Merge 8ecae19 into 3f1bf57

DESCRIPTION

@@ -1,24 +1,25 @@
 Package: caretEnsemble
 Type: Package
 Title: Ensembles of Caret Models
-Version: 1.0.5
-Date: 2015-01-14
+Version: 2.0.0.9000
+Date: 2016-01-31
 Authors@R: c(person(c("Zachary", "A."), "Deane-Mayer", role = c("aut", "cre"),
     email = "zach.mayer@gmail.com"),
     person(c("Jared", "E."), "Knowles", role=c("aut"),
     email="jknowles@gmail.com"))
 URL: https://github.com/zachmayer/caretEnsemble
 BugReports: https://github.com/zachmayer/caretEnsemble/issues
-Description: Functions for creating ensembles of caret models: caretList,
-    caretEnsemble, and caretStack.  caretList is a convenience function for
-    fitting multiple caret::train models to the same dataset. caretEnsemble will
-    make a linear combination of these models using greedy forward selection,
-    and caretStack will make linear or non-linear combinations of these models,
-    using a caret::train model as a meta-model.
+Description: Functions for creating ensembles of caret models: caretList
+    and caretStack.  caretList is a convenience function for fitting multiple
+    caret::train models to the same dataset. caretStack will make linear or
+    non-linear combinations of these models, using a caret::train model as a
+    meta-model, and caretEnsemble will make a robust linear combination of
+    models using a glm.
 Depends:
-    R (>= 3.1.0),
+    R (>= 3.2.0),
     caret
 Suggests:
+    caTools,
     testthat,
     lintr,
     randomForest,
@@ -35,7 +36,6 @@ Suggests:
     gbm,
     klaR
 Imports:
-    caTools,
     pbapply,
     ggplot2,
     digest,
@@ -46,3 +46,4 @@ Imports:
     data.table
 License: MIT + file LICENSE
 VignetteBuilder: knitr
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,12 +1,12 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(autoplot,caretEnsemble)
 S3method(c,caretList)
 S3method(c,train)
 S3method(getMetric,train)
+S3method(getMetricSD,train)
 S3method(plot,caretEnsemble)
 S3method(plot,caretStack)
-S3method(predict,caretEnsemble)
 S3method(predict,caretList)
 S3method(predict,caretStack)
 S3method(print,caretStack)
@@ -18,14 +18,14 @@ export(caretList)
 export(caretModelSpec)
 export(caretStack)
 export(getMetric)
-export(greedOptAUC)
-export(greedOptRMSE)
-export(safeOptAUC)
+export(getMetricSD)
+export(is.caretEnsemble)
+export(is.caretList)
+export(is.caretStack)
 import(caret)
 import(ggplot2)
 import(grid)
 import(plyr)
-importFrom(caTools,colAUC)
 importFrom(data.table,data.table)
 importFrom(data.table,dcast.data.table)
 importFrom(data.table,rbindlist)

R/caretEnsemble-package.R

@@ -0,0 +1,65 @@
+#' caretEnsemble: Make ensembles of caret models.
+#'
+#' Functions for creating ensembles of caret models: caretList and caretStack
+#' @docType package
+#' @name caretEnsemble
+NULL
+
+#' @title caretList of classification models
+#' @name models.class
+#' @description Data for the caretEnsemble package
+#' @docType data
+#' @rdname data
+#' @author Zachary Deane-Mayer \email{zach.mayer@@gmail.com}
+#' @keywords data
+NULL
+
+#' @title caretList of regression models
+#' @name models.reg
+#' @docType data
+#' @rdname data
+#' @author Zachary Deane-Mayer \email{zach.mayer@@gmail.com}
+#' @keywords data
+NULL
+
+#' @title data for classification
+#' @name X.class
+#' @docType data
+#' @rdname data
+#' @author Zachary Deane-Mayer \email{zach.mayer@@gmail.com}
+#' @keywords data
+NULL
+
+#' @title data for classification
+#' @name Y.class
+#' @docType data
+#' @rdname data
+#' @references \url{data_blah.com}
+#' @keywords data
+NULL
+
+#' @title data for classification
+#' @name X.reg
+#' @docType data
+#' @rdname data
+#' @author Zachary Deane-Mayer \email{zach.mayer@@gmail.com}
+#' @keywords data
+NULL
+
+#' @title data for regression
+#' @name Y.reg
+#' @docType data
+#' @rdname data
+#' @author Zachary Deane-Mayer \email{zach.mayer@@gmail.com}
+#' @keywords data
+NULL
+
+#Hack to make data.table functions work with devtools::load_all
+#http://stackoverflow.com/questions/23252231/r-data-table-breaks-in-exported-functions
+#http://r.789695.n4.nabble.com/Import-problem-with-data-table-in-packages-td4665958.html
+assign(".datatable.aware", TRUE)
+
+#Avoid false positives in R CMD CHECK:
+utils::globalVariables(
+  c(".fitted", ".resid", "method", "id", "yhat",
+    "ymax", "yavg", "ymin", "metric", "metricSD", "n"))