adding imports and more s3classes

MichaelChirico · Sep 15, 2016 · 9b4e3fe · 9b4e3fe
1 parent 10ebaee
commit 9b4e3fe
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diff --git a/deprecated/normalize2Reference.R b/deprecated/normalize2Reference.R
@@ -1,3 +1,4 @@
+#' @importFrom stats approx
 "normalize2Reference" <-
   function (data, refData = NULL, ties = TRUE) 
 {

diff --git a/pkg/caret/NAMESPACE b/pkg/caret/NAMESPACE
@@ -1,10 +1,5 @@
-useDynLib(caret)
-importFrom(ModelMetrics, auc)
-import(foreach, methods, plyr, reshape2, ggplot2, lattice, nlme)
-importFrom(car, powerTransform, yjPower)
-importFrom(grDevices, extendrange)
-importFrom(stats, .checkMFClasses, .getXlevels, aggregate, anova,
-           approx, as.formula, binom.test, complete.cases, contrasts,
+
+importFrom(stats, 
            cor, cov, delete.response, dist,
            fitted.values, loess, mahalanobis,
            mcnemar.test, median, model.frame, model.matrix,
@@ -18,132 +13,3 @@ importFrom(utils, capture.output, getFromNamespace, head,
            install.packages, installed.packages, object.size, flush.console, menu, stack,
            modifyList, combn
            )
-
-
-S3method(train,       formula)
-S3method(rfe,         formula)
-
-
-S3method(varImp, train)
-S3method(varImp, rpart)
-S3method(varImp, randomForest)
-S3method(varImp, gbm)
-S3method(varImp, classbagg)
-S3method(varImp, regbagg)
-S3method(varImp, pamrtrained)
-S3method(varImp, lm)
-S3method(varImp, glm)
-S3method(varImp, mvr)
-S3method(varImp, earth)
-S3method(varImp, bagEarth)
-S3method(varImp, bagFDA)
-S3method(varImp, RandomForest)
-S3method(varImp, dsa)
-S3method(varImp, plsda)
-S3method(varImp, fda)
-S3method(varImp, multinom)
-S3method(varImp, cubist)
-S3method(varImp, RRF)
-S3method(varImp, PART)
-S3method(varImp, JRip)
-S3method(varImp, C5.0)
-S3method(varImp, nnet)
-S3method(varImp, glmnet)
-S3method(varImp, gam)
-S3method(varImp, gafs)
-S3method(varImp, safs)
-
-S3method(densityplot, train)
-S3method(histogram,   train)
-S3method(stripplot,   train)
-S3method(xyplot,      train)
-
-
-S3method(plot,  train)
-S3method(plot,  gafs)
-S3method(plot,  safs)
-
-S3method(confusionMatrix,  train)
-S3method(confusionMatrix,  rfe)
-S3method(confusionMatrix,  sbf)
-
-S3method(print, train)
-S3method(print, varImp.train)
-S3method(print, confusionMatrix)
-S3method(print, confusionMatrix.train)
-S3method(print, confusionMatrix.rfe)
-S3method(print, confusionMatrix.sbf)
-S3method(print, knn3)
-S3method(print, plsda)
-S3method(print, splsda)
-S3method(print, bagEarth)
-S3method(print, bagFDA)
-S3method(print, summary.bagEarth)
-S3method(print, summary.bagFDA)
-S3method(print, preProcess)
-S3method(print, pcaNNet)
-
-
-S3method(print, gafs)
-S3method(print, safs)
-
-S3method(predict, plsda)
-S3method(predict, splsda)
-S3method(predict, knn3)
-S3method(predict, bagEarth)
-S3method(predict, bagFDA)
-S3method(predict, preProcess)
-S3method(predict, pcaNNet)
-S3method(predict, list)
-S3method(predict, train)
-
-S3method(predict, gafs)
-S3method(predict, safs)
-
-S3method(summary, bagEarth)
-S3method(summary, bagFDA)
-
-S3method(format, bagEarth)
-
-S3method(predictors, train)
-S3method(predictors, terms)
-S3method(predictors, formula)
-S3method(predictors, list)
-S3method(predictors, default)
-S3method(predictors, gafs)
-S3method(predictors, safs)
-
-S3method(confusionMatrix, table)
-
-
-
-S3method(as.table,  confusionMatrix)
-S3method(as.matrix, confusionMatrix)
-
-S3method(update, gafs)
-S3method(update, safs)
-
-
-S3method(levels, train)
-
-S3method(ggplot, train)
-S3method(ggplot, rfe)
-
-
-S3method(oob_pred, train)
-S3method(oob_pred, rfe)
-S3method(oob_pred, sbf)
-S3method(oob_pred, list)
-
-S3method(gafs, default)
-S3method(safs, default)
-
-S3method(trim, train)
-
-S3method(spatialSign, matrix)
-S3method(spatialSign, data.frame)
-
-S3method(knn3, matrix)
-S3method(knn3, data.frame)
-S3method(knn3, formula)
-
diff --git a/pkg/caret/R/aaa.R b/pkg/caret/R/aaa.R
@@ -15,6 +15,10 @@
 ##
 ## and other examples.
 
+
+#' @useDynLib caret
+#' @import methods plyr reshape2 ggplot2 lattice nlme
+
 ###################################################################
 ## Global Variables
 ###################################################################
@@ -223,6 +227,8 @@ defaultSummary <- function(data, lev = NULL, model = NULL)
   postResample(data[,"pred"], data[,"obs"])
 }
 
+
+#' @importFrom ModelMetrics auc
 #' @export
 twoClassSummary <- function (data, lev = NULL, model = NULL)
 {
@@ -242,6 +248,7 @@ twoClassSummary <- function (data, lev = NULL, model = NULL)
   out
 }
 
+#' @importFrom stats complete.cases
 #' @export
 mnLogLoss <- function(data, lev = NULL, model = NULL){
   if(is.null(lev)) stop("'lev' cannot be NULL")

diff --git a/pkg/caret/R/adaptive.R b/pkg/caret/R/adaptive.R
@@ -2,7 +2,8 @@
 ##       add na.action to all eval functions
 ##       change multiplier and alpha to confidence
 
-
+#' @importFrom stats complete.cases
+#' @import foreach
 adaptiveWorkflow <- function(x, y, wts, info, method, ppOpts, ctrl, lev, 
                              metric, maximize, testing = FALSE, ...) {
   loadNamespace("caret")

diff --git a/pkg/caret/R/avNNet.R b/pkg/caret/R/avNNet.R
@@ -5,6 +5,7 @@ avNNet <- function (x, ...)
 
 
 ## this is a near copy of nnet.formula
+#' @importFrom stats .getXlevels contrasts
 #' @export
 avNNet.formula <- function (formula, data, weights, ...,
                             repeats = 5,
@@ -48,6 +49,7 @@ avNNet.formula <- function (formula, data, weights, ...,
   res
 }
 
+#' @import foreach
 #' @export 
 avNNet.default <- function(x, y, repeats = 5, 
                            bag = FALSE, allowParallel = TRUE,
@@ -106,6 +108,7 @@ print.avNNet <- function (x, ...)
   invisible(x)
 }
 
+#' @importFrom stats .checkMFClasses
 #' @export
 predict.avNNet <- function(object, newdata, type = c("raw", "class", "prob"), ...)
   {

diff --git a/pkg/caret/R/bag.R b/pkg/caret/R/bag.R
@@ -115,7 +115,7 @@ bagControl <- function(fit = NULL, predict = NULL, aggregate = NULL, downSample
 
 
 
-
+#' @importFrom stats contrasts
 #' @export
 "bag.formula" <-
   function (formula, data = NULL,..., subset, weights, na.action = na.omit) 

diff --git a/pkg/caret/R/bagEarth.R b/pkg/caret/R/bagEarth.R
@@ -70,6 +70,7 @@
             class = "bagEarth")
 }
 
+#' @importFrom stats contrasts
 #' @export
 "bagEarth.formula" <-
   function (formula, data = NULL, B = 50, summary = mean, keepX = TRUE, ..., subset, weights = NULL, na.action = na.omit) 
@@ -157,7 +158,7 @@
 
 }
 
-
+#' @export
 print.bagEarth <- function (x, ...) 
 {
   cat("\nCall:\n", deparse(x$call), "\n\n", sep = "")
@@ -190,6 +191,7 @@ print.bagEarth <- function (x, ...)
   out
 }
 
+#' @export
 "print.summary.bagEarth" <-
   function(x, digits = max(3, getOption("digits") - 3), ...)
 {

diff --git a/pkg/caret/R/bagFDA.R b/pkg/caret/R/bagFDA.R
@@ -46,6 +46,7 @@ function(x, y, weights = NULL, B = 50, keepX = TRUE, ...)
                   weights = !is.null(weights), dots = list(...)), class = "bagFDA")
 }
 
+#' @importFrom stats contrasts
 #' @export
 "bagFDA.formula" <-
 function (formula, data = NULL, B = 50, keepX = TRUE, ..., subset, weights = NULL, na.action = na.omit) 
@@ -73,7 +74,7 @@ function (formula, data = NULL, B = 50, keepX = TRUE, ..., subset, weights = NUL
    out
 }
 
-
+#' @export
 "print.bagFDA" <-
 function (x, ...) 
 {
@@ -162,6 +163,7 @@ function(object, ...)
    out
 }
 
+#' @export
 "print.summary.bagFDA" <-
 function(x, digits = max(3, getOption("digits") - 3), ...)
 {

diff --git a/pkg/caret/R/calibration.R b/pkg/caret/R/calibration.R
@@ -55,7 +55,7 @@ print.calibration <- function(x, ...)
   invisible(x)
 }
 
-
+#' @importFrom stats binom.test
 calibCalc <- function(x, class = levels(obs)[1], cuts = 11) {
   if(length(cuts) == 1) {
     num_cuts <- cuts
@@ -94,6 +94,8 @@ calibCalc <- function(x, class = levels(obs)[1], cuts = 11) {
 plot.calibration <- function(x, y = NULL, ...) 
   xyplot(x = x, data = NULL, ...)
 
+#' @importFrom stats as.formula
+#' @importFrom grDevices extendrange
 #' @export
 xyplot.calibration <- function(x, data = NULL, ...){
   lFormula <- "Percent ~ midpoint"

diff --git a/pkg/caret/R/classLevels.R b/pkg/caret/R/classLevels.R
@@ -1,4 +1,5 @@
 
+#' @export
 levels.train <- function(x, ...) {
   if(any(names(x) == "levels")) {
     out <- x$levels

diff --git a/pkg/caret/R/common_code.R b/pkg/caret/R/common_code.R
@@ -78,10 +78,12 @@ change_text <- function(old, new, p, show_diff = TRUE) {
   num_text
 }
 
+#' @export
 predictors.gafs <- function(x, ...) {
  x$best_vars
 }
 
+#' @export
 predictors.safs <- function(x, ...) {
   x$best_vars
 }

diff --git a/pkg/caret/R/confusionMatrix.R b/pkg/caret/R/confusionMatrix.R
@@ -52,6 +52,8 @@ confusionMatrix.default <- function(data, reference,
   getFromNamespace("confusionMatrix.table", "caret")(classTable, positive, prevalence = prevalence, mode = mode)
 }
 
+#' @importFrom stats binom.test
+#' @export
 confusionMatrix.table <- function(data, positive = NULL, 
                                   prevalence = NULL, mode = "sens_spec", ...){
   requireNamespaceQuietStop("e1071")
@@ -157,7 +159,7 @@ confusionMatrix.table <- function(data, positive = NULL,
     class = "confusionMatrix")
 }
 
-
+#' @export
 as.matrix.confusionMatrix <- function(x, what = "xtabs", ...){
   if(!(what %in% c("xtabs", "overall", "classes")))
     stop("what must be either xtabs, overall or classes")
@@ -231,6 +233,7 @@ train_resampledCM <- function(x) {
   resampledCM
 }
 
+#' @export
 as.table.confusionMatrix <- function(x, ...)  x$table
 
 #' @export
@@ -283,9 +286,13 @@ confusionMatrix.train <- function(data, norm = "overall", dnn = c("Prediction",
   out
 }
 
+#' @export
 confusionMatrix.rfe <- confusionMatrix.train
+
+#' @export
 confusionMatrix.sbf <- confusionMatrix.train
 
+#' @export
 print.confusionMatrix.train <- function(x, digits = 1, ...){
   cat(x$text, "\n")
   normText <- switch(x$norm,
@@ -308,7 +315,10 @@ print.confusionMatrix.train <- function(x, digits = 1, ...){
   invisible(x)
 }
 
+#' @export
 print.confusionMatrix.rfe <- print.confusionMatrix.train
+
+#' @export
 print.confusionMatrix.sbf <- print.confusionMatrix.train
 
 resampName <- function(x, numbers = TRUE){

diff --git a/pkg/caret/R/dummyVar.R b/pkg/caret/R/dummyVar.R
@@ -42,6 +42,7 @@ contr.dummy <- function(n, ...)
     UseMethod("dummyVars")
   }
 
+#' @importFrom stats as.formula
 #' @export
 dummyVars.default <- function (formula, data, sep = ".", levelsOnly = FALSE, fullRank = FALSE, ...) 
 {

diff --git a/pkg/caret/R/filterVarImp.R b/pkg/caret/R/filterVarImp.R
@@ -1,4 +1,7 @@
 
+
+#' @importFrom ModelMetrics auc
+
 rocPerCol <- function(dat, cls){
   auc(cls, dat)
 }

diff --git a/pkg/caret/R/findCorrelation.R b/pkg/caret/R/findCorrelation.R
@@ -1,4 +1,5 @@
 
+#' @importFrom stats complete.cases
 findCorrelation_fast <- function(x, cutoff = .90, verbose = FALSE){
   if(any(!complete.cases(x)))
     stop("The correlation matrix has some missing values.")

diff --git a/pkg/caret/R/format.bagEarth.R b/pkg/caret/R/format.bagEarth.R
@@ -1,3 +1,5 @@
+
+#' @export
 format.bagEarth <- function(x, file = "", cat = TRUE, ...) 
 {
   requireNamespaceQuietStop("earth")