Changes for resubmission to CRAN

R/manip-methods.R

@@ -457,7 +457,7 @@ pinTips <- function(tree, tids, lngs, end_ages, tree_age) {
   spn_data[tree@all, 'end'] <- tmp_spn_data[['end']]
   rm(tmp_spn_data)
   rid <- tree@root
-  #　add oldest to youngest
+  # add oldest to youngest
   ordrd <- order(end_ages, decreasing=TRUE)
   plyr::m_ply(ordrd, .pin)
   tree

R/node-declaration.R

@@ -22,9 +22,13 @@
 }
 
 #' @name Node-class
+#' @aliases Node-method
 #' @param x \code{Node} object
 #' @param object \code{Node} object
 #' @param i slot name
+#' @param j missing
+#' @param ... missing
+#' @param drop missing
 #' @title Node-class
 #' @description The \code{Node} is an S4 class used for displaying node information.
 #' It is only generated when a user implements the \code{[[]]} on a tree. Information
@@ -57,28 +61,24 @@ setClass ('Node', representation=representation (
   tip='logical')         # T/F tip node?
 )
 #' @rdname Node-class
-#' @aliases Node-method
 #' @exportMethod as.character
 setMethod ('as.character', c('x'='Node'),
            function(x) {
              paste0('Node Obj. [ID=', x@id, ']')
            })
 #' @rdname Node-class
-#' @aliases Node-method
 #' @exportMethod show
 setMethod ('show', 'Node',
            function(object){
              cat(summary(object))
            })
 #' @rdname Node-class
-#' @aliases Node-method
 #' @exportMethod print
 setMethod ('print', 'Node',
            function(x){
              print(summary(x))
            })
 #' @rdname Node-class
-#' @aliases Node-method
 #' @exportMethod summary
 setMethod ('summary', c('object'='Node'),
            function(object){
@@ -110,9 +110,10 @@ setMethod ('summary', c('object'='Node'),
              cat(msg)
            })
 
+#' @rdname Node-class
 #' @exportMethod [
-setMethod('[', c('Node', 'character'),
-          function(x, i) {
+setMethod('[', c('Node', 'character', 'missing', 'missing'),
+          function(x, i, j, ..., drop=TRUE) {
             if(!i %in% slotNames(x)) {
               stop(paste0(i, '  not in node'))
             }

R/server-methods.R

@@ -78,7 +78,7 @@ searchTxnyms <- function (tree, cache=FALSE, parent=NULL, clean=TRUE,
 #' @description Resolve taxonomic names via the Global Names Resolver.
 #' @details Returns dataframe containing GNR metadata for each name wames
 #' that cannot be resolved are returned as NA. Various datasources are 
-#' available, see \url{http://resolver.globalnames.biodinfo.org/data_sources} for a
+#' available, see \url{http://resolver.globalnames.org/data_sources} for a
 #' list and IDs. Default is 4 for NCBI.
 #' @param nms vector of names
 #' @param batch size of the batches to be queried

R/treeman-declaration.R

@@ -6,12 +6,15 @@
 
 #' @name TreeMan-class
 #' @title TreeMan-class
+#' @aliases TreeMan-method
 #' @description S4 class for representing phylogenetic trees as a list of nodes.
 #' @param x \code{TreeMan} object
 #' @param i node ID or slot name
 #' @param object \code{TreeMan} object
 #' @param max.level \code{str()} maximum number of levels to show
 #' @param ... additional tree objects
+#' @param j missing
+#' @param drop missing
 #' @slot ndlst list of nodes
 #' @slot nds vector of node ids that are internal nodes
 #' @slot nnds numeric of number of internal nodes in tree
@@ -101,7 +104,6 @@ setClass('TreeMan', representation=representation(
 
 # Accessor methods
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod [[
 setMethod('[[', c('TreeMan', 'character'),
           function(x, i) {
@@ -124,10 +126,8 @@ setMethod('[[', c('TreeMan', 'character'),
             .newNd(x, i)
           })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
-#' @exportMethod [
-setMethod('[', c('TreeMan', 'character'),
-          function(x, i) {
+setMethod('[', c('TreeMan', 'character', 'missing', 'missing'),
+          function(x, i, j, ..., drop=TRUE) {
             slt_nms <- slotNames(x)
             slt_nms <- slt_nms[slt_nms != 'ndlst']
             slt_nms <- slt_nms[slt_nms != 'ndmtrx']
@@ -151,30 +151,26 @@ setMethod('[', c('TreeMan', 'character'),
 
 # display methods
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod as.character
 setMethod('as.character', c('x'='TreeMan'),
           function(x) {
             paste0('TreeMan Object of [', length(x@tips),'] tips')
           })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod show
 setMethod('show', 'TreeMan',
           function(object){
             msg <- as.character(object)
             cat(msg)
           })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod print
 setMethod('print', 'TreeMan',
           function(x){
             msg <- as.character(x)
             print(msg)
           })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod str
 setMethod('str', c('object'='TreeMan'),
           function(object, max.level=2L, ...) {
@@ -184,7 +180,6 @@ setMethod('str', c('object'='TreeMan'),
             str@default(object, max.level=max.level, ...)
           })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod summary
 setMethod('summary', c('object'='TreeMan'),
           function(object){

R/treemen-declaration.R

@@ -1,10 +1,13 @@
 #' @name TreeMen-class
 #' @title TreeMen-class
+#' @aliases TreeMen-method
 #' @param x \code{TreeMen} object
 #' @param i tree index (integer or character)
 #' @param object \code{TreeMen} object
 #' @param max.level \code{str()} maximum level
 #' @param ... additional tree objects
+#' @param j missing
+#' @param drop missing
 #' @description S4 class for multiple phylogenetic trees
 #' @slot treelst list of \code{TreeMan} objects
 #' @slot ntips sum of tips per tree
@@ -70,7 +73,6 @@ setGeneric("cTrees", signature=c("x"),
              standardGeneric("cTrees")
            })
 #' @rdname TreeMan-class
-#' @aliases TreeMan-method
 #' @exportMethod cTrees
 setMethod("cTrees", c("TreeMan"),
           function(x, ...) {
@@ -80,7 +82,6 @@ setMethod("cTrees", c("TreeMan"),
             x
             })
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod cTrees
 setMethod('cTrees', c('TreeMen'),
           function(x, ...) {
@@ -90,7 +91,6 @@ setMethod('cTrees', c('TreeMen'),
 
 # Accessor methods
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod [[
 setMethod('[[', c('TreeMen', 'ANY'),
           function(x, i) {
@@ -103,8 +103,8 @@ setMethod('[[', c('TreeMen', 'ANY'),
 #' @aliases TreeMen-method
 #' Extract slots from a list of trees
 #' @exportMethod [
-setMethod('[', c('TreeMen', 'character'),
-          function(x, i) {
+setMethod('[', c('TreeMen', 'character', 'missing', 'missing'),
+          function(x, i, j, ..., drop=TRUE) {
             if(!i %in% slotNames(x)) {
               stop(paste0(i, '  not in tree'))
             }
@@ -129,22 +129,19 @@ setAs(from="list", to="TreeMen", def=function(from, to) {
 
 # display methods
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod as.character
 setMethod('as.character', c('x'='TreeMen'),
           function(x) {
             paste0('TreeMen Object of [', x@ntrees,'] trees')
           })
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod show
 setMethod('show', 'TreeMen',
           function(object){
             msg <- as.character(object)
             cat(msg)
           })
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod str
 setMethod('str', c('object'='TreeMen'),
           function(object, max.level=2L, ...) {
@@ -154,15 +151,13 @@ setMethod('str', c('object'='TreeMen'),
             str@default(object, max.level=max.level, ...)
           })
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod print
 setMethod('print', c('x'='TreeMen'),
           function(x){
             msg <- as.character(x)
             print(msg)
           })
 #' @rdname TreeMen-class
-#' @aliases TreeMen-method
 #' @exportMethod summary
 setMethod('summary', c('object'='TreeMen'),
           function(object){

R/update-methods.R

@@ -65,7 +65,7 @@ updateSlts <- function(tree) {
 #' @param ... \code{as.big.matrix()} additional arguments
 #' @seealso
 #' \code{\link{updateSlts}}, \code{\link{rmNdmtrx}},
-#' \url{https://cran.r-project.org/web/packages/bigmemory/index.html}
+#' \url{https://cran.r-project.org/package=bigmemory}
 #' @export
 #' @examples
 #' # library(treeman)

README.md

@@ -1,5 +1,5 @@
 # treeman
-[![Build Status](https://travis-ci.org/DomBennett/treeman.svg)](https://travis-ci.org/DomBennett/treeman)[![Coverage Status](https://coveralls.io/repos/DomBennett/treeman/badge.svg?branch=master&service=github)](https://coveralls.io/github/DomBennett/treeman?branch=master)[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/treeman)](https://cran.r-project.org/web/packages/treeman/index.html)[![Rdoc](http://www.rdocumentation.org/badges/version/treeman)](http://www.rdocumentation.org/packages/treeman) 
+[![Build Status](https://travis-ci.org/DomBennett/treeman.svg)](https://travis-ci.org/DomBennett/treeman)[![Coverage Status](https://coveralls.io/repos/DomBennett/treeman/badge.svg?branch=master&service=github)](https://coveralls.io/github/DomBennett/treeman?branch=master)[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/treeman)](https://CRAN.R-project.org/package=treeman)[![Rdoc](http://www.rdocumentation.org/badges/version/treeman)](http://www.rdocumentation.org/packages/treeman) 
 
 > An R package for manipulating phylogentic trees using an intuitive S4 class structure.