Displaying 3 results from an estimated 3 matches for "tree4".
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2012 Apr 13
1
Coding columns for survival analysis
...when a live tree is first observed, "alive" for when a
tree is found alive and is not just found, and "mort" when it was
previously alive but is now dead.
Given the following:
> tree_live = data.frame(tree =
c("tree1","tree2","tree3","tree4","tree5"), live1 = c(0,0,0,1,1), live2
= c(0,0,1,1,0), live3 = c(0,1,1,0,0), live4 = c(1,1,0,0,0), live5 = c(1,
0, 0, 0, 0))
tree live1 live2 live3 live4 live5
1 tree1 0 0 0 1 1
2 tree2 0 0 1 1 0
3 tree3 0 1 1...
2006 Apr 28
1
unrooted tree and margins, ape package
...of the plotting region. Below is an example of one of the trees.
cat("(((((R3:500.0,R4:500.0):439.0,L._amplexicaule:500.0):494.8,((W4:500.0,R1:500.0):499.0,
W2:500.0):500.0):495.8,(W5:500.0,R2:500.0):491.8):500.0,W1:500.0);",
file = "clustal.tre", sep = "\n")
clustal.tree4 <- read.tree("clustal.tre")
plot(clustal.tree4, type="unrooted", no.margin=TRUE,
font=c(1,1,3,1,1,1,1,1,1))
unlink("clustal.tre")
text.lab < -c(99.2,99.0,87.8,100.0,99.8,98.4)
node.lab <- c(3:8)
nodelabels(text=text.lab, node=node.lab, cex=.7)
Any help or g...
2006 Jan 17
0
Cannot convert from phylo to hclust , error!!???
...p
library(ade4)
library(cluster)
library(stats)
library(ape)
data<-read.table(file="in.matrix",header=FALSE,sep="\t",row.names=1)
dis<-dist.binary(data,method=5,diag=TRUE)
clust<-hclust(dis)
tree1<-as.phylo(clust)
tree2<-as.phylo(clust)
tree3<-as.phylo(clust)
tree4<-as.phylo(clust)
tree5<-as.phylo(clust)
liste <-list(tree1,tree2,tree3,tree4,tree5)
cons<-consensus(liste,p=0.5)
cons_clust <-as.hclust(cons)
Error in "[<-"(`*tmp*`, i, value = numeric(0)) :
nothing to replace
david