[Phylobase-commits] r896 - pkg/R

[noreply at r-forge.r-project.org]

Author: francois
Date: 2014-03-31 18:24:15 +0200 (Mon, 31 Mar 2014)
New Revision: 896

Modified:
   pkg/R/checkdata.R
   pkg/R/class-phylo4d.R
   pkg/R/methods-multiphylo4.R
   pkg/R/methods-phylo4.R
   pkg/R/methods-phylo4d.R
Log:
added @include field in roxygen doc to create proper Collate field in DESCRIPTION

Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2014-03-31 15:59:33 UTC (rev 895)
+++ pkg/R/checkdata.R	2014-03-31 16:24:15 UTC (rev 896)
@@ -42,6 +42,8 @@
 #' trees.  See \code{\link{coerce-methods}} for translation functions and
 #' \code{\link{phylobase.options} to change some of the default options of the
 #' validator.}
+#' @include RcppExports.R
+#' @include phylo4.R
 #' @keywords misc
 checkPhylo4 <- function(object) {
     ct <- checkTree(object)

Modified: pkg/R/class-phylo4d.R
===================================================================
--- pkg/R/class-phylo4d.R	2014-03-31 15:59:33 UTC (rev 895)
+++ pkg/R/class-phylo4d.R	2014-03-31 16:24:15 UTC (rev 896)
@@ -35,6 +35,7 @@
 #' \code{\link{checkPhylo4}} function to check the validity of \code{phylo4}
 #' trees.
 #' @keywords classes
+#' @include formatData.R
 #' @examples
 #'   example(read.tree, "ape")
 #'   obj <- phylo4d(as(tree.owls.bis,"phylo4"), data.frame(wing=1:3))

Modified: pkg/R/methods-multiphylo4.R
===================================================================
--- pkg/R/methods-multiphylo4.R	2014-03-31 15:59:33 UTC (rev 895)
+++ pkg/R/methods-multiphylo4.R	2014-03-31 16:24:15 UTC (rev 896)
@@ -9,3 +9,5 @@
 #' @aliases multiPhylo-class multiPhylo4-class multiPhylo4d-class tbind
 #' @docType class
 #' @keywords classes
+#' @include class-multiphylo4.R
+NULL

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2014-03-31 15:59:33 UTC (rev 895)
+++ pkg/R/methods-phylo4.R	2014-03-31 16:24:15 UTC (rev 896)
@@ -115,6 +115,10 @@
 #' \item{isUltrametric}{\code{signature(object = "phylo4")}: whether the tree
 #' is ultrametric} }
 #' @keywords methods
+#' @include RcppExports.R
+#' @include phylo4.R
+#' @include checkdata.R
+#' @include class-phylo4.R
 #' @examples
 #' 
 #' data(geospiza)

Modified: pkg/R/methods-phylo4d.R
===================================================================
--- pkg/R/methods-phylo4d.R	2014-03-31 15:59:33 UTC (rev 895)
+++ pkg/R/methods-phylo4d.R	2014-03-31 16:24:15 UTC (rev 896)
@@ -43,6 +43,10 @@
 #' @author Ben Bolker, Thibaut Jombart, Francois Michonneau
 #' @seealso \code{\link{phylo4d}}
 #' @keywords methods
+#' @include RcppExports.R
+#' @include phylo4.R
+#' @include checkdata.R
+#' @include class-phylo4d.R
 #' @examples
 #' 
 #'    data(geospiza)