[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. ![screen shot 2016-06-27 at 10 28 20 am](https://cloud.githubusercontent.com/assets/15318264/16392008/a14cf472-3c5e-11e6-9ce5-490ed1a52249.png) ![screen shot 2016-06-27 at 10 28 35 am](https://cloud.githubusercontent.com/assets/15318264/16392009/a14e333c-3c5e-11e6-8bd7-c2e9ba71f8e2.png) Author: Junyang Qian <junyangq@databricks.com> Closes #13927 from junyangq/SPARK-16143.
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@ -233,9 +233,10 @@ setMethod("predict", signature(object = "GeneralizedLinearRegressionModel"),
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# Makes predictions from a naive Bayes model or a model produced by spark.naiveBayes(),
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# similarly to R package e1071's predict.
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#' @rdname spark.naiveBayes
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#' @param newData A SparkDataFrame for testing
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#' @return \code{predict} returns a SparkDataFrame containing predicted labeled in a column named
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#' "prediction"
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#' @rdname spark.naiveBayes
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#' @export
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#' @note predict(NaiveBayesModel) since 2.0.0
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setMethod("predict", signature(object = "NaiveBayesModel"),
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@ -439,25 +440,16 @@ setMethod("write.ml", signature(object = "NaiveBayesModel", path = "character"),
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invisible(callJMethod(writer, "save", path))
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})
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#' Save fitted MLlib model to the input path
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#'
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#' Save the AFT survival regression model to the input path.
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#'
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#' @param object A fitted AFT survival regression model
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#' @param path The directory where the model is saved
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#' @param overwrite Overwrites or not if the output path already exists. Default is FALSE
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# Saves the AFT survival regression model to the input path.
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#' @param path The directory where the model is savedist containing the model's coefficien
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#' which means throw exception if the output path exists.
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#'
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#' @rdname write.ml
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#' @rdname spark.survreg
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#' @name write.ml
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#' @export
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#' @examples
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#' \dontrun{
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#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx)
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#' path <- "path/to/model"
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#' write.ml(model, path)
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#' }
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#' @note write.ml(AFTSurvivalRegressionModel, character) since 2.0.0
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#' @seealso \link{read.ml}
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setMethod("write.ml", signature(object = "AFTSurvivalRegressionModel", path = "character"),
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function(object, path, overwrite = FALSE) {
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writer <- callJMethod(object@jobj, "write")
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@ -542,15 +534,18 @@ read.ml <- function(path) {
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}
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}
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#' Fit an accelerated failure time (AFT) survival regression model.
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#' Accelerated Failure Time (AFT) Survival Regression Model
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#'
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#' Fit an accelerated failure time (AFT) survival regression model on a Spark DataFrame.
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#' \code{spark.survreg} fits an accelerated failure time (AFT) survival regression model on
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#' a SparkDataFrame. Users can call \code{summary} to get a summary of the fitted AFT model,
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#' \code{predict} to make predictions on new data, and \code{write.ml}/\code{read.ml} to
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#' save/load fitted models.
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#'
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#' @param data SparkDataFrame for training.
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#' @param data A SparkDataFrame for training
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#' @param formula A symbolic description of the model to be fitted. Currently only a few formula
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#' operators are supported, including '~', ':', '+', and '-'.
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#' Note that operator '.' is not supported currently.
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#' @return a fitted AFT survival regression model
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#' Note that operator '.' is not supported currently
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#' @return \code{spark.survreg} returns a fitted AFT survival regression model
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#' @rdname spark.survreg
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#' @seealso survival: \url{https://cran.r-project.org/web/packages/survival/}
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#' @export
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@ -558,6 +553,19 @@ read.ml <- function(path) {
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#' \dontrun{
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#' df <- createDataFrame(ovarian)
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#' model <- spark.survreg(df, Surv(futime, fustat) ~ ecog_ps + rx)
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#'
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#' # get a summary of the model
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#' summary(model)
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#'
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#' # make predictions
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#' predicted <- predict(model, df)
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#' showDF(predicted)
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#'
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#' # save and load the model
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#' path <- "path/to/model"
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#' write.ml(model, path)
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#' savedModel <- read.ml(path)
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#' summary(savedModel)
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#' }
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#' @note spark.survreg since 2.0.0
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setMethod("spark.survreg", signature(data = "SparkDataFrame", formula = "formula"),
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@ -569,20 +577,14 @@ setMethod("spark.survreg", signature(data = "SparkDataFrame", formula = "formula
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})
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#' Get the summary of an AFT survival regression model
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#'
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#' Returns the summary of an AFT survival regression model produced by spark.survreg(),
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#' similarly to R's summary().
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#'
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#' @param object a fitted AFT survival regression model
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#' @return coefficients the model's coefficients, intercept and log(scale).
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#' @rdname summary
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# Returns a summary of the AFT survival regression model produced by spark.survreg,
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# similarly to R's summary().
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#' @param object A fitted AFT survival regression model
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#' @return \code{summary} returns a list containing the model's coefficients,
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#' intercept and log(scale)
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#' @rdname spark.survreg
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#' @export
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#' @examples
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#' \dontrun{
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#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx)
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#' summary(model)
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#' }
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#' @note summary(AFTSurvivalRegressionModel) since 2.0.0
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setMethod("summary", signature(object = "AFTSurvivalRegressionModel"),
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function(object, ...) {
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@ -595,20 +597,14 @@ setMethod("summary", signature(object = "AFTSurvivalRegressionModel"),
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return(list(coefficients = coefficients))
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})
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#' Predicted values based on model
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#'
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#' Makes predictions from an AFT survival regression model or a model produced by spark.survreg(),
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#' similarly to R package survival's predict.
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#'
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#' @param object A fitted AFT survival regression model
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#' @rdname predict
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# Makes predictions from an AFT survival regression model or a model produced by
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# spark.survreg, similarly to R package survival's predict.
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#' @param newData A SparkDataFrame for testing
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#' @return \code{predict} returns a SparkDataFrame containing predicted values
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#' on the original scale of the data (mean predicted value at scale = 1.0)
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#' @rdname spark.survreg
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#' @export
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#' @examples
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#' \dontrun{
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#' model <- spark.survreg(trainingData, Surv(futime, fustat) ~ ecog_ps + rx)
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#' predicted <- predict(model, testData)
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#' showDF(predicted)
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#' }
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#' @note predict(AFTSurvivalRegressionModel) since 2.0.0
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setMethod("predict", signature(object = "AFTSurvivalRegressionModel"),
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function(object, newData) {
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