From fdc708dad5db567503d286af0c1ab021cc46cea5 Mon Sep 17 00:00:00 2001 From: Joel Therrien Date: Wed, 19 Jun 2019 13:14:11 -0700 Subject: [PATCH] New features - Add support for making predictions without specifying training data Add support for adding trees to an existing forest Add support for toggling displayProgress Also reduced the size of the package by removing some unused dependency classes. --- DESCRIPTION | 2 +- NAMESPACE | 2 + R/addTrees.R | 128 ++++++++++++++++++ R/connectToData.R | 37 +++++ R/java_classes_directory.R | 10 ++ R/loadData.R | 7 +- R/loadForest.R | 7 +- R/predict.R | 37 +++-- R/train.R | 93 +++++++------ .../ca/joeltherrien/randomforest/Main.class | Bin 11299 -> 11471 bytes .../ForestTrainer$ForestTrainerBuilder.class | Bin 5130 -> 5130 bytes .../ForestTrainer$TreeInMemoryWorker.class | Bin 2113 -> 2113 bytes .../tree/ForestTrainer$TreeSavedWorker.class | Bin 2985 -> 2267 bytes .../randomforest/tree/ForestTrainer.class | Bin 12742 -> 16012 bytes 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-> 0 bytes .../snakeyaml/tokens/WhitespaceToken.class | Bin 733 -> 0 bytes man/addTrees.Rd | 36 +++++ man/connectToData.Rd | 34 +++++ man/predict.JRandomForest.Rd | 11 +- man/train.Rd | 43 +++--- tests/testthat/test_adding_new_trees.R | 71 ++++++++++ tests/testthat/test_deterministic_forests.R | 37 ++++- tests/testthat/test_factors.R | 4 +- tests/testthat/test_na.R | 4 +- .../testthat/test_predicting_training_data.R | 32 +++++ tests/testthat/test_running.R | 4 +- tests/testthat/test_running_environment.R | 6 +- tests/testthat/test_saving_loading.R | 3 +- tests/testthat/test_saving_offline.R | 2 +- ...test_verify_response_not_used_in_formula.R | 14 +- 152 files changed, 526 insertions(+), 98 deletions(-) create mode 100644 R/addTrees.R create mode 100644 R/connectToData.R delete mode 100644 inst/java/com/fasterxml/jackson/core/JsonTokenId.class delete mode 100644 inst/java/com/fasterxml/jackson/core/JsonpCharacterEscapes.class delete mode 100644 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man/connectToData.Rd create mode 100644 tests/testthat/test_adding_new_trees.R create mode 100644 tests/testthat/test_predicting_training_data.R diff --git a/DESCRIPTION b/DESCRIPTION index 2bc850f..cd1054d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: largeRCRF Type: Package Title: Large Random Competing Risk Forests, Java Implementation Run in R -Version: 0.0.0.9037 +Version: 0.0.0.9038 Authors@R: person("Joel", "Therrien", email = "joel@joeltherrien.ca", role = c("aut", "cre")) Description: This package is used for training competing risk random forests on larger scale datasets. It currently only supports training models, running predictions, plotting those predictions (they are curves), diff --git a/NAMESPACE b/NAMESPACE index 22ff28f..f728caa 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -25,6 +25,8 @@ export(LogRankSplitFinder) export(MeanResponseCombiner) export(Numeric) export(WeightedVarianceSplitFinder) +export(addTrees) +export(connectToData) export(extractCHF) export(extractCIF) export(extractMortalities) diff --git a/R/addTrees.R b/R/addTrees.R new file mode 100644 index 0000000..75331ee --- /dev/null +++ b/R/addTrees.R @@ -0,0 +1,128 @@ + + + +#' Add Trees +#' +#' Add more trees to an existing forest. Most parameters are extracted from the +#' previous forest. +#' +#' @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 +#' 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. +#' @param cores The number of cores to be used for training the new trees. +#' @param displayProgress A logical indicating whether the progress should be +#' displayed to console; default is \code{TRUE}. Useful to set to FALSE in +#' some automated situations. +#' +#' @return A new forest with the original and additional trees. +#' @export +#' +addTrees <- function(forest, numTreesToAdd, savePath = NULL, savePath.overwrite = c("warn", "delete", "merge"), cores = getCores(), displayProgress = TRUE){ + if(is.null(forest$dataset)){ + stop("Training dataset must be connected to forest before more trees can be added; this can be done manually by using connectToData") + } + + numTreesToAdd <- as.integer(numTreesToAdd) + + if(numTreesToAdd <= 0){ + stop("numTreesToAdd must be a positive integer") + } + + if(is.null(savePath.overwrite) | length(savePath.overwrite)==0 | !(savePath.overwrite[1] %in% c("warn", "delete", "merge"))){ + stop("savePath.overwrite must be one of c(\"warn\", \"delete\", \"merge\")") + } + + newTreeCount <- forest$params$ntree + as.integer(numTreesToAdd) + + treeTrainer <- createTreeTrainer(responseCombiner=forest$params$nodeResponseCombiner, + splitFinder=forest$params$splitFinder, + covariateList=forest$covariateList, + numberOfSplits=forest$params$numberOfSplits, + nodeSize=forest$params$nodeSize, + maxNodeDepth=forest$params$maxNodeDepth, + mtry=forest$params$mtry, + splitPureNodes=forest$params$splitPureNodes) + + forestTrainer <- createForestTrainer(treeTrainer=treeTrainer, + covariateList=forest$covariateList, + treeResponseCombiner=forest$params$forestResponseCombiner, + dataset=forest$dataset, + ntree=forest$params$ntree + numTreesToAdd, + randomSeed=forest$params$randomSeed, + saveTreeLocation=savePath, + displayProgress=displayProgress) + + params <- list( + splitFinder=forest$params$splitFinder, + nodeResponseCombiner=forest$params$nodeResponseCombiner, + forestResponseCombiner=forest$params$forestResponseCombiner, + ntree=forest$params$ntree + numTreesToAdd, + numberOfSplits=forest$params$numberOfSplits, + mtry=forest$params$mtry, + nodeSize=forest$params$nodeSize, + splitPureNodes=forest$params$splitPureNodes, + maxNodeDepth = forest$params$maxNodeDepth, + randomSeed=forest$params$randomSeed + ) + + initial.forest.optional <- .object_Optional(forest$javaObject) + + # We'll be saving an offline version of the forest + if(!is.null(savePath)){ + + if(file.exists(savePath)){ # we might have to remove the folder or display an error + + if(savePath.overwrite[1] == "warn"){ + stop(paste(savePath, "already exists; will not modify it. Please remove/rename it or set the savePath.overwrite to either 'delete' or 'merge'")) + } else if(savePath.overwrite[1] == "delete"){ + unlink(savePath, recursive=TRUE) + } else if(savePath.overwrite[1] == "merge"){ + warning("Assuming that the previous forest at savePath is the provided forest argument; if not true then your results will be suspect") + initial.forest.optional <- .object_Optional(NULL) # Java backend requires we be explicit about whether we're providing an in-memory initial forest or starting from a previous directory + } + + } + + if(savePath.overwrite[1] != "merge"){ + dir.create(savePath) + } + + # First save forest components (so that if the training crashes mid-way through it can theoretically be recovered by the user) + saveForestComponents(savePath, + covariateList=forest$covariateList, + params=params, + forestCall=match.call()) + + if(cores > 1){ + .jcall(forestTrainer, "V", "trainParallelOnDisk", initial.forest.optional, as.integer(cores)) + } else { + .jcall(forestTrainer, "V", "trainSerialOnDisk", initial.forest.optional) + } + + # Need to now load forest trees back into memory + forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", savePath, forest$params$forestResponseCombiner$javaObject) + + + } + else{ # save directly into memory + if(cores > 1){ + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", initial.forest.optional, as.integer(cores)) + } else { + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory", initial.forest.optional) + } + } + + + + + forestObject <- list(call=match.call(), params=params, javaObject=forest.java, covariateList=forest$covariateList, dataset=forest$dataset) + + class(forestObject) <- "JRandomForest" + return(forestObject) + +} diff --git a/R/connectToData.R b/R/connectToData.R new file mode 100644 index 0000000..2b6bd75 --- /dev/null +++ b/R/connectToData.R @@ -0,0 +1,37 @@ +#' Connect To Data +#' +#' When a trained forest is saved, the training dataset is not saved alongside +#' it. When it's loaded back up, it can be more convenient (and in some cases +#' necessary) to import the training dataset back into the Java environment so +#' that it's readily accessible. There are only two functions that look for the +#' training dataset: \code{predict}, where you can easily just specify an +#' alternative dataset, or \code{\link{addTrees}}, which requires the training +#' dataset be connected. +#' @param forest The forest to connect data too +#' @param responses The responses in the data; aka the left hand side of the formula +#' @param covariateData A data.frame containing all of the covariates used in the training dataset +#' @return The same forest, but connected to the training data. +#' @export +#' @examples +#' data <- data.frame(x1=rnorm(1000), x2=rnorm(1000), y=rnorm(1000)) +#' forest <- train(y~x1+x2, data, ntree=100, numberOfSplits=0, nodeSize=1, mtry=1) +#' forest$dataset <- NULL # what the forest looks like after being loaded +#' +#' forest <- connectToData(forest, data$y, data) +connectToData <- function(forest, responses, covariateData){ + covariateList <- forest$covariateList + + numCovariates <- .jcall(covariateList, "I", "size") + covariateNames <- character(numCovariates) + + for(j in 1:numCovariates){ + covariate <- .jcall(covariateList, makeResponse(.class_Object), "get", as.integer(j-1)) + covariate <- .jcast(covariate, .class_Covariate) + covariateNames[j] <- .jcall(covariate, makeResponse(.class_String), "getName") + } + + forest$dataset <- loadData(covariateData, covariateNames, responses, covariateList)$dataset + + return(forest) + +} \ No newline at end of file diff --git a/R/java_classes_directory.R b/R/java_classes_directory.R index c94728f..00d271a 100644 --- a/R/java_classes_directory.R +++ b/R/java_classes_directory.R @@ -50,6 +50,16 @@ .class_LogRankSplitFinder <- "ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder" .class_WeightedVarianceSplitFinder <- "ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder" +.object_Optional <- function(forest=NULL){ + if(is.null(forest)){ + return(.jcall("java/util/Optional", "Ljava/util/Optional;", "empty")) + } else{ + forest <- .jcast(forest, .class_Object) + return(.jcall("java/util/Optional", "Ljava/util/Optional;", "of", forest)) + } + +} + # When a class object is returned, rJava often often wants L prepended and ; appended. # So a list that returns "java/lang/Object" should show "Ljava/lang/Object;" # This function does that. diff --git a/R/loadData.R b/R/loadData.R index ded0e6e..9e870c2 100644 --- a/R/loadData.R +++ b/R/loadData.R @@ -1,10 +1,13 @@ -loadData <- function(data, xVarNames, responses){ +loadData <- function(data, xVarNames, responses, covariateList.java = NULL){ if(class(responses) == "integer" | class(responses) == "numeric"){ responses <- Numeric(responses) } - covariateList.java <- getCovariateList(data, xVarNames) + # connectToData provides a pre-created covariate list we can re-use + if(is.null(covariateList.java)){ + covariateList.java <- getCovariateList(data, xVarNames) + } textColumns <- list() for(j in 1:length(xVarNames)){ diff --git a/R/loadForest.R b/R/loadForest.R index 524a24f..d4600a2 100644 --- a/R/loadForest.R +++ b/R/loadForest.R @@ -43,7 +43,7 @@ loadForest <- function(directory){ params$forestResponseCombiner$javaObject <- forestResponseCombiner.java forest <- loadForestArgumentsSpecified(directory, params$nodeResponseCombiner, params$splitFinder, params$forestResponseCombiner, covariateList, call, - params$ntree, params$numberOfSplits, params$mtry, params$nodeSize, params$maxNodeDepth, params$splitPureNodes) + params$ntree, params$numberOfSplits, params$mtry, params$nodeSize, params$maxNodeDepth, params$splitPureNodes, params$randomSeed) return(forest) @@ -56,7 +56,7 @@ loadForest <- function(directory){ # I'd appreciate knowing that someone's going to use it first (email me; see # README). loadForestArgumentsSpecified <- function(treeDirectory, nodeResponseCombiner, splitFinder, forestResponseCombiner, - covariateList.java, call, ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE){ + covariateList.java, call, ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE, randomSeed=NULL){ params <- list( splitFinder=splitFinder, @@ -67,7 +67,8 @@ loadForestArgumentsSpecified <- function(treeDirectory, nodeResponseCombiner, sp mtry=mtry, nodeSize=nodeSize, splitPureNodes=splitPureNodes, - maxNodeDepth = maxNodeDepth + maxNodeDepth=maxNodeDepth, + randomSeed=randomSeed ) forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", treeDirectory, forestResponseCombiner$javaObject) diff --git a/R/predict.R b/R/predict.R index 383aa7e..aa21ee1 100644 --- a/R/predict.R +++ b/R/predict.R @@ -6,9 +6,9 @@ #' #' @param forest A forest that was previously \code{\link{train}}ed #' @param newData The new data containing all of the previous predictor -#' covariates. Note that even if predictions are being made on the training -#' set, the dataset must be specified. \code{largeRCRF} doesn't keep track of -#' the dataset after the forest is trained. +#' 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 +#' specify it. #' @param parallel A logical indicating whether multiple cores should be #' utilized when making the predictions. Available as an option because it's #' been observed that using Java's \code{parallelStream} can be unstable on @@ -16,7 +16,8 @@ #' get strange errors while predicting. #' @param out.of.bag A logical indicating whether predictions should be based on #' '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{FALSE}. +#' on data that was used in the training. Default value is \code{TRUE} if +#' \code{newData} is \code{NULL}, otherwise \code{FALSE}. #' @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 @@ -50,18 +51,33 @@ #' forest <- train(CR_Response(delta, u) ~ x1 + x2, data, ntree=100, 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=FALSE){ +predict.JRandomForest <- function(forest, newData=NULL, parallel=TRUE, out.of.bag=NULL){ + + if(is.null(newData) & is.null(forest$dataset)){ + stop("forest doesn't have a copy of the training data loaded (this happens if you just loaded it); please manually specify newData and possibly out.of.bag") + } + if(is.null(newData)){ - stop("newData must be specified, even if predictions are on the training set") + predictionDataList <- forest$dataset + + if(is.null(out.of.bag)){ + out.of.bag <- TRUE + } + } + else{ # newData is provided + if(is.null(out.of.bag)){ + out.of.bag <- FALSE + } + + predictionDataList <- loadPredictionData(newData, forest$covariateList) } + numRows <- .jcall(predictionDataList, "I", "size") + forestObject <- forest$javaObject - covariateList <- forest$covariateList predictionClass <- forest$params$forestResponseCombiner$outputClass convertToRFunction <- forest$params$forestResponseCombiner$convertToRFunction - predictionDataList <- loadPredictionData(newData, covariateList) - if(parallel){ function.to.use <- "evaluate" } @@ -82,8 +98,7 @@ predict.JRandomForest <- function(forest, newData=NULL, parallel=TRUE, out.of.ba predictions <- list() } - - for(i in 1:nrow(newData)){ + for(i in 1:numRows){ prediction <- .jcall(predictionsJava, makeResponse(.class_Object), "get", as.integer(i-1)) prediction <- convertToRFunction(prediction, forest) diff --git a/R/train.R b/R/train.R index 2756130..f0d3186 100644 --- a/R/train.R +++ b/R/train.R @@ -30,10 +30,12 @@ getCores <- function(){ #' #' @param responses An R list of the responses. See \code{\link{CR_Response}} #' for an example function. +#' @param data A data.frame containing the columns of the predictors and +#' responses; not relevant if you're not using the formula version of +#' \code{train}. #' @param covariateData A data.frame containing only the columns of the -#' covariates you wish to use in your training (unless you're using the -#' \code{formula} version of \code{train}, in which case it should contain the -#' response as well). +#' covariates you wish to use in your training (not relevant if you're using +#' the formula version of \code{train}). #' @param splitFinder A split finder that's used to score splits in the random #' forest training algorithm. See \code{\link{Competing Risk Split Finders}} #' or \code{\link{WeightedVarianceSplitFinder}}. If you don't specify one, @@ -78,10 +80,10 @@ getCores <- function(){ #' split a pure node. If set to FALSE, then before every split it will check #' that every response is the same, and if so, not split. If set to TRUE it #' forgoes that check and splits it. Prediction accuracy won't change under -#' any sensible \code{nodeResponseCombiner}; as all terminal nodes from a split -#' pure node should give the same prediction, so this parameter only affects -#' performance. If your response is continuous you'll likely experience faster -#' train times by setting it to TRUE. Default value is TRUE. +#' any sensible \code{nodeResponseCombiner}; as all terminal nodes from a +#' split pure node should give the same prediction, so this parameter only +#' affects performance. If your response is continuous you'll likely +#' experience faster train times by setting it to TRUE. Default value is TRUE. #' @param savePath If set, this parameter will save each tree of the random #' forest in this directory as the forest is trained. Use this parameter if #' you need to save memory while training. See also \code{\link{loadForest}} @@ -98,21 +100,24 @@ getCores <- function(){ #' a crash. #' @param cores This parameter specifies how many trees will be simultaneously #' trained. By default the package attempts to detect how many cores you have -#' by using the \code{parallel} package and using all of them. You may -#' specify a lower number if you wish. It is not recommended to specify a -#' number greater than the number of available cores as this will hurt -#' performance with no available benefit. +#' by using the \code{parallel} package and using all of them. You may specify +#' a lower number if you wish. It is not recommended to specify a number +#' greater than the number of available cores as this will hurt performance +#' with no available benefit. #' @param randomSeed This parameter specifies a random seed if reproducible, -#' deterministic forests are desired. +#' deterministic forests are desired. +#' @param displayProgress A logical indicating whether the progress should be +#' displayed to console; default is \code{TRUE}. Useful to set to FALSE in +#' some automated situations. #' @export #' @return A \code{JRandomForest} object. You may call \code{predict} or #' \code{print} on it. #' @seealso \code{\link{predict.JRandomForest}} -#' @note If saving memory is a concern, you can replace \code{covariateData} -#' with an environment containing one element called \code{data} as the actual -#' dataset. After the data has been imported into Java, but before the forest -#' training begins, the dataset in the environment is deleted, freeing up -#' memory in R. +#' @note If saving memory is a concern, you can replace \code{covariateData} or +#' \code{data} with an environment containing one element called \code{data} +#' as the actual dataset. After the data has been imported into Java, but +#' before the forest training begins, the dataset in the environment is +#' deleted, freeing up memory in R. #' @examples #' # Regression Example #' x1 <- rnorm(1000) @@ -150,7 +155,7 @@ train <- function(x, ...) UseMethod("train") #' @rdname train #' @export -train.default <- function(responses, covariateData, splitFinder = splitFinderDefault(responses), nodeResponseCombiner = nodeResponseCombinerDefault(responses), forestResponseCombiner = forestResponseCombinerDefault(responses), ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE, savePath=NULL, savePath.overwrite=c("warn", "delete", "merge"), cores = getCores(), randomSeed = NULL){ +train.default <- function(responses, covariateData, splitFinder = splitFinderDefault(responses), nodeResponseCombiner = nodeResponseCombinerDefault(responses), forestResponseCombiner = forestResponseCombinerDefault(responses), ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE, savePath=NULL, savePath.overwrite=c("warn", "delete", "merge"), cores = getCores(), randomSeed = NULL, displayProgress = TRUE){ # Some quick checks on parameters ntree <- as.integer(ntree) @@ -223,7 +228,8 @@ train.default <- function(responses, covariateData, splitFinder = splitFinderDef dataset=dataset$dataset, ntree=ntree, randomSeed=randomSeed, - saveTreeLocation=savePath) + saveTreeLocation=savePath, + displayProgress=displayProgress) params <- list( splitFinder=splitFinder, @@ -235,7 +241,7 @@ train.default <- function(responses, covariateData, splitFinder = splitFinderDef nodeSize=nodeSize, splitPureNodes=splitPureNodes, maxNodeDepth = maxNodeDepth, - savePath=savePath + randomSeed=randomSeed ) # We'll be saving an offline version of the forest @@ -262,9 +268,9 @@ train.default <- function(responses, covariateData, splitFinder = splitFinderDef forestCall=match.call()) if(cores > 1){ - .jcall(forestTrainer, "V", "trainParallelOnDisk", as.integer(cores)) + .jcall(forestTrainer, "V", "trainParallelOnDisk", .object_Optional(), as.integer(cores)) } else { - .jcall(forestTrainer, "V", "trainSerialOnDisk") + .jcall(forestTrainer, "V", "trainSerialOnDisk", .object_Optional()) } # Need to now load forest trees back into memory @@ -274,16 +280,16 @@ train.default <- function(responses, covariateData, splitFinder = splitFinderDef } else{ # save directly into memory if(cores > 1){ - forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", as.integer(cores)) + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", .object_Optional(), as.integer(cores)) } else { - forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory") + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory", .object_Optional()) } } - forestObject <- list(call=match.call(), params=params, javaObject=forest.java, covariateList=dataset$covariateList) + forestObject <- list(call=match.call(), params=params, javaObject=forest.java, covariateList=dataset$covariateList, dataset=dataset$dataset) class(forestObject) <- "JRandomForest" return(forestObject) @@ -298,19 +304,19 @@ train.default <- function(responses, covariateData, splitFinder = splitFinderDef #' @param formula You may specify the response and covariates as a formula #' instead; make sure the response in the formula is still properly #' constructed; see \code{responses} -train.formula <- function(formula, covariateData, ...){ +train.formula <- function(formula, data, ...){ # Having an R copy of the data loaded at the same time can be wasteful; we # also allow users to provide an environment of the data which gets removed # after being imported into Java env <- NULL - if(class(covariateData) == "environment"){ - if(is.null(covariateData$data)){ + if(class(data) == "environment"){ + if(is.null(data$data)){ stop("When providing an environment with the dataset, the environment must contain an item called 'data'") } - env <- covariateData - covariateData <- env$data + env <- data + data <- env$data } yVar <- formula[[2]] @@ -319,25 +325,25 @@ train.formula <- function(formula, covariateData, ...){ variablesToDrop <- character(0) # yVar is a call object; as.character(yVar) will be the different components, including the parameters. - # if the length of yVar is > 1 then it's a function call. If the length is 1, and it's not in covariateData, + # if the length of yVar is > 1 then it's a function call. If the length is 1, and it's not in data, # then we also need to explicitly evaluate it - if(class(yVar)=="call" || !(as.character(yVar) %in% colnames(covariateData))){ + if(class(yVar)=="call" || !(as.character(yVar) %in% colnames(data))){ # yVar is a function like CompetingRiskResponses - responses <- eval(expr=yVar, envir=covariateData) + responses <- eval(expr=yVar, envir=data) if(class(formula[[3]]) == "name" && as.character(formula[[3]])=="."){ - # do any of the variables match data in covariateData? We need to track that so we can drop them later - variablesToDrop <- as.character(yVar)[as.character(yVar) %in% names(covariateData)] + # do any of the variables match data in data? We need to track that so we can drop them later + variablesToDrop <- as.character(yVar)[as.character(yVar) %in% names(data)] } formula[[2]] <- NULL - } else if(class(yVar)=="name"){ # and implicitly yVar is contained in covariateData + } else if(class(yVar)=="name"){ # and implicitly yVar is contained in data variablesToDrop <- as.character(yVar) } # Includes responses which we may need to later cut out - mf <- model.frame(formula=formula, data=covariateData, na.action=na.pass) + mf <- model.frame(formula=formula, data=data, na.action=na.pass) if(is.null(responses)){ responses <- model.response(mf) @@ -349,7 +355,7 @@ train.formula <- function(formula, covariateData, ...){ # If environment was provided instead of data if(!is.null(env)){ env$data <- mf - rm(covariateData) + rm(data) forest <- train.default(responses, env, ...) } else{ forest <- train.default(responses, mf, ...) @@ -363,7 +369,14 @@ train.formula <- function(formula, covariateData, ...){ return(forest) } -createForestTrainer <- function(treeTrainer, covariateList, treeResponseCombiner, dataset, ntree, randomSeed, saveTreeLocation){ +createForestTrainer <- function(treeTrainer, + covariateList, + treeResponseCombiner, + dataset, + ntree, + randomSeed, + saveTreeLocation, + displayProgress){ builderClassReturned <- makeResponse(.class_ForestTrainer_Builder) builder <- .jcall(.class_ForestTrainer, builderClassReturned, "builder") @@ -373,7 +386,7 @@ createForestTrainer <- function(treeTrainer, covariateList, treeResponseCombiner builder <- .jcall(builder, builderClassReturned, "treeResponseCombiner", treeResponseCombiner$javaObject) builder <- .jcall(builder, builderClassReturned, "data", dataset) builder <- .jcall(builder, builderClassReturned, "ntree", as.integer(ntree)) - builder <- .jcall(builder, builderClassReturned, "displayProgress", TRUE) + builder <- .jcall(builder, builderClassReturned, "displayProgress", displayProgress) if(!is.null(randomSeed)){ builder <- .jcall(builder, 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forest.} + +\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 +previously saved forest.} + +\item{savePath.overwrite}{If \code{savePath} is pointing to an existing +directory, possibly containing another forest, this specifies what should +be done.} + +\item{cores}{The number of cores to be used for training the new trees.} + +\item{displayProgress}{A logical indicating whether the progress should be +displayed to console; default is \code{TRUE}. Useful to set to FALSE in +some automated situations.} +} +\value{ +A new forest with the original and additional trees. +} +\description{ +Add more trees to an existing forest. Most parameters are extracted from the +previous forest. +} diff --git a/man/connectToData.Rd b/man/connectToData.Rd new file mode 100644 index 0000000..331e357 --- /dev/null +++ b/man/connectToData.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/connectToData.R +\name{connectToData} +\alias{connectToData} +\title{Connect To Data} +\usage{ +connectToData(forest, responses, covariateData) +} +\arguments{ +\item{forest}{The forest to connect data too} + +\item{responses}{The responses in the data; aka the left hand side of the formula} + +\item{covariateData}{A data.frame containing all of the covariates used in the training dataset} +} +\value{ +The same forest, but connected to the training data. +} +\description{ +When a trained forest is saved, the training dataset is not saved alongside +it. When it's loaded back up, it can be more convenient (and in some cases +necessary) to import the training dataset back into the Java environment so +that it's readily accessible. There are only two functions that look for the +training dataset: \code{predict}, where you can easily just specify an +alternative dataset, or \code{\link{addTrees}}, which requires the training +dataset be connected. +} +\examples{ +data <- data.frame(x1=rnorm(1000), x2=rnorm(1000), y=rnorm(1000)) +forest <- train(y~x1+x2, data, ntree=100, numberOfSplits=0, nodeSize=1, mtry=1) +forest$dataset <- NULL # what the forest looks like after being loaded + +forest <- connectToData(forest, data$y, data) +} diff --git a/man/predict.JRandomForest.Rd b/man/predict.JRandomForest.Rd index 7bf71d8..83f3297 100644 --- a/man/predict.JRandomForest.Rd +++ b/man/predict.JRandomForest.Rd @@ -5,15 +5,15 @@ \title{Predict} \usage{ \method{predict}{JRandomForest}(forest, newData = NULL, - parallel = TRUE, out.of.bag = FALSE) + parallel = TRUE, out.of.bag = NULL) } \arguments{ \item{forest}{A forest that was previously \code{\link{train}}ed} \item{newData}{The new data containing all of the previous predictor -covariates. Note that even if predictions are being made on the training -set, the dataset must be specified. \code{largeRCRF} doesn't keep track of -the dataset after the forest is trained.} +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 +specify it.} \item{parallel}{A logical indicating whether multiple cores should be utilized when making the predictions. Available as an option because it's @@ -23,7 +23,8 @@ get strange errors while predicting.} \item{out.of.bag}{A logical indicating whether predictions should be based on '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{FALSE}.} +on data that was used in the training. Default value is \code{TRUE} if +\code{newData} is \code{NULL}, otherwise \code{FALSE}.} } \value{ A list of responses corresponding with each row of \code{newData} if diff --git a/man/train.Rd b/man/train.Rd index e6beb19..1b08007 100644 --- a/man/train.Rd +++ b/man/train.Rd @@ -15,18 +15,17 @@ train(x, ...) ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 1e+05, splitPureNodes = TRUE, savePath = NULL, savePath.overwrite = c("warn", "delete", "merge"), - cores = getCores(), randomSeed = NULL) + cores = getCores(), randomSeed = NULL, displayProgress = TRUE) -\method{train}{formula}(formula, covariateData, ...) +\method{train}{formula}(formula, data, ...) } \arguments{ \item{responses}{An R list of the responses. See \code{\link{CR_Response}} for an example function.} \item{covariateData}{A data.frame containing only the columns of the -covariates you wish to use in your training (unless you're using the -\code{formula} version of \code{train}, in which case it should contain the -response as well).} +covariates you wish to use in your training (not relevant if you're using +the formula version of \code{train}).} \item{splitFinder}{A split finder that's used to score splits in the random forest training algorithm. See \code{\link{Competing Risk Split Finders}} @@ -80,10 +79,10 @@ number and tree depth is controlled by \code{nodeSize}.} split a pure node. If set to FALSE, then before every split it will check that every response is the same, and if so, not split. If set to TRUE it forgoes that check and splits it. Prediction accuracy won't change under -any sensible \code{nodeResponseCombiner}; as all terminal nodes from a split -pure node should give the same prediction, so this parameter only affects -performance. If your response is continuous you'll likely experience faster -train times by setting it to TRUE. Default value is TRUE.} +any sensible \code{nodeResponseCombiner}; as all terminal nodes from a +split pure node should give the same prediction, so this parameter only +affects performance. If your response is continuous you'll likely +experience faster train times by setting it to TRUE. Default value is TRUE.} \item{savePath}{If set, this parameter will save each tree of the random forest in this directory as the forest is trained. Use this parameter if @@ -103,17 +102,25 @@ a crash.} \item{cores}{This parameter specifies how many trees will be simultaneously trained. By default the package attempts to detect how many cores you have -by using the \code{parallel} package and using all of them. You may -specify a lower number if you wish. It is not recommended to specify a -number greater than the number of available cores as this will hurt -performance with no available benefit.} +by using the \code{parallel} package and using all of them. You may specify +a lower number if you wish. It is not recommended to specify a number +greater than the number of available cores as this will hurt performance +with no available benefit.} \item{randomSeed}{This parameter specifies a random seed if reproducible, deterministic forests are desired.} +\item{displayProgress}{A logical indicating whether the progress should be +displayed to console; default is \code{TRUE}. Useful to set to FALSE in +some automated situations.} + \item{formula}{You may specify the response and covariates as a formula instead; make sure the response in the formula is still properly constructed; see \code{responses}} + +\item{data}{A data.frame containing the columns of the predictors and +responses; not relevant if you're not using the formula version of +\code{train}.} } \value{ A \code{JRandomForest} object. You may call \code{predict} or @@ -133,11 +140,11 @@ from the data (so feel free to not specify them), and \code{splitFinder} can be inferred but you might want to change its default. } \note{ -If saving memory is a concern, you can replace \code{covariateData} - with an environment containing one element called \code{data} as the actual - dataset. After the data has been imported into Java, but before the forest - training begins, the dataset in the environment is deleted, freeing up - memory in R. +If saving memory is a concern, you can replace \code{covariateData} or + \code{data} with an environment containing one element called \code{data} + as the actual dataset. After the data has been imported into Java, but + before the forest training begins, the dataset in the environment is + deleted, freeing up memory in R. } \examples{ # Regression Example diff --git a/tests/testthat/test_adding_new_trees.R b/tests/testthat/test_adding_new_trees.R new file mode 100644 index 0000000..08a1172 --- /dev/null +++ b/tests/testthat/test_adding_new_trees.R @@ -0,0 +1,71 @@ +context("Add trees on existing forest") + +test_that("Can add trees on existing forest", { + + trainingData <- data.frame(x=rnorm(100)) + trainingData$T <- rexp(100) + abs(trainingData$x) + trainingData$delta <- sample(0:2, size = 100, replace=TRUE) + + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) + + predictions <- predict(forest) + + forest.more <- addTrees(forest, 50, cores=2, displayProgress=FALSE) # test multi-core + + predictions <- predict(forest) + + forest.more <- addTrees(forest.more, 50, cores=1, displayProgress=FALSE) # test single-core + + expect_true(T) # show Ok if we got this far + +}) + +test_that("Test adding trees on saved forest - using delete", { + + expect_false(file.exists("trees")) # Folder shouldn't exist yet + + trainingData <- data.frame(x=rnorm(100)) + trainingData$T <- rexp(100) + abs(trainingData$x) + trainingData$delta <- sample(0:2, size = 100, replace=TRUE) + + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, + mtry=1, nodeSize=5, cores=2, + savePath="trees", displayProgress=FALSE + ) + + forest.more <- addTrees(forest, 50, cores=2, savePath = "trees", savePath.overwrite="delete", displayProgress=FALSE) + + predictions <- predict(forest) + + unlink("trees", recursive=TRUE) + + expect_true(T) # show Ok if we got this far + +}) + +test_that("Test adding trees on saved forest - using merge", { + + expect_false(file.exists("trees")) # Folder shouldn't exist yet + + trainingData <- data.frame(x=rnorm(100)) + trainingData$T <- rexp(100) + abs(trainingData$x) + trainingData$delta <- sample(0:2, size = 100, replace=TRUE) + + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, + mtry=1, nodeSize=5, cores=2, + savePath="trees", displayProgress=FALSE + ) + + expect_warning( + addTrees(forest, 50, + cores=2, + savePath = "trees", + savePath.overwrite="merge", + displayProgress=FALSE), + "Assuming that the previous forest at savePath is the provided forest argument; if not true then your results will be suspect" ) + + unlink("trees", recursive=TRUE) + + expect_true(T) # show Ok if we got this far + +}) \ No newline at end of file diff --git a/tests/testthat/test_deterministic_forests.R b/tests/testthat/test_deterministic_forests.R index 7e18231..f03c66f 100644 --- a/tests/testthat/test_deterministic_forests.R +++ b/tests/testthat/test_deterministic_forests.R @@ -9,11 +9,11 @@ test_that("Two forests produce identical results", { data <- data.frame(x1, x2, y) forest1 <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, - randomSeed=5) + randomSeed=5, displayProgress=FALSE) forest2 <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, - randomSeed=5) + randomSeed=5, displayProgress=FALSE) newData <- data.frame(x1=rnorm(10), x2=rnorm(10)) predictions1 <- predict(forest1, newData) @@ -35,15 +35,17 @@ test_that("Finishing an interrupted forest produces the same results as having f data <- data.frame(x1, x2, y) forest1 <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, - randomSeed=6) + randomSeed=6, displayProgress=FALSE) forest2.incomplete <- train(y ~ x1 + x2, data, ntree=50, numberOfSplits = 5, mtry = 1, nodeSize = 5, - randomSeed=6, savePath="trees_deterministic_forests") + randomSeed=6, savePath="trees_deterministic_forests", + displayProgress=FALSE) forest2.complete <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, randomSeed=6, savePath="trees_deterministic_forests", - savePath.overwrite="merge") + savePath.overwrite="merge", + displayProgress=FALSE) newData <- data.frame(x1=rnorm(10), x2=rnorm(10)) @@ -56,3 +58,28 @@ test_that("Finishing an interrupted forest produces the same results as having f unlink("trees_deterministic_forests", recursive=TRUE) }) + +test_that("Adding trees is equivalent to training all at once", { + + x1 <- rnorm(100) + x2 <- rnorm(100) + y <- 1 + x1 + x2 + rnorm(100) + + data <- data.frame(x1, x2, y) + forest1 <- train(y ~ x1 + x2, data, + ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, + randomSeed=5, displayProgress=FALSE) + + forest2 <- train(y ~ x1 + x2, data, + ntree=50, numberOfSplits = 5, mtry = 1, nodeSize = 5, + randomSeed=5, displayProgress=FALSE) + forest2 <- addTrees(forest2, 50, displayProgress=FALSE) + + newData <- data.frame(x1=rnorm(10), x2=rnorm(10)) + predictions1 <- predict(forest1, newData) + predictions2 <- predict(forest2, newData) + + expect_equal(round(predictions1, digits=6), round(predictions2, digits=6)) + + +}) diff --git a/tests/testthat/test_factors.R b/tests/testthat/test_factors.R index ca94e99..4b4b413 100644 --- a/tests/testthat/test_factors.R +++ b/tests/testthat/test_factors.R @@ -10,7 +10,7 @@ test_that("Competing Risks doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(CR_Response(delta, Time) ~ x + z, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(CR_Response(delta, Time) ~ x + z, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) @@ -27,7 +27,7 @@ test_that("Regresssion doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(y ~ x + z, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(y ~ x + z, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) diff --git a/tests/testthat/test_na.R b/tests/testthat/test_na.R index ebf8ab1..ee0e299 100644 --- a/tests/testthat/test_na.R +++ b/tests/testthat/test_na.R @@ -11,7 +11,7 @@ test_that("Competing Risks doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(CR_Response(delta, Time) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(CR_Response(delta, Time) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) @@ -29,7 +29,7 @@ test_that("Regresssion doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(y ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(y ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) diff --git a/tests/testthat/test_predicting_training_data.R b/tests/testthat/test_predicting_training_data.R new file mode 100644 index 0000000..59330f4 --- /dev/null +++ b/tests/testthat/test_predicting_training_data.R @@ -0,0 +1,32 @@ +context("Predict without re-specifying training data") + +test_that("Can predict without new data", { + + trainingData <- data.frame(x=rnorm(100)) + trainingData$T <- rexp(100) + abs(trainingData$x) + trainingData$delta <- sample(0:2, size = 100, replace=TRUE) + + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) + + predictions <- predict(forest) + + expect_true(T) # show Ok if we got this far + +}) + +test_that("Can connect new data", { + + trainingData <- data.frame(x=rnorm(100)) + trainingData$T <- rexp(100) + abs(trainingData$x) + trainingData$delta <- sample(0:2, size = 100, replace=TRUE) + + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) + + forest$dataset <- NULL + forest <- connectToData(forest, CR_Response(trainingData$delta, trainingData$T), trainingData) + + predictions <- predict(forest) + + expect_true(T) # show Ok if we got this far + +}) \ No newline at end of file diff --git a/tests/testthat/test_running.R b/tests/testthat/test_running.R index 34d42e4..b235b61 100644 --- a/tests/testthat/test_running.R +++ b/tests/testthat/test_running.R @@ -9,7 +9,7 @@ test_that("Competing Risks doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(CR_Response(delta, T) ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) @@ -25,7 +25,7 @@ test_that("Regresssion doesn't crash", { testData <- sampleData[1:5,] trainingData <- sampleData[6:100,] - forest <- train(y ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(y ~ x, trainingData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) predictions <- predict(forest, testData) diff --git a/tests/testthat/test_running_environment.R b/tests/testthat/test_running_environment.R index 199de65..1941eab 100644 --- a/tests/testthat/test_running_environment.R +++ b/tests/testthat/test_running_environment.R @@ -13,12 +13,16 @@ test_that("Training with environment works", { e$data <- trainingData rm(trainingData) - forest <- train(CR_Response(delta, T) ~ x, e, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2) + forest <- train(CR_Response(delta, T) ~ x, e, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=2, displayProgress=FALSE) expect_null(e$data) predictions <- predict(forest, testData) + forest <- addTrees(forest, 50, displayProgress = FALSE) + + predictions <- predict(forest, testData) + expect_true(T) # show Ok if we got this far }) diff --git a/tests/testthat/test_saving_loading.R b/tests/testthat/test_saving_loading.R index 19ae578..1d7a425 100644 --- a/tests/testthat/test_saving_loading.R +++ b/tests/testthat/test_saving_loading.R @@ -10,7 +10,8 @@ test_that("Can save & load regression example", { data <- data.frame(x1, x2, y) forest <- train(y ~ x1 + x2, data, - ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5) + ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, + displayProgress=FALSE) saveForest(forest, "trees_saving_loading") diff --git a/tests/testthat/test_saving_offline.R b/tests/testthat/test_saving_offline.R index 9d2ac9b..123d157 100644 --- a/tests/testthat/test_saving_offline.R +++ b/tests/testthat/test_saving_offline.R @@ -11,7 +11,7 @@ test_that("Can save a random forest while training, and use it afterward", { data <- data.frame(x1, x2, y) forest <- train(y ~ x1 + x2, data, ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5, - savePath="trees") + savePath="trees", displayProgress=FALSE) expect_true(file.exists("trees")) # Something should have been saved diff --git a/tests/testthat/test_verify_response_not_used_in_formula.R b/tests/testthat/test_verify_response_not_used_in_formula.R index 7a97d91..72e30f0 100644 --- a/tests/testthat/test_verify_response_not_used_in_formula.R +++ b/tests/testthat/test_verify_response_not_used_in_formula.R @@ -6,7 +6,13 @@ test_that("CompetingRisks - response not included", { sampleData$Time <- rexp(100) + abs(sampleData$x) sampleData$delta <- sample(0:2, size = 100, replace=TRUE) - forest <- train(CR_Response(delta, Time) ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1) + forest <- train(CR_Response(delta, Time) ~ ., sampleData, + ntree=50, + numberOfSplits=0, + mtry=1, + nodeSize=5, + cores=1, + displayProgress=FALSE) expect_equal(rJava::.jcall(forest$covariateList, "I", "size"), 1) @@ -19,7 +25,7 @@ test_that("CompetingRisksWithCensorTimes - response not included", { sampleData$CensorTime <- rexp(100) + abs(sampleData$x) sampleData$delta <- sample(0:2, size = 100, replace=TRUE) - forest <- train(CR_Response(delta, Time, CensorTime) ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1) + forest <- train(CR_Response(delta, Time, CensorTime) ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1, displayProgress=FALSE) expect_equal(rJava::.jcall(forest$covariateList, "I", "size"), 1) @@ -30,7 +36,7 @@ test_that("Regression - response not included", { sampleData <- data.frame(x=rnorm(100)) sampleData$y <- rexp(100) + sampleData$x - forest <- train(y ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1) + forest <- train(y ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1, displayProgress=FALSE) expect_equal(rJava::.jcall(forest$covariateList, "I", "size"), 1) @@ -41,7 +47,7 @@ test_that("Regression - response not included (with Numeric)", { sampleData <- data.frame(x=rnorm(100)) sampleData$y <- rexp(100) + sampleData$x - forest <- train(Numeric(y) ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1) + forest <- train(Numeric(y) ~ ., sampleData, ntree=50, numberOfSplits=0, mtry=1, nodeSize=5, cores=1, displayProgress=FALSE) expect_equal(rJava::.jcall(forest$covariateList, "I", "size"), 1)