If data are not sequence alignment an
phyDat object then there are generic functions
as.phyDat() in phangorn to transform a matrices and data.frames into
For example you can read in your data with
read.csv(), but you might need to transpose your data. For matrices
as.phyDat() assumes that the entries each row belongs to one individual (taxa), but for data.frame each column. For binary data you can transform these with a command like (depending how you coded them):
as.phyDat(data, type="USER", levels = c(0, 1)) as.phyDat(data, type="USER", levels = c(TRUE, FALSE))
Often you also have missing data (e.g.
-) which you want to code as ambiguous character.
In this case your code may look like:
as.phyDat(data, type="USER", levels = c("0", "1"), , ambiguity="-")
More information is avaiable in one of the vignettes (type
vignette("phangorn-specials", package = "phangorn") in R).