Hello,
I am trying to preform a comparative analysis using the partial mantel
method. However, i am having trouble creating compatible matrices. I can
create matrices from my numerical data using the 'distance(x, method)'
function from ecodist, but the row/column names are out put as numbers.
While when i create a phyo-distance matrix using 'cophenetic(x)' from
APE,
the row/column names are the taxa names. Different data sets incorporate
different taxa from the tree, which requires me to prune it for each data
set, meaning I cannot just convert the taxa names to corresponding numbers
in the data matrix (because the numbers will change for each data set).
Anyways, my question is, is there an easy way to label the row/column names
with the taxa names? A different distance matrix function perhaps? When I
import the data I convert the taxa names to row names (row.names(data) <-
as.character(data$taxanames). Why these don't transfer over when I create a
distance matrix, I don't know.
Thank you,
Charlie
--
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Charles G. Willis
Department of Organismic and Evolutionary Biology
22 Divinity Ave Cambridge MA 02139
HP (857) 488-2506
WP (617) 496-3890
cgwillis@oeb.harvard.edu
http://www.people.fas.harvard.edu/%7Ecgwillis/
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