tothuhien / Rlsd2

An R-wrapper for lsd2

Rlsd2

This package is developped as an R-wrapper for lsd2 (https://github.com/tothuhien/lsd2). For now, the package is only tested under Unix and Mac systems.

All options and file format used here are the same as the original lsd2, but this R package also accepts some R-object inputs. Users could refer to that the original lsd2 for better documentation.

To install it (some packages are required: devtools, ape, treeio):

devtools::install_github("tothuhien/Rlsd2")

Example of using it:

library(Rlsd2)
result <- lsd2(inputTree="data/D750_11_10_rooted.tree", 
               inputDate="data/D750_11_10.date", 
               outFile = "data/test_lsd2", seqLen=1000)

Another example with R-object input

tree <- read.tree("data/D750_11_10_rooted.tree")
dateTbl <- read.table("data/D750_11_10.date",skip=1,colClasses = "character")
date <- dateTbl[,2]
names(date) <- dateTbl[,1]
result <- lsd2(inputTree=tree, inputDate=date, 
               outFile = "data/test_lsd2", seqLen=1000)

?lsd2 for help page