Repository: spark Updated Branches: refs/heads/branch-2.0 c7704099d -> 4c4f7775c
[SPARK-16143][R] group AFT survival regression methods docs in a single Rd ## What changes were proposed in this pull request? This PR groups `spark.survreg`, `summary(AFT)`, `predict(AFT)`, `write.ml(AFT)` for survival regression into a single Rd. ## How was this patch tested? Manually checked generated HTML doc. See attached screenshots.   Author: Junyang Qian <junya...@databricks.com> Closes #13927 from junyangq/SPARK-16143. (cherry picked from commit 1b7fc5817203db5a56489b289fb1a0dd44b2e26b) Signed-off-by: Xiangrui Meng <m...@databricks.com> Project: http://git-wip-us.apache.org/repos/asf/spark/repo Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/4c4f7775 Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/4c4f7775 Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/4c4f7775 Branch: refs/heads/branch-2.0 Commit: 4c4f7775cbf5dd69e688350ee59a9319bcaa56fe Parents: c770409 Author: Junyang Qian <junya...@databricks.com> Authored: Mon Jun 27 20:32:27 2016 -0700 Committer: Xiangrui Meng <m...@databricks.com> Committed: Mon Jun 27 20:32:35 2016 -0700 ---------------------------------------------------------------------- R/pkg/R/mllib.R | 88 +++++++++++++++++++++++++--------------------------- 1 file changed, 42 insertions(+), 46 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/spark/blob/4c4f7775/R/pkg/R/mllib.R ---------------------------------------------------------------------- diff --git a/R/pkg/R/mllib.R b/R/pkg/R/mllib.R index 853cfce..8e6c2dd 100644 --- a/R/pkg/R/mllib.R +++ b/R/pkg/R/mllib.R @@ -233,9 +233,10 @@ setMethod("predict", signature(object = "GeneralizedLinearRegressionModel"), # Makes predictions from a naive Bayes model or a model produced by spark.naiveBayes(), # similarly to R package e1071's predict. -#' @rdname spark.naiveBayes +#' @param newData A SparkDataFrame for testing #' @return \code{predict} returns a SparkDataFrame containing predicted labeled in a column named #' "prediction" +#' @rdname spark.naiveBayes #' @export #' @note predict(NaiveBayesModel) since 2.0.0 setMethod("predict", signature(object = "NaiveBayesModel"), @@ -439,25 +440,16 @@ setMethod("write.ml", signature(object = "NaiveBayesModel", path = "character"), invisible(callJMethod(writer, "save", path)) }) -#' Save fitted MLlib model to the input path -#' -#' Save the AFT survival regression model to the input path. -#' -#' @param object A fitted AFT survival regression model -#' @param path The directory where the model is saved -#' @param overwrite Overwrites or not if the output path already exists. Default is FALSE +# Saves the AFT survival regression model to the input path. + +#' @param path The directory where the model is savedist containing the model's coefficien #' which means throw exception if the output path exists. #' -#' @rdname write.ml +#' @rdname spark.survreg #' @name write.ml #' @export -#' @examples -#' \dontrun{ -#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx) -#' path <- "path/to/model" -#' write.ml(model, path) -#' } #' @note write.ml(AFTSurvivalRegressionModel, character) since 2.0.0 +#' @seealso \link{read.ml} setMethod("write.ml", signature(object = "AFTSurvivalRegressionModel", path = "character"), function(object, path, overwrite = FALSE) { writer <- callJMethod(object@jobj, "write") @@ -542,15 +534,18 @@ read.ml <- function(path) { } } -#' Fit an accelerated failure time (AFT) survival regression model. +#' Accelerated Failure Time (AFT) Survival Regression Model #' -#' Fit an accelerated failure time (AFT) survival regression model on a Spark DataFrame. +#' \code{spark.survreg} fits an accelerated failure time (AFT) survival regression model on +#' a SparkDataFrame. Users can call \code{summary} to get a summary of the fitted AFT model, +#' \code{predict} to make predictions on new data, and \code{write.ml}/\code{read.ml} to +#' save/load fitted models. #' -#' @param data SparkDataFrame for training. +#' @param data A SparkDataFrame for training #' @param formula A symbolic description of the model to be fitted. Currently only a few formula #' operators are supported, including '~', ':', '+', and '-'. -#' Note that operator '.' is not supported currently. -#' @return a fitted AFT survival regression model +#' Note that operator '.' is not supported currently +#' @return \code{spark.survreg} returns a fitted AFT survival regression model #' @rdname spark.survreg #' @seealso survival: \url{https://cran.r-project.org/web/packages/survival/} #' @export @@ -558,6 +553,19 @@ read.ml <- function(path) { #' \dontrun{ #' df <- createDataFrame(ovarian) #' model <- spark.survreg(df, Surv(futime, fustat) ~ ecog_ps + rx) +#' +#' # get a summary of the model +#' summary(model) +#' +#' # make predictions +#' predicted <- predict(model, df) +#' showDF(predicted) +#' +#' # save and load the model +#' path <- "path/to/model" +#' write.ml(model, path) +#' savedModel <- read.ml(path) +#' summary(savedModel) #' } #' @note spark.survreg since 2.0.0 setMethod("spark.survreg", signature(data = "SparkDataFrame", formula = "formula"), @@ -569,20 +577,14 @@ setMethod("spark.survreg", signature(data = "SparkDataFrame", formula = "formula }) -#' Get the summary of an AFT survival regression model -#' -#' Returns the summary of an AFT survival regression model produced by spark.survreg(), -#' similarly to R's summary(). -#' -#' @param object a fitted AFT survival regression model -#' @return coefficients the model's coefficients, intercept and log(scale). -#' @rdname summary +# Returns a summary of the AFT survival regression model produced by spark.survreg, +# similarly to R's summary(). + +#' @param object A fitted AFT survival regression model +#' @return \code{summary} returns a list containing the model's coefficients, +#' intercept and log(scale) +#' @rdname spark.survreg #' @export -#' @examples -#' \dontrun{ -#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx) -#' summary(model) -#' } #' @note summary(AFTSurvivalRegressionModel) since 2.0.0 setMethod("summary", signature(object = "AFTSurvivalRegressionModel"), function(object, ...) { @@ -595,20 +597,14 @@ setMethod("summary", signature(object = "AFTSurvivalRegressionModel"), return(list(coefficients = coefficients)) }) -#' Predicted values based on model -#' -#' Makes predictions from an AFT survival regression model or a model produced by spark.survreg(), -#' similarly to R package survival's predict. -#' -#' @param object A fitted AFT survival regression model -#' @rdname predict +# Makes predictions from an AFT survival regression model or a model produced by +# spark.survreg, similarly to R package survival's predict. + +#' @param newData A SparkDataFrame for testing +#' @return \code{predict} returns a SparkDataFrame containing predicted values +#' on the original scale of the data (mean predicted value at scale = 1.0) +#' @rdname spark.survreg #' @export -#' @examples -#' \dontrun{ -#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx) -#' predicted <- predict(model, testData) -#' showDF(predicted) -#' } #' @note predict(AFTSurvivalRegressionModel) since 2.0.0 setMethod("predict", signature(object = "AFTSurvivalRegressionModel"), function(object, newData) { --------------------------------------------------------------------- To unsubscribe, e-mail: commits-unsubscr...@spark.apache.org For additional commands, e-mail: commits-h...@spark.apache.org
