/spacodiR/R/spacodi.calc.R
http://github.com/eastman/spacodiR · R · 152 lines · 128 code · 16 blank · 8 comment · 43 complexity · 4ae3a5c75c1be88ba2caf75608d90a14 MD5 · raw file
- spacodi.calc <-function(sp.plot, phy = NULL, sp.traits = NULL, all.together=TRUE, prune=TRUE, pairwise=FALSE,...){
- if(!missing(phy) && !missing(sp.traits)) stop("Please supply either a phylogeny or a trait matrix, but not both.")
- rematrix=function(arr, names){
- n=sqrt(length(arr))
- counter=1
- M=matrix(0,n,n)
- for(i in 1:n){
- j=i+1
- while(j<=n) {
- M[i,j]=arr[counter]
- counter=counter+1
- j=j+1
- }
- }
- M[lower.tri(M)]=t(M)[lower.tri(t(M))]
- dimnames(M)[[1]]<-dimnames(M)[[2]]<-names
- return(M)
- }
-
- # determine type of abundance
- stripped=unname(unlist(c(sp.plot)))
- if(all(!is.na(match(stripped, c(0,1))))) {
- abundt = 0 # presence|absence
- } else if(all(!is.na(match(range(stripped), c(0,1)))) && length(unique(stripped))>2) {
- abundt = 1 # relative abundance
- } else {
- abundt = 2 # abundance (n.individuals)
- }
-
- # iter is 1 unless more than a single trait is being used for separate analyses
- iter=1
- traits.tmp<-distmat<-NULL
-
- # INTERPRET whether to compute trait diversity or phylogenetic diversity & prepare data
- if(!missing(phy)) {
- # distmat is phylogenetic: Pst
- sp.data=match.spacodi.data(sp.plot=sp.plot, phy=phy, prune=prune, ...)
- sp.plot=sp.data$sp.plot
- phy=sp.data$sp.tree
- if(check.distmat(phy)) distmat <- phy else distmat <- cophen(phy)
-
- } else if(missing(sp.traits) & missing(phy)) {
- # distmat is null: Ist
- distmat <- matrix(1, ncol = nrow(sp.plot), nrow = nrow(sp.plot))
-
- } else if(!missing(sp.traits)){
- # distmat is trait-based: Tst
- if(class(sp.traits)=="dist") sp.traits=as.matrix(sp.traits)
- if(ncol(sp.traits)==1) all.together=TRUE
- if(all(is.null(names(sp.traits)))) names(sp.traits)=paste("trt",seq(1:ncol(sp.traits)),sep="")
- if(all.together==TRUE | check.distmat(sp.traits)) {
- sp.data=match.spacodi.data(sp.plot=sp.plot, sp.traits=sp.traits, prune=prune, ...)
- sp.plot=sp.data$sp.plot
- sp.traits=sp.data$sp.traits
- if(check.distmat(sp.traits)) distmat=sp.traits else distmat=as.matrix(dist(sp.traits))
- } else {
- iter=ncol(sp.traits)
- traits.tmp=lapply(1:ncol(sp.traits), function(x) {
- trait.tt<-data.frame(sp.traits[,x])
- row.names(trait.tt)<-row.names(sp.traits)
- sp.data<-match.spacodi.data(sp.plot=sp.plot, sp.traits=trait.tt, prune=prune, ...)
- distmat <- as.matrix(dist(sp.data$sp.traits))
- return(list(distmat=distmat, sp.plot=sp.data$sp.plot))
- }
- )
- }
- } else if(is.null(distmat)){
- stop("Cannot decipher input object(s).")
- }
-
- if(is.null(names(sp.plot))) pnames=paste("plt",seq(1,ncol(sp.plot)),sep=".") else pnames=names(sp.plot)
-
- # PREPARE output
- gen.out=list()
- prw.out=list()
-
- for(tt in 1:iter) {
- if(is.null(traits.tmp)) {
- sp.plot <- as.matrix(sp.plot)
- } else {
- sp.plot <- as.matrix(traits.tmp[[tt]]$sp.plot)
- distmat <- as.matrix(traits.tmp[[tt]]$distmat)
- }
-
- diag(distmat) <- 0
- np <- ncol(sp.plot)
- out <- NA
- out <- .C("spacodi",
- np = as.integer(np),
- ns = as.integer(nrow(sp.plot)),
- sp.plot = as.double(as.vector(sp.plot)),
- distmat = as.double(as.vector(as.matrix(distmat))),
- abundtype = as.integer(abundt),
- Ndclass = as.integer(0),
- dclass = as.double(c(0,0)),
- Ist = 0,
- Pst = 0,
- Bst = 0,
- PIst = 0,
- pairwiseIst = as.double(as.vector(matrix(0,np,np))),
- pairwisePst = as.double(as.vector(matrix(0,np,np))),
- pairwiseBst = as.double(as.vector(matrix(0,np,np))),
- pairwisePIst = as.double(as.vector(matrix(0,np,np))),
- PACKAGE="spacodiR"
- )
-
- # compile results for phylogenetic turnover
- if(missing(phy) & missing(sp.traits)) {
- r.out=as.numeric(out[8])
- names(r.out)="Ist"
- gen.out[[tt]]=as.data.frame(t(r.out))
- if(pairwise) {
- prw.out[[tt]]=list(rematrix(unlist(out[12]),pnames))
- names(prw.out[[tt]])<-paste("pairwise","Ist",sep=".")
- }
- } else if(!missing(phy)){
- r.out=as.numeric(c(out[8:11]))
- names(r.out)<-c("Ist","Pst","Bst","PIst")
- gen.out[[tt]]=as.data.frame(t(r.out))
- if(pairwise) {
- prw.out[[tt]]=lapply(out[12:15], function(x) rematrix(x,pnames))
- names(prw.out[[tt]])<-paste("pairwise",c("Ist","Pst","Bst","PIst"),sep=".")
- }
- } else if(!missing(sp.traits)) {
- r.out=as.numeric(c(out[8:11]))
- names(r.out)=c("Ist","Tst","Ust","TAUst")
- gen.out[[tt]]=as.data.frame(t(r.out))
- if(pairwise) {
- prw.out[[tt]]=lapply(out[12:15], function(x) rematrix(x,pnames))
- names(prw.out[[tt]])<-paste("pairwise",c("Ist","Tst","Ust","TAUst"),sep=".")
- }
- }
- }
- if(iter>1 & !all.together) {
- RES=lapply(1:iter, function(x) {
- if(pairwise) return(c(gen.out[[x]], prw.out[[x]])) else return(c(gen.out[[x]]))
- }
- )
- names(RES)<-names(sp.traits)
- } else {
- prw.out=unlist(prw.out,recursive=FALSE)
- gen.out=unlist(gen.out,recursive=FALSE)
- if(pairwise) RES=c(gen.out,prw.out) else RES=gen.out
- }
-
- return(unlist(list(RES,sp.plot=list(sp.plot),sp.tree=list(phy),sp.traits=list(sp.traits)),recursive=FALSE))
- }