I'll be trying to get a new version of phytools on CRAN in advance of the
I will be teaching with Transmitting Science in Barcelona next week.
Consequently, I just
a whole bunch of new updates to GitHub. Most of these pertain to minor bugs
& fixes, but I also renamed the function
densityTree to rectify an unidentified (by me) S3 method
incompatibility. This makes it even more confusing to distinguish this function
from the similarly named, and similarly purposed, phangorn function
densiTree. Both allow the user to visualize a posterior density
of phylogenies from (say) a Bayesian analysis; however different plotting
methods & options are used internally, and my function (now
densityTree) can also plot mapped stochastic character
histories. For example:
##  '0.5.19'
## 100 phylogenetic trees
## A B C D E F G H I J K L M N O P Q R ## "b" "a" "b" "b" "b" "b" "b" "b" "a" "b" "b" "a" "a" "a" "a" "a" "b" "b" ## S T U V W X Y Z ## "a" "a" "a" "a" "a" "a" "a" "a"
## make stochastic character histories for x on trees mtrees<-make.simmap(trees,x,message=FALSE) mtrees
## 100 phylogenetic trees with mapped discrete characters
## plot posterior density using densityTree colors<-setNames(c("red","blue"),sort(unique(x))) densityTree(mtrees,colors=colors,nodes="inner",ftype="i",lwd=5, method="plotSimmap") add.simmap.legend(colors=colors,prompt=FALSE,x=par()$usr+0.1, y=par()$usr-1)
After I submit to CRAN (hopefully soon) I will post a longer note documenting all the updates from the previous CRAN version. This version of phytools can be obtained from GitHub using the devtools package:
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