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noticed typo that suppressed multithreading #130

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noticed typo that suppressed multithreading #130

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a7f25ef
noticed typo that suppressed multithreading
brj1 Jan 9, 2025
af607bd
fixed bug with write.beast indexing the data wrong
brj1 Feb 18, 2025
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2 changes: 1 addition & 1 deletion R/beast.R
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ read.beast <- function(file, threads = 1, verbose = FALSE) {
text <- readLines(file)

treetext <- read.treetext_beast(text)
stats <- read.stats_beast(text, treetext, threads = 1, verbose = FALSE)
stats <- read.stats_beast(text, treetext, threads = threads, verbose = verbose)
phylo <- read.nexus(file)

if (length(treetext) == 1) {
Expand Down
24 changes: 14 additions & 10 deletions R/write-beast.R
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Original file line number Diff line number Diff line change
Expand Up @@ -216,6 +216,7 @@ write_beast_newick <- write.beast.newick
}

add.internal <- function(i) {
char.i <- as.character(i) # make sure we are indexing node_anno by name and not index
cp("(")
desc <- kids[[i]]
for (j in desc) {
Expand All @@ -231,13 +232,13 @@ write_beast_newick <- write.beast.newick
if (is.null(node_anno)) {
if (id_as_label) nl <- to_nodelab(edge, i)
else nl <- node.label[i - n]
} else if (!is.na(node_anno[i])) {
if (id_as_label) nl <- paste0(to_nodelab(edge, i), node_anno[i])
else nl <- paste0(node.label[i - n], node_anno[i])
} else if (!is.na(node_anno[char.i])) {
if (id_as_label) nl <- paste0(to_nodelab(edge, i), node_anno[char.i])
else nl <- paste0(node.label[i - n], node_anno[char.i])
}
cp(nl)
} else if (i %in% edge[,1] && !is.null(node_anno)) {
cp(node_anno[i])
cp(node_anno[char.i])
}
if (brl) {
cp(":")
Expand All @@ -246,13 +247,15 @@ write_beast_newick <- write.beast.newick
}

add.terminal <- function(i) {
char.i <- as.character(i) # make sure we are indexing node_anno by name and not index
ii <- edge[i, 2]
if (is.null(node_anno) || is.na(node_anno[ii])) {
char.ii <- as.character(ii)
if (is.null(node_anno) || is.na(node_anno[char.ii])) {
if (id_as_label) tl <- to_tiplab(edge, ii)
else tl <- tip.label[ii]
} else {
if (id_as_label) tl <- paste0(to_tiplab(edge, ii), node_anno[ii])
else tl <- paste0(tip.label[ii], node_anno[ii])
if (id_as_label) tl <- paste0(to_tiplab(edge, ii), node_anno[char.ii])
else tl <- paste0(tip.label[ii], node_anno[char.ii])
}
cp(tl)
if (brl) {
Expand Down Expand Up @@ -293,6 +296,7 @@ write_beast_newick <- write.beast.newick
#getRoot <- function(edge)
# edge[, 1][!match(edge[, 1], edge[, 2], 0)][1]
root <- getRoot(edge) # replaced n+1 with root - root has not be n+1
char.root <- as.character(root)
desc <- kids[[root]]
for (j in desc) {
if (j %in% edge[,1]) add.internal(j)
Expand All @@ -305,14 +309,14 @@ write_beast_newick <- write.beast.newick
cp(")")
if (nodelab) {
if (!is.null(node_anno) && !is.na(node_anno[root])) {
if(id_as_label) cp(paste0(to_nodelab(edge, root), node_anno[root]))
else cp(paste0(node.label[1], node_anno[root]))
if(id_as_label) cp(paste0(to_nodelab(edge, root), node_anno[char.root]))
else cp(paste0(node.label[1], node_anno[char.root]))
} else {
if (id_as_label) cp(to_nodelab(edge, root))
else cp(node.label[1])
}
} else if (!is.null(node_anno) && !is.na(node_anno[root])) {
cp(node_anno[root])
cp(node_anno[char.root])
}
cp(";")
} else {
Expand Down