Dear Diogo,
the following function should give you the p-values (physo.obs.p) you
are looking for:
# obs : observed phylosor-values (distance matrix)
# rand : list of distance matrices from the "phylosor.rnd"-function
ses.physo <- function(obs, rand){
rand <- t(as.data.frame(lapply(rand, as.vector)))
physo.obs <- as.numeric(obs)
physo.mean <- apply(rand, MARGIN = 2, FUN = mean, na.rm = TRUE)
physo.sd <- apply(rand, MARGIN = 2, FUN = sd, na.rm = TRUE)
physo.ses <- (physo.obs - physo.mean)/physo.sd
physo.obs.rank <- apply(X = rbind(physo.obs, rand), MARGIN = 2, FUN =
rank)[1, ]
physo.obs.rank <- ifelse(is.na(physo.mean), NA, physo.obs.rank)
data.frame(physo.obs, physo.mean, physo.sd, physo.obs.rank,
physo.ses, physo.obs.p = physo.obs.rank/(dim(rand)[1] + 1))
}
# code heavily borrowed from Steven Kembel's "ses.mpd"-function
Good luck,
Oliver
--
Oliver Purschke, PhD
Department of Biology
Biodiversity Unit
Sölvegatan 37, SE-223 62 Lund, Sweden
+46 (0)73 891 1048 (mobile, SE)
+46 (0)46 222 8976 (office, SE)
+49 (0)1522 916 2980 (mobile, DE)
skype: oliverpurschke
oliver.pursc...@nateko.lu.se
www.lu.se/o.o.i.s/27001
http://www.mendeley.com/profiles/oliver-purschke/
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