I just
added
a print method for the ancestral state estimation function,
fastAnc
. Here is a quick demo of how it works:
library(devtools)
install_github("liamrevell/phytools",quiet=TRUE)
library(phytools)
## Loading required package: ape
## Loading required package: maps
Simulate a tree & data:
x<-fastBM(tree<-rtree(n=12))
tree
##
## Phylogenetic tree with 12 tips and 11 internal nodes.
##
## Tip labels:
## t5, t6, t8, t7, t3, t4, ...
##
## Rooted; includes branch lengths.
x
## t5 t6 t8 t7 t3 t4
## 0.08020791 0.90090545 -0.52120123 -0.70089226 0.60523627 0.32977174
## t10 t2 t12 t11 t1 t9
## -1.35329157 -0.41231935 -0.12192103 0.56163234 -1.40509098 -1.52915450
obj<-fastAnc(tree,x)
obj
## Ancestral character estimates using fastAnc:
## 13 14 15 16 17 18 19
## -0.613584 -0.333720 0.311369 -0.667771 -0.805572 -0.640828 0.133491
## 20 21 22 23
## -0.665823 -1.137190 -0.402258 0.504335
obj<-fastAnc(tree,x,CI=TRUE)
obj
## Ancestral character estimates using fastAnc:
## 13 14 15 16 17 18 19
## -0.613584 -0.333720 0.311369 -0.667771 -0.805572 -0.640828 0.133491
## 20 21 22 23
## -0.665823 -1.137190 -0.402258 0.504335
##
## Lower & upper 95% CIs:
## lower upper
## 13 -1.872864 0.645696
## 14 -1.649728 0.982288
## 15 -0.648504 1.271242
## 16 -1.773040 0.437499
## 17 -1.911716 0.300572
## 18 -1.048660 -0.232996
## 19 -0.697674 0.964656
## 20 -1.724715 0.393068
## 21 -1.890327 -0.384054
## 22 -1.274650 0.470134
## 23 0.242778 0.765892
print(obj,printlen=6)
## Ancestral character estimates using fastAnc:
## 13 14 15 16 17 18
## -0.613584 -0.33372 0.311369 -0.667771 -0.805572 -0.640828 ....
##
## Lower & upper 95% CIs:
## lower upper
## 13 -1.872864 0.645696
## 14 -1.649728 0.982288
## 15 -0.648504 1.271242
## 16 -1.77304 0.437499
## 17 -1.911716 0.300572
## 18 -1.04866 -0.232996
## .... ....
That's it.
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