Created
September 18, 2017 19:44
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getGroups w/ edges
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getGroups <- function(tree, get_edges=TRUE) { | |
.fillInRes <- function(i) { | |
res <- vector('list', length=2) | |
names(res) <- c('g1', 'g2') | |
res[['g1']] <- which(edge.tips[i, ] == 1) | |
res[['g2']] <- which(edge.tips[i, ] == 0) | |
res | |
} | |
.addEdges <- function(i) { | |
res[[i]][['edglngth']] <<- edglngths[[i]] | |
NULL | |
} | |
edge.tips <- .Call("bifurcations", PACKAGE="phylofactor", | |
as.integer(tree$edge[, 1]), | |
as.integer(tree$edge[, 2]), | |
as.integer(length(tree$tip.label))) | |
res <- lapply(1:nrow(edge.tips), .fillInRes) | |
names(res) <- 1:nrow(tree$edge) # remove this line after testing | |
if(is.rooted(tree)) { | |
root <- length(tree$tip.label) + 1 | |
rootedges <- which(tree$edge[ ,1] == root) | |
edglngths <- tree$edge.length | |
rootedglngth <- sum(edglngths[rootedges]) | |
edglngths[rootedges[1]] <- rootedglngth | |
pull <- 1:nrow(tree$edge) %in% rootedges[-1] | |
edglngths <- edglngths[!pull] | |
res <- res[!pull] | |
} else { | |
edglngths <- tree$edge.length | |
} | |
if(get_edges) { | |
lapply(1:length(res), .addEdges) | |
} | |
res | |
} | |
# n.b. having labels in 'res' will make the code marginally slower | |
# TESTING | |
plotWEdgeInf <- function() { | |
# plot w/ edge number and length | |
plot(tree, no.margin=TRUE) | |
edgelabels(text=round(tree$edge.length, 2), adj=-.5) | |
edgelabels() | |
} | |
polytomise <- function(tree, n) { | |
# make polytomies for random n internal nodes | |
intnds <- length(tree$tip.label):nrow(tree$edge) | |
edges <- which(tree$edge[ ,2] %in% intnds) | |
tree$edge.length[sample(edges, 3)] <- 0 | |
tree <- di2multi(tree) | |
tree | |
} | |
library(phylofactor) | |
# test bifurcating and rooted tree | |
tree <- rtree(10) | |
tree$tip.label <- 1:10 | |
plotWEdgeInf() | |
res <- getGroups(tree) | |
res[['1']] # res contains edge numbers as names | |
# test polytmous and unrooted tree | |
tree <- unroot(tree) | |
plotWEdgeInf() | |
res <- getGroups(tree) | |
res[['1']] | |
# test tree with multiple polytomies | |
tree <- polytomise(rtree(10), 3) | |
tree$tip.label <- 1:10 | |
plotWEdgeInf() | |
res <- getGroups(tree) |
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You might want to remove l18 in the future