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fixed bug when some node labels are blank in read.beast #63

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fixed bug when some node labels are blank in read.beast #63

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1a95584
fixed bug when some node labels are blank in read.beast
Aug 5, 2021
f8bcc81
fixed bug in read.beast with duplicate node labels and node labels wi…
Aug 6, 2021
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,7 @@ importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(filenamer,filename)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(magrittr,"%>%")
Expand All @@ -170,6 +171,7 @@ importFrom(methods,missingArg)
importFrom(methods,new)
importFrom(methods,setGeneric)
importFrom(methods,slot)
importFrom(purrr,is_numeric)
importFrom(rlang,.data)
importFrom(rlang,enexpr)
importFrom(rlang,quo)
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7 changes: 7 additions & 0 deletions R/beast.R
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Expand Up @@ -71,6 +71,7 @@ read.beast.newick <- function(file) {
return(obj)
}

#' @importFrom filenamer filename
BEAST <- function(file, treetext, stats, phylo) {
stats$node <- gsub("\"*'*", "", stats$node)

Expand Down Expand Up @@ -142,6 +143,7 @@ read.stats_beast <- function(beast, trees) {



##' @importFrom purrr is_numeric
read.stats_beast_internal <- function(beast, tree) {
##tree <- gsub(" ", "", tree)
## tree2 <- gsub("\\[[^\\[]*\\]", "", tree)
Expand Down Expand Up @@ -350,6 +352,11 @@ add_pseudo_nodelabel <- function(phylo) {
## treetext)
## }
}
# assign blank labels
if (any(phylo$node.label == "")) {
blanks <- sum(phylo$node.label == "")
phylo$node.label[phylo$node.label == ""] <- paste("X", 1:blanks, sep="")
}
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I don't think this method can solve the problem. when the tree contained X1 of node label or the same node label. This method can't also solve the problem.

for example

> xx <- '((1[&x="1"]:1,2[&x="2"]:1)5[&x="3"]:1,(3[&x="4"]:1,4[&x="5"]:1)X1[&x="6"]:1)[&x="7"];'
> trda <- read.beast.newick(textConnection(xx))
> trda@data
# A tibble: 7 x 2
      x node
  <dbl> <chr>
1     1 1
2     2 2
3     3 6
4     4 3
5     5 4
6     6 5
7     7 5

I think all node.label can be replace with

nnode <- phylo$Nnode
phylo$node.label <- paste("X", 1:nnode, sep="")

Even node.label is not NULL sometimes. because the node.label does not effect the following calculation.

## if tip.label contains () which will broken node name extraction
phylo$tip.label <- gsub("[\\(\\)]", "_", phylo$tip.label)

Expand Down