From 9217c72cf9d6c9700ca078bb4ba3d8ead0cdbc1e Mon Sep 17 00:00:00 2001 From: Joel Therrien Date: Fri, 31 May 2019 15:13:24 -0700 Subject: [PATCH] Initial commit for pre-release development version --- .Rbuildignore | 2 + .gitignore | 3 + DESCRIPTION | 19 + NAMESPACE | 39 ++ R/CR_Response.R | 106 +++++ R/Numeric.R | 25 ++ R/cr_components.R | 202 +++++++++ R/cr_naiveConcordance.R | 52 +++ R/cr_predictions.R | 142 ++++++ R/create_java_covariates.R | 57 +++ R/defaults.R | 52 +++ R/java_classes_directory.R | 57 +++ R/loadData.R | 83 ++++ R/load_forest.R | 75 ++++ R/misc.R | 101 +++++ R/predict.R | 96 ++++ R/recover_forest.R | 37 ++ R/regressionComponents.R | 80 ++++ R/save_forest.R | 94 ++++ R/train.R | 417 ++++++++++++++++++ R/wrapFunction.R | 12 + R/zzz.R | 7 + .../randomforest/Bootstrapper.class | Bin 0 -> 1273 bytes .../randomforest/CovariateRow.class | Bin 0 -> 4467 bytes .../ca/joeltherrien/randomforest/Main.class | Bin 0 -> 11299 bytes .../ca/joeltherrien/randomforest/Row.class | Bin 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tests/testthat/test_cr_naive_concordance.R | 14 + tests/testthat/test_creating_cr_components.R | 17 + tests/testthat/test_deterministic_forests.R | 58 +++ tests/testthat/test_factors.R | 36 ++ tests/testthat/test_na.R | 38 ++ tests/testthat/test_responses_length_1.R | 17 + tests/testthat/test_running.R | 34 ++ tests/testthat/test_running_environment.R | 24 + tests/testthat/test_saving_loading.R | 26 ++ tests/testthat/test_saving_offline.R | 29 ++ ...test_verify_response_not_used_in_formula.R | 48 ++ 1170 files changed, 2798 insertions(+) create mode 100644 .Rbuildignore create mode 100644 .gitignore create mode 100644 DESCRIPTION create mode 100644 NAMESPACE create mode 100644 R/CR_Response.R create mode 100644 R/Numeric.R create mode 100644 R/cr_components.R create mode 100644 R/cr_naiveConcordance.R create mode 100644 R/cr_predictions.R create mode 100644 R/create_java_covariates.R create mode 100644 R/defaults.R create mode 100644 R/java_classes_directory.R create mode 100644 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inst/java/org/yaml/snakeyaml/util/UriEncoder.class create mode 100644 man/CR_FunctionCombiner.Rd create mode 100644 man/CR_Response.Rd create mode 100644 man/CR_ResponseCombiner.Rd create mode 100644 man/CompetingRiskPredictions.Rd create mode 100644 man/CompetingRiskSplitFinders.Rd create mode 100644 man/MeanResponseCombiner.Rd create mode 100644 man/Numeric.Rd create mode 100644 man/WeightedVarianceSplitFinder.Rd create mode 100644 man/convertRListToJava.Rd create mode 100644 man/load_forest.Rd create mode 100644 man/naiveConcordance.Rd create mode 100644 man/predict.JRandomForest.Rd create mode 100644 man/save_forest.Rd create mode 100644 man/train.Rd create mode 100644 tests/testthat.R create mode 100644 tests/testthat/test_cr_naive_concordance.R create mode 100644 tests/testthat/test_creating_cr_components.R create mode 100644 tests/testthat/test_deterministic_forests.R create mode 100644 tests/testthat/test_factors.R create mode 100644 tests/testthat/test_na.R create mode 100644 tests/testthat/test_responses_length_1.R create mode 100644 tests/testthat/test_running.R create mode 100644 tests/testthat/test_running_environment.R create mode 100644 tests/testthat/test_saving_loading.R create mode 100644 tests/testthat/test_saving_offline.R create mode 100644 tests/testthat/test_verify_response_not_used_in_formula.R diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..861651b --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +*.Rproj +.Rproj.user +copyJar diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..2188eef --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,19 @@ +Package: largeRCRF +Type: Package +Title: Large Random Competing Risk Forests, Java Implementation Run in R +Version: 0.0.0.9036 +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), + and some simple error analysis using concordance measures. +License: GPL-3 +Encoding: UTF-8 +LazyData: true +Imports: + rJava (>= 0.9-9) +Suggests: + parallel, + testthat +Depends: R (>= 3.4.2) +SystemRequirements: Java JDK 1.8 or higher +RoxygenNote: 6.1.1 diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..0892a93 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,39 @@ +# Generated by roxygen2: do not edit by hand + +S3method(extractCHF,CompetingRiskFunctions) +S3method(extractCHF,CompetingRiskFunctions.List) +S3method(extractCIF,CompetingRiskFunctions) +S3method(extractCIF,CompetingRiskFunctions.List) +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) +S3method(print,JRandomForest) +S3method(print,ResponseCombiner) +S3method(print,SplitFinder) +S3method(train,default) +S3method(train,formula) +export(CR_FunctionCombiner) +export(CR_Response) +export(CR_ResponseCombiner) +export(GrayLogRankSplitFinder) +export(LogRankSplitFinder) +export(MeanResponseCombiner) +export(Numeric) +export(WeightedVarianceSplitFinder) +export(convertRListToJava) +export(extractCHF) +export(extractCIF) +export(extractMortalities) +export(extractSurvivorCurve) +export(load_covariate_list_from_settings) +export(load_forest) +export(load_forest_args_provided) +export(naiveConcordance) +export(save_forest) +export(train) +import(rJava) diff --git a/R/CR_Response.R b/R/CR_Response.R new file mode 100644 index 0000000..e4be1a5 --- /dev/null +++ b/R/CR_Response.R @@ -0,0 +1,106 @@ + +#' Competing Risk Response +#' +#' Takes vectors of event time and event type and turns it into the internal +#' objects used throughout the package. The result of this function shouldn't be +#' used directly, but should instead by provided as the \code{y} parameter in +#' \code{\link{train}}. +#' +#' @param delta A vector of integers detailing the event that occurred. A value +#' of 0 denotes that censoring occurred first and that time was recorded. +#' @param u A vector of numerics detailing the recorded event times (possibly +#' censored). +#' @param C If the censoring times are known for all observations, they can be +#' included which allows for \code{\link{GrayLogRankSplitFinder}} to be used. +#' Default is \code{NULL}. +#' +#' @details To be clear, if T1,...TJ are the J different competing risks, and C +#' is the censoring time, then \code{u[i] = min(T1[i], ...TJ[i], C[i])}; and +#' \code{delta[i]} denotes which time was the minimum, with a value of 0 if +#' C[i] was the smallest. +#' @export +#' @examples +#' T1 <- rexp(10) +#' T2 <- rweibull(10, 2, 2) +#' C <- rexp(10) +#' +#' u <- pmin(T1, T2, C) +#' delta <- ifelse(u == T1, 1, ifelse(u == T2, 2, 0)) +#' +#' responses <- CR_Response(delta, u) +#' # Then use responses in train +CR_Response <- function(delta, u, C = NULL){ + if(is.null(C)){ + return(Java_CompetingRiskResponses(delta, u)) + } else{ + return(Java_CompetingRiskResponsesWithCensorTimes(delta, u, C)) + } +} + + +# Internal function +Java_CompetingRiskResponses <- function(delta, u){ + + if(length(delta) != length(u)){ + stop("delta and u must be of the same length") + } + + if(anyNA(delta) | is.null(delta)){ + stop("delta must be specified") + } + + if(anyNA(u) | is.null(u)){ + stop("u must be specified") + } + + delta <- as.integer(delta) + u <- as.double(u) + + delta.java <- .jarray(delta, contents.class="I") + u.java <- .jarray(u, contents.class="D") + + responses.java.list <- .jcall(.class_RUtils, makeResponse(.class_List), + "importCompetingRiskResponses", delta.java, u.java) + + responses <- list(javaObject=responses.java.list, eventIndicator=delta, eventTime=u) + class(responses) <- "CompetingRiskResponses" + + return(responses) +} + +# Internal function +Java_CompetingRiskResponsesWithCensorTimes <- function(delta, u, C){ + + if(length(delta) != length(u) | length(u) != length(C)){ + stop("delta, u, and C must be of the same length") + } + + if(anyNA(delta) | is.null(delta)){ + stop("delta must be specified") + } + + if(anyNA(u) | is.null(u)){ + stop("u must be specified") + } + + if(anyNA(C) | is.null(C)){ + stop("C must be specified") + } + + delta <- as.integer(delta) + u <- as.double(u) + C <- as.double(C) + + delta.java <- .jarray(delta, contents.class="I") + u.java <- .jarray(u, contents.class="D") + C.java <- .jarray(C, contents.class="D") + + responses.java.list <- .jcall(.class_RUtils, makeResponse(.class_List), + "importCompetingRiskResponsesWithCensorTimes", delta.java, u.java, C.java) + + responses <- list(javaObject=responses.java.list, eventIndicator=delta, eventTime=u, censorTime=C) + class(responses) <- "CompetingRiskResponsesWithCensorTimes" + + return(responses) +} + diff --git a/R/Numeric.R b/R/Numeric.R new file mode 100644 index 0000000..6eadf01 --- /dev/null +++ b/R/Numeric.R @@ -0,0 +1,25 @@ + +#' Numeric +#' +#' An internal function that converts an R vector of numerics or integers into an R list containing java.lang.Double objects. This method does not need to be used directly by the user, as \code{\link{train}} will automatically handle numeric responses if you're working in the regression settings. +#' @param y The R vector of numbers +#' @export +#' @return An R list containing rJava Doubles. +#' @keywords internal +#' @examples +#' x <- Numeric(1:5) +#' class(x[[1]]) +Numeric <- function(y){ + y <- as.double(y) + + javaList <- .jcall(.class_RUtils, + makeResponse(.class_List), + "importNumericResponse", + y) + + responses <- list(javaObject=javaList, y=y) + + class(responses) <- "JNumeric" + + return(responses) +} diff --git a/R/cr_components.R b/R/cr_components.R new file mode 100644 index 0000000..19c70c8 --- /dev/null +++ b/R/cr_components.R @@ -0,0 +1,202 @@ + +#' Competing Risk Function Combiner +#' +#' Creates a CompetingRiskFunctionCombiner rJava object, which is used +#' internally for constructing a forest. The forest uses it when creating +#' predictions to average the cumulative incidence curves, cause-specific +#' cumulative hazard functions, and Kaplan-Meier curves generated by each tree +#' into individual functions. +#' +#' The user only needs to pass this object into \code{\link{train}} as the +#' \code{forestResponseCombiner} parameter. +#' +#' @return A response combiner object to be used in \code{\link{train}}; not +#' useful on its own. However, internally, a response combiner object is a +#' list consisting of the following objects: \describe{ +#' \item{\code{javaObject}}{The java object used in the algorithm} +#' \item{\code{call}}{The call (used in \code{print})} +#' \item{\code{outputClass}}{The R class of the outputs; used in +#' \code{\link{predict.JRandomForest}}} \item{\code{convertToRFunction}}{An R +#' function that converts a Java prediction from the combiner into R output +#' that is readable by a user.} } +#' +#' @param events A vector of integers specifying which competing risk events's +#' functions should be processed. This should correspond to all of the +#' competing risk events that can occur, from 1 to the largest number. +#' @param times An optional numeric vector that forces the output functions to +#' only update at these time points. Pre-specifying the values can result in +#' faster performance when predicting, however if the times are not exhaustive +#' then the resulting curves will not update at that point (they'll be flat). +#' If left blank, the package will default to using all of the time points. +#' @export +#' @examples +#' T1 <- rexp(1000) +#' T2 <- rweibull(1000, 1, 2) +#' C <- rexp(1000) +#' +#' u <- round(pmin(T1, T2, C)) +#' # ... +#' +#' forestCombiner <- CR_FunctionCombiner(1:2) # there are two possible events +#' # or, since we know that u is always an integer +#' forestCombiner <- CR_FunctionCombiner(1:2, 0:max(u)) +CR_FunctionCombiner <- function(events, times = NULL){ + # need to first change events into array of int + eventArray <- .jarray(events, "I") + + if(is.null(times)){ + timeArray <- .jnull(class="[D") + } + else{ + timeArray <- .jarray(as.numeric(times), "D") + } + + javaObject <- .jnew(.class_CompetingRiskFunctionCombiner, eventArray, timeArray) + javaObject <- .jcast(javaObject, .class_ResponseCombiner) + + combiner <- list(javaObject=javaObject, + call=match.call(), + events=events, + outputClass="CompetingRiskFunctions", + convertToRFunction=convertCompetingRiskFunctions) + class(combiner) <- "ResponseCombiner" + + return(combiner) +} + +#' Competing Risk Response Combiner +#' +#' Creates a CompetingRiskResponseCombiner rJava object, which is used +#' internally for constructing a forest. It is used when each tree in the forest +#' is constructed, as it combines response level information (u & delta) into +#' functions such as cumulative incidence curves, cause-specific cumulative +#' hazard functions, and an overall Kaplan-Meier curve. This combination is done +#' for each terminal node for each tree. +#' +#' The user only needs to pass this object into \code{\link{train}} as the +#' \code{nodeResponseCombiner} parameter. +#' +#' @return A response combiner object to be used in \code{\link{train}}; not +#' useful on its own. However, internally, a response combiner object is a +#' list consisting of the following objects: \describe{ +#' \item{\code{javaObject}}{The java object used in the algorithm} +#' \item{\code{call}}{The call (used in \code{print})} +#' \item{\code{outputClass}}{The R class of the outputs; used in +#' \code{\link{predict.JRandomForest}}} \item{\code{convertToRFunction}}{An R +#' function that converts a Java prediction from the combiner into R output +#' that is readable by a user.} } +#' +#' @param events A vector of integers specifying which competing risk events's +#' functions should be processed. This should correspond to all of the +#' competing risk events that can occur, from 1 to the largest number. +#' @export +#' @examples +#' T1 <- rexp(1000) +#' T2 <- rweibull(1000, 1, 2) +#' C <- rexp(1000) +#' +#' u <- round(pmin(T1, T2, C)) +#' # ... +#' +#' forestCombiner <- CR_ResponseCombiner(1:2) # there are two possible events +CR_ResponseCombiner <- function(events){ + # need to first change events into array of int + eventArray <- .jarray(events, "I") + + + javaObject <- .jnew(.class_CompetingRiskResponseCombiner, eventArray) + javaObject <- .jcast(javaObject, .class_ResponseCombiner) + + combiner <- list(javaObject=javaObject, + call=match.call(), + outputClass="CompetingRiskFunctions", + convertToRFunction=convertCompetingRiskFunctions + ) + class(combiner) <- "ResponseCombiner" + + return(combiner) +} + + +#' Competing Risk Split Finders +#' +#' Creates a SplitFinder rJava Java object, which is then used internally when +#' training a competing risk random forest. The split finder is responsible for +#' finding the best split according to the logic of the split finder. +#' +#' These split finders require that the response be \code{\link{CR_Response}}. +#' +#' The user only needs to pass this object into \code{\link{train}} as the +#' \code{splitFinder} parameter. +#' +#' @return An internal rJava Java object used in \code{\link{train}}. +#' @note The Gray log-rank split finder \strong{requires} that the response +#' include the censoring time. +#' @param events A vector of integers specifying which competing risk events +#' should be focused on when determining differences. Currently, equal weights +#' will be assigned to all included groups. +#' @param eventsOfFocus The split finder will only maximize differences +#' between the two groups with respect to these specified events. Default is +#' \code{NULL}, which will cause the split finder to focus on all events +#' included in \code{events}. +#' @details Roughly speaking, the Gray log-rank split finder looks at +#' differences between the cumulative incidence functions of the two groups, +#' while the plain log-rank split finder look at differences between the +#' cause-specific hazard functions. See the references for a more detailed +#' discussion. +#' @references Kogalur, U., Ishwaran, H. Random Forests for Survival, +#' Regression, and Classification: A Parallel Package for a General +#' Implemention of Breiman's Random Forests: Theory and Specifications. URL +#' https://kogalur.github.io/randomForestSRC/theory.html#section8.2 +#' +#' Ishwaran, H., et. al. (2014) Random survival forests for competing risks, +#' Biostatistics (2014), 15, 4, pp. 757–773 +#' +#' @name CompetingRiskSplitFinders +NULL + +#' @rdname CompetingRiskSplitFinders +#' @export +#' @examples splitFinder <- GrayLogRankSplitFinder(1:2) +GrayLogRankSplitFinder <- function(events, eventsOfFocus = NULL){ + return(java.LogRankSplitFinder(events, eventsOfFocus, .class_GrayLogRankSplitFinder, match.call())) +} + +#' @rdname CompetingRiskSplitFinders +#' @export +#' @examples splitFinder <- LogRankSplitFinder(1:2) +LogRankSplitFinder <- function(events, eventsOfFocus = NULL){ + return(java.LogRankSplitFinder(events, eventsOfFocus, .class_LogRankSplitFinder, match.call())) +} + +# Internal function for creating a competing risk split finder +java.LogRankSplitFinder <- function(events, eventsOfFocus, java.class, call = match.call()){ + events <- sort(events) + + if(is.null(eventsOfFocus)){ + eventsOfFocus <- events + } + + # Check the events + if(any(diff(events) != 1) | min(events) != 1){ + stop("The events provided for creating a log rank split finder do not run from 1 to the maximum") + } + + if(any(!(eventsOfFocus %in% events))){ + stop("There's an event of focus for the log rank split finder that's not included in the events vector") + } + + events <- .jarray(as.integer(events)) + eventsOfFocus <- .jarray(as.integer(eventsOfFocus)) + + javaObject <- .jnew(java.class, eventsOfFocus, events) + javaObject <- .jcast(javaObject, .class_SplitFinder) + + splitFinder <- list(javaObject=javaObject, call=call) + class(splitFinder) <- "SplitFinder" + + return(splitFinder) +} + + + diff --git a/R/cr_naiveConcordance.R b/R/cr_naiveConcordance.R new file mode 100644 index 0000000..356e4f6 --- /dev/null +++ b/R/cr_naiveConcordance.R @@ -0,0 +1,52 @@ + +#' Naive Concordance +#' +#' Used to calculate a concordance index error. The user needs to supply a list +#' of mortalities, with each item in the list being a vector for the specific +#' events. To calculate mortalities a user should look to +#' \code{\link{extractMortalities}}. +#' +#' @return A vector of 1 minus the concordance scores, with each element +#' corresponding to one of the events. To be clear, the lower the score the +#' more accurate the model was. +#' +#' @param responses A list of responses corresponding to the provided +#' mortalities; use \code{\link{CR_Response}}. +#' @param predictedMortalities A list of mortality vectors; each element of the +#' list should correspond to one of the events in the order of event 1 to J, +#' and should be a vector of the same length as responses. +#' @export +naiveConcordance <- function(responses, predictedMortalities){ + if(is.null(responses)){ + stop("responses cannot be null") + } + + if(is.null(predictedMortalities)){ + stop("predictedMortalities cannot be null") + } + if(!is.list(predictedMortalities)){ + stop("predictedMortalities must be a list") + } + + responseList = responses$javaObject + responseLength = .jcall(responseList, "I", "size") + + events = as.integer(1:length(predictedMortalities)) + + concordances = numeric(length(predictedMortalities)) + + for(event in events){ + if(length(predictedMortalities[[event]]) != responseLength){ + stop("Every mortality vector in predictedMortalities must be the same length as responses") + } + + # Need to turn predictedMortalities into an array of doubles + mortality = .jarray(predictedMortalities[[event]], "D") + + concordances[event] = 1 - .jcall(.class_CompetingRiskUtils, "D", "calculateConcordance", responseList, mortality, event) + + } + + return(concordances) + +} diff --git a/R/cr_predictions.R b/R/cr_predictions.R new file mode 100644 index 0000000..ee0b7e8 --- /dev/null +++ b/R/cr_predictions.R @@ -0,0 +1,142 @@ + + +convertCompetingRiskFunctionsSlow <- function(javaObject, forest){ + events <- forest$params$forestResponseCombiner$events + lst <- list(javaObject = javaObject, events = events) + + rightContinuousStepFunctionResponseClass <- makeResponse(.class_RightContinuousStepFunction) + + kaplanMeier <- .jcall(javaObject, rightContinuousStepFunctionResponseClass, "getSurvivalCurve") + + lst$time.interest <- .jcall(.class_RUtils, "[D", "extractTimes", kaplanMeier) + lst$survivorCurve <- .jcall(.class_RUtils, "[D", "extractY", kaplanMeier) + + lst$cif <- matrix(nrow=length(lst$time.interest), ncol=length(events)) + lst$chf <- matrix(nrow=length(lst$time.interest), ncol=length(events)) + + for(i in events){ + cif <- .jcall(javaObject, rightContinuousStepFunctionResponseClass, "getCumulativeIncidenceFunction", as.integer(i)) + lst$cif[,i] <- .jcall(.class_RUtils, "[D", "extractY", cif) + + chf <- .jcall(javaObject, rightContinuousStepFunctionResponseClass, "getCauseSpecificHazardFunction", as.integer(i)) + lst$chf[,i] <- .jcall(.class_RUtils, "[D", "extractY", chf) + } + + class(lst) <- "CompetingRiskFunctions" + return(lst) +} + +convertCompetingRiskFunctions <- compiler::cmpfun(convertCompetingRiskFunctionsSlow) + + +#' Competing Risk Predictions +#' +#' @param x The predictions output from a competing risk random forest. +#' @param event The event who's CIF/CHF/Mortality you are interested in. +#' @param time The time to evaluate the mortality for (relevant only for +#' \code{extractMortalities}). +#' +#' @name CompetingRiskPredictions +NULL + +#' @rdname CompetingRiskPredictions +#' @export +#' @description +#' \code{extractCIF} extracts the cumulative incidence function for a prediction. +extractCIF <- function (x, event) { + UseMethod("extractCIF", x) +} + +#' @export +extractCIF.CompetingRiskFunctions <- function(prediction, event){ + fun <- stepfun(prediction$time.interest, c(0, prediction$cif[,event])) + + class(fun) <- "function" + attr(fun, "call") <- sys.call() + return(fun) +} + +#' @export +extractCIF.CompetingRiskFunctions.List <- function(predictions, event){ + return(lapply(predictions, extractCIF.CompetingRiskFunctions, event)) +} + +#' @rdname CompetingRiskPredictions +#' @export +#' @description +#' \code{extractCHF} extracts the cause-specific cumulative hazard function for a prediction. +extractCHF <- function (x, event) { + UseMethod("extractCHF", x) +} + +#' @export +extractCHF.CompetingRiskFunctions <- function(prediction, event){ + fun <- stepfun(prediction$time.interest, c(0, prediction$chf[,event])) + + class(fun) <- "function" + attr(fun, "call") <- sys.call() + return(fun) +} + +#' @export +extractCHF.CompetingRiskFunctions.List <- function(predictions, event){ + return(lapply(predictions, extractCHF.CompetingRiskFunctions, event)) +} + + +#' @rdname CompetingRiskPredictions +#' @export +#' @description \code{extractSurvivorCurve} extracts the Kaplan-Meier estimator +#' of the overall survivor curve for a prediction. +extractSurvivorCurve <- function (x) { + UseMethod("extractSurvivorCurve", x) +} + +#' @export +extractSurvivorCurve.CompetingRiskFunctions <- function(prediction){ + fun <- stepfun(prediction$time.interest, c(1, prediction$survivorCurve)) + + class(fun) <- "function" + attr(fun, "call") <- sys.call() + return(fun) +} + +#' @export +extractSurvivorCurve.CompetingRiskFunctions.List <- function(predictions){ + return(lapply(predictions, extractSurvivorCurve.CompetingRiskFunctions)) +} + +#' @rdname CompetingRiskPredictions +#' @export +#' @description \code{extractMortalities} extracts the cause-specific +#' mortalities for a function, which here is the CIF integrated from 0 to +#' \code{time}. +extractMortalities <- function(x, event, time){ + UseMethod("extractMortalities", x) +} + +#' @export +extractMortalities.CompetingRiskFunctions <- function(prediction, event, time){ + if(is.null(event) | anyNA(event)){ + stop("event must be specified") + } + + if(is.null(time) | anyNA(time)){ + stop("time must be specified") + } + + return(.jcall(prediction$javaObject, "D", "calculateEventSpecificMortality", as.integer(event), time)) +} + +#' @export +extractMortalities.CompetingRiskFunctions.List <- function(predictions, event, time){ + if(is.null(event) | anyNA(event)){ + stop("event must be specified") + } + + if(is.null(time) | anyNA(time)){ + stop("time must be specified") + } + + return(as.numeric(lapply(predictions, extractMortalities.CompetingRiskFunctions, event, time))) +} \ No newline at end of file diff --git a/R/create_java_covariates.R b/R/create_java_covariates.R new file mode 100644 index 0000000..a096d98 --- /dev/null +++ b/R/create_java_covariates.R @@ -0,0 +1,57 @@ +# These functions are not exported, so I won't create their documentation either. +# I.e. it's not a mistake that the documentation below lacks the " ' " on each line. + +# Covariates +# +# Creates a covariate for use in the Java code. These functions don't need to +# be directly run by a user, as loadData and train will detect, create and use +# such covariate objects. +# +# @name covariates +# +# @param name The name of the covariate, that later values will be placed +# under. +# @return An internal rJava object for later internal use. +# @keywords internal +# @examples +# # This is unnecessary for a user to do +# +# # Create a covariate +# booleanCovariate <- Java_BooleanCovariate("x1") +# factorCovariate <- Java_FactorCovariate("x2", c("cat", "dog", "mouse")) +# numericCovariate <- Java_NumericCovariate("x3") +# +# # Call the approriate Java method +# # The Java createValue method always takes in a String +# value1 <- .jcall(booleanCovariate, "Lca/joeltherrien/randomforest/covariates/Covariate$Value;", "createValue", "true") +# value2 <- .jcall(factorCovariate, "Lca/joeltherrien/randomforest/covariates/Covariate$Value;", "createValue", "dog") +# value3 <- .jcall(numericCovariate, "Lca/joeltherrien/randomforest/covariates/Covariate$Value;", "createValue", "3.14") +NULL + +# @rdname covariates +Java_BooleanCovariate <- function(name, index){ + covariate <- .jnew(.class_BooleanCovariate, name, as.integer(index)) + covariate <- .jcast(covariate, .class_Object) # needed for later adding it into Java Lists + + return(covariate) +} + +# @rdname covariates +# @param levels The levels of the factor as a character vector +Java_FactorCovariate <- function(name, index, levels){ + levelsArray <- .jarray(levels, makeResponse(.class_String)) + levelsList <- .jcall("java/util/Arrays", "Ljava/util/List;", "asList", .jcast(levelsArray, "[Ljava/lang/Object;")) + + covariate <- .jnew(.class_FactorCovariate, name, as.integer(index), levelsList) + covariate <- .jcast(covariate, .class_Object) # needed for later adding it into Java Lists + + return(covariate) +} + +# @rdname covariates +Java_NumericCovariate <- function(name, index){ + covariate <- .jnew(.class_NumericCovariate, name, as.integer(index)) + covariate <- .jcast(covariate, .class_Object) # needed for later adding it into Java Lists + + return(covariate) +} diff --git a/R/defaults.R b/R/defaults.R new file mode 100644 index 0000000..94e8e68 --- /dev/null +++ b/R/defaults.R @@ -0,0 +1,52 @@ +splitFinderDefault <- function(responses){ + if(class(responses) == "CompetingRiskResponses"){ + # get all of the events + deltas <- unique(sort(responses$eventIndicator)) + deltas <- deltas[!(deltas %in% as.integer(0))] + + return(LogRankSplitFinder(deltas)) + } else if(class(responses) == "CompetingRiskResponsesWithCensorTimes"){ + # get all of the events + deltas <- sort(unique(responses$eventIndicator)) + deltas <- deltas[!(deltas %in% as.integer(0))] + + return(GrayLogRankSplitFinder(deltas)) + } + else if(class(responses) == "numeric" | class(responses) == "integer" | class(responses) == "JNumeric"){ + return(WeightedVarianceSplitFinder()) + } + else{ + stop("Unable to determine an appropriate split finder for this response; please specify one manually.") + } +} + + +nodeResponseCombinerDefault <- function(responses){ + if(class(responses) == "CompetingRiskResponses" | class(responses) == "CompetingRiskResponsesWithCensorTimes"){ + # get all of the events + deltas <- unique(sort(responses$eventIndicator)) + deltas <- deltas[!(deltas %in% as.integer(0))] + + return(CR_ResponseCombiner(deltas)) + } else if(class(responses) == "numeric" | class(responses) == "integer" | class(responses) == "JNumeric"){ + return(MeanResponseCombiner()) + } + else{ + stop("Unable to determine an appropriate node response combiner for this response; please specify one manually") + } +} + +forestResponseCombinerDefault <- function(responses){ + if(class(responses) == "CompetingRiskResponses" | class(responses) == "CompetingRiskResponsesWithCensorTimes"){ + # get all of the events + deltas <- unique(sort(responses$eventIndicator)) + deltas <- deltas[!(deltas %in% as.integer(0))] + + return(CR_FunctionCombiner(deltas)) + } else if(class(responses) == "numeric" | class(responses) == "integer" | class(responses) == "JNumeric"){ + return(MeanResponseCombiner()) + } + else{ + stop("Unable to determine an appropriate forest response combiner for this response; please specify one manually.") + } +} diff --git a/R/java_classes_directory.R b/R/java_classes_directory.R new file mode 100644 index 0000000..f382cf7 --- /dev/null +++ b/R/java_classes_directory.R @@ -0,0 +1,57 @@ +# This file keeps track of the different Java classes used +# Whenever refactoring happens in the Java code, this file should be updated and (hopefully) nothing will break. + +# General Java objects +.class_Object <- "java/lang/Object" +.class_String <- "java/lang/String" +.class_List <- "java/util/List" +.class_ArrayList <- "java/util/ArrayList" +.class_Collection <- "java/util/Collection" +.class_Serializable <- "java/io/Serializable" +.class_File <- "java/io/File" + +# Utility Classes +.class_DataUtils <- "ca/joeltherrien/randomforest/utils/DataUtils" +.class_RUtils <- "ca/joeltherrien/randomforest/utils/RUtils" +.class_CompetingRiskUtils <- "ca/joeltherrien/randomforest/responses/competingrisk/CompetingRiskUtils" +.class_Settings <- "ca/joeltherrien/randomforest/Settings" + +# Misc. Classes +.class_RightContinuousStepFunction <- "ca/joeltherrien/randomforest/utils/RightContinuousStepFunction" + + # TreeTrainer & its Builder +.class_TreeTrainer <- "ca/joeltherrien/randomforest/tree/TreeTrainer" +.class_TreeTrainer_Builder <- "ca/joeltherrien/randomforest/tree/TreeTrainer$TreeTrainerBuilder" + +# ForestTrainer & its Builder +.class_ForestTrainer <- "ca/joeltherrien/randomforest/tree/ForestTrainer" +.class_ForestTrainer_Builder <- "ca/joeltherrien/randomforest/tree/ForestTrainer$ForestTrainerBuilder" + + +# Covariate classes +.class_Covariate <- "ca/joeltherrien/randomforest/covariates/Covariate" +.class_BooleanCovariate <- "ca/joeltherrien/randomforest/covariates/bool/BooleanCovariate" +.class_FactorCovariate <- "ca/joeltherrien/randomforest/covariates/factor/FactorCovariate" +.class_NumericCovariate <- "ca/joeltherrien/randomforest/covariates/numeric/NumericCovariate" + +# Forest class +.class_Forest <- "ca/joeltherrien/randomforest/tree/Forest" + +# ResponseCombiner classes +.class_ResponseCombiner <- "ca/joeltherrien/randomforest/tree/ResponseCombiner" +.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" + +# SplitFinder classes +.class_SplitFinder <- "ca/joeltherrien/randomforest/tree/SplitFinder" +.class_GrayLogRankSplitFinder <- "ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/GrayLogRankSplitFinder" +.class_LogRankSplitFinder <- "ca/joeltherrien/randomforest/responses/competingrisk/splitfinder/LogRankSplitFinder" +.class_WeightedVarianceSplitFinder <- "ca/joeltherrien/randomforest/responses/regression/WeightedVarianceSplitFinder" + +# 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 +makeResponse <- function(className){ + return(paste0("L", className, ";")) +} \ No newline at end of file diff --git a/R/loadData.R b/R/loadData.R new file mode 100644 index 0000000..ded0e6e --- /dev/null +++ b/R/loadData.R @@ -0,0 +1,83 @@ +loadData <- function(data, xVarNames, responses){ + + if(class(responses) == "integer" | class(responses) == "numeric"){ + responses <- Numeric(responses) + } + + covariateList.java <- getCovariateList(data, xVarNames) + + textColumns <- list() + for(j in 1:length(xVarNames)){ + textColumns[[j]] <- .jarray(as.character(data[,xVarNames[j]]), "S") + } + textData <- convertRListToJava(textColumns) + + rowList <- .jcall(.class_RUtils, makeResponse(.class_List), "importDataWithResponses", + responses$javaObject, covariateList.java, textData) + + return(list(covariateList=covariateList.java, dataset=rowList)) + +} + +getCovariateList <- function(data, xvarNames){ + covariateList <- .jcast(.jnew(.class_ArrayList, length(xvarNames)), .class_List) + + for(i in 1:length(xvarNames)){ + xName = xvarNames[i] + + column <- data[,xName] + + if(class(column) == "numeric" | class(column) == "integer"){ + covariate <- Java_NumericCovariate(xName, i-1) + } + else if(class(column) == "logical"){ + covariate <- Java_BooleanCovariate(xName, i-1) + } + else if(class(column) == "factor"){ + lvls <- levels(column) + covariate <- Java_FactorCovariate(xName, i-1, lvls) + } + else{ + stop("Unknown column type") + } + + .jcall(covariateList, "Z", "add", covariate) + + } + + return(covariateList) + +} + +loadPredictionData <- function(newData, covariateList.java){ + + xVarNames <- character(.jcall(covariateList.java, "I", "size")) + for(j in 1:length(xVarNames)){ + covariate.java <- .jcast( + .jcall(covariateList.java, makeResponse(.class_Object), "get", as.integer(j-1)), + .class_Covariate + ) + + xVarNames[j] <- .jcall(covariate.java, makeResponse(.class_String), "getName") + } + + if(any(!(xVarNames %in% names(newData)))){ + varsMissing = xVarNames[!(xVarNames %in% names(newData))] + + error <- paste0("The following covariates are not present in newdata: ", paste(varsMissing, collapse = ", ")) + stop(error) + } + + textColumns <- list() + for(j in 1:length(xVarNames)){ + textColumns[[j]] <- .jarray(as.character(newData[,xVarNames[j]]), "S") + } + textData <- convertRListToJava(textColumns) + + rowList <- .jcall(.class_RUtils, makeResponse(.class_List), + "importData", covariateList.java, textData) + + + return(rowList) +} + diff --git a/R/load_forest.R b/R/load_forest.R new file mode 100644 index 0000000..22aa554 --- /dev/null +++ b/R/load_forest.R @@ -0,0 +1,75 @@ + + +#' Load Random Forest +#' +#' Loads a random forest that was saved using \code{\link{save_forest}}. +#' +#' @param forest The directory created that saved the previous forest. +#' @return A JForest object; see \code{\link{train}} for details. +#' @export +#' @seealso \code{\link{train}}, \code{\link{save_forest}} +#' @examples +#' # Regression Example +#' 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) +#' +#' save_forest(forest, "trees") +#' new_forest <- load_forest("trees") +load_forest <- function(directory){ + + # First load the response combiners and the split finders + nodeResponseCombiner.java <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/nodeResponseCombiner.jData")) + nodeResponseCombiner.java <- .jcast(nodeResponseCombiner.java, .class_ResponseCombiner) + + splitFinder.java <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/splitFinder.jData")) + 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) + + covariateList <- .jcall(.class_DataUtils, makeResponse(.class_Object), "loadObject", paste0(directory, "/covariateList.jData")) + covariateList <- .jcast(covariateList, .class_List) + + params <- readRDS(paste0(directory, "/parameters.rData")) + call <- readRDS(paste0(directory, "/call.rData")) + + params$nodeResponseCombiner$javaObject <- nodeResponseCombiner.java + params$splitFinder$javaObject <- splitFinder.java + params$forestResponseCombiner$javaObject <- forestResponseCombiner.java + + forest <- load_forest_args_provided(directory, params$nodeResponseCombiner, params$splitFinder, params$forestResponseCombiner, covariateList, call, + params$ntree, params$numberOfSplits, params$mtry, params$nodeSize, params$maxNodeDepth, params$splitPureNodes) + + return(forest) + +} + +#' @export +load_forest_args_provided <- function(treeDirectory, nodeResponseCombiner, splitFinder, forestResponseCombiner, + covariateList.java, call, ntree, numberOfSplits, mtry, nodeSize, maxNodeDepth = 100000, splitPureNodes=TRUE){ + + params <- list( + splitFinder=splitFinder, + nodeResponseCombiner=nodeResponseCombiner, + forestResponseCombiner=forestResponseCombiner, + ntree=ntree, + numberOfSplits=numberOfSplits, + mtry=mtry, + nodeSize=nodeSize, + splitPureNodes=splitPureNodes, + maxNodeDepth = maxNodeDepth + ) + + forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", treeDirectory, forestResponseCombiner$javaObject) + + forestObject <- list(call=call, javaObject=forest.java, covariateList=covariateList.java, params=params) + class(forestObject) <- "JRandomForest" + + return(forestObject) + +} \ No newline at end of file diff --git a/R/misc.R b/R/misc.R new file mode 100644 index 0000000..2f931ed --- /dev/null +++ b/R/misc.R @@ -0,0 +1,101 @@ +#' convertRListToJava +#' +#' An internal function that converts an R list of rJava objects into a +#' java.util.List rJava object containing those objects. It's used internally, +#' and is only available because it's used in some examples that demonstrate what +#' other objects do. +#' @param lst The R list containing rJava objects +#' @export +#' @return An rJava List object to be used internally. +#' @keywords internal +#' @examples +#' x <- Numeric(1:5) +#' class(x) +#' x <- convertRListToJava(x) +#' class(x) +convertRListToJava <- function(lst){ + javaList <- .jnew(.class_ArrayList, as.integer(length(lst))) + javaList <- .jcast(javaList, .class_List) + + for (item in lst){ + if (class(item) != "jobjRef" & class(item) != "jarrayRef"){ + stop("All items in the list must be rJava Java objects") + } + + .jcall(javaList, "Z", "add", .jcast(item, .class_Object)) + } + + return(javaList) +} + +#' @export +print.SplitFinder = function(splitFinder) print(splitFinder$call) + +#' @export +print.ResponseCombiner = function(combiner) print(combiner$call) + +#' @export +print.JRandomForest <- function(forest){ + cat("Call:\n") + print(forest$call) + cat("\nParameters:\n") + cat("\tSplit Finder: "); print(forest$params$splitFinder$call) + cat("\tTerminal Node Response Combiner: "); print(forest$params$nodeResponseCombiner$call) + cat("\tForest Response Combiner: "); print(forest$params$forestResponseCombiner$call) + cat("\t# of trees: "); cat(forest$params$ntree); cat("\n") + cat("\t# of Splits: "); cat(forest$params$numberOfSplits); cat("\n") + cat("\t# of Covariates to try: "); cat(forest$params$mtry); cat("\n") + cat("\tNode Size: "); cat(forest$params$nodeSize); cat("\n") + cat("\tMax Node Depth: "); cat(forest$params$maxNodeDepth); cat("\n") + + cat("Try using me with predict() or one of the relevant commands to determine error\n") +} + +#' @export +print.CompetingRiskFunctions.List <- function(lst){ + cat("Number of predictions: ") + cat(length(lst)) + + cat("\n\nSee the help page ?CompetingRiskPredictions for a list of relevant functions on how to use this object.\n") +} + +#' @export +print.CompetingRiskFunctions <- function(functions){ + mx <- ncol(functions$cif) + cat(mx); cat(" CIFs available\n") + cat(mx); cat(" CHFs available\n") + cat("An overall survival curve available\n") + cat("\nSee the help page ?CompetingRiskPredictions for a list of relevant functions on how to use this object.\n") + +} + +#' @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") + } + + } + + plot(mat[,2] ~ mat[,1], col=col, type=type, xlab=xlab, ylab=ylab, ...) + } + else{ + points(mat[,2] ~ mat[,1], col=col, type=type, xlab=xlab, ylab=ylab, ...) + } + +} diff --git a/R/predict.R b/R/predict.R new file mode 100644 index 0000000..bf54099 --- /dev/null +++ b/R/predict.R @@ -0,0 +1,96 @@ + + +#' Predict +#' +#' Predict on the random forest. +#' +#' @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. +#' @param parallel A logical indicating whether multiple cores should be +#' utilized when making the predictions. Available as an option because it's +#' been observed by this author that using Java's \code{parallelStream} can be +#' unstable on some systems. Default value is \code{TRUE}. +#' @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}. +#' @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 +#' @examples +#' # Regression Example +#' x1 <- rnorm(1000) +#' x2 <- rnorm(1000) +#' y <- 1 + x1 + x2 + rnorm(1000) +#' +#' data <- data.frame(x1, x2, y) +#' forest <- train(y ~ x1 + x2, data, WeightedVarianceSplitFinder(), MeanResponseCombiner(), MeanResponseCombiner(), ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5) +#' +#' # Fix x2 to be 0 +#' newData <- data.frame(x1 = seq(from=-2, to=2, by=0.5), x2 = 0) +#' ypred <- predict(forest, newData) +#' +#' plot(ypred ~ newData$x1, type="l") +#' +#' # Competing Risk Example +#' x1 <- abs(rnorm(1000)) +#' x2 <- abs(rnorm(1000)) +#' +#' T1 <- rexp(1000, rate=x1) +#' T2 <- rweibull(1000, shape=x1, scale=x2) +#' C <- rexp(1000) +#' u <- pmin(T1, T2, C) +#' delta <- ifelse(u==T1, 1, ifelse(u==T2, 2, 0)) +#' +#' data <- data.frame(x1, x2) +#' +#' forest <- train(CR_Response(delta, u) ~ x1 + x2, data, +#' LogRankSplitFinder(1:2), CompetingRiskResponseCombiner(1:2), CompetingRiskFunctionCombiner(1:2), ntree=100, numberOfSplits=5, mtry=1, nodeSize=10) +#' newData <- data.frame(x1 = c(-1, 0, 1), x2 = 0) +#' ypred <- predict(forest, newData) +predict.JRandomForest <- function(forest, newData=NULL, parallel=TRUE, out.of.bag=FALSE){ + if(is.null(newData)){ + stop("newData must be specified, even if predictions are on the training set") + } + + forestObject <- forest$javaObject + covariateList <- forest$covariateList + predictionClass <- forest$params$forestResponseCombiner$outputClass + convertToRFunction <- forest$params$forestResponseCombiner$convertToRFunction + + predictionDataList <- loadPredictionData(newData, covariateList) + + if(parallel){ + function.to.use <- "evaluate" + } + else{ + function.to.use <- "evaluateSerial" + } + + if(out.of.bag){ + function.to.use <- paste0(function.to.use, "OOB") + } + + predictionsJava <- .jcall(forestObject, makeResponse(.class_List), function.to.use, predictionDataList) + + if(predictionClass == "numeric"){ + predictions <- vector(length=nrow(newData), mode="numeric") + } + else{ + predictions <- list() + } + + + for(i in 1:nrow(newData)){ + prediction <- .jcall(predictionsJava, makeResponse(.class_Object), "get", as.integer(i-1)) + prediction <- convertToRFunction(prediction, forest) + + predictions[[i]] <- prediction + } + + class(predictions) <- paste0(predictionClass, ".List") + + return(predictions) +} diff --git a/R/recover_forest.R b/R/recover_forest.R new file mode 100644 index 0000000..fc6f267 --- /dev/null +++ b/R/recover_forest.R @@ -0,0 +1,37 @@ + +recover_forest_predictable <- function(tree_directory, settingsPath) { + + settings.java <- load_settings(settingsPath) + + nodeResponseCombiner.java <- .jcall(settings.java, makeResponse(.class_ResponseCombiner), "getResponseCombiner") + splitFinder.java <- .jcall(settings.java, makeResponse(.class_SplitFinder), "getSplitFinder") + forestResponseCombiner.java <- .jcall(settings.java, makeResponse(.class_ResponseCombiner), "getTreeCombiner") + + covariateList <- .jcall(settings.java, makeResponse(.class_List), "getCovariates") + + params <- readRDS(paste0(directory, "/parameters.rData")) + call <- readRDS(paste0(directory, "/call.rData")) + + params$nodeResponseCombiner$javaObject <- nodeResponseCombiner.java + params$splitFinder$javaObject <- splitFinder.java + params$forestResponseCombiner$javaObject <- forestResponseCombiner.java + + forest <- load_forest_args_provided(directory, params$nodeResponseCombiner, params$splitFinder, params$forestResponseCombiner, covariateList, params, call) + + return(forest) + +} + +load_settings <- function(settingsPath) { + settingsFile <- .jnew(.class_File, settingsPath) + settings.java <- .jcall(.class_Settings, makeResponse(.class_Settings), "load", settingsFile) + + return(settings.java) +} + +#' @export +load_covariate_list_from_settings <- function(settingsPath){ + settings.java = load_settings(settingsPath) + covariateList <- .jcall(settings.java, makeResponse(.class_List), "getCovariates") + return(covariateList) +} \ No newline at end of file diff --git a/R/regressionComponents.R b/R/regressionComponents.R new file mode 100644 index 0000000..6d304d6 --- /dev/null +++ b/R/regressionComponents.R @@ -0,0 +1,80 @@ + +#' WeightedVarianceSplitFinder +#' +#' This split finder is used in regression random forests. When a split is made, +#' this finder computes the sample variance in each group (divided by n, not +#' n-1); it then minimizes the the sum of these variances, each of them weighted +#' by their sample size divided by the total sample size of that node. +#' +#' @note There are other split finders that are used in regression random +#' forests that are not included in this package. This package is oriented +#' toward the competing risk side of survival analysis; the regression options +#' are provided as an example of how extensible the back-end Java package is. +#' If you are interested in using this package for regression (or other uses), +#' feel free to write your own components. It's really not hard to write these +#' components; the WeightedVarianceSplitFinder Java class is quite short; most +#' of the code is to reuse calculations from previous considered splits. +#' @export +#' @return A split finder object to be used in \code{\link{train}}; not +#' useful on its own. +#' @examples +#' splitFinder <- WeightedVarianceSplitFinder() +#' # You would then use it in train() +#' +#' @references https://kogalur.github.io/randomForestSRC/theory.html#section8.3 +WeightedVarianceSplitFinder <- function(){ + javaObject <- .jnew(.class_WeightedVarianceSplitFinder) + javaObject <- .jcast(javaObject, .class_SplitFinder) + + splitFinder <- list(javaObject=javaObject, call=match.call()) + class(splitFinder) <- "SplitFinder" + + return(splitFinder) +} + +#' MeanResponseCombiner +#' +#' This response combiner is used in regression random forests, where the +#' response in the data is a single number that needs to be averaged in each +#' terminal node, and then averaged across trees. This response combiner is +#' appropriate as an argument for both the \code{nodeResponseCombiner} and +#' \code{forestResponseCombiner} parameters in \code{\link{train}} when doing +#' regression. +#' @export +#' @return A response combiner object to be used in \code{\link{train}}; not +#' useful on its own. However, internally, a response combiner object is a +#' list consisting of the following objects: +#' \describe{ +#' \item{\code{javaObject}}{The java object used in the algorithm} +#' \item{\code{call}}{The call (used in \code{print})} +#' \item{\code{outputClass}}{The R class of the outputs; used in \code{\link{predict.JRandomForest}}} +#' \item{\code{convertToRFunction}}{An R function that converts a Java prediction from the combiner into R output that is readable by a user.} +#' } +#' +#' @examples +#' responseCombiner <- MeanResponseCombiner() +#' # You would then use it in train() +#' +#' # However; I'll show an internal Java method to make it clear what it does +#' # Note that you should never have to do the following +#' x <- 1:3 +#' x <- convertRListToJava(Numeric(x)) +#' +#' # will output a Java object containing 2 +#' output <- rJava::.jcall(responseCombiner$javaObject, "Ljava/lang/Double;", "combine", x) +#' responseCombiner$convertToRFunction(output) +#' +MeanResponseCombiner <- function(){ + javaObject <- .jnew(.class_MeanResponseCombiner) + javaObject <- .jcast(javaObject, .class_ResponseCombiner) + + combiner <- list(javaObject=javaObject, call=match.call(), outputClass="numeric") + combiner$convertToRFunction <- function(javaObject, ...){ + return(.jcall(javaObject, "D", "doubleValue")) + } + + + class(combiner) <- "ResponseCombiner" + + return(combiner) +} diff --git a/R/save_forest.R b/R/save_forest.R new file mode 100644 index 0000000..d5c1d3a --- /dev/null +++ b/R/save_forest.R @@ -0,0 +1,94 @@ + + +#' Save Random Forests +#' +#' Saves a random forest for later use, given that the base R +#' \code{\link{base::save}} function doesn't work for this package. +#' +#' @param forest The forest to save. +#' @param directory The directory that should be created to save the trees in. +#' Note that if the directory already exists, an error will be displayed +#' unless \code{overwrite} is set to TRUE. +#' @param overwrite Should the function overwrite an existing forest; FALSE by +#' default. + +#' @export +#' @seealso \code{\link{train}}, \code{\link{load_forest}} +#' @examples +#' # Regression Example +#' x1 <- rnorm(1000) +#' x2 <- rnorm(1000) +#' y <- 1 + x1 + x2 + rnorm(1000) +#' +#' data <- data.frame(x1, x2, y) +#' forest <- train(y ~ x1 + x2, data, +#' ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5) +#' +#' save_forest(forest, "trees") +#' new_forest <- load_forest("trees") +save_forest <- function(forest, directory, overwrite=FALSE){ + check_and_create_directory(directory, overwrite) + + saveTrees(forest, directory) + + # Next save the response combiners and the split finders + saveForestComponents(directory, + covariateList=forest$covariateList, + params=forest$params, + forestCall=forest$call) + +} + +saveTrees <- function(forest, directory){ + # This function assumes that directory is free for us to write in. + + forest.java <- forest$javaObject + + # First save the trees + tree.collection.java <- .jcall(forest.java, makeResponse(.class_List), "getTrees") + numberOfTrees <- forest$params$ntree + width = round(log10(numberOfTrees))+1 + treeNames <- paste0(directory, "/tree-", formatC(1:numberOfTrees, width=width, format="d", flag="0"), ".tree") + for(i in 1:numberOfTrees){ + treeName <-treeNames[i] + tree.java <- .jcall(tree.collection.java, makeResponse(.class_Object), "get", as.integer(i-1)) + tree.java <- .jcast(tree.java, .class_Serializable) + .jcall(.class_DataUtils, "V", "saveObject", tree.java, treeName) + } + +} + +saveForestComponents <- function(directory, covariateList, params, forestCall){ + + nodeResponseCombiner <- params$nodeResponseCombiner + nodeResponseCombiner.java <- .jcast(nodeResponseCombiner$javaObject, .class_Serializable) + .jcall(.class_DataUtils, "V", "saveObject", nodeResponseCombiner.java, paste0(directory, "/nodeResponseCombiner.jData")) + nodeResponseCombiner$javaObject <- NULL + + splitFinder <- params$splitFinder + splitFinder.java <- .jcast(splitFinder$javaObject, .class_Serializable) + .jcall(.class_DataUtils, "V", "saveObject", splitFinder.java, paste0(directory, "/splitFinder.jData")) + splitFinder$javaObject <- NULL + + forestResponseCombiner <- params$forestResponseCombiner + forestResponseCombiner.java <- .jcast(forestResponseCombiner$javaObject, .class_Serializable) + .jcall(.class_DataUtils, "V", "saveObject", forestResponseCombiner.java, paste0(directory, "/forestResponseCombiner.jData")) + forestResponseCombiner$javaObject <- NULL + + covariateList <- .jcast(covariateList, .class_Serializable) + .jcall(.class_DataUtils, "V", "saveObject", covariateList, paste0(directory, "/covariateList.jData")) + + saveRDS(object=params, file=paste0(directory, "/parameters.rData")) + saveRDS(object=forestCall, file=paste0(directory, "/call.rData")) +} + +check_and_create_directory <- function(directory, overwrite){ + if(file.exists(directory) & !overwrite){ + stop(paste(directory, "already exists; will not modify it. Please remove/rename it or set overwrite=TRUE")) + } + else if(file.exists(directory) & overwrite){ + unlink(directory) + } + + dir.create(directory) +} \ No newline at end of file diff --git a/R/train.R b/R/train.R new file mode 100644 index 0000000..a70752a --- /dev/null +++ b/R/train.R @@ -0,0 +1,417 @@ + +getCores <- function(){ + cores <- NA + if (requireNamespace("parallel", quietly = TRUE)){ + cores <- parallel::detectCores() + } + + if (is.na(cores)){ + message("Unable to detect how many cores are available; defaulting to only using one. Feel free to override this by pre-specifying the cores argument.") + cores <- 1 + } + + return(cores) +} + +#' Train Random Forests +#' +#' Trains the random forest. The type of response the random forest can be +#' trained on varies depending on the \code{splitFinder}, +#' \code{nodeResponseCombiner}, and the \code{forestResponseCombiner} +#' parameters. Make sure these are compatible with each other, and with the +#' response you plug in. \code{splitFinder} should work on the responses you are +#' providing; \code{nodeResponseCombiner} should combine these responses into +#' some intermediate product, and \code{forestResponseCombiner} combines these +#' intermediate products into the final output product. +#' +#' @param responses An R list of the responses. See \code{\link{CR_Response}} +#' for an example function. +#' @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). +#' @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, +#' this function tries to pick one based on the response. For +#' \code{\link{CR_Response}} wihtout censor times, it will pick a +#' \code{\link{LogRankSplitFinder}}; while if censor times were provided it +#' will pick \code{\link{GrayLogRankSplitFinder}}; for integer or numeric +#' responses it picks a \code{\link{WeightedVarianceSplitFinder}}. +#' @param nodeResponseCombiner A response combiner that's used to combine +#' responses for each terminal node in a tree (regression example; average the +#' observations in each tree into a single number). See +#' \code{\link{CompetingRiskResponseCombiner}} or +#' \code{\link{MeanResponseCombiner}}. If you don't specify one, this function +#' tries to pick one based on the response. For \code{\link{CR_Response}} it +#' picks a \code{\link{CompetingRiskResponseCombiner}}; for integer or numeric +#' responses it picks a \code{\link{MeanResponseCombiner}}. +#' @param forestResponseCombiner A response combiner that's used to combine +#' predictions across trees into one final result (regression example; average +#' the prediction of each tree into a single number). See +#' \code{\link{CompetingRiskFunctionCombiner}} or +#' \code{\link{MeanResponseCombiner}}. If you don't specify one, this function +#' tries to pick one based on the response. For \code{\link{CR_Response}} it +#' picks a \code{\link{CompetingRiskFunctionCombiner}}; for integer or numeric +#' responses it picks a \code{\link{MeanResponseCombiner}}. +#' @param ntree An integer that specifies how many trees should be trained. +#' @param numberOfSplits A tuning parameter specifying how many random splits +#' should be tried for a covariate; a value of 0 means all splits will be +#' tried (with an exception for factors, who might have too many splits to +#' feasibly compute). +#' @param mtry A tuning parameter specifying how many covariates will be +#' randomly chosen to be tried in the splitting process. This value must be at +#' least 1. +#' @param nodeSize The algorithm will not attempt to split a node that has +#' observations less than 2*\code{nodeSize}; this results in terminal nodes +#' having a size of roughly \code{nodeSize} (true sizes may be both smaller or +#' greater). This value must be at least 1. +#' @param maxNodeDepth This parameter is analogous to \code{nodeSize} in that it +#' helps keep trees shorter; by default maxNodeDepth is an extremely high +#' number and tree depth is controlled by \code{nodeSize}. +#' @param splitPureNodes This parameter determines whether the algorithm will +#' 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 just splits. 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. +#' @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{load_forest}} +#' @param savePath.overwrite This parameter controls the behaviour for what +#' happens if \code{savePath} is pointing to an existing directory. If set to +#' \code{warn} (default) then \code{train} refuses to proceed. If set to +#' \code{delete} then all the contents in that folder are deleted for the new +#' forest to be trained. Note that all contents are deleted, even those files +#' not related to \code{largeRCRF}. Use only if you're sure it's safe. If set +#' to \code{merge}, then the files describing the forest (such as its +#' parameters) are overwritten but the saved trees are not. The algorithm +#' 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 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. +#' @param randomSeed This parameter specifies a random seed if reproducible, +#' deterministic forests are desired. The number o1 +#' @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. +#' @examples +#' # Regression Example +#' x1 <- rnorm(1000) +#' x2 <- rnorm(1000) +#' y <- 1 + x1 + x2 + rnorm(1000) +#' +#' data <- data.frame(x1, x2, y) +#' forest <- train(y ~ x1 + x2, data, WeightedVarianceSplitFinder(), MeanResponseCombiner(), MeanResponseCombiner(), ntree=100, numberOfSplits = 5, mtry = 1, nodeSize = 5) +#' +#' # Fix x2 to be 0 +#' newData <- data.frame(x1 = seq(from=-2, to=2, by=0.5), x2 = 0) +#' ypred <- predict(forest, newData) +#' +#' plot(ypred ~ newData$x1, type="l") +#' +#' # Competing Risk Example +#' x1 <- abs(rnorm(1000)) +#' x2 <- abs(rnorm(1000)) +#' +#' T1 <- rexp(1000, rate=x1) +#' T2 <- rweibull(1000, shape=x1, scale=x2) +#' C <- rexp(1000) +#' u <- pmin(T1, T2, C) +#' delta <- ifelse(u==T1, 1, ifelse(u==T2, 2, 0)) +#' +#' data <- data.frame(x1, x2) +#' +#' forest <- train(CompetingRiskResponses(delta, u) ~ x1 + x2, data, +#' LogRankSplitFinder(1:2), CompetingRiskResponseCombiner(1:2), CompetingRiskFunctionCombiner(1:2), ntree=100, numberOfSplits=5, mtry=1, nodeSize=10) +#' newData <- data.frame(x1 = c(-1, 0, 1), x2 = 0) +#' ypred <- predict(forest, newData) +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){ + + # Some quick checks on parameters + ntree <- as.integer(ntree) + numberOfSplits <- as.integer(numberOfSplits) + mtry <- as.integer(mtry) + nodeSize <- as.integer(nodeSize) + maxNodeDepth <- as.integer(maxNodeDepth) + cores <- as.integer(cores) + + if (ntree <= 0){ + stop("ntree must be strictly positive.") + } + if (numberOfSplits < 0){ + stop("numberOfSplits cannot be negative.") + } + if (mtry <= 0){ + stop("mtry must be strictly positive. If you want to try all covariates, you can set it to be very large.") + } + if (nodeSize <= 0){ + stop("nodeSize must be strictly positive.") + } + if (maxNodeDepth <= 0){ + stop("maxNodeDepth must be strictly positive") + } + if (cores <= 0){ + stop("cores must be strictly positive") + } + + 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\")") + } + + + if(class(nodeResponseCombiner) != "ResponseCombiner"){ + stop("nodeResponseCombiner must be a ResponseCombiner") + } + if(class(splitFinder) != "SplitFinder"){ + stop("splitFinder must be a SplitFinder") + } + if(class(forestResponseCombiner) != "ResponseCombiner"){ + stop("forestResponseCombiner must be a ResponseCombiner") + } + + if(class(covariateData)=="environment"){ + if(is.null(covariateData$data)){ + stop("When providing an environment with the dataset, the environment must contain an item called 'data'") + } + dataset <- loadData(covariateData$data, colnames(covariateData$data), responses) + covariateData$data <- NULL # save memory, hopefully + gc() # explicitly try to save memory + } + else{ + dataset <- loadData(covariateData, colnames(covariateData), responses) + } + + + + treeTrainer <- createTreeTrainer(responseCombiner=nodeResponseCombiner, + splitFinder=splitFinder, + covariateList=dataset$covariateList, + numberOfSplits=numberOfSplits, + nodeSize=nodeSize, + maxNodeDepth=maxNodeDepth, + mtry=mtry, + splitPureNodes=splitPureNodes) + + forestTrainer <- createForestTrainer(treeTrainer=treeTrainer, + covariateList=dataset$covariateList, + treeResponseCombiner=forestResponseCombiner, + dataset=dataset$dataset, + ntree=ntree, + randomSeed=randomSeed, + saveTreeLocation=savePath) + + params <- list( + splitFinder=splitFinder, + nodeResponseCombiner=nodeResponseCombiner, + forestResponseCombiner=forestResponseCombiner, + ntree=ntree, + numberOfSplits=numberOfSplits, + mtry=mtry, + nodeSize=nodeSize, + splitPureNodes=splitPureNodes, + maxNodeDepth = maxNodeDepth, + savePath=savePath + ) + + # 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) + } + + } + + 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=dataset$covariateList, + params=params, + forestCall=match.call()) + + if(cores > 1){ + .jcall(forestTrainer, "V", "trainParallelOnDisk", as.integer(cores)) + } else { + .jcall(forestTrainer, "V", "trainSerialOnDisk") + } + + # Need to now load forest trees back into memory + forest.java <- .jcall(.class_DataUtils, makeResponse(.class_Forest), "loadForest", savePath, forestResponseCombiner$javaObject) + + + } + else{ # save directly into memory + if(cores > 1){ + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainParallelInMemory", as.integer(cores)) + } else { + forest.java <- .jcall(forestTrainer, makeResponse(.class_Forest), "trainSerialInMemory") + } + } + + + + + forestObject <- list(call=match.call(), params=params, javaObject=forest.java, covariateList=dataset$covariateList) + + # TODO - remove redundant code if tests pass + #forestObject$params <- list( + # splitFinder=splitFinder, + # nodeResponseCombiner=nodeResponseCombiner, + # forestResponseCombiner=forestResponseCombiner, + # ntree=ntree, + # numberOfSplits=numberOfSplits, + # mtry=mtry, + # nodeSize=nodeSize, + # splitPureNodes=splitPureNodes, + # maxNodeDepth = maxNodeDepth, + # savePath=savePath + #) + + class(forestObject) <- "JRandomForest" + return(forestObject) + +} + + + + +#' @rdname train +#' @export +#' @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, ...){ + + # 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$data)){ + stop("When providing an environment with the dataset, the environment must contain an item called 'data'") + } + + env <- covariateData + covariateData <- env$data + } + + yVar <- formula[[2]] + + responses <- NULL + 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, + # then we also need to explicitly evaluate it + if(class(yVar)=="call" || !(as.character(yVar) %in% colnames(covariateData))){ + # yVar is a function like CompetingRiskResponses + responses <- eval(expr=yVar, envir=covariateData) + + 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)] + } + + formula[[2]] <- NULL + + } else if(class(yVar)=="name"){ # and implicitly yVar is contained in covariateData + 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) + + if(is.null(responses)){ + responses <- model.response(mf) + } + + # remove any response variables + mf <- mf[,!(names(mf) %in% variablesToDrop), drop=FALSE] + + # If environment was provided instead of data + if(!is.null(env)){ + env$data <- mf + rm(covariateData) + forest <- train.default(responses, env, ...) + } else{ + forest <- train.default(responses, mf, ...) + } + + + + forest$call <- match.call() + forest$formula <- formula + + return(forest) +} + +createForestTrainer <- function(treeTrainer, covariateList, treeResponseCombiner, dataset, ntree, randomSeed, saveTreeLocation){ + builderClassReturned <- makeResponse(.class_ForestTrainer_Builder) + + builder <- .jcall(.class_ForestTrainer, builderClassReturned, "builder") + + builder <- .jcall(builder, builderClassReturned, "treeTrainer", treeTrainer) + builder <- .jcall(builder, builderClassReturned, "covariates", covariateList) + builder <- .jcall(builder, builderClassReturned, "treeResponseCombiner", treeResponseCombiner$javaObject) + builder <- .jcall(builder, builderClassReturned, "data", dataset) + builder <- .jcall(builder, builderClassReturned, "ntree", as.integer(ntree)) + builder <- .jcall(builder, builderClassReturned, "displayProgress", TRUE) + + if(!is.null(randomSeed)){ + builder <- .jcall(builder, builderClassReturned, "randomSeed", .jlong(randomSeed)) + } + else{ + builder <- .jcall(builder, builderClassReturned, "randomSeed", .jlong(as.integer(Sys.time()))) + } + + if(!is.null(saveTreeLocation)){ + builder <- .jcall(builder, builderClassReturned, "saveTreeLocation", saveTreeLocation) + } + + + forestTrainer <- .jcall(builder, makeResponse(.class_ForestTrainer), "build") + return(forestTrainer) +} + +createTreeTrainer <- function(responseCombiner, splitFinder, covariateList, numberOfSplits, nodeSize, maxNodeDepth, mtry, splitPureNodes){ + builderClassReturned <- makeResponse(.class_TreeTrainer_Builder) + + builder <- .jcall(.class_TreeTrainer, builderClassReturned, "builder") + + builder <- .jcall(builder, builderClassReturned, "responseCombiner", responseCombiner$javaObject) + builder <- .jcall(builder, builderClassReturned, "splitFinder", splitFinder$javaObject) + builder <- .jcall(builder, builderClassReturned, "covariates", covariateList) + builder <- .jcall(builder, builderClassReturned, "numberOfSplits", as.integer(numberOfSplits)) + builder <- .jcall(builder, builderClassReturned, "nodeSize", as.integer(nodeSize)) + builder <- .jcall(builder, builderClassReturned, "maxNodeDepth", as.integer(maxNodeDepth)) + builder <- .jcall(builder, builderClassReturned, "mtry", as.integer(mtry)) + builder <- .jcall(builder, builderClassReturned, "checkNodePurity", !splitPureNodes) + + treeTrainer <- .jcall(builder, makeResponse(.class_TreeTrainer), "build") + return(treeTrainer) +} diff --git a/R/wrapFunction.R b/R/wrapFunction.R new file mode 100644 index 0000000..1151fac --- /dev/null +++ b/R/wrapFunction.R @@ -0,0 +1,12 @@ +wrapFunction <- function(mf){ + f <- function(x){ + + y <- vector(mode="numeric", length=length(x)) + for(i in 1:length(x)){ + y[i] <- .jcall(mf, "D", "evaluate", x[i]) + } + + return(y) + + } +} diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..9edb824 --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,7 @@ +.onLoad <- function(libname, pkgname) { + # rJava needs to be initialized with the path to the class files + .jpackage(pkgname, lib.loc=libname, morePaths = "inst/java/") +} + +#' @import rJava +NULL diff --git a/inst/java/ca/joeltherrien/randomforest/Bootstrapper.class 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