## Saturday, March 5, 2016

### Bug fixes and updates for phytools; new name for `density.tree` to fix S3 method incompatibility

I'll be trying to get a new version of phytools on CRAN in advance of the workshop I will be teaching with Transmitting Science in Barcelona next week. Consequently, I just pushed a whole bunch of new updates to GitHub. Most of these pertain to minor bugs & fixes, but I also renamed the function `density.tree` as `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:

``````library(phytools)
packageVersion("phytools")
``````
``````## [1] '0.5.19'
``````
``````trees
``````
``````## 100 phylogenetic trees
``````
``````x
``````
``````##   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")
y=par()\$usr[4]-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:

``````library(devtools)
install_github("liamrevell/phytools")
``````