Hi All,
I am using the ape R package to extract interspecific distances from a
pairwise distance matrix.
Consider the woodmouse example.
library(ape)
data(woodmouse)
dists <- dist.dna(woodmouse, model = "raw", as.matrix = TRUE)
isSymmetric(dists) # TRUE
dists[upper.tri(dists, diag = FALSE)] <- NA # replace upper triangle
with NA and then subset to get lower triangular matrix
isSymmetric(dists) # FALSE
dists # this is a matrix
labs <- labels(woodmouse) # get species names
res <- outer(labs, labs, "==") # get cases where matrix elements are
equal
inter <- na.omit(dists[!res]) # get interspecific distances by taking
elements that are not equal
The problem I am facing is that I need 'inter' to be a matrix instead of a
vector, so that I can tell which distances belong to which pairs of
specimens. The 'inter' matrix should have the same row and column names as
the 'dists' variable. Simply doing
as.matrix(inter)
will not suffice in this case since row names and column names are not
preserved.
Once I have a matrix of only interspecific distances, I can then find
nearest neighbours for all species in my dataset and continue from there.
I feel it is an easy solution, but something is just not clicking.
Any ideas?
Please let me know if anything is unclear.
Thanks.
Cheers,
Jarrett
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