, error,
     return(out)
 }
 
+#' Combine default parameters and command line arguments
+#'
+#' @param args the command line arguments
+#' @param defaults default algorithm parameters
+#' @return a combined list with both the default parameter settings and those 
+#' provided on the command line. If a parameter is in the default list that is 
+#' specified on the command line the command line parameter takes precedence.
 make.param.list <- function(args, defaults)
 {
     params <- defaults
@@ -106,6 +145,14 @@ make.param.list <- function(args, defaults)
     return(params)
 }
 
+#' Write output to a file or stdout
+#'
+#' This function takes an output list generated by \code{\link{prepare.result}} 
+#' and writes it out as JSON to a file if provided or stdout otherwise.
+#'
+#' @param out experimental results as a list
+#' @param filename (optional) output file to write to
+#'
 dump.output <- function(out, filename) {
     json.out <- toJSON(out, pretty=T)
     if (!is.null(filename))
@@ -114,6 +161,16 @@ dump.output <- function(out, filename) {
         cat(json.out, '\n')
 }
 
+#' Exit with SKIP status due to multidimensional data
+#'
+#' This is a shorthand for \code{\link{exit.with.error}} where the error is 
+#' already set for methods that don't handle multidimensional data. Writes out 
+#' the data and exits.
+#'
+#' @param data  original data loaded by \code{\link{load.dataset}}
+#' @param args command line arguments
+#' @param params combined hyperparameters generated by 
+#' \code{\link{make.param.list}}
 exit.error.multidim <- function(data, args, params) {
     status = 'SKIP'
     error = 'This method has no support for multidimensional data.'
@@ -122,6 +179,13 @@ exit.error.multidim <- function(data, args, params) {
     quit(save='no')
 }
 
+#' Exit with FAIL status and a custom error message
+#'
+#' @param data  original data loaded by \code{\link{load.dataset}}
+#' @param args command line arguments
+#' @param params combined hyperparameters generated by 
+#' \code{\link{make.param.list}}
+#' @param error custom error message
 exit.with.error <- function(data, args, params, error) {
     status = 'FAIL'
     out <- prepare.result(data, args$input, status, error, params, NULL, NULL)
@@ -129,6 +193,14 @@ exit.with.error <- function(data, args, params, error) {
     quit(save='no')
 }
 
+#' Exit with SUCCESS status
+#'
+#' @param data  original data loaded by \code{\link{load.dataset}}
+#' @param args command line arguments
+#' @param params combined hyperparameters generated by 
+#' \code{\link{make.param.list}}
+#' @param locations detected change point locations (0-based!)
+#' @param runtime runtime in seconds
 exit.success <- function(data, args, params, locations, runtime) {
     status = 'SUCCESS'
     error = NULL