2nd Release candidate V1.1.4

Clean up S3 methods
Remove tests from CRAN release (until I can reduce the run times)

Author: ehrlinger

.Rbuildignore

@@ -8,9 +8,11 @@ cran-comments.md
 ^\.Rprofile$
 Sweave.sty
 useR2014.pdf
-vignettes/figure/
 jss.cls
 jss.bst
 jsslogo.jpg
 framed.sty
+^vignettes/fig-rf/*
+^vignettes/fig-rfs/*
+^tests/*
 

.travis.yml

@@ -5,7 +5,7 @@
 #   https://github.com/craigcitro/r-travis/wiki
 
 language: r
-
+sudo: required
 os:
   - linux
   - osx

NAMESPACE

@@ -1,22 +1,35 @@
 # Generated by roxygen2 (4.1.0): do not edit by hand
 
+S3method(gg_error,rfsrc)
+S3method(gg_interaction,default)
+S3method(gg_interaction,rfsrc)
+S3method(gg_minimal_depth,default)
+S3method(gg_minimal_depth,rfsrc)
+S3method(gg_minimal_vimp,default)
+S3method(gg_minimal_vimp,rfsrc)
+S3method(gg_partial,rfsrc)
+S3method(plot,gg_error)
+S3method(plot,gg_interaction)
+S3method(plot,gg_minimal_depth)
+S3method(plot,gg_minimal_vimp)
+S3method(plot,gg_partial)
+S3method(plot,gg_partial_list)
+S3method(plot,gg_rfsrc)
+S3method(plot,gg_roc)
+S3method(plot,gg_survival)
+S3method(plot,gg_variable)
+S3method(plot,gg_vimp)
+S3method(print,gg_minimal_depth)
 export(calc_auc)
-export(calc_roc)
 export(calc_roc.rfsrc)
 export(combine.gg_partial)
-export(combine.gg_partial_list)
 export(gg_error)
-export(gg_error.rfsrc)
 export(gg_interaction)
-export(gg_interaction.rfsrc)
 export(gg_minimal_depth)
-export(gg_minimal_depth.rfsrc)
 export(gg_minimal_vimp)
-export(gg_minimal_vimp.rfsrc)
 export(gg_partial)
-export(gg_partial.rfsrc)
 export(gg_partial_coplot)
-export(gg_partial_coplot.ggRandomForests)
+export(gg_partial_coplot.rfsrc)
 export(gg_rfsrc)
 export(gg_rfsrc.rfsrc)
 export(gg_roc)
@@ -29,22 +42,9 @@ export(gg_vimp.rfsrc)
 export(kaplan)
 export(nelson)
 export(partial.rfsrc)
-export(plot.gg_error)
-export(plot.gg_interaction)
-export(plot.gg_minimal_depth)
-export(plot.gg_minimal_vimp)
-export(plot.gg_partial)
-export(plot.gg_partial_list)
-export(plot.gg_rfsrc)
-export(plot.gg_roc)
-export(plot.gg_survival)
-export(plot.gg_variable)
-export(plot.gg_vimp)
-export(print.gg_minimal_depth)
 export(quantile_pts)
 export(rfsrc_cache_datasets)
 export(surface_matrix)
-export(surface_matrix.gg_partial_coplot)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,annotate)

NEWS

@@ -1,7 +1,6 @@
 Package: ggRandomForests
 Version: 1.1.4
 
-
 ggRandomForests v1.1.4
 ===================
 * `combine.gg_partial` bug when giving a single variable plot.variable object.
@@ -15,9 +14,11 @@ ggRandomForests v1.1.4
 * Vignette updates for JSS submission of "ggRandomForests: Exploring Random Forest Survival".
 * Vignette updates for arXiv submission of ggRandomForests: Random Forests for Regression
 
-* Setup continuous code testing with Travis-CI and Coveralls.
-* Improved unit tests to implemnt code test coverage using `covr` package.
 * Some optimizations to reduce package size.
+* Remove all tests from CRAN build to optimise R CMD CHECK times.
+* Remove pdf vignette figure from CRAN build.
+* Return S3method calls to NAMESPACE for "S3 methods exported but not registered" for R V3.2+.
+  
 * Misc Bug Fixes.
 
 ggRandomForests v1.1.3

R/calc_roc.R

@@ -38,14 +38,13 @@
 #' 
 #' @importFrom parallel mclapply
 #' 
-#' @export calc_roc calc_roc.rfsrc
 #' @examples
 #' ## Taken from the gg_roc example
 #' # rfsrc_iris <- rfsrc(Species ~ ., data = iris)
 #' data(rfsrc_iris)
 #' gg_dta <- calc_roc.rfsrc(rfsrc_iris, rfsrc_iris$yvar, which.outcome=1, oob=TRUE)
 #' gg_dta <- calc_roc.rfsrc(rfsrc_iris, rfsrc_iris$yvar, which.outcome=1, oob=FALSE)
-#' 
+#' @export
 
 calc_roc.rfsrc <- function(object, yvar, which.outcome="all", oob=TRUE){
   if(!is.factor(yvar)) yvar <- factor(yvar)
@@ -134,9 +133,8 @@ calc_roc <- calc_roc.rfsrc
 #' 
 #' calc_auc(gg_dta)
 #' 
-#' @export calc_auc
 #' @aliases calc_auc calc_auc.gg_roc
-#' 
+#' @export
 calc_auc <- function(x){
   ## Use the trapeziod rule, basically calc
   ##

R/combine.gg_partial.R

@@ -21,7 +21,6 @@
 #'  
 #'  @return \code{\link{gg_partial}}  or \code{gg_partial_list} based on class of x and y.
 #'  
-#'  @export combine.gg_partial_list combine.gg_partial
 #'  @aliases combine.gg_partial combine.gg_partial_list
 #' 
 #' @importFrom parallel mclapply
@@ -64,7 +63,7 @@
 #' 
 #
 # Tested in the gg_partial testthat file.
-
+#' @export
 combine.gg_partial <- function(x, y, lbls, ...){
   return(combine.gg_partial_list(x, y, lbls, ...))
 }

R/gg_error.R

@@ -31,8 +31,6 @@
 #' @return \code{gg_error} \code{data.frame} with one column indicating the tree number, 
 #' and the remaining columns from the \code{randomForestSRC::rfsrc$err.rate} return value. 
 #' 
-#' @export gg_error.rfsrc gg_error
-#' 
 #' @seealso \code{\link{plot.gg_error}} \code{rfsrc} \code{plot.rfsrc}
 #' 
 #' @references
@@ -115,10 +113,11 @@
 #' gg_dta <- gg_error(rfsrc_pbc)
 #' plot(gg_dta)
 #' 
+#' @export 
 gg_error <- function (object, ...) {
   UseMethod("gg_error", object)
 }
-
+#' @export 
 gg_error.rfsrc <- function(object, ...) {
   ## Check that the input obect is of the correct type.
   if (!inherits(object, "rfsrc")){

R/gg_interaction.R

@@ -36,7 +36,6 @@
 #' \code{randomForestSRC::vimp}
 #' \code{\link{plot.gg_interaction}} 
 #' 
-#' @export gg_interaction gg_interaction.rfsrc 
 #' @aliases gg_interaction
 #' 
 #' @importFrom randomForestSRC find.interaction
@@ -122,11 +121,11 @@
 #' plot(gg_dta, panel=TRUE)
 #' }
 #' 
-
-# gg_interaction <- function (object, ...) {
-#   UseMethod("gg_interaction", object)
-# }
-
+#' @export 
+gg_interaction <- function (object, ...) {
+  UseMethod("gg_interaction", object)
+}
+#' @export
 gg_interaction.rfsrc <- function(object, ...){
   if (inherits(object, "rfsrc")) {
     # If we called this with a rfsrc object, we need to run find.interaction.
@@ -151,4 +150,6 @@ gg_interaction.rfsrc <- function(object, ...){
 
   invisible(gg_dta)
 }
-gg_interaction <- gg_interaction.rfsrc
+# 
+#' @export
+gg_interaction.default <- gg_interaction.rfsrc

R/gg_minimal_depth.R

@@ -31,7 +31,6 @@
 #' @return \code{gg_minimal_depth} object, A modified list of variables from the 
 #' \code{randomForestSRC::var.select} function, ordered by minimal depth rank. 
 #' 
-#' @export gg_minimal_depth gg_minimal_depth.rfsrc 
 #' @aliases gg_minimal_depth gg_minimal_depth.rfsrc
 #' 
 #' @seealso \code{randomForestSRC::var.select} \code{\link{plot.gg_minimal_depth}}
@@ -110,7 +109,12 @@
 #' gg_dta <- gg_minimal_depth(varsel_pbc)
 #' plot(gg_dta)
 #' 
+#' @export
+gg_minimal_depth <- function (object, ...) {
+  UseMethod("gg_minimal_depth", object)
+}
 
+#' @export
 gg_minimal_depth.rfsrc <- function (object, ...){
 
   if (inherits(object, "rfsrc") == TRUE){
@@ -139,4 +143,6 @@ gg_minimal_depth.rfsrc <- function (object, ...){
   invisible(vsel) 
 }
 
-gg_minimal_depth <- gg_minimal_depth.rfsrc                     
+#' @export
+gg_minimal_depth.default <- 
+  gg_minimal_depth.rfsrc

R/gg_minimal_vimp.R

@@ -19,16 +19,13 @@
 #' 
 #' @param object A \code{randomForestSRC::rfsrc} object, \code{randomForestSRC::predict}
 #'  object or the list from the \code{randomForestSRC::var.select.rfsrc} function.
-#' @param event an optional vector of logical values (event indicator) for 
-#' shaping the points in when plotting.
 #' @param ... optional arguments passed to the \code{randomForestSRC::var.select} function 
 #'  if operating on an \code{randomForestSRC::rfsrc} object. 
-#'  
+#' 
 #'  @return \code{gg_minimal_vimp} comparison object.
 #'  
 #'  @seealso \code{\link{plot.gg_minimal_vimp}} \code{randomForestSRC::var.select}
 #'  
-#'  @export gg_minimal_vimp gg_minimal_vimp.rfsrc
 #'  @aliases gg_minimal_vimp
 #'  
 #' @examples
@@ -105,8 +102,12 @@
 #' 
 #' gg_dta <- gg_minimal_vimp(varsel_pbc)
 #' plot(gg_dta)
-
-gg_minimal_vimp.rfsrc <- function(object, event, ...){
+#' @export
+gg_minimal_vimp <- function (object, ...) {
+  UseMethod("gg_minimal_vimp", object)
+}
+#' @export
+gg_minimal_vimp.rfsrc <- function(object, ...){
 
   if (inherits(object, "rfsrc") == TRUE){
     vsel <- var.select(object, ...)
@@ -138,4 +139,6 @@ gg_minimal_vimp.rfsrc <- function(object, event, ...){
   class(gg_dta) <- c("gg_minimal_vimp", class(gg_dta))
   invisible(gg_dta)
 }
-gg_minimal_vimp <- gg_minimal_vimp.rfsrc
+
+#' @export
+gg_minimal_vimp.default <- gg_minimal_vimp.rfsrc