Use inherits (#247)

* use inherits * oopsie * fix tests: * UTF-8 * fix note * fuckity shit * lol * i guess you dont need the vingettes * ddddd * bump version * notes * fix urls * more fixes * couple more fixes * remove dead badges * update news * fix comment * fix link * copyright
zachmayer · Dec 13, 2019 · 8a6496f · 8a6496f
1 parent 48e6ecd
commit 8a6496f
Show file tree

Hide file tree

Showing 69 changed files with 43 additions and 1,060 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,5 @@ inst/docs
 inst/examples
 travis_wait_*
 .github/*
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
@@ -128,3 +128,5 @@ pip-log.txt
 .RHistory
 .Rproj.user
 caretEnsemble_test_plots.png
+doc
+Meta
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,9 @@
+Encoding: UTF-8
 Package: caretEnsemble
 Type: Package
 Title: Ensembles of Caret Models
-Version: 2.0.0
-Date: 2016-02-06
+Version: 2.0.1
+Date: 2019-12-11
 Authors@R: c(person(c("Zachary", "A."), "Deane-Mayer", role = c("aut", "cre"),
     email = "[email protected]"),
     person(c("Jared", "E."), "Knowles", role=c("aut"),
@@ -47,4 +48,4 @@ Imports:
     caret
 License: MIT + file LICENSE
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.1.1
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2013-2015
+YEAR: 2013-2019
 COPYRIGHT HOLDER: Zachary Albert Mayer
diff --git a/NAMESPACE b/NAMESPACE
@@ -70,6 +70,7 @@ importFrom(stats,coef)
 importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,model.response)
+importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stats,qnorm)
 importFrom(stats,reshape)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,8 @@
 #NEWS 
 
+## caretEnsemble 2.0.1
+- Minor fixes to support R 4.0
+
 ## caretEnsemble 2.0.0
 - caretEnsemble now inherits from caretStack
 - Removed the optimizers and now use a glm for caretEnsemble (optimizers will be added back ase caret.train models in a future release)
@@ -8,7 +11,6 @@
 - Fixed the build on travis and locally
 
 ## caretEnsemble 1.0.5
-
 - Change output for predict functions to better align with other predict methods 
 in R (predict.caretEnsemble and predict.caretStack)
 - Update documentation for predict methods to better explain the model disagreement 
@@ -18,5 +20,4 @@ calculation
 calculation
 
 ## caretEnsemble 1.0 - First CRAN release
-
-* caretEnsemble is a new package for making ensembles of [caret](http://cran.r-project.org/web/packages/caret/index.html) models.
+- caretEnsemble is a new package for making ensembles of [caret](https://CRAN.R-project.org/package=caret/) models.
diff --git a/R/S3GenericExtenstions.R b/R/S3GenericExtenstions.R
@@ -34,8 +34,8 @@
 c.caretList <- function(...) {
 
   new_model_list <- unlist(lapply(list(...), function(x) {
-    if(class(x)[1] != "caretList") {
-      if(class(x)[1] != "train") stop("class of modelList1 must be 'caretList' or 'train'")
+    if(! inherits(x, "caretList")) {
+      if(! inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
 
       ## assuming this is a single train object
       x <- list(x)
@@ -81,8 +81,8 @@ c.caretList <- function(...) {
 c.train <- function(...) {
 
   new_model_list <- unlist(lapply(list(...), function(x) {
-    if(class(x)[1] != "caretList") {
-      if(class(x)[1] != "train") stop("class of modelList1 must be 'caretList' or 'train'")
+    if(! inherits(x, "caretList")) {
+      if(! inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
 
       ## assuming this is a single train object
       x <- list(x)

diff --git a/R/caretEnsemble-package.R b/R/caretEnsemble-package.R
@@ -37,7 +37,6 @@ NULL
 #' @name Y.class
 #' @docType data
 #' @rdname data
-#' @references \url{data_blah.com}
 #' @keywords data
 NULL
 

diff --git a/R/caretEnsemble.R b/R/caretEnsemble.R
@@ -293,7 +293,7 @@ multiResiduals <- function(object, ...){
 fortify <- function(model, data = NULL, ...){
   data <- extractModFrame(model)
   data$y <- model$models[[1]]$trainingData$.outcome
-  if(class(data$y) != "numeric"){
+  if(!inherits(data$y, "numeric")){
     data$y <- as.character(data$y)
     z <- table(data$y)
     prevOutcome <- names(z)[z == max(z)]

diff --git a/R/caretList.R b/R/caretList.R
@@ -64,10 +64,10 @@ methodCheck <- function(x){
         "(e.g. getModelInfo(\"gbm\", regex=F))"))
     }
   })
-  models <- do.call(rbind, models)
+  models <- do.call(rbind, models)  # Could use data.table to be more efficient with lots of models
 
   # Ensure that all non-custom models are valid
-  native_models <- subset(models, type == "native")$model
+  native_models <- subset(models, get('type') == "native")$model
   bad_models <- setdiff(native_models, supported_models)
 
   if(length(bad_models)>0){
@@ -282,7 +282,7 @@ as.caretList.default <- function(object){
 #' @export
 #' @method as.caretList list
 as.caretList.list <- function(object){
-  if(!(class(object) == "list")){
+  if(! inherits(object, "list")){
     stop("object must be a list of caret models")
   }
   # Check that each element in the list is of class train
@@ -350,8 +350,8 @@ predict.caretList <- function(object, newdata = NULL, ..., verbose = FALSE){
       stop(paste("Unknown model type:", type))
     }
   })
-  if(class(preds) != "matrix" & class(preds) != "data.frame"){
-    if(class(preds) == "character" | class(preds) == "factor"){
+  if(! inherits(preds, "matrix") & ! inherits(preds, "data.frame")){
+    if(inherits(preds, "character") | inherits(preds, "factor")){
       preds <- as.character(preds) # drop factorization
     }
     preds <- as.matrix(t(preds))

diff --git a/R/caretStack.R b/R/caretStack.R
@@ -77,7 +77,7 @@ predict.caretStack <- function(
   if(type == "Classification"){
     out <- predict(object$ens_model, newdata=preds, na.action=na.action, ...)
     # Need a check here
-    if(class(out) %in% c("data.frame", "matrix")){
+    if(inherits(out, c("data.frame", "matrix"))){
       # Return probability predictions for only one of the classes
       # as determined by configured default response class level
       est <- out[, getBinaryTargetLevel(), drop = TRUE]
@@ -157,6 +157,7 @@ summary.caretStack <- function(object, ...){
 #' @description This is a function to print a caretStack.
 #' @param x An object of class caretStack
 #' @param ... ignored
+#' @importFrom stats na.omit
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/README.md b/README.md
@@ -1,11 +1,9 @@
 [![Build Status](http://img.shields.io/travis/zachmayer/caretEnsemble.svg?style=flat)](https://travis-ci.org/zachmayer/caretEnsemble)
 [![Coverage Status](http://img.shields.io/coveralls/zachmayer/caretEnsemble.svg?style=flat)](https://coveralls.io/r/zachmayer/caretEnsemble)
-[![Github Issues](http://githubbadges.herokuapp.com/zachmayer/caretEnsemble/issues.svg)](https://github.com/zachmayer/caretEnsemble/issues)
-[![Pending Pull-Requests](http://githubbadges.herokuapp.com/zachmayer/caretEnsemble/pulls.svg?style=flat)](https://github.com/zachmayer/caretEnsemble/pulls)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/caretEnsemble)](http://cran.r-project.org/web/packages/caretEnsemble)
-[![Downloads](http://cranlogs.r-pkg.org/badges/caretEnsemble)](http://cran.rstudio.com/package=caretEnsemble)
-[![License](http://img.shields.io/:license-mit-blue.svg?style=flat)](http://badges.mit-license.org)
-[![Badges](http://img.shields.io/:badges-9/9-438cf0.svg?style=flat)](https://github.com/badges/badgerbadgerbadger)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/caretEnsemble)](https://CRAN.R-project.org/package=caretEnsemble/)
+[![Downloads](http://cranlogs.r-pkg.org/badges/caretEnsemble)](https://CRAN.R-project.org/package=caretEnsemble/)
+[![License](http://img.shields.io/:license-mit-blue.svg?style=flat)](https://badges.mit-license.org)
+[![Badges](http://img.shields.io/:badges-7/7-438cf0.svg?style=flat)](https://github.com/badges/badgerbadgerbadger)
 [![Join the chat at https://gitter.im/zachmayer/caretEnsemble](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/zachmayer/caretEnsemble?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 # caretEnsemble: [(Read the vignette!)](https://htmlpreview.github.io/?https://github.com/zachmayer/caretEnsemble/blob/master/inst/doc/caretEnsemble-intro.html)
@@ -14,7 +12,7 @@ Framework for fitting multiple [caret models](https://github.com/topepo/caret) u
 
 caretEnsemble was inspired by [medley](https://github.com/mewo2/medley), which in turn was inspired by Caruana et. al.'s (2004) paper [Ensemble Selection from Libraries of Models.](http://www.cs.cornell.edu/~caruana/ctp/ct.papers/caruana.icml04.icdm06long.pdf)
 
-# Install the stable version from [CRAN](http://cran.r-project.org/web/packages/caretEnsemble/):
+# Install the stable version from [CRAN](https://CRAN.R-project.org/package=caretEnsemble/):
 ```{R}
 install.packages('caretEnsemble')
 ```
@@ -30,4 +28,4 @@ devtools::install_github('zachmayer/[email protected]')
 ```
 
 # Code of Conduct:
-Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+Please note that this project is released with a [Contributor Code of Conduct](https://github.com/zachmayer/caretEnsemble/blob/master/.github/CONTRIBUTING.md). By participating in this project you agree to abide by its terms.
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,14 +1,7 @@
 ## Test environments
-* local OS X install, R 3.1.2
-* ubuntu 12.04 (on travis-ci), R 3.1.2
-* win-builder (devel and release)
+* local OS X install, R 3.6.1
+* ubuntu 16.04, R 3.6.0
+* win-builder (R-release, R-devel, R-devel ATC, R-oldrelease)
 
 ## R CMD check results
-There were no ERRORs, WARNINGs, or NOTES. 
-
-## Downstream dependencies
-I have also run R CMD check on downstream dependencies of caretEnsemble 
-(https://github.com/wch/checkresults/blob/master/httr/r-release). All packages 
-that I could install passed except:
-
-* XYZ:...
+There were no ERRORs, WARNINGs, or NOTEs
diff --git a/inst/doc/caretEnsemble-intro.R b/inst/doc/caretEnsemble-intro.R