version 0.2.0

cran · Feb 13, 2012 · c2957d5 · c2957d5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,21 @@
 Package: cvTools
 Type: Package
 Title: Cross-validation tools for regression models
-Version: 0.1.1
-Date: 2011-12-07
+Version: 0.2.0
+Date: 2012-02-13
 Author: Andreas Alfons
 Maintainer: Andreas Alfons <andreas.alfons@econ.kuleuven.be>
 Depends: R (>= 2.11.0), lattice, robustbase
-Description: Tools that allow developers to write functions
-    for cross-validation with minimal programming effort
-    and assist users with model selection.
+Imports: lattice, robustbase, stats
+Description: Tools that allow developers to write functions for
+        cross-validation with minimal programming effort and assist
+        users with model selection.
 License: GPL (>= 2)
 LazyLoad: yes
-Collate: 'accessors.R' 'aggregate.R' 'bwplot.R' 'cost.R' 'cvExamples.R'
-        'cvFit.R' 'cvFolds.R' 'cvReshape.R' 'cvSelect.R' 'cvTool.R'
-        'cvTuning.R' 'densityplot.R' 'dotplot.R' 'plot.R' 'print.R'
-        'subset.R' 'summary.R' 'utils.R' 'xyplot.R'
-Packaged: 2011-12-07 00:15:47 UTC; andi
+Collate: 'accessors.R' 'aggregate.R' 'bwplot.R' 'cost.R' 'cvFit.R'
+        'cvFolds.R' 'cvReshape.R' 'cvSelect.R' 'cvTool.R' 'cvTuning.R'
+        'densityplot.R' 'dotplot.R' 'plot.R' 'print.R' 'repCV.R'
+        'selectBest.R' 'subset.R' 'summary.R' 'utils.R' 'xyplot.R'
+Packaged: 2012-02-13 12:16:53 UTC; andi
 Repository: CRAN
-Date/Publication: 2011-12-07 17:07:24
+Date/Publication: 2012-02-13 12:46:49
diff --git a/MD5 b/MD5
@@ -1,29 +1,29 @@
-fc040270f59e000d737131e2b62d01db *DESCRIPTION
-09f63cf33f60f752d33ada7aa00cef61 *NAMESPACE
-19be3e29185ca04d81133a9659f53317 *NEWS
-48b2c3810a8fa90471c4fb6b6b788287 *R/accessors.R
-c68ea945f1d98b9627184222b4778e7e *R/aggregate.R
-e7c1113e14898697bf4df600190488ca *R/bwplot.R
-9242c02087bdbf1ef6de9063204d01db *R/cost.R
-c8918b91b5a1ebcf3936d735331e6cd2 *R/cvExamples.R
-363bb51711414f00f592c27762fa7dfd *R/cvFit.R
-955411a4d1383a14960fd7e600e42f18 *R/cvFolds.R
-5c16b115a94f3f32febef99071c3ed27 *R/cvReshape.R
-968bb75ef4547e519a001b753aff8c7a *R/cvSelect.R
-2006b0398493afc3b078eb2ffcb15d1c *R/cvTool.R
-5502a11380c02e285d7f5909aa0ee639 *R/cvTuning.R
-9c0195b959a2bb550f7d4ab02213cb7c *R/densityplot.R
-140d36e327ab204880902dea1e0faead *R/dotplot.R
-3f47fa5b135279093e3d104a13028481 *R/plot.R
-7505ece24c6dbd1c721dbdd7c7fd57c6 *R/print.R
-fe6b97561c271e8416ad2f8a9e669aeb *R/subset.R
-6450e0cd3117c8c262fb51dff4acd43c *R/summary.R
-e4d7f1157a58ac610fb9b64d119dd7df *R/utils.R
-930e428a62aa12bd92b3284e0a01ba2d *R/xyplot.R
+573d9de879faf2769d8d184ba369d017 *DESCRIPTION
+3dfbab2b529557b78684f7246de5ed96 *NAMESPACE
+13816a1032489b3be4aa53aa7a7f96b9 *NEWS
+b397301b6de28042cd36de56b50ce145 *R/accessors.R
+38b3a4b29c70ac2da562c21d00691c3c *R/aggregate.R
+0c07168914e5627f96633e5dff9138e3 *R/bwplot.R
+5ccfa919b733b028d5dabe8ec847a502 *R/cost.R
+edecaa067584204843f2abfc0a124115 *R/cvFit.R
+24398fd63f63f6438b805663588163f0 *R/cvFolds.R
+91ff198fd41846d46fe00de82f7d686d *R/cvReshape.R
+a86e39c97e83a9f282b87fffbb0546ad *R/cvSelect.R
+74457ff168a8944717d900a486453546 *R/cvTool.R
+5afeae9df0fd300f7704d0576606f236 *R/cvTuning.R
+e4fdd61e76c8343e764aa239570bfa19 *R/densityplot.R
+8d546cc39ae0b64871ccbaba493ab8c0 *R/dotplot.R
+e649978d04434760d0e622c066e8d38a *R/plot.R
+dcb0694d7a8837b2912ca5194fc6755e *R/print.R
+07f4f56b8fde6df81e7920b4c6294c52 *R/repCV.R
+14aea30357b3ca1031c8ab6c45731a03 *R/selectBest.R
+f33204bb96e326b4327b0517b943918d *R/subset.R
+a47692a042ebfe144e37b3d9fa5678be *R/summary.R
+abe4bec9e985980935d52c0ed3965a79 *R/utils.R
+c6ecc2da7c715f45ca435e7ef4918067 *R/xyplot.R
 a7fb93ab8b8c87287ee6ae3532e4e084 *inst/doc/examples/example-accessors.R
 96c17ca35116c5919d0a4b920e6faa6b *inst/doc/examples/example-aggregate.R
 7e93e37e153121cfdac1595571d540b0 *inst/doc/examples/example-bwplot.R
-91fa09a4b5fe431149023f32cd24bdfc *inst/doc/examples/example-cvExamples.R
 6ed9c05c84a4f14609db195d00973eae *inst/doc/examples/example-cvFit.R
 1ba5d997426d14332ef3e5b9d2ed0615 *inst/doc/examples/example-cvReshape.R
 a03e81f822a631f313e955e132a33b66 *inst/doc/examples/example-cvSelect.R
@@ -32,24 +32,25 @@ a03e81f822a631f313e955e132a33b66 *inst/doc/examples/example-cvSelect.R
 c3d7eedf0be5f2bb054397e7cd7fd742 *inst/doc/examples/example-densityplot.R
 5bbb84a057d8895cf7b841b409d33cc6 *inst/doc/examples/example-dotplot.R
 ef335dd66da19918ce14c845a881dce7 *inst/doc/examples/example-plot.R
+16d5323935a11f27615ffdbe7887a191 *inst/doc/examples/example-repCV.R
 331c3a0cf8fbedb337fb28d8d8447656 *inst/doc/examples/example-subset.R
 09ff2ea3c53522657e74e01ffa7096a6 *inst/doc/examples/example-summary.R
 0f3e66e0c10f34c66c4dc03aea3bc4ff *inst/doc/examples/example-xyplot.R
-be6185c1028975e4e5c3c6fd18af5a5e *man/accessors.Rd
-3524598663d42b47033adc6bacd5b0a6 *man/aggregate.cv.Rd
-31c631cfd97fa2a05fc7b965e85742c9 *man/bwplot.cv.Rd
-91ae69b7a16565e3bbe68ebce06bcefb *man/cost.Rd
-b20d201b4d21c2fd98de29c5d7641dcc *man/cvExamples.Rd
-076f5f90aeb28478fd60928c401f5313 *man/cvFit.Rd
-3f8e6b06af39a887dccf57313e32bbab *man/cvFolds.Rd
-ec22fe85e4c369d3bb39b1e47e4e5f08 *man/cvReshape.Rd
-36b2534a6791129e4b53ee3f92c99d63 *man/cvSelect.Rd
-37fd0a86766164550615de28c1a608c2 *man/cvTool.Rd
-662b7d4f9b4d93d4cf52c94e8cb79293 *man/cvTools-package.Rd
-8c50fa742d6bb9df66a319661de391a1 *man/cvTuning.Rd
-5c318a3eb87222d45b88d44409a00a3f *man/densityplot.cv.Rd
-aad5bcb236f1525ec16c49231d3efdfb *man/dotplot.cvSelect.Rd
-38708544ed1937f12776aab5b4c70200 *man/plot.cv.Rd
-43a068f6a1de41cd04d490d2b5d85aa0 *man/subset.cv.Rd
-62bf8cc5e7c8ee3f81d21d7fe1cb0ebd *man/summary.cv.Rd
-c7a712546a3b40294f26aae6bf3c2587 *man/xyplot.cvSelect.Rd
+be915e96939dffdcd8b6e4b0b18bcca6 *man/accessors.Rd
+04a6badc4198b636bb1748bf66abbe3c *man/aggregate.cv.Rd
+ac323b29b7a1b77e70469fe7dff488c2 *man/bwplot.cv.Rd
+2f1283c243c880f1be5a4c57c3f40e8e *man/cost.Rd
+e7b5173b7ba6dd4c31c00aae1702d137 *man/cvFit.Rd
+c3455f9c21a42fce405f2b739c8f99c8 *man/cvFolds.Rd
+d522a615775388e3cd7326fb9bb70ab8 *man/cvReshape.Rd
+606429e762e9b2820cc98366d2f8cbf8 *man/cvSelect.Rd
+6988e084820a825fde952e4553351958 *man/cvTool.Rd
+a037ae4b626e316ba8b3531a52dde51e *man/cvTools-package.Rd
+90ca3ce5b98c2db1ce24a93039ec182b *man/cvTuning.Rd
+1f1e5620a7f0540c04a0fdb00791b050 *man/densityplot.cv.Rd
+8c31e99ae44736c8f8c9e0ffb3f2fcd8 *man/dotplot.cv.Rd
+fa9ee4c80126a4530aeef5f01c5afc1b *man/plot.cv.Rd
+02cea1c011bbcfb20cf8dd4d01f63eca *man/repCV.Rd
+c1215e7f730038ccf0a241fdaf961ce7 *man/subset.cv.Rd
+7543745fa1ff706e65d790c5ecd8b9b6 *man/summary.cv.Rd
+80a2e79f72aa22aab6c1e3ecf4db8bbf *man/xyplot.cv.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,26 +1,3 @@
-export("cvNames<-")
-export("fits<-")
-export(cvFit)
-export(cvFolds)
-export(cvLm)
-export(cvLmrob)
-export(cvLts)
-export(cvNames)
-export(cvReshape)
-export(cvSelect)
-export(cvTool)
-export(cvTuning)
-export(fits)
-export(mape)
-export(mspe)
-export(ncv)
-export(nfits)
-export(rmspe)
-export(rtmspe)
-export(tmspe)
-import(lattice)
-import(robustbase)
-import(stats)
 S3method("cvNames<-",cv)
 S3method("cvNames<-",cvSelect)
 S3method("fits<-",cv)
@@ -41,6 +18,7 @@ S3method(cvTuning,"function")
 S3method(cvTuning,call)
 S3method(densityplot,cv)
 S3method(densityplot,cvSelect)
+S3method(dotplot,cv)
 S3method(dotplot,cvSelect)
 S3method(fits,cv)
 S3method(fits,cvSelect)
@@ -58,10 +36,38 @@ S3method(print,cvTuning)
 S3method(print,summary.cv)
 S3method(print,summary.cvSelect)
 S3method(print,summary.cvTuning)
+S3method(repCV,lm)
+S3method(repCV,lmrob)
+S3method(repCV,lts)
 S3method(subset,cv)
 S3method(subset,cvSelect)
 S3method(summary,cv)
 S3method(summary,cvSelect)
 S3method(summary,cvTuning)
+S3method(xyplot,cv)
 S3method(xyplot,cvSelect)
 S3method(xyplot,cvTuning)
+export("cvNames<-")
+export("fits<-")
+export(cvFit)
+export(cvFolds)
+export(cvLm)
+export(cvLmrob)
+export(cvLts)
+export(cvNames)
+export(cvReshape)
+export(cvSelect)
+export(cvTool)
+export(cvTuning)
+export(fits)
+export(mape)
+export(mspe)
+export(ncv)
+export(nfits)
+export(repCV)
+export(rmspe)
+export(rtmspe)
+export(tmspe)
+import(lattice)
+import(robustbase)
+import(stats)
diff --git a/NEWS b/NEWS
@@ -1,3 +1,25 @@
+Changes in cvTools version 0.2.0
+
+    + New generic function repCV() for (repeated) K-fold cross-validation.  The 
+      example functions cvLm(), cvLmrob() and cvLts() are now aliases for the 
+      respective methods.
+
+    + Bugfix in cvFit(): default names are retained if cvTool() returns a 
+      1x1 matrix.
+
+    + Bugfix in plot.cvSelect(): default handling of argument 'method' no 
+      longer throws error in case of only one replication.
+
+    + Added functionality to incorporate standard errors.
+
+    + cvSelect() and cvTuning() now allow to specify criterion for selecting 
+      the best model via the argument 'selectBest'.
+
+    + New xyplot() and dotplot() methods for class "cv".
+
+
+
 Changes in cvTools version 0.1.1
 
     + Added different types of obtaining CV folds.
+
diff --git a/R/accessors.R b/R/accessors.R
@@ -1,6 +1,6 @@
 # ----------------------
 # Author: Andreas Alfons
-#         K.U.Leuven
+#         KU Leuven
 # ----------------------
 
 #' Access or set information on cross-validation results
@@ -63,7 +63,7 @@ cvNames.cvSelect <- function(x) names(x$cv)[-1]
 #' @S3method cvNames<- cv
 "cvNames<-.cv" <- function(x, value) {
     object <- x
-    names(object$cv) <- value
+    names(object$cv) <- names(object$sd) <- value
     if(!is.null(x$reps)) colnames(object$reps) <- value
     eval.parent(substitute(x <- object))
 }
@@ -73,7 +73,7 @@ cvNames.cvSelect <- function(x) names(x$cv)[-1]
     object <- x
     names(object$best) <- value
     value <- c("Fit", value)
-    names(object$cv) <- value
+    names(object$cv) <- names(object$sd) <- value
     if(!is.null(x$reps)) names(object$reps) <- value
     eval.parent(substitute(x <- object))
 }
@@ -104,7 +104,7 @@ fits.cvSelect <- function(x) x$cv$Fit
 "fits<-.cvSelect" <- function(x, value) {
     object <- x
     if(is.factor(value)) value <- factor(as.character(value), levels=value)
-    object$cv$Fit <- value
+    object$cv$Fit <- object$sd$Fit <- value
     if(!is.null(reps <- x$reps)) {
         indices <- match(reps$Fit, x$cv$Fit, nomatch=0)
         object$reps$Fit <- value[indices]

diff --git a/R/aggregate.R b/R/aggregate.R
@@ -1,6 +1,6 @@
 # ----------------------
 # Author: Andreas Alfons
-#         K.U.Leuven
+#         KU Leuven
 # ----------------------
 
 #' Aggregate cross-validation results

diff --git a/R/bwplot.R b/R/bwplot.R
@@ -1,6 +1,6 @@
 # ----------------------
 # Author: Andreas Alfons
-#         K.U.Leuven
+#         KU Leuven
 # ----------------------
 
 #' Box-and-whisker plots of cross-validation results
@@ -46,7 +46,7 @@
 
 bwplot.cv <- function(x, data, select = NULL, ...) {
     # initializations
-    if(x$R == 1) stop("density plot is only meaningful for repeated CV")
+    if(x$R == 1) stop("box plot is only meaningful for repeated CV")
     # construct data frame in lattice format and call internal function
     CV <- getLatticeData(x, select)
     localBwplot(CV, ...)