Nothing
cNST<-function(beta.obs, beta.rand.list, group, Dmax=1,
between.group=FALSE,SES=FALSE,RC=FALSE,
output.detail=FALSE)
{
beta.obs=as.matrix(beta.obs)
beta.r1=as.matrix(beta.rand.list[[1]])
if(sum(rownames(beta.obs)!=rownames(beta.r1))>0){stop("sample IDs in beta.obs and beta.rand.list do not match.")}
obs3=dist.3col(beta.obs)
obs=as.numeric(obs3[,3])
dist.ran=sapply(1:length(beta.rand.list),function(i){as.numeric(dist.3col(beta.rand.list[[i]])[,3])})
if(min(min(obs,na.rm = TRUE),min(dist.ran,na.rm = TRUE))<0){stop("beta diversity value should not be negative.")}
if(!is.na(Dmax)){if(Dmax<(max(max(obs,na.rm = TRUE),max(dist.ran,na.rm = TRUE)))){stop("Some beta diversity values are larger than Dmax. Please check.")}}
rand.mean=apply(dist.ran, 1, mean,na.rm=TRUE)
if(SES)
{
rand.sd=apply(dist.ran,1,stats::sd,na.rm=TRUE)
ses=obs3
ses[,3]=(obs-rand.mean)/rand.sd
ses[which(obs==rand.mean),3]=0
colnames(ses)[3]=paste0("SES.",colnames(obs3)[3])
}
if(RC)
{
obsmm=matrix(obs,nrow=nrow(dist.ran),ncol=ncol(dist.ran))
a1=rowSums(dist.ran>obsmm,na.rm = TRUE)/ncol(dist.ran)
a2=rowSums(dist.ran==obsmm,na.rm = TRUE)/ncol(dist.ran)
rc=obs3
rc[,3]=(0.5-(a1+(a2/2)))*2
colnames(rc)[3]=paste0("RC.",colnames(obs3)[3])
}
if(is.na(Dmax))
{
rand.amax=apply(dist.ran, 1, max,na.rm=TRUE)
rand.bmax=apply(dist.ran, 1, function(v){max(stats::density(v,na.rm = TRUE)$x)})
d.up1=(sum((obs<=1)*(rand.amax<=1))==length(obs))*(rand.bmax>1)
rand.max=d.up1+((1-d.up1)*rand.bmax)
Dmax=max(obs,rand.max)
}
GD=rand.mean/cbind(dist.ran,obs) # G / D and G / Gk
EC=(Dmax-rand.mean)/(Dmax-cbind(dist.ran,obs)) # E / C and E / Ek
EC[is.nan(EC)]=1
ECGD=EC
ECGD[which(EC>1)]=GD[which(EC>1)]
Cij=(Dmax-obs)/Dmax
Eij=(Dmax-rand.mean)/Dmax
Dsij=obs/Dmax
Gsij=rand.mean/Dmax
####
ECijx=Eij/Cij; CEijx=Cij/Eij
ECijx[is.nan(ECijx)]=1
CEijx[is.nan(CEijx)]=1
DGijx=Dsij/Gsij;GDijx=Gsij/Dsij
DGijx[is.nan(DGijx)]=1
GDijx[is.nan(GDijx)]=1
MSTij = (ECijx) * (DGijx)
MSTij[which(MSTij > 1)] = ((CEijx) * (GDijx))[which(MSTij > 1)]
#####
#MSTij=(Eij/Cij)*(Dsij/Gsij)
#MSTij[which(MSTij>1)]=((Cij/Eij)*(Gsij/Dsij))[which(MSTij>1)]
indexs=data.frame(obs3[,1:2],D.ij=obs,G.ij=rand.mean,Ds.ij=Dsij,
Gs.ij=Gsij,C.ij=Cij, E.ij=Eij, ST.ij=ECGD[,ncol(ECGD)],MST.ij=MSTij)
colnames(indexs)[3:ncol(indexs)]=paste0(colnames(indexs)[3:ncol(indexs)],".",colnames(obs3)[3])
STmin=Eij
STmin[which(obs>rand.mean)]=(1-Eij)[which(obs>rand.mean)]
grp.lev=unique(group[,1])
outi<-outij<-list()
if(between.group){outik<-outikj<-list();bgi=1}
for(i in 1:length(grp.lev))
{
sampi=rownames(group)[which(group[,1]==grp.lev[i])]
ni=length(sampi)
idi=which((obs3[,1] %in% sampi)&(obs3[,2] %in% sampi))
ECGDi=ECGD[idi,,drop=FALSE]
ECGD.mi=colMeans(ECGDi,na.rm = TRUE)
STi.max=max(ECGD.mi,na.rm = TRUE)
STi.min=mean(STmin[idi])
STi=ECGD.mi[[length(ECGD.mi)]]
if(STi==STi.min){NSTi=0}else{NSTi=(STi-STi.min)/(STi.max-STi.min)}
MSTi=mean(MSTij[idi],na.rm=TRUE)
outi[[i]]=data.frame(group=grp.lev[i],size=length(idi),ST.i=STi,NST.i=NSTi,MST.i=MSTi,stringsAsFactors = FALSE)
STij=ECGD[idi,ncol(ECGD)]
NSTij=(STij-STi.min)/(STi.max-STi.min)
MSTiji=MSTij[idi]
outij[[i]]=data.frame(group=rep(grp.lev[i],length(idi)),
obs3[idi,1:2,drop=FALSE],C.ij=Cij[idi],E.ij=Eij[idi],
ST.ij=STij,NST.ij=NSTij,MST.ij=MSTiji,stringsAsFactors = FALSE)
if(SES)
{
ses.i=mean(as.numeric(ses[idi,3]),na.rm = TRUE)
outi[[i]]=data.frame(outi[[i]],SES.i=ses.i,stringsAsFactors = FALSE)
outij[[i]]=data.frame(outij[[i]],SES.ij=as.numeric(ses[idi,3]),stringsAsFactors = FALSE)
}
if(RC)
{
rc.i=mean(as.numeric(rc[idi,3]),na.rm = TRUE)
outi[[i]]=data.frame(outi[[i]],RC.i=rc.i,stringsAsFactors = FALSE)
outij[[i]]=data.frame(outij[[i]],RC.ij=as.numeric(rc[idi,3]),stringsAsFactors = FALSE)
}
if(between.group)
{
if(i<length(grp.lev))
{
for(k in (i+1):length(grp.lev))
{
sampk=rownames(group)[which(group[,1]==grp.lev[k])]
nk=length(sampk)
idik=which(((obs3[,1] %in% sampi)&(obs3[,2] %in% sampk))|((obs3[,1] %in% sampk)&(obs3[,2] %in% sampi)))
ECGDik=ECGD[idik,,drop=FALSE]
ECGD.mik=colMeans(ECGDik)
STik.max=max(ECGD.mik)
STik.min=mean(STmin[idik])
STik=ECGD.mik[[length(ECGD.mik)]]
if(STik==STik.min){NSTik=0}else{NSTik=(STik-STik.min)/(STik.max-STik.min)}
MSTik=mean(MSTij[idik])
outik[[bgi]]=data.frame(group=paste0(grp.lev[i],".vs.",grp.lev[k]),size=length(idik),
ST.i=STik,NST.i=NSTik,MST.i=MSTik,stringsAsFactors = FALSE)
STikj=ECGD[idik,ncol(ECGD)]
NSTikj=(STikj-STik.min)/(STik.max-STik.min)
MSTikj=MSTij[idik]
outikj[[bgi]]=data.frame(group=rep(paste0(grp.lev[i],".vs.",grp.lev[k]),length(idik)),
obs3[idik,1:2,drop=FALSE],C.ij=Cij[idik],E.ij=Eij[idik],
ST.ij=STikj,NST.ij=NSTikj,MST.ij=MSTikj,stringsAsFactors = FALSE)
if(SES)
{
sesik=mean(as.numeric(ses[idik,3]),na.rm = TRUE)
outik[[bgi]]=data.frame(outik[[bgi]],SES.i=sesik,stringsAsFactors = FALSE)
outikj[[bgi]]=data.frame(outikj[[bgi]],SES.ij=as.numeric(ses[idik,3]),stringsAsFactors = FALSE)
}
if(RC)
{
rcik=mean(as.numeric(rc[idik,3]),na.rm = TRUE)
outik[[bgi]]=data.frame(outik[[bgi]],RC.i=rcik,stringsAsFactors = FALSE)
outikj[[bgi]]=data.frame(outikj[[bgi]],RC.ij=as.numeric(rc[idik,3]),stringsAsFactors = FALSE)
}
bgi=bgi+1
}
}
}
}
outi=Reduce(rbind,outi)
outij=Reduce(rbind,outij)
colnames(outi)[3:ncol(outi)]=paste0(colnames(outi)[3:ncol(outi)],".",colnames(obs3)[3])
colnames(outij)[4:ncol(outij)]=paste0(colnames(outij)[4:ncol(outij)],".",colnames(obs3)[3])
output=list(index.pair=indexs,index.grp=outi,index.pair.grp=outij,Dmax=Dmax)
if(between.group)
{
outik=Reduce(rbind,outik)
outikj=Reduce(rbind,outikj)
colnames(outik)[3:ncol(outik)]=paste0(colnames(outik)[3:ncol(outik)],".",colnames(obs3)[3])
colnames(outikj)[4:ncol(outikj)]=paste0(colnames(outikj)[4:ncol(outikj)],".",colnames(obs3)[3])
output=c(output,list(index.between=outik,index.pair.between=outikj))
}
if(SES){output$index.pair=data.frame(output$index.pair,ses[,3,drop=FALSE],stringsAsFactors = FALSE)}
if(RC){output$index.pair=data.frame(output$index.pair,rc[,3,drop=FALSE],stringsAsFactors = FALSE)}
if(output.detail)
{
details=list(rand.mean=rand.mean,Dmax=Dmax,obs3=obs3,dist.ran=dist.ran,group=group)
output=c(output,list(details=details))
}
output
}
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