Add support for 'offline' forests

NAMESPACE

@@ -26,6 +26,7 @@ export(Numeric)
 export(WeightedVarianceSplitFinder)
 export(addTrees)
 export(connectToData)
+export(convertToOnlineForest)
 export(extractCHF)
 export(extractCIF)
 export(extractMortalities)

R/addTrees.R

@@ -14,6 +14,10 @@
 #' @param savePath.overwrite If \code{savePath} is pointing to an existing
 #'   directory, possibly containing another forest, this specifies what should
 #'   be done.
+#' @param forest.output This parameter only applies if \code{savePath} has been
+#'   set; set to 'online' (default) and the saved forest will be loaded into
+#'   memory after being trained. Set to 'offline' and the forest is not saved
+#'   into memory, but can still be used in a memory unintensive manner.
 #' @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
@@ -22,7 +26,11 @@
 #' @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){
+addTrees <- function(forest, numTreesToAdd, savePath = NULL,
+                     savePath.overwrite = c("warn", "delete", "merge"),
+                     forest.output = c("online", "offline"), 
+                     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")
   }
@@ -37,6 +45,10 @@ addTrees <- function(forest, numTreesToAdd, savePath = NULL, savePath.overwrite
     stop("savePath.overwrite must be one of c(\"warn\", \"delete\", \"merge\")")
   }
   
+  if(is.null(forest.output) | length(forest.output)==0 | !(forest.output[1] %in% c("online", "offline"))){
+    stop("forest.output must be one of c(\"online\", \"offline\")")
+  }
+  
   newTreeCount <- forest$params$ntree + as.integer(numTreesToAdd)
   
   treeTrainer <- createTreeTrainer(responseCombiner=forest$params$nodeResponseCombiner,
@@ -98,22 +110,23 @@ addTrees <- function(forest, numTreesToAdd, savePath = NULL, savePath.overwrite
                          params=params,
                          forestCall=match.call())
     
+    forest.java <- NULL
     if(cores > 1){
-      .jcall(forestTrainer, "V", "trainParallelOnDisk", initial.forest.optional, as.integer(cores))
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OfflineForest), "trainParallelOnDisk", initial.forest.optional, as.integer(cores))
     } else {
-      .jcall(forestTrainer, "V", "trainSerialOnDisk", initial.forest.optional)
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OfflineForest), "trainSerialOnDisk", initial.forest.optional)
     }
     
-    # Need to now load forest trees back into memory
+    if(forest.output[1] == "online"){
-    forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", savePath, forest$params$forestResponseCombiner$javaObject)
+      forest.java <- convertToOnlineForest.Java(forest.java)
-    
+    }
     
   }
   else{ # save directly into memory
     if(cores > 1){
-      forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", initial.forest.optional, as.integer(cores))
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OnlineForest), "trainParallelInMemory", initial.forest.optional, as.integer(cores))
     } else {
-      forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory", initial.forest.optional)
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OnlineForest), "trainSerialInMemory", initial.forest.optional)
     }
   }
   

R/convertToOnlineForest.R

@@ -0,0 +1,38 @@
+
+#' Convert to Online Forest
+#'
+#' Some forests are too large to store in memory and have been saved to disk.
+#' They can still be used, but their performance is much slower. If there's
+#' enough memory, they can easily be converted into an in-memory forest that is
+#' faster to use.
+#'
+#' @param forest The offline forest.
+#'
+#' @return An online, in memory forst.
+#' @export
+#' 
+convertToOnlineForest <- function(forest){
+  old.forest.object <- forest$javaObject
+  
+  if(getJavaClass(old.forest.object) == "ca.joeltherrien.randomforest.tree.OnlineForest"){
+    
+    warning("forest is already in-memory")
+    return(forest)
+    
+  } else if(getJavaClass(old.forest.object) == "ca.joeltherrien.randomforest.tree.OfflineForest"){
+    
+    forest$javaObject <- convertToOnlineForest.Java(old.forest.object)
+    return(forest)
+    
+  } else{
+    stop("'forest' is not an online or offline forest")
+  }
+  
+}
+
+# Internal function
+convertToOnlineForest.Java <- function(forest.java){
+  offline.forest <- .jcast(forest.java, .class_OfflineForest)
+  online.forest <- .jcall(offline.forest, makeResponse(.class_OnlineForest), "createOnlineCopy")
+  return(online.forest)
+}

R/cr_components.R

@@ -42,7 +42,7 @@ CR_FunctionCombiner <- function(events, times = NULL){
   }
 
   javaObject <- .jnew(.class_CompetingRiskFunctionCombiner, eventArray, timeArray)
-  javaObject <- .jcast(javaObject, .class_ResponseCombiner)
+  javaObject <- .jcast(javaObject, .class_ForestResponseCombiner)
 
   combiner <- list(javaObject=javaObject,
                    call=match.call(),

R/java_classes_directory.R

@@ -11,6 +11,7 @@
 .class_Serializable <- "java/io/Serializable"
 .class_File <- "java/io/File"
 .class_Random <- "java/util/Random"
+.class_Class <- "java/lang/Class"
 
 # Utility Classes
 .class_DataUtils <- "ca/joeltherrien/randomforest/utils/DataUtils"
@@ -41,9 +42,12 @@
 
 # Forest class
 .class_Forest <- "ca/joeltherrien/randomforest/tree/Forest"
+.class_OnlineForest <- "ca/joeltherrien/randomforest/tree/OnlineForest"
+.class_OfflineForest <- "ca/joeltherrien/randomforest/tree/OfflineForest"
 
 # ResponseCombiner classes
 .class_ResponseCombiner <- "ca/joeltherrien/randomforest/tree/ResponseCombiner"
+.class_ForestResponseCombiner <- "ca/joeltherrien/randomforest/tree/ForestResponseCombiner"
 .class_CompetingRiskResponseCombiner <- "ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskResponseCombiner"
 .class_CompetingRiskFunctionCombiner <- "ca/joeltherrien/randomforest/responses/competingrisk/combiner/CompetingRiskFunctionCombiner"
 .class_MeanResponseCombiner <- "ca/joeltherrien/randomforest/responses/regression/MeanResponseCombiner"
@@ -77,4 +81,10 @@
 # This function does that.
 makeResponse <- function(className){
   return(paste0("L", className, ";"))
-}
+}
+
+getJavaClass <- function(object){
+  class <- .jcall(object, makeResponse(.class_Class), "getClass")
+  className <- .jcall(class, "S", "getName")
+  return(className)
+}

R/loadForest.R

@@ -5,6 +5,12 @@
 #' Loads a random forest that was saved using \code{\link{saveForest}}.
 #'
 #' @param directory The directory created that saved the previous forest.
+#' @param forest.output Specifies whether the forest loaded should be loaded
+#'   into memory, or reflect the saved files where only one tree is loaded at a
+#'   time.
+#' @param maxTreeNum If for some reason you only want to load the number of
+#'   trees up until a certain point, you can specify maxTreeNum as a single
+#'   number.
 #' @return A JForest object; see \code{\link{train}} for details.
 #' @export
 #' @seealso \code{\link{train}}, \code{\link{saveForest}}
@@ -20,7 +26,11 @@
 #'
 #' saveForest(forest, "trees")
 #' new_forest <- loadForest("trees")
-loadForest <- function(directory){
+loadForest <- function(directory, forest.output = c("online", "offline"), maxTreeNum = NULL){
+  
+  if(is.null(forest.output) | length(forest.output)==0 | !(forest.output[1] %in% c("online", "offline"))){
+    stop("forest.output must be one of c(\"online\", \"offline\")")
+  }
   
   # First load the response combiners and the split finders
   nodeResponseCombiner.java <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/nodeResponseCombiner.jData"))
@@ -30,7 +40,7 @@ loadForest <- function(directory){
   splitFinder.java <- .jcast(splitFinder.java, .class_SplitFinder)
   
   forestResponseCombiner.java <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/forestResponseCombiner.jData"))
-  forestResponseCombiner.java <- .jcast(forestResponseCombiner.java, .class_ResponseCombiner)
+  forestResponseCombiner.java <- .jcast(forestResponseCombiner.java, .class_ForestResponseCombiner)
   
   covariateList <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/covariateList.jData"))
   covariateList <- .jcast(covariateList, .class_List)
@@ -42,8 +52,11 @@ loadForest <- function(directory){
   params$splitFinder$javaObject <- splitFinder.java
   params$forestResponseCombiner$javaObject <- forestResponseCombiner.java
   
-  forest <- loadForestArgumentsSpecified(directory, params$nodeResponseCombiner, params$splitFinder, params$forestResponseCombiner, covariateList, call,
+  forest <- loadForestArgumentsSpecified(directory, params$nodeResponseCombiner, params$splitFinder, 
-                                      params$ntree, params$numberOfSplits, params$mtry, params$nodeSize, params$maxNodeDepth, params$splitPureNodes, params$randomSeed)
+                                         params$forestResponseCombiner, covariateList, call,
+                                         params$ntree, params$numberOfSplits, params$mtry,
+                                         params$nodeSize, params$maxNodeDepth, params$splitPureNodes,
+                                         params$randomSeed, forest.output, maxTreeNum)
   
   return(forest)
   
@@ -55,8 +68,11 @@ loadForest <- function(directory){
 # that uses the Java version's settings yaml file to recreate the forest, but
 # I'd appreciate knowing that someone's going to use it first (email me; see
 # README).
-loadForestArgumentsSpecified <- function(treeDirectory, nodeResponseCombiner, splitFinder, forestResponseCombiner, 
+loadForestArgumentsSpecified <- function(treeDirectory, nodeResponseCombiner, splitFinder,
-                                 covariateList.java, call, ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE, randomSeed=NULL){
+                                         forestResponseCombiner, covariateList.java, call,
+                                         ntree, numberOfSplits, mtry, nodeSize,
+                                         maxNodeDepth = 100000, splitPureNodes=TRUE,
+                                         randomSeed=NULL, forest.output = "online", maxTreeNum = NULL){
   
   params <- list(
     splitFinder=splitFinder,
@@ -71,7 +87,33 @@ loadForestArgumentsSpecified <- function(treeDirectory, nodeResponseCombiner, sp
     randomSeed=randomSeed
   )
   
-  forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", treeDirectory, forestResponseCombiner$javaObject)
+  forest.java <- NULL
+  if(forest.output[1] == "online"){
+    castedForestResponseCombiner <- .jcast(forestResponseCombiner$javaObject, .class_ResponseCombiner) # OnlineForest constructor takes a ResponseCombiner
+    
+    if(is.null(maxTreeNum)){
+      forest.java <- .jcall(.class_DataUtils, makeResponse(.class_OnlineForest), "loadOnlineForest",
+                            treeDirectory, castedForestResponseCombiner)
+    } else{
+      tree.file.array <- .jcall(.class_RUtils, paste0("[", makeResponse(.class_File)), "getTreeFileArray", 
+                                treeDirectory, as.integer(maxTreeNum), evalArray = FALSE)
+      forest.java <- .jcall(.class_DataUtils, makeResponse(.class_OnlineForest), "loadOnlineForest",
+                            tree.file.array, castedForestResponseCombiner)
+      
+    }
+    
+  } else{ # offline forest
+    if(is.null(maxTreeNum)){
+      path.as.file <- .jnew(.class_File, treeDirectory)
+      forest.java <- .jnew(.class_OfflineForest, path.as.file, forestResponseCombiner$javaObject)
+    } else{
+      tree.file.array <- .jcall(.class_RUtils, paste0("[", makeResponse(.class_File)), "getTreeFileArray", 
+                                treeDirectory, as.integer(maxTreeNum), evalArray = FALSE)
+      forest.java <- .jnew(.class_OfflineForest, tree.file.array, forestResponseCombiner$javaObject)
+    }
+  }
+  
+  
   
   forestObject <- list(call=call, javaObject=forest.java, covariateList=covariateList.java, params=params)
   class(forestObject) <- "JRandomForest"

R/regressionComponents.R

@@ -48,7 +48,7 @@ WeightedVarianceSplitFinder <- function(){
 #'
 MeanResponseCombiner <- function(){
   javaObject <- .jnew(.class_MeanResponseCombiner)
-  javaObject <- .jcast(javaObject, .class_ResponseCombiner)
+  javaObject <- .jcast(javaObject, .class_ForestResponseCombiner)
 
   combiner <- list(javaObject=javaObject, call=match.call(), outputClass="numeric")
   combiner$convertToRFunction <- function(javaObject, ...){

R/train.R

@@ -18,7 +18,7 @@ train.internal <- function(dataset, splitFinder,
                            nodeResponseCombiner, forestResponseCombiner, ntree, 
                            numberOfSplits, mtry, nodeSize, maxNodeDepth, 
                            splitPureNodes, savePath, savePath.overwrite, 
-                           cores, randomSeed, displayProgress){
+                           forest.output, cores, randomSeed, displayProgress){
   
   # Some quick checks on parameters
   ntree <- as.integer(ntree)
@@ -51,6 +51,10 @@ train.internal <- function(dataset, splitFinder,
     stop("savePath.overwrite must be one of c(\"warn\", \"delete\", \"merge\")")
   }
   
+  if(is.null(forest.output) | length(forest.output)==0 | !(forest.output[1] %in% c("online", "offline"))){
+    stop("forest.output must be one of c(\"online\", \"offline\")")
+  }
+  
   if(is.null(splitFinder)){
     splitFinder <- splitFinderDefault(dataset$responses)
   }
@@ -129,22 +133,23 @@ train.internal <- function(dataset, splitFinder,
                          params=params,
                          forestCall=match.call())
     
+    forest.java <- NULL
     if(cores > 1){
-      .jcall(forestTrainer, "V", "trainParallelOnDisk", .object_Optional(), as.integer(cores))
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OfflineForest), "trainParallelOnDisk", .object_Optional(), as.integer(cores))
     } else {
-      .jcall(forestTrainer, "V", "trainSerialOnDisk", .object_Optional())
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OfflineForest), "trainSerialOnDisk", .object_Optional())
     }
     
-    # Need to now load forest trees back into memory
+    if(forest.output[1] == "online"){
-    forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", savePath, forestResponseCombiner$javaObject)
+      forest.java <- convertToOnlineForest.Java(forest.java)
-    
+    }
-    
+
   }
   else{ # save directly into memory
     if(cores > 1){
-      forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", .object_Optional(), as.integer(cores))
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OnlineForest), "trainParallelInMemory", .object_Optional(), as.integer(cores))
     } else {
-      forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory", .object_Optional())
+      forest.java <- .jcall(forestTrainer, makeResponse(.class_OnlineForest), "trainSerialInMemory", .object_Optional())
     }
   }
   
@@ -253,6 +258,10 @@ train.internal <- function(dataset, splitFinder,
 #'   assumes (without checking) that the existing trees are from a previous run
 #'   and starts from where it left off. This option is useful if recovering from
 #'   a crash.
+#' @param forest.output This parameter only applies if \code{savePath} has been
+#'   set; set to 'online' (default) and the saved forest will be loaded into
+#'   memory after being trained. Set to 'offline' and the forest is not saved
+#'   into memory, but can still be used in a memory unintensive manner.
 #' @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
@@ -311,7 +320,8 @@ train.internal <- function(dataset, splitFinder,
 train <- function(formula, data, splitFinder = NULL, nodeResponseCombiner = NULL,
                   forestResponseCombiner = NULL, ntree, numberOfSplits, mtry,
                   nodeSize, maxNodeDepth = 100000, na.penalty = TRUE, splitPureNodes=TRUE, 
-                  savePath=NULL, savePath.overwrite=c("warn", "delete", "merge"), 
+                  savePath = NULL, savePath.overwrite = c("warn", "delete", "merge"), 
+                  forest.output = c("online", "offline"),
                   cores = getCores(), randomSeed = NULL, displayProgress = TRUE){
   
   dataset <- processFormula(formula, data, na.penalty = na.penalty)
@@ -322,8 +332,8 @@ train <- function(formula, data, splitFinder = NULL, nodeResponseCombiner = NULL
                            ntree = ntree, numberOfSplits = numberOfSplits,
                            mtry = mtry, nodeSize = nodeSize, maxNodeDepth = maxNodeDepth,
                            splitPureNodes = splitPureNodes, savePath = savePath,
-                           savePath.overwrite = savePath.overwrite, cores = cores,
+                           savePath.overwrite = savePath.overwrite, forest.output = forest.output,
-                           randomSeed = randomSeed, displayProgress = displayProgress)
+                           cores = cores, randomSeed = randomSeed, displayProgress = displayProgress)
   
   forest$call <- match.call()
   forest$formula <- formula
@@ -370,8 +380,10 @@ createTreeTrainer <- function(responseCombiner, splitFinder, covariateList, numb
   builderClassReturned <- makeResponse(.class_TreeTrainer_Builder)
 
   builder <- .jcall(.class_TreeTrainer, builderClassReturned, "builder")
-
+  
-  builder <- .jcall(builder, builderClassReturned, "responseCombiner", responseCombiner$javaObject)
+  responseCombinerCasted <- .jcast(responseCombiner$javaObject, .class_ResponseCombiner) # might need to cast a ForestResponseCombiner down
+  
+  builder <- .jcall(builder, builderClassReturned, "responseCombiner", responseCombinerCasted)
   builder <- .jcall(builder, builderClassReturned, "splitFinder", splitFinder$javaObject)
   builder <- .jcall(builder, builderClassReturned, "covariates", covariateList)
   builder <- .jcall(builder, builderClassReturned, "numberOfSplits", as.integer(numberOfSplits))

man/addTrees.Rd

@@ -6,7 +6,8 @@
 \usage{
 addTrees(forest, numTreesToAdd, savePath = NULL,
   savePath.overwrite = c("warn", "delete", "merge"),
-  cores = getCores(), displayProgress = TRUE)
+  forest.output = c("online", "offline"), cores = getCores(),
+  displayProgress = TRUE)
 }
 \arguments{
 \item{forest}{An existing forest.}
@@ -21,6 +22,11 @@ a previously saved forest.}
 directory, possibly containing another forest, this specifies what should
 be done.}
 
+\item{forest.output}{This parameter only applies if \code{savePath} has been
+set; set to 'online' (default) and the saved forest will be loaded into
+memory after being trained. Set to 'offline' and the forest is not saved
+into memory, but can still be used in a memory unintensive manner.}
+
 \item{cores}{The number of cores to be used for training the new trees.}
 
 \item{displayProgress}{A logical indicating whether the progress should be

man/convertToOnlineForest.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convertToOnlineForest.R
+\name{convertToOnlineForest}
+\alias{convertToOnlineForest}
+\title{Convert to Online Forest}
+\usage{
+convertToOnlineForest(forest)
+}
+\arguments{
+\item{forest}{The offline forest.}
+}
+\value{
+An online, in memory forst.
+}
+\description{
+Some forests are too large to store in memory and have been saved to disk.
+They can still be used, but their performance is much slower. If there's
+enough memory, they can easily be converted into an in-memory forest that is
+faster to use.
+}

man/loadForest.Rd

@@ -4,10 +4,19 @@
 \alias{loadForest}
 \title{Load Random Forest}
 \usage{
-loadForest(directory)
+loadForest(directory, forest.output = c("online", "offline"),
+  maxTreeNum = NULL)
 }
 \arguments{
 \item{directory}{The directory created that saved the previous forest.}
+
+\item{forest.output}{Specifies whether the forest loaded should be loaded
+into memory, or reflect the saved files where only one tree is loaded at a
+time.}
+
+\item{maxTreeNum}{If for some reason you only want to load the number of
+trees up until a certain point, you can specify maxTreeNum as a single
+number.}
 }
 \value{
 A JForest object; see \code{\link{train}} for details.

man/train.Rd

@@ -8,7 +8,8 @@ train(formula, data, splitFinder = NULL, nodeResponseCombiner = NULL,
   forestResponseCombiner = NULL, ntree, numberOfSplits, mtry, nodeSize,
   maxNodeDepth = 1e+05, na.penalty = TRUE, splitPureNodes = TRUE,
   savePath = NULL, savePath.overwrite = c("warn", "delete", "merge"),
-  cores = getCores(), randomSeed = NULL, displayProgress = TRUE)
+  forest.output = c("online", "offline"), cores = getCores(),
+  randomSeed = NULL, displayProgress = TRUE)
 }
 \arguments{
 \item{formula}{You may specify the response and covariates as a formula
@@ -106,6 +107,11 @@ assumes (without checking) that the existing trees are from a previous run
 and starts from where it left off. This option is useful if recovering from
 a crash.}
 
+\item{forest.output}{This parameter only applies if \code{savePath} has been
+set; set to 'online' (default) and the saved forest will be loaded into
+memory after being trained. Set to 'offline' and the forest is not saved
+into memory, but can still be used in a memory unintensive manner.}
+
 \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

tests/testthat/test_adding_new_trees.R

@@ -1,6 +1,6 @@
 context("Add trees on existing forest")
 
-test_that("Can add trees on existing forest", {
+test_that("Can add trees on existing online forest", {
 
   trainingData <- data.frame(x=rnorm(100))
   trainingData$T <- rexp(100) + abs(trainingData$x)
@@ -20,6 +20,44 @@ test_that("Can add trees on existing forest", {
   
 })
 
+test_that("Can add trees on existing offline forest", {
+  
+  if(file.exists("trees")){ # folder could exist from a previous failed test; delete it
+    unlink("trees", recursive=TRUE)
+  }
+  
+  
+  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, 
+                  forestResponseCombiner = CR_FunctionCombiner(events = 1:2, times = 0:10), # TODO - remove specifing times; this is workaround around unimplemented feature for offline forests
+                  cores=2, displayProgress=FALSE, savePath="trees",
+                  forest.output = "offline")
+  warning("TODO - need to implement feature; test workaround in the meantime")
+  
+  predictions <- predict(forest)
+  
+  warning_message <- "Assuming that the previous forest at savePath is the provided forest argument; if not true then your results will be suspect"
+  
+  forest.more <- expect_warning(addTrees(forest, 50, cores=2, displayProgress=FALSE,
+                          savePath="trees", savePath.overwrite = "merge",
+                          forest.output = "offline"), fixed=warning_message) # test multi-core
+  
+  predictions <- predict(forest)
+  
+  forest.more <- expect_warning(addTrees(forest, 50, cores=1, displayProgress=FALSE,
+                                         savePath="trees", savePath.overwrite = "merge",
+                                         forest.output = "offline"), fixed=warning_message) # test single-core
+  
+  expect_true(T) # show Ok if we got this far
+  
+  unlink("trees", recursive=TRUE)
+  
+})
+
 test_that("Test adding trees on saved forest - using delete", {
   
   if(file.exists("trees")){ # folder could exist from a previous failed test; delete it

tests/testthat/test_saving_loading.R

@@ -2,7 +2,11 @@ context("Train, save, and load without error")
 
 test_that("Can save & load regression example", {
 
-  expect_false(file.exists("trees_saving_loading")) # Folder shouldn't exist yet
+  if(file.exists("trees_saving_loading")){
+    unlink("trees_saving_loading", recursive=TRUE)
+  }
+  
+  expect_false(file.exists("trees_saving_loading")) # Folder shouldn't exist at this point
   
   x1 <- rnorm(1000)
   x2 <- rnorm(1000)

tests/testthat/test_saving_offline.R

@@ -13,7 +13,7 @@ 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", displayProgress=FALSE)
+                  savePath="trees", forest.output = "online", displayProgress=FALSE)
   
   expect_true(file.exists("trees")) # Something should have been saved
   
@@ -26,6 +26,39 @@ test_that("Can save a random forest while training, and use it afterward", {
   predictions <- predict(newforest, newData)
   
   
+  unlink("trees", recursive=TRUE)
+  
+})
+
+test_that("Can save a random forest while training, and use it afterward with pure offline forest", {
+  
+  if(file.exists("trees")){ # folder could exist from a previous failed test; delete it
+    unlink("trees", recursive=TRUE)
+  }
+  
+  x1 <- rnorm(1000)
+  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, mtry = 1, nodeSize = 5,
+                  savePath="trees", forest.output = "offline", displayProgress=FALSE)
+  
+  expect_true(file.exists("trees")) # Something should have been saved
+  
+  # try making a little prediction to verify it works
+  newData <- data.frame(x1=seq(from=-3, to=3, by=0.5), x2=0)
+  predictions <- predict(forest, newData)
+  
+  # Also make sure we can load the forest too
+  newforest <- loadForest("trees")
+  predictions <- predict(newforest, newData)
+  
+  # Last, make sure we can take the forest online
+  onlineForest <- convertToOnlineForest(forest)
+  predictions <- predict(onlineForest, newData)
+  
   unlink("trees", recursive=TRUE)
   
 })