big documentaiton push to comply with R CMD Check

.Rbuildignore

@@ -1,5 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.eslintrc$
 Readme.Rmd
 docs/
-man/

DESCRIPTION

@@ -1,24 +1,29 @@
 Package: phylocanvas
 Title: Interactive phylogenetic trees using phylocanvas
-Version: 0.0.0.92
+Version: 0.0.0.93
 Authors@R: person("zachary", "charlop-powers", email = "zach.charlop.powers@gmail.com", role = c("aut", "cre"))
 Description: A package to allow use of the phylocanvas JS library from R.
 URL: https://github.com/zachcp/phylocanvas
 BugReports: https://github.com/zachcp/phylocanvas/issues
 Depends:
     R (>= 3.3.1)
 Imports:
-  ape (>= 4.0),
-  phylobase,
-  htmlwidgets,
-  magrittr,
-  methods (>= 3.3.0)
+    ape (>= 4.0),
+    phylobase,
+    htmlwidgets,
+    magrittr,
+    methods (>= 3.3.0)
 Suggests:
-  knitr,
-  rmarkdown,
-  dplyr
-License: MIT
+    knitr,
+    rmarkdown
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 5.0.1
 VignetteBuilder: knitr
+Collate:
+    'load.tree.R'
+    'as.tree.R'
+    'get.descendants.R'
+    'nodes.branches.R'
+    'phylocanvas.R'

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(as.tree)
+export(as_tree)
 export(collapse_branch)
 export(get.descendants)
 export(highlight_node)

R/as.tree.R

@@ -1,26 +1,40 @@
-#' as.tree
+#' as_tree
 #'
 #' Convert objects to newick strings
 #'
-#' @importFrom ape write.tree
-#' @importFrom ape read.tree
-#' @importFrom methods as
-#' @export
+#' @param phy Required. phy is either a \code{\link[ape]{phylo}} class object,
+#' \code{\link[phylobase]{phylo4}} class object, or a character that can be a newick
+#'  literal or apath to newick-containing file.
+#' @importClassesFrom phylobase phylo4
 #'
-setGeneric("as.tree", function(phy, id) {standardGeneric("as.tree")})
+#' @docType methods
+#' @rdname as_tree-methods
 #'
-setMethod("as.tree", "phylo", function(phy, id) {
+#' @export
+setGeneric("as_tree", function(phy) {standardGeneric("as_tree")})
+################################################################################
+#' @aliases as_tree, phylo, phylo-method
+#' @rdname as_tree-methods
+#' @importFrom ape write.tree
+setMethod("as_tree", "phylo", function(phy) {
   write.tree(phy, file="")
 })
-#'
-setMethod("as.tree", "phylo4", function(phy, id) {
+################################################################################
+#' @aliases as_tree, phylo4, phylo4-method
+#' @rdname as_tree-methods
+#' @importFrom methods as
+setMethod("as_tree", "phylo4", function(phy) {
   phy <- as(phy, "phylo")
-  as.tree(phy)
+  as_tree(phy)
 })
-setMethod("as.tree", "character", function(phy, id) {
+################################################################################
+#' @aliases as_tree, character, character-method
+#' @rdname as_tree-methods
+#' @include load.tree.R
+setMethod("as_tree", "character", function(phy) {
   if (file.exists(phy)) {
     newphy <- NULL
-    try(newphy <- read.tree(phy))
+    try(newphy <- load.tree(phy))
     if (!is.null(newphy)) {
       return(newphy)
     }

R/get.descendants.R

@@ -1,9 +1,9 @@
 #' get descendants
 #'
-#' get the names of the tips of descendantds given a tree
+#' get the names of the tips of descendants given a tree
 #' and the name of an internal node.
 #'
-#' @param tree Required. A \code{\link[phlobase] phloy4} object.
+#' @param tree Required. A \code{\link[phylobase]{phylo4}} object.
 #' @param nodename Required. A character corresponding to an internal node.
 #'
 #' @return a character vector of descendant names

R/load.tree.R

@@ -4,15 +4,15 @@
 #'
 #' this is the recommended way to load a tree for use with phylocanvas. The reason is that
 #' all of the javascript selector methods require that the nodes are named and the
-#' selection of nodes based on names is straightforward with \code{\link[phylobase] phylo4}
+#' selection of nodes based on names is straightforward with \code{\link[phylobase]{phylo4}}
 #' objects. Therefore this function will read your newick tree, add names, and return a
-#'  \code{\link[phylobase] phylo4}  object that can be easily manipulated and subsetted
+#'  \code{\link[phylobase]{phylo4}}  object that can be easily manipulated and subsetted
 #' generating custom displays.
 #'
 #' @param treefile Required. Path of phylogenetic tree to read
 #' @param ... Optional. Pass any other arguments to read.tree
 #'
-#' @return a \code{\link[phylobase] phylo4} tree object.
+#' @return a \code{\link[phylobase]{phylo4}} tree object.
 #'
 #' @importFrom ape read.tree
 #' @importFrom ape makeNodeLabel

R/nodes.branches.R

@@ -92,8 +92,8 @@ highlight_node <- function(phycnv, nodeid) {
 #' @param linewidth Optional. Default \code{1}.
 #' @param labelcolor Optional. Default \code{"black"}. Label color. Colors are strings in the format of names, rgb strings or hex values.
 #' @param labeltextsize Optional.Default \code{20}. Label size.
-#' @param linefont Optional. Default \code{"Arial"}. Label font.
-#' @param lineformat Optional. Default \code{"bold"}. Label format.
+#' @param labelfont Optional. Default \code{"Arial"}. Label font.
+#' @param labelformat Optional. Default \code{"bold"}. Label format.
 #'
 #' @seealso \url{http://phylocanvas.org/docs/features/#style-branches-individually}
 #' @export
@@ -105,7 +105,7 @@ style_node <- function(phycnv, nodeid,
                        strokecolor= "black",
                        fillcolor ='black',
                        linewidth = 1,
-                       labelcolour='black',
+                       labelcolor='black',
                        labeltextsize=20, #// points
                        labelfont ='Arial',
                        labelformat = 'bold'
@@ -121,7 +121,7 @@ style_node <- function(phycnv, nodeid,
       lineWidth = linewidth
     ),
     labelStyle = list(
-      colour=labelcolour,
+      colour=labelcolor,
       textSize=labeltextsize,
       font =labelfont,
       format = labelformat

R/phylocanvas.R

@@ -4,17 +4,23 @@
 #'
 #' @import htmlwidgets
 #'
-#' @param tree Required. Newick string of a phyloseq tree, \code{\link[ape] phylo} class object, or path to newick-containing file.
-#' @param nodestyles. Optional. Default \code{NULL}. Let nodes b stylized.
-#' @param treetype. Optional. Default \code{"rectangular"}. Can be one of "rectengular", "circular",
+#' @param tree Required. Newick string of a phyloseq tree, \code{\link[ape]{phylo}} class object,
+#' \code{\link[phylobase]{phylo4}} class object,, or path to newick-containing file.
+#' @param nodestyles Optional. Default \code{NULL}. Let nodes b stylized.
+#' @param treetype Optional. Default \code{"rectangular"}. Can be one of "rectengular", "circular",
 #' "hierarchical", "diagonal", or "radial".
 #' @param nodesize Optional. Default \code{30}. Global nodesize.
 #' @param textsize Optional. Default \code{30}. Global textsize.
+#' @param linewidth Optional. Default \code{3}. Global linewidth.
 #' @param showlabels Optional. Default \code{TRUE}. Whether to show labels.
 #' @param showhistory Optional. Default \code{FALSE}. Whether to use/show the history plugin.
 #' @param showcontextmenu Optional. Default \code{TRUE}. Whether to use/show the mouse context menu.
 #' @param showscalebar Optional. Default \code{FALSE}. Whether to use/show the scalebar.
 #' @param alignlabels Optional. Default \code{FALSE}. Whether to align node labels
+#' @param width Optional. Default \code{NULL}. HTMLWidget width
+#' @param height Optional. Default \code{NULL}. HTMLWidget width
+#' @param elementId Optional. Default \code{NULL}. HTMLWidget ID
+
 #' @export
 phylocanvas <- function(tree,
                         treetype = "rectangular",
@@ -31,7 +37,7 @@ phylocanvas <- function(tree,
 
   # forward options using x
   x = list(
-    tree=as.tree(tree),
+    tree=as_tree(tree),
     treetype=treetype,
     nodesize=nodesize,
     textsize=textsize,