@@ -62,5 +62,5 @@ BugReports: https://github.com/YuLab-SMU/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization

-RoxygenNote: 7.1.2

+RoxygenNote: 7.2.0

 Roxygen: list(markdown = TRUE)

@@ -81,7 +81,7 @@ layoutEqualAngle <- function(model, branch.length = "branch.length"){

     ## Get number of tips for each node in tree.

   ## nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

   ## self_include = TRUE to return itself if the input node is a tip

-  nb.sp <- vapply(1:N, function(i) length(offspring(tree, i, tiponly = TRUE, self_include = TRUE)), numeric(1))

+  nb.sp <- vapply(1:N, function(i) length(suppressMessages(offspring(tree, i, tiponly = TRUE, self_include = TRUE))), numeric(1))

     ## Get list of node id's.

     nodes <- getNodes_by_postorder(tree)

@@ -97,6 +97,9 @@ layoutEqualAngle <- function(model, branch.length = "branch.length"){

         end <- df[curNode, "end"]

         cur_x = df[curNode, "x"]

         cur_y = df[curNode, "y"]

+

+        total_angle = end - start

+

         for (child in children) {

             ## Get the number of tips for child node.

             ntip.child <- nb.sp[child]

@@ -104,7 +107,8 @@ layoutEqualAngle <- function(model, branch.length = "branch.length"){

             ## Calculated in half radians.

             ## alpha: angle of segment for i-th child with ntips_ij tips.

             ## alpha = (left_angle - right_angle) * (ntips_ij)/(ntips_current)

-            alpha <- (end - start) * ntip.child / curNtip

+            ## alpha <- (end - start) * ntip.child / curNtip

+            alpha <- total_angle * ntip.child / curNtip

             ## beta = angle of line from parent node to i-th child.

             beta <- start + alpha / 2

@@ -68,7 +68,5 @@ For demonstration of this function, please refer to chapter 8.3 of

 \url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

 }

 \author{

-Guangchuang Yu

-

 Guangchuang Yu

 }

@@ -21,12 +21,14 @@ tree as data.frame with equal angle layout.

 }

 \references{

 The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"

-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children

+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.

+

+\if{html}{\out{<div class="sourceCode">}}\preformatted{Leafs are subtrees with no children

 Initialise tree using equal angle algorithm

 tree_df = equal_angle(tree)

 nodes = get list of nodes in tree_df breadth-first

 nodes = remove tip nodes.

-}

+}\if{html}{\out{</div>}}

 }

@@ -52,6 +52,6 @@ below to see their documentation.

   \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}

-  \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}

+  \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}

 }}