Nothing
pair.attributes <-
function(mod){
ptab <- mod$results
spp <- unique(c(ptab$sp1,ptab$sp2))
profiles <- data.frame(spp=c(), rand=c(),pos=c(), neg=c(), num_rand=c(),num_pos=c(), num_neg=c())
for (i in as.character(spp)){
spptab <- ptab[ptab$sp1 == i| ptab$sp2 == i,]
pos <- nrow(spptab[spptab$p_gt < 0.05,])
neg <- nrow(spptab[spptab$p_lt < 0.05,])
rand <- nrow(spptab) - (pos + neg)
total <- rand + pos + neg
if (total == 0){
profiles[i,"pos"] <- 0
profiles[i,"neg"] <- 0
profiles[i,"rand"] <- 100
profiles[i,"num_pos"] <- pos
profiles[i,"num_neg"] <- neg
profiles[i,"num_rand"] <- rand
profiles[i,"spp"] <- i
}else{
profiles[i,"pos"] <- round(pos / total * 100,2)
profiles[i,"neg"] <- round(neg / total * 100,2)
profiles[i,"rand"] <- round(rand / total * 100,2)
profiles[i,"num_pos"] <- pos
profiles[i,"num_neg"] <- neg
profiles[i,"num_rand"] <- rand
profiles[i,"spp"] <- i
}
}
profiles$cooccur <- profiles$pos + profiles$neg
profiles <- profiles[with(profiles,order(cooccur)),]
## Reorder fullname based on the the sum of the other columns
profiles$spp <- factor(x=profiles$spp,ordered=T,levels=profiles$spp)
profiles$cooccur <- NULL
if ("sp1_name" %in% colnames(ptab)){
spp_key <- unique(data.frame(sppnum=c(ptab$sp1,ptab$sp2),sppname=c(as.character(ptab$sp1_name),as.character(ptab$sp2_name))))
names <- merge(x=data.frame(order=1:length(row.names(profiles)),profiles),y=spp_key,by.x="spp",by.y="sppnum",all.x=T)
names <- names[with(names,order(order)),]
names$order <- NULL
names$spp <- NULL
names[order(match(names$sppname,mod$spp.names)),]
}else{
profiles[order(match(profiles$spp,mod$spp.names)),]
}
}
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