Nothing
effect.sizes <-
function(mod, standardized=TRUE, matrix=FALSE){
ptab <- mod$results
if ("sp1_name" %in% colnames(ptab)){
sp1 <- as.character(ptab$sp1_name)
sp2 <- as.character(ptab$sp2_name)
}else{
sp1 <- ptab$sp1
sp2 <- ptab$sp2
}
if (standardized==T){
# ORIGINAL effs <- data.frame(sp1,sp2,effect=as.numeric(((ptab$obs_cooccur - ptab$exp_cooccur)/mod$sites)))
Nmat <- mod$sites
rawtab <- mod$results
rawsp1 <- rawtab$sp1
rawsp2 <- rawtab$sp2
rawobs <- ptab$obs_cooccur
rawexp <- ptab$exp_cooccur
effs <- data.frame()
for (i in 1:length(sp1)){
effs <- rbind(effs,data.frame(sp1[i],sp2[i],effect=as.numeric(((rawobs[i] - rawexp[i])/Nmat[rawsp1[i],rawsp2[i]]))))
}
colnames(effs) <- c("sp1","sp2","effects")
}else{
effs <- data.frame(sp1,sp2,effect=as.numeric((ptab$obs_cooccur - ptab$exp_cooccur)))
}
if (matrix==F){
effs
}else{
effs_1 <- effs
effs_2 <- effs[,c(2,1,3)]
colnames(effs_2) <- c("sp1","sp2","effects")
effs <- rbind(effs_1,effs_2)
effs <- recast(data=effs,formula=sp1~sp2,measure.var="effects",id.var=c("sp1","sp2"))
#m <- as.matrix(effs[[1]])
#rns <- effs[[2]][[1]]
#cns <- effs[[2]][[2]]
#row.names(m) <- as.character(rns$sp1)
#colnames(m) <- as.character(cns$sp2)
#m <- effs[mod$spp.names,mod$spp.names]
#as.dist(as.matrix(m))
row.names(effs) <- effs$sp1
effs$sp1 <- NULL
effs <- as.matrix(effs)
effs <- effs[mod$spp.names,mod$spp.names]
as.dist(as.matrix(effs))
}
}
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