Slight cleanup

No more warnings from devtools::check()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: largeRCRF
 Type: Package
 Title: Large Random Competing Risks Forests
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person("Joel", "Therrien", email = "joel_therrien@sfu.ca", role = c("aut", "cre", "cph")),
     person("Jiguo", "Cao", email = "jiguo_cao@sfu.ca", role = c("aut", "dgs"))

NAMESPACE

@@ -8,7 +8,6 @@ S3method(extractMortalities,CompetingRiskFunctions)
 S3method(extractMortalities,CompetingRiskFunctions.List)
 S3method(extractSurvivorCurve,CompetingRiskFunctions)
 S3method(extractSurvivorCurve,CompetingRiskFunctions.List)
-S3method(plot,JMatrixPlottable)
 S3method(predict,JRandomForest)
 S3method(print,CompetingRiskFunctions)
 S3method(print,CompetingRiskFunctions.List)

R/cr_predictions.R

@@ -47,8 +47,8 @@ extractCIF <- function (x, event) {
 }
 
 #' @export
-extractCIF.CompetingRiskFunctions <- function(prediction, event){
+extractCIF.CompetingRiskFunctions <- function(x, event){
-  fun <- stats::stepfun(prediction$time.interest, c(0, prediction$cif[,event]))
+  fun <- stats::stepfun(x$time.interest, c(0, x$cif[,event]))
   
   class(fun) <- "function"
   attr(fun, "call") <- sys.call()
@@ -56,8 +56,8 @@ extractCIF.CompetingRiskFunctions <- function(prediction, event){
 }
 
 #' @export
-extractCIF.CompetingRiskFunctions.List <- function(predictions, event){
+extractCIF.CompetingRiskFunctions.List <- function(x, event){
-  return(lapply(predictions, extractCIF.CompetingRiskFunctions, event))
+  return(lapply(x, extractCIF.CompetingRiskFunctions, event))
 }
 
 #' @rdname CompetingRiskPredictions
@@ -69,8 +69,8 @@ extractCHF <- function (x, event) {
 }
 
 #' @export
-extractCHF.CompetingRiskFunctions <- function(prediction, event){
+extractCHF.CompetingRiskFunctions <- function(x, event){
-  fun <- stats::stepfun(prediction$time.interest, c(0, prediction$chf[,event]))
+  fun <- stats::stepfun(x$time.interest, c(0, x$chf[,event]))
   
   class(fun) <- "function"
   attr(fun, "call") <- sys.call()
@@ -78,8 +78,8 @@ extractCHF.CompetingRiskFunctions <- function(prediction, event){
 }
 
 #' @export
-extractCHF.CompetingRiskFunctions.List <- function(predictions, event){
+extractCHF.CompetingRiskFunctions.List <- function(x, event){
-  return(lapply(predictions, extractCHF.CompetingRiskFunctions, event))
+  return(lapply(x, extractCHF.CompetingRiskFunctions, event))
 }
 
 
@@ -92,8 +92,8 @@ extractSurvivorCurve <- function (x) {
 }
 
 #' @export
-extractSurvivorCurve.CompetingRiskFunctions <- function(prediction){
+extractSurvivorCurve.CompetingRiskFunctions <- function(x){
-  fun <- stats::stepfun(prediction$time.interest, c(1, prediction$survivorCurve))
+  fun <- stats::stepfun(x$time.interest, c(1, x$survivorCurve))
   
   class(fun) <- "function"
   attr(fun, "call") <- sys.call()
@@ -101,8 +101,8 @@ extractSurvivorCurve.CompetingRiskFunctions <- function(prediction){
 }
 
 #' @export
-extractSurvivorCurve.CompetingRiskFunctions.List <- function(predictions){
+extractSurvivorCurve.CompetingRiskFunctions.List <- function(x){
-  return(lapply(predictions, extractSurvivorCurve.CompetingRiskFunctions))
+  return(lapply(x, extractSurvivorCurve.CompetingRiskFunctions))
 }
 
 #' @rdname CompetingRiskPredictions
@@ -115,7 +115,7 @@ extractMortalities <- function(x, event, time){
 }
 
 #' @export
-extractMortalities.CompetingRiskFunctions <- function(prediction, event, time){
+extractMortalities.CompetingRiskFunctions <- function(x, event, time){
   if(is.null(event) | anyNA(event)){
     stop("event must be specified")
   }
@@ -124,11 +124,11 @@ extractMortalities.CompetingRiskFunctions <- function(prediction, event, time){
     stop("time must be specified")
   }
   
-  return(.jcall(prediction$javaObject, "D", "calculateEventSpecificMortality", as.integer(event), time))
+  return(.jcall(x$javaObject, "D", "calculateEventSpecificMortality", as.integer(event), time))
 }
 
 #' @export
-extractMortalities.CompetingRiskFunctions.List <- function(predictions, event, time){
+extractMortalities.CompetingRiskFunctions.List <- function(x, event, time){
   if(is.null(event) | anyNA(event)){
     stop("event must be specified")
   }
@@ -137,5 +137,5 @@ extractMortalities.CompetingRiskFunctions.List <- function(predictions, event, t
     stop("time must be specified")
   }
   
-  return(as.numeric(lapply(predictions, extractMortalities.CompetingRiskFunctions, event, time)))
+  return(as.numeric(lapply(x, extractMortalities.CompetingRiskFunctions, event, time)))
 }

R/misc.R

@@ -15,39 +15,39 @@ convertRListToJava <- function(lst){
 }
 
 #' @export
-print.SplitFinder = function(splitFinder) print(splitFinder$call)
+print.SplitFinder = function(x, ...) print(x$call)
 
 #' @export
-print.ResponseCombiner = function(combiner) print(combiner$call)
+print.ResponseCombiner = function(x, ...) print(x$call)
 
 #' @export
-print.JRandomForest <- function(forest){
+print.JRandomForest <- function(x, ...){
   cat("Call:\n")
-  print(forest$call)
+  print(x$call)
   cat("\nParameters:\n")
-  cat("\tSplit Finder: "); print(forest$params$splitFinder$call)
+  cat("\tSplit Finder: "); print(x$params$splitFinder$call)
-  cat("\tTerminal Node Response Combiner: "); print(forest$params$nodeResponseCombiner$call)
+  cat("\tTerminal Node Response Combiner: "); print(x$params$nodeResponseCombiner$call)
-  cat("\tForest Response Combiner: "); print(forest$params$forestResponseCombiner$call)
+  cat("\tForest Response Combiner: "); print(x$params$forestResponseCombiner$call)
-  cat("\t# of trees: "); cat(forest$params$ntree); cat("\n")
+  cat("\t# of trees: "); cat(x$params$ntree); cat("\n")
-  cat("\t# of Splits: "); cat(forest$params$numberOfSplits); cat("\n")
+  cat("\t# of Splits: "); cat(x$params$numberOfSplits); cat("\n")
-  cat("\t# of Covariates to try: "); cat(forest$params$mtry); cat("\n")
+  cat("\t# of Covariates to try: "); cat(x$params$mtry); cat("\n")
-  cat("\tNode Size: "); cat(forest$params$nodeSize); cat("\n")
+  cat("\tNode Size: "); cat(x$params$nodeSize); cat("\n")
-  cat("\tMax Node Depth: "); cat(forest$params$maxNodeDepth); cat("\n")
+  cat("\tMax Node Depth: "); cat(x$params$maxNodeDepth); cat("\n")
 
   cat("Try using me with predict() or one of the relevant commands to determine error\n")
 }
 
 #' @export
-print.CompetingRiskFunctions.List <- function(lst){
+print.CompetingRiskFunctions.List <- function(x, ...){
   cat("Number of predictions: ")
-  cat(length(lst))
+  cat(length(x))
 
   cat("\n\nSee the help page ?CompetingRiskPredictions for a list of relevant functions on how to use this object.\n")
 }
 
 #' @export
-print.CompetingRiskFunctions <- function(functions){
+print.CompetingRiskFunctions <- function(x, ...){
-  mx <- ncol(functions$cif)
+  mx <- ncol(x$cif)
   cat(mx); cat(" CIFs available\n")
   cat(mx); cat(" CHFs available\n")
   cat("An overall survival curve available\n")
@@ -55,33 +55,4 @@ print.CompetingRiskFunctions <- function(functions){
 
 }
 
-#' @export
-plot.JMatrixPlottable <- function(mat, add=FALSE, type="s", xlab="Time", ylab=NULL, col="black", ...){
-  if(!add){
-    if(is.null(ylab)){
-      matType <- attr(mat, "type")
-      event <- attr(mat, "event")
 
-      if(matType == "cif"){
-        ylab <- paste0("CIF-", event, "(t)")
-      }
-      else if(matType == "chf"){
-        ylab <- paste0("CHF(t)-", event, "(t)")
-      }
-      else if(matType == "kaplanMeier"){
-        ylab <- "S-hat(t)"
-      }
-      else{
-        ylab <- "Y"
-        warning("Unknown type attribute in plottable object")
-      }
-
-    }
-
-    graphics::plot(mat[,2] ~ mat[,1], col=col, type=type, xlab=xlab, ylab=ylab, ...)
-  }
-  else{
-    graphics::points(mat[,2] ~ mat[,1], col=col, type=type, xlab=xlab, ylab=ylab, ...)
-  }
-
-}

R/predict.R

@@ -4,10 +4,10 @@
 #'
 #' Predict on the random forest.
 #'
-#' @param forest A forest that was previously \code{\link{train}}ed
+#' @param object A forest that was previously \code{\link{train}}ed
 #' @param newData The new data containing all of the previous predictor
 #'   covariates. Can be NULL if you want to use the training dataset, and
-#'   \code{forest} hasn't been loaded from the disk; otherwise you'll have to
+#'   \code{object} hasn't been loaded from the disk; otherwise you'll have to
 #'   specify it.
 #' @param parallel A logical indicating whether multiple cores should be
 #'   utilized when making the predictions. Available as an option because it's
@@ -18,6 +18,8 @@
 #'   'out of bag' trees; set only to \code{TRUE} if you're running predictions
 #'   on data that was used in the training. Default value is \code{TRUE} if
 #'   \code{newData} is \code{NULL}, otherwise \code{FALSE}.
+#' @param ... Other parameters that may one day get passed onto other functions;
+#'   currently not used.
 #' @return A list of responses corresponding with each row of \code{newData} if
 #'   it's a non-regression random forest; otherwise it returns a numeric vector.
 #' @export
@@ -28,7 +30,7 @@
 #' y <- 1 + x1 + x2 + rnorm(1000)
 #'
 #' data <- data.frame(x1, x2, y)
-#' forest <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, 
+#' forest <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5,
 #'     mtry = 1, nodeSize = 5)
 #'
 #' # Fix x2 to be 0
@@ -53,7 +55,10 @@
 #'    numberOfSplits=5, mtry=1, nodeSize=10)
 #' newData <- data.frame(x1 = c(-1, 0, 1), x2 = 0)
 #' ypred <- predict(forest, newData)
-predict.JRandomForest <- function(forest, newData=NULL, parallel=TRUE, out.of.bag=NULL){
+predict.JRandomForest <- function(object, newData=NULL, parallel=TRUE, out.of.bag=NULL, ...){
+  
+  # slight renaming
+  forest <- object
   
   if(is.null(newData) & is.null(forest$dataset)){
     stop("forest doesn't have a copy of the training data loaded (this happens if you just loaded it); please manually specify newData and possibly out.of.bag")

README.md

@@ -1,66 +1,66 @@
-# README
+# README
-
+
-This R package is used to train random competing risks forests, ideally for large data.
+This R package is used to train random competing risks forests, ideally for large data.
-It's based heavily off of [randomForestSRC](https://github.com/kogalur/randomForestSRC/), although there are some differences.
+It's based heavily off of [randomForestSRC](https://github.com/kogalur/randomForestSRC/), although there are some differences.
-
+
-This package is still in a pre-release state and so it not yet available on CRAN.
+This package is still in a pre-release state and so it not yet available on CRAN.
-To install it now, in R install the `devtools` package and run the following command:
+To install it now, in R install the `devtools` package and run the following command:
-```
+```
-R> devtools::install_git("https://github.com/jatherrien/largeRCRF.git")
+R> devtools::install_git("https://github.com/jatherrien/largeRCRF.git")
-```
+```
-
+
-## System Requirements
+## System Requirements
-
+
-You need:
+You need:
-
+
-* R version 3.4.2 or greater
+* R version 3.4.0 or greater
-* The `rJava` package version 0.9-9 or greater
+* The `rJava` package version 0.9-9 or greater
-* A Java runtime version 1.8 or greater
+* A Java runtime version 1.8 or greater
-
+
-## Troubleshooting
+## Troubleshooting
-
+
-### I get an `OutOfMemoryException` error but I have plenty of RAM
+### I get an `OutOfMemoryException` error but I have plenty of RAM
-
+
-`largeRCRF` makes use of the Java virtual machine, which unfortunately restricts itself by default to a quarter of your system memory. 
+`largeRCRF` makes use of the Java virtual machine, which unfortunately restricts itself by default to a quarter of your system memory. 
-You can override the default by including **before** loading `largeRCRF` or any other `rJava` based package the following line:
+You can override the default by including **before** loading `largeRCRF` or any other `rJava` based package the following line:
-
+
-```
+```
-R> options(java.parameters <- c("-Xmx13G", "-Xms13G"))
+R> options(java.parameters <- c("-Xmx13G", "-Xms13G"))
-```
+```
-
+
-with `13G` replaced with a little less than your available system memory.
+with `13G` replaced with a little less than your available system memory.
-
+
-### I get an `OutOfMemoryException` error and I'm short on RAM
+### I get an `OutOfMemoryException` error and I'm short on RAM
-
+
-Obviously if you're short on RAM there is a limit on how large of a dataset you can train,
+Obviously if you're short on RAM there is a limit on how large of a dataset you can train,
-but there are some techniques you can use to limit how much `largeRCRF` needs.
+but there are some techniques you can use to limit how much `largeRCRF` needs.
-
+
-* If your training dataset is large you might not want both R and `largeRCRF` to have their own separate copies 
+* If your training dataset is large you might not want both R and `largeRCRF` to have their own separate copies 
-(limitations due to Java require `largeRCRF` have its own copy). When specifying the `data` parameter into `train`, 
+(limitations due to Java require `largeRCRF` have its own copy). When specifying the `data` parameter into `train`, 
-instead provide an environment containing one object called `data` which is the dataset. `largeRCRF` will delete that variable
+instead provide an environment containing one object called `data` which is the dataset. `largeRCRF` will delete that variable
-after importing it into the Java environment.
+after importing it into the Java environment.
-
+
-Example:
+Example:
-```
+```
-R> data.env <- new.env()
+R> data.env <- new.env()
-R> data.env$data <- trainingData
+R> data.env$data <- trainingData
-R> rm(trainingData)
+R> rm(trainingData)
-R> model <- train(..., data=data.env, ...)
+R> model <- train(..., data=data.env, ...)
-```
+```
-
+
-* Each core that is training trees requires its own memory; you can try limiting `largeRCRF` to train only one tree at a time by specifiying `cores=1`.
+* Each core that is training trees requires its own memory; you can try limiting `largeRCRF` to train only one tree at a time by specifiying `cores=1`.
-
+
-* By default `largeRCRF` keeps the entire forest loaded in memory during training, 
+* By default `largeRCRF` keeps the entire forest loaded in memory during training, 
-when in practice only the trees being trained on need to be loaded. 
+when in practice only the trees being trained on need to be loaded. 
-You can specify `savePath` to give a directory for `largeRCRF` to save trees in during training,
+You can specify `savePath` to give a directory for `largeRCRF` to save trees in during training,
-which will allow to `largeRCRF` to conserve memory for only those trees being currently trained.
+which will allow to `largeRCRF` to conserve memory for only those trees being currently trained.
-
+
-### Training stalls immediately at 0 trees and the CPU is idle
+### Training stalls immediately at 0 trees and the CPU is idle
-
+
-This issue has been observed before on one particular system (and only on that system) but it's not clear what causes it. 
+This issue has been observed before on one particular system (and only on that system) but it's not clear what causes it. 
-It would be appreciated if you could report this bug to [joelt@sfu.ca](mailto:joelt@sfu.ca) and give your operating system
+It would be appreciated if you could report this bug to [joelt@sfu.ca](mailto:joelt@sfu.ca) and give your operating system
-and the version of Java installed (the entire output of `java --version`). 
+and the version of Java installed (the entire output of `java --version`). 
-
+
-As a workaround, this issue seems to occur randomly; so try restarting your code to see if it runs.
+As a workaround, this issue seems to occur randomly; so try restarting your code to see if it runs.
-
+
-
+

man/predict.JRandomForest.Rd

@@ -4,15 +4,15 @@
 \alias{predict.JRandomForest}
 \title{Predict}
 \usage{
-\method{predict}{JRandomForest}(forest, newData = NULL,
+\method{predict}{JRandomForest}(object, newData = NULL,
-  parallel = TRUE, out.of.bag = NULL)
+  parallel = TRUE, out.of.bag = NULL, ...)
 }
 \arguments{
-\item{forest}{A forest that was previously \code{\link{train}}ed}
+\item{object}{A forest that was previously \code{\link{train}}ed}
 
 \item{newData}{The new data containing all of the previous predictor
 covariates. Can be NULL if you want to use the training dataset, and
-\code{forest} hasn't been loaded from the disk; otherwise you'll have to
+\code{object} hasn't been loaded from the disk; otherwise you'll have to
 specify it.}
 
 \item{parallel}{A logical indicating whether multiple cores should be
@@ -25,6 +25,9 @@ get strange errors while predicting.}
 'out of bag' trees; set only to \code{TRUE} if you're running predictions
 on data that was used in the training. Default value is \code{TRUE} if
 \code{newData} is \code{NULL}, otherwise \code{FALSE}.}
+
+\item{...}{Other parameters that may one day get passed onto other functions;
+currently not used.}
 }
 \value{
 A list of responses corresponding with each row of \code{newData} if
@@ -40,7 +43,7 @@ x2 <- rnorm(1000)
 y <- 1 + x1 + x2 + rnorm(1000)
 
 data <- data.frame(x1, x2, y)
-forest <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, 
+forest <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5,
     mtry = 1, nodeSize = 5)
 
 # Fix x2 to be 0