New function to simulate species trees from genus-level tree

I just added a function to phytools to automate the task of attaching species-level subtrees simulated under a Yule process to a backbone genus-level tree. I described this here last week.

Here is how it works:

## first update phytools
library(devtools)
install_github("liamrevell/phytools")

## load
library(phytools)
## here's our hypothetical genus tree:
genus.tree

## 
## Phylogenetic tree with 16 tips and 15 internal nodes.
## 
## Tip labels:
##  Vkfns, Ikfxnyht, Qkyca, Bnlpd, Wkpws, Bkhq, ...
## 
## Rooted; includes branch lengths.

plotTree(genus.tree,ftype="i")

## here are our tips to add
tips

##  [1] "Ikfxnyht_opqcfh" "Ikfxnyht_nvaocw" "Ikfxnyht_knzcyf"
##  [4] "Qkyca_pzdukv"    "Qkyca_jukdfi"    "Qkyca_ritdjl"   
##  [7] "Qkyca_agrjou"    "Qkyca_qoyafl"    "Qkyca_qrfsbu"   
## [10] "Bnlpd_hidqnw"    "Bnlpd_wlthqi"    "Bnlpd_gayokd"   
## [13] "Bnlpd_lqjspu"    "Wkpws_xbahqo"    "Wkpws_pwdnuv"   
## [16] "Bkhq_hqdkbx"     "Bkhq_ojrbaw"     "Bkhq_pzwyfq"    
## [19] "Bkhq_dejpxs"     "Bkhq_efnyzp"     "Bkhq_kymfvj"    
## [22] "Bgln_tfuizj"     "Bgln_tpdsuf"     "Bgln_ycaqrs"    
## [25] "Bgln_havrzp"     "Bgln_bonyms"     "Bgln_nhquvm"    
## [28] "Nrztfp_blunwa"   "Iakywem_jqhxdr"  "Lhkrtyl_usqjhl" 
## [31] "Lhkrtyl_nbjhyc"  "Lhkrtyl_wmhkcd"  "Lhkrtyl_wmdkqp" 
## [34] "Lhkrtyl_dfhlkj"  "Lhkrtyl_kpadxb"  "Javcgbph_qvgmrh"
## [37] "Javcgbph_vzqfir" "Ctfioy_yjuxhp"   "Ctfioy_bcgonv"  
## [40] "Yrvp_prchgs"     "Yrvp_zcjuqx"     "Yrvp_usjbyc"    
## [43] "Hmvlk_nymqow"    "Hmvlk_ktjxnq"    "Hmvlk_crtdau"   
## [46] "Hmvlk_hemxwi"    "Hmvlk_xygpmk"    "Hmvlk_hxofgw"   
## [49] "Fioxrcyl_pecahk" "Fioxrcyl_uifsdv" "Okmfyg_ahxljq"

## add them:
species.tree<-genus.to.species.tree(genus.tree,tips)
plotTree(species.tree,ftype="i",fsize=0.7)

That's it.

Obviously, the data & tree above were simulated. Here is code used in simulation

## first let's simulate our genus tree:
foo<-function() paste(sample(LETTERS,1),paste(sample(letters,
    round(runif(1,min=3,max=7))),collapse=""),sep="")
genera<-replicate(16,foo())
genus.tree<-pbtree(n=length(genera),tip.label=genera,scale=80)
genus.tree$edge.length[which(genus.tree$edge[,2]<=Ntip(genus.tree))]<-
    genus.tree$edge.length[which(genus.tree$edge[,2]<=Ntip(genus.tree))]+20
tips<-c()
for(i in 1:Ntip(genus.tree)){
    n.genus<-sample(0:6,1)
    if(n.genus>0) for(j in 1:n.genus) 
        tips<-c(tips,paste(genus.tree$tip.label[i],
        paste(sample(letters,6),collapse=""),sep="_"))
}