Merge branch 'master' into 1.0.4-develop

R/CR_Response.R

@@ -8,7 +8,7 @@
 #'
 #' @param delta A vector of integers detailing the event that occurred. A value
 #'   of 0 denotes that censoring occurred first and that time was recorded.
-#' @param u A vector of numerics detailing the recorded event times (possibly
+#' @param u A numeric vector detailing the recorded event times (possibly
 #'   censored).
 #' @param C If the censoring times are known for all observations, they can be
 #'   included which allows for \code{\link{GrayLogRankSplitFinder}} to be used.

R/Numeric.R

@@ -1,7 +1,10 @@
 
 #' Numeric
 #'
-#' An internal function that converts an R vector of numerics or integers into an R list containing java.lang.Double objects. This method does not need to be used directly by the user, as \code{\link{train}} will automatically handle numeric responses if you're working in the regression settings.
+#' An internal function that converts an R vector of numerics or integers into
+#' an R list containing java.lang.Double objects. This method does not need to
+#' be used directly by the user, as \code{\link{train}} will automatically
+#' handle numeric responses if you're working in the regression settings.
 #' @param y The R vector of numbers
 #' @export
 #' @return An R list containing rJava Doubles.

R/addTrees.R

@@ -9,8 +9,8 @@
 #' @param forest An existing forest.
 #' @param numTreesToAdd The number of trees to add.
 #' @param savePath If saving the forest, the directory to save to. Default is
-#'   \code{NULL}. Note that you need to respecify the path if you're modifying a
+#'   \code{NULL}. Note that you need to re-specify the path if you're modifying
-#'   previously saved forest.
+#'   a previously saved forest.
 #' @param savePath.overwrite If \code{savePath} is pointing to an existing
 #'   directory, possibly containing another forest, this specifies what should
 #'   be done.

R/cr_components.R

@@ -10,7 +10,7 @@
 #' The user only needs to pass this object into \code{\link{train}} as the
 #' \code{forestResponseCombiner} parameter.
 #'
-#' @param events A vector of integers specifying which competing risk events's
+#' @param events A vector of integers specifying which competing risks event
 #'   functions should be processed. This should correspond to all of the
 #'   competing risk events that can occur, from 1 to the largest number.
 #' @param times An optional numeric vector that forces the output functions to
@@ -66,7 +66,7 @@ CR_FunctionCombiner <- function(events, times = NULL){
 #' The user only needs to pass this object into \code{\link{train}} as the
 #' \code{nodeResponseCombiner} parameter.
 #'
-#' @param events A vector of integers specifying which competing risk events's
+#' @param events A vector of integers specifying which competing risks event
 #'   functions should be processed. This should correspond to all of the
 #'   competing risk events that can occur, from 1 to the largest number.
 #' @export

R/cr_predictions.R

@@ -48,6 +48,10 @@ extractCIF <- function (x, event) {
 
 #' @export
 extractCIF.CompetingRiskFunctions <- function(x, event){
+  if(is.null(event) | anyNA(event)){
+    stop("event must be specified")
+  }
+  
   fun <- stats::stepfun(x$time.interest, c(0, x$cif[,event]))
   
   class(fun) <- "function"
@@ -57,6 +61,10 @@ extractCIF.CompetingRiskFunctions <- function(x, event){
 
 #' @export
 extractCIF.CompetingRiskFunctions.List <- function(x, event){
+  if(is.null(event) | anyNA(event)){
+    stop("event must be specified")
+  }
+  
   return(lapply(x, extractCIF.CompetingRiskFunctions, event))
 }
 
@@ -70,6 +78,10 @@ extractCHF <- function (x, event) {
 
 #' @export
 extractCHF.CompetingRiskFunctions <- function(x, event){
+  if(is.null(event) | anyNA(event)){
+    stop("event must be specified")
+  }
+  
   fun <- stats::stepfun(x$time.interest, c(0, x$chf[,event]))
   
   class(fun) <- "function"
@@ -79,6 +91,10 @@ extractCHF.CompetingRiskFunctions <- function(x, event){
 
 #' @export
 extractCHF.CompetingRiskFunctions.List <- function(x, event){
+  if(is.null(event) | anyNA(event)){
+    stop("event must be specified")
+  }
+  
   return(lapply(x, extractCHF.CompetingRiskFunctions, event))
 }
 

R/zzz.R

@@ -4,7 +4,7 @@
   # it's in the inst folder which won't be present if the package was actually
   # loaded from the R library). Thus with morePaths we make sure it loads up the
   # jar in this situation.
-  .jpackage(pkgname, lib.loc=libname, morePaths="inst/java/largeRCRF-1.0-SNAPSHOT.jar")
+  .jpackage(pkgname, lib.loc=libname, morePaths="inst/java/largeRCRF-library-1.0-SNAPSHOT.jar")
   
 }
 

java/OBTAINING.md

@@ -1,5 +1,5 @@
-The Java source code for this package can be obtained at https://github.com/jatherrien/largeRCRF-Java, and is also licensed under the GPL-3 license. You can include it with your modifications into the R package by following these steps: 
+The Java source code for this package can be obtained at https://github.com/jatherrien/largeRCRF-Java, and is also licensed under the GPL-3 license. You can include it with your modifications into the R package by following these steps: 
-
+
-* Delete the Jar file in `inst/java/`
+* Delete the Jar file in `inst/java/`
-* Build the Java code in its own separate directory using `mvn clean package` in the root of the directory (same folder containing `README.md`). Make sure you have [Maven](https://maven.apache.org/) installed.
+* Build the Java code in its own separate directory using `mvn clean package` in the root of the directory (same folder containing `README.md`). Make sure you have [Maven](https://maven.apache.org/) installed.
-* Copy the `library/target/largeRCRF-library/1.0-SNAPSHOT.jar` file produced in the Java directory into `inst/java/`
+* Copy the `library/target/largeRCRF-library-1.0-SNAPSHOT.jar` file produced in the Java directory into `inst/java/`

man/CR_FunctionCombiner.Rd

@@ -7,7 +7,7 @@
 CR_FunctionCombiner(events, times = NULL)
 }
 \arguments{
-\item{events}{A vector of integers specifying which competing risk events's
+\item{events}{A vector of integers specifying which competing risks event
 functions should be processed. This should correspond to all of the
 competing risk events that can occur, from 1 to the largest number.}
 

man/CR_Response.Rd

@@ -10,7 +10,7 @@ CR_Response(delta, u, C = NULL)
 \item{delta}{A vector of integers detailing the event that occurred. A value
 of 0 denotes that censoring occurred first and that time was recorded.}
 
-\item{u}{A vector of numerics detailing the recorded event times (possibly
+\item{u}{A numeric vector detailing the recorded event times (possibly
 censored).}
 
 \item{C}{If the censoring times are known for all observations, they can be

man/CR_ResponseCombiner.Rd

@@ -7,7 +7,7 @@
 CR_ResponseCombiner(events)
 }
 \arguments{
-\item{events}{A vector of integers specifying which competing risk events's
+\item{events}{A vector of integers specifying which competing risks event
 functions should be processed. This should correspond to all of the
 competing risk events that can occur, from 1 to the largest number.}
 }

man/Numeric.Rd

@@ -13,7 +13,10 @@ Numeric(y)
 An R list containing rJava Doubles.
 }
 \description{
-An internal function that converts an R vector of numerics or integers into an R list containing java.lang.Double objects. This method does not need to be used directly by the user, as \code{\link{train}} will automatically handle numeric responses if you're working in the regression settings.
+An internal function that converts an R vector of numerics or integers into
+an R list containing java.lang.Double objects. This method does not need to
+be used directly by the user, as \code{\link{train}} will automatically
+handle numeric responses if you're working in the regression settings.
 }
 \examples{
 x <- Numeric(1:5)

man/addTrees.Rd

@@ -14,8 +14,8 @@ addTrees(forest, numTreesToAdd, savePath = NULL,
 \item{numTreesToAdd}{The number of trees to add.}
 
 \item{savePath}{If saving the forest, the directory to save to. Default is
-\code{NULL}. Note that you need to respecify the path if you're modifying a
+\code{NULL}. Note that you need to re-specify the path if you're modifying
-previously saved forest.}
+a previously saved forest.}
 
 \item{savePath.overwrite}{If \code{savePath} is pointing to an existing
 directory, possibly containing another forest, this specifies what should