library(ape)
library(MASS)
library(phytools)
## Loading required package: maps
CompareRates.multTrait<-function(phy,x,TraitCov=T,ms.err=NULL,ms.cov=NULL){
build.chol<-function(b){
c.mat<-matrix(0,nrow = p,ncol = p)
c.mat[lower.tri(c.mat)]<-b[-1]
c.mat[p,p]<-exp(b[1])
c.mat[1,1]<-sqrt(sum((c.mat[p,])^2))
if(p>2){
for(i in 2:(p-1)){
c.mat[i,i]<-ifelse((c.mat[1,1]^2-sum((c.mat[i,])^2))>0,sqrt(c.mat[1,1]^2-sum((c.mat[i,])^2)),0)
}
}
return(c.mat)
}
x<-as.matrix(x)
N<-nrow(x)
p<-ncol(x)
C<-vcv.phylo(phy)
C<-C[rownames(x),rownames(x)]
I<-diag(1,N)
if (is.matrix(ms.err)){
ms.err<-as.matrix(ms.err[rownames(x),])}
if (is.matrix(ms.cov)){
ms.cov<-as.matrix(ms.cov[rownames(x),])}
a.obs<-colSums(solve(C)) %*% x / sum(solve(C))
one<-matrix(1,N,1)
R.obs<-t(x-one%*%a.obs)%*%solve(C)%*%(x-one%*%a.obs)/N
IIDcon<-function(trait=trait,mu=mu,sigma=sigma,C=C){
z<- (trait-mu)/sigma
eC<-eigen(C)
D.n5<-diag(1/sqrt(eC$values))
C.neg.5<-eC$vectors%*%D.n5%*%t(eC$vectors)
return(C.neg.5%*%trait)
}
a.obs.pmm<-array(NA,p)
R.obs.pmm<-array(NA,c(p,p))
IIDtrait<-array(NA,dim(x))
h.array<-array(NA,p)
for(Index in 1:p){
h<-phylosig(tree=phy,x=x[,Index],method="lambda")$lambda
h.array[Index]<-h
Sh<-h^2*C + (1-h^2)*I
assign(paste("Sh",Index,sep=""),Sh)
a.obs.pmm[Index]<-colSums(solve(Sh)) %*% x[,Index] / sum(solve(Sh))
R.obs.pmm[Index,Index]<-t(x[,Index]-one%*%a.obs.pmm[Index])%*%solve(Sh)%*%(x[,Index]-one%*%a.obs.pmm[Index])/N
IIDtrait[,Index]<-IIDcon(trait=x[,Index],mu=a.obs.pmm[Index],sigma=R.obs.pmm[Index,Index],C=Sh)
}
for(i in 1: (p-1)){
for( j in (i+1):p){
R.obs.pmm[i,j]<-R.obs.pmm[j,i]<- cov(IIDtrait[,i],IIDtrait[,j])
}
}
dim(a.obs.pmm)
a.obs.pmm<-matrix(a.obs.pmm,nrow=1,ncol=p)
a.obs.pmm
dim(a.obs.pmm)
R.obs.pmm
D<-matrix(0,N*p,p)
for(i in 1:(N*p)){
for(j in 1:p){
if((j-1)*N < i && i<=j*N){
D[i,j]=1.0
}
}
}
y<-as.matrix(as.vector(x))
if (TraitCov==F){R.obs.pmm<-diag(diag(R.obs.pmm),p)}
Sh1
Sh2
h1<-h.array[1]
h2<-h.array[2]
h12<-(h1+h2)/2
Sh12 <- h12^2*C + (1-h12^2)*I
RkronSh<-rbind(cbind(R.obs.pmm[1,1]*Sh1,R.obs.pmm[1,2]*Sh12),
cbind(R.obs.pmm[1,2]*Sh12,R.obs.pmm[2,2]*Sh2))
RkronSh
LLik.obs.pmm<-ifelse(is.matrix(ms.err)==TRUE,
-t(y-D%*%t(a.obs.pmm))%*%ginv((RkronSh+diag(as.vector(ms.err))))%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant((RkronSh+ diag(as.vector(ms.err))))$modulus[1]/2,
-t(y-D%*%t(a.obs.pmm))%*%ginv(RkronSh)%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant(RkronSh)$modulus[1]/2)
sigma.mn.pmm<-mean(diag(R.obs.pmm))
if(is.matrix(ms.err) && is.matrix(ms.cov)){
within.spp<-cbind(ms.err,ms.cov)
rc.label<-NULL
for(i in 1:p){
rc.label<-rbind(rc.label,c(i,i))
}
for(j in 2:p){
if(i!=j&&i<j){
rc.label<-rbind(rc.label,c(i,j))
}
}
m.e<-NULL
for(i in 1:p){
temp<-NULL
for(j in 1:p){
for(k in 1:nrow(rc.label)){
if(setequal(c(i,j),rc.label[k,])==T)
{tmp<-cbind(tmp,diag(within.spp[,k]))}
}
}
m.e<-rbind(m.e,tmp)
}
}
R<-R.obs.pmm
param<-c(sigma.mn.pmm,0.5,0.5)
names(param)<-c("sigma","h1","h2")
lik.covF.pmm<-function(param){
h1<-param["h1"]
h2<-param["h2"]
sigma<-param["sigma"]
h12<-(h1+h2)/2
Sh12 <- h12^2*C + (1-h12^2)*I
diag(R)<-sigma.mn.pmm
RkronSh<-rbind(cbind(R[1,1]*Sh1,R[1,2]*Sh12),
cbind(R[1,2]*Sh12,R[2,2]*Sh2))
LLik<-ifelse(is.matrix(ms.err)==TRUE,
-t(y-D%*%t(a.obs.pmm))%*%ginv((RkronSh+m.e))%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant((RkronSh+ m.e))$modulus[1]/2,
-t(y-D%*%t(a.obs.pmm))%*%ginv(RkronSh)%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant(RkronSh)$modulus[1]/2)
if(LLik==-Inf){LLik<--1e+10}
return(-LLik)
}
lik.covT.pmm<-function(param){
h1<-param["h1"]
h2<-param["h2"]
sigma<-param["sigma"]
R.offd<-param["R.offd"]
h12<-(h1+h2)/2
Sh12 <- h12^2*C + (1-h12^2)*I
low.chol<-build.chol(c(sigma,R.offd))
R<-low.chol%*%t(low.chol)
RkronSh<-rbind(cbind(R[1,1]*Sh1,R[1,2]*Sh12),
cbind(R[1,2]*Sh12,R[2,2]*Sh2))
LLik <- ifelse(is.matrix(ms.err)==TRUE,
-t(y-D%*%t(a.obs.pmm))%*%ginv(RkronSh+m.e)%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant(RkronSh+m.e)$modulus[1]/2,
-t(y-D%*%t(a.obs.pmm))%*%ginv(RkronSh)%*%(y-D%*%t(a.obs.pmm))/2-N*p*log(2*pi)/2-determinant(RkronSh)$modulus[1]/2
)
if(LLik==-Inf){LLik<--le+10}
return(-LLik)
}
sigma.upper<-2*max(apply(x,2,sd))
p0<-c(0.5,0.5,sigma.mn.pmm)
names(p0)<-c("h1","h2","sigma")
if(TraitCov==F){model.pmm<-optim(p0,fn=lik.covF.pmm,method
="L-BFGS-B",lower = c(0,0,0),upper=c(1,1,sigma.upper))}
R.offd<-rep(0,(p*(p-1)/2))
p0<-c(0.5,0.5,sigma.mn.pmm,0)
names(p0)<-c("h1","h2","sigma","R.offd")
if(TraitCov==T){model1.pmm<-
optim(par=p0,fn=lik.covT.pmm,method="L-BFGS-B",lower = c(0,0,0,0),upper=c(1,1,sigma.upper,sigma.upper))
}
if(TraitCov==F){R.constr.pmm<-diag(model.pmm$par["sigma"],p)}
if(TraitCov==T){
chol.mat<-build.chol(model1.pmm$par[c("sigma","R.offd")])
R.constr.pmm<-chol.mat%*%t(chol.mat)
}
if(model1.pmm$convergence==0){
message.pmm<-"Optimization has converged."}else{
message.pmm<-"Optim may not have converrged.
Consideer changing startt value or lower/upper limits."}
LRT.pmm<-(-2*((-model1.pmm$value-LLik.obs.pmm)))
LRT.prob.pmm<-pchisq(LRT.pmm, (p-1),lower.tail = FALSE)
AIC.obs.pmm<- -2*LLik.obs.pmm+2*p+2*p+2*p #(2p twice: 1x for rates, 1x for anc.states,1x for h)
AIC.common.pmm<--2*(-model1.pmm$value)+2+2*p+2*p #(2*1:for 1 rate 2p for anc.states)
return(
list(
Robs.pmm=R.obs.pmm,
Rconstrained.pmm=R.constr.pmm,
Lobs.pmm=LLik.obs.pmm,
Lconstrained.pmm=(-model1.pmm$value),
LRTest.pmm=LRT.pmm,
Prob.pmm=LRT.prob.pmm,
AICc.obs.pmm=AIC.obs.pmm,
AICc.constrained.pmm=AIC.common.pmm,
optimmessage.pmm=message.pmm
)
)
}
### Sample code
phy<-rcoal(5)
plot(phy)
x<- matrix(c(rnorm(5,2,1),rnorm(5,0,0.5)),ncol=2)
rownames(x)<-phy$tip.label#LETTERS[1:N]
CompareRates.multTrait(phy=phy,x=x,TraitCov=T,ms.err=NULL,ms.cov=NULL)
## $Robs.pmm
## [,1] [,2]
## [1,] 0.5396813 -0.1249293
## [2,] -0.1249293 0.2374261
##
## $Rconstrained.pmm
## [,1] [,2]
## [1,] 1 0
## [2,] 0 1
##
## $Lobs.pmm
## [1] -8.124351
##
## $Lconstrained.pmm
## [1] -10.08756
##
## $LRTest.pmm
## [1] 3.926419
##
## $Prob.pmm
## [1] 0.04753307
##
## $AICc.obs.pmm
## [1] 28.2487
##
## $AICc.constrained.pmm
## [1] 30.17512
##
## $optimmessage.pmm
## [1] "Optimization has converged."
#####
tree<-read.tree("http://tonyjhwueng.info/phyrates/ple.nwk")
plot(tree)
tree$tip.label
## [1] "Plethodon_dorsalis" "Plethodon_ventralis"
## [3] "Plethodon_angusticlavius" "Plethodon_welleri"
## [5] "Plethodon_punctatus" "Plethodon_wehrlei"
## [7] "Plethodon_websteri" "Plethodon_teyahalee"
## [9] "Plethodon_cylindraceus" "Plethodon_variolatus"
## [11] "Plethodon_chlorobryonis" "Plethodon_chattahoochee"
## [13] "Plethodon_cheoah" "Plethodon_shermani"
## [15] "Plethodon_amplus" "Plethodon_meridianus"
## [17] "Plethodon_montanus" "Plethodon_albagula"
## [19] "Plethodon_sequoyah" "Plethodon_ocmulgee"
## [21] "Plethodon_savannah" "Plethodon_grobmani"
## [23] "Plethodon_kisatchie" "Plethodon_mississippi"
## [25] "Plethodon_kiamichi" "Plethodon_aureolus"
## [27] "Plethodon_glutinosus" "Plethodon_jordani"
## [29] "Plethodon_metcalfi" "Plethodon_ouachitae"
## [31] "Plethodon_fourchensis" "Plethodon_caddoensis"
## [33] "Plethodon_kentucki" "Plethodon_petraeus"
## [35] "Plethodon_yonahlossee" "Plethodon_hubrichti"
## [37] "Plethodon_nettingi" "Plethodon_richmondi"
## [39] "Plethodon_electromorphus" "Plethodon_cinereus"
## [41] "Plethodon_shenandoah" "Plethodon_hoffmani"
## [43] "Plethodon_virginia" "Plethodon_serratus"
df<-read.csv("http://tonyjhwueng.info/phyrates/Adams2012-SystBiolData.csv")
spX<-strsplit(as.character(df$X),"_")
phy<-tree
spX<-strsplit(as.character(df$X),"_")
spname<-array(NA,length(phy$tip.label))
for(Index in 1:length(phy$tip.label)){
spname[Index]<-paste("Plethodon_", spX[[Index]][2],sep="")
}
spname
## [1] "Plethodon_albagula" "Plethodon_amplus"
## [3] "Plethodon_angusticlavius" "Plethodon_aureolus"
## [5] "Plethodon_caddoensis" "Plethodon_chattahoochee"
## [7] "Plethodon_cheoah" "Plethodon_chlorobryonis"
## [9] "Plethodon_cinereus" "Plethodon_cylindraceus"
## [11] "Plethodon_dorsalis" "Plethodon_electromorphus"
## [13] "Plethodon_fourchensis" "Plethodon_glutinosus"
## [15] "Plethodon_grobmani" "Plethodon_hoffmani"
## [17] "Plethodon_hubrichti" "Plethodon_jordani"
## [19] "Plethodon_kentucki" "Plethodon_kiamichi"
## [21] "Plethodon_kisatchie" "Plethodon_meridianus"
## [23] "Plethodon_metcalfi" "Plethodon_mississippi"
## [25] "Plethodon_montanus" "Plethodon_nettingi"
## [27] "Plethodon_ocmulgee" "Plethodon_ouachitae"
## [29] "Plethodon_petraeus" "Plethodon_punctatus"
## [31] "Plethodon_richmondi" "Plethodon_savannah"
## [33] "Plethodon_sequoyah" "Plethodon_serratus"
## [35] "Plethodon_shenandoah" "Plethodon_shermani"
## [37] "Plethodon_teyahalee" "Plethodon_variolatus"
## [39] "Plethodon_ventralis" "Plethodon_virginia"
## [41] "Plethodon_websteri" "Plethodon_wehrlei"
## [43] "Plethodon_welleri" "Plethodon_yonahlossee"
df$X<-spname
HeadLength<-df$HeadLength
names(HeadLength)<-spname
BodyWidth<-df$BodyWidth
names(BodyWidth)<-spname
HeadLength<-HeadLength[phy$tip.label]
BodyWidth<-BodyWidth[phy$tip.label]
x<-cbind(HeadLength,BodyWidth)
CompareRates.multTrait(phy=phy,x=x,TraitCov=T,ms.err=NULL,ms.cov=NULL)
## $Robs.pmm
## [,1] [,2]
## [1,] 0.2222583 0.1252084
## [2,] 0.1252084 0.1251008
##
## $Rconstrained.pmm
## [,1] [,2]
## [1,] 1.0166341 0.1300416
## [2,] 0.1300416 1.0166341
##
## $Lobs.pmm
## [1] -126.824
##
## $Lconstrained.pmm
## [1] -187.8177
##
## $LRTest.pmm
## [1] 121.9874
##
## $Prob.pmm
## [1] 2.323066e-28
##
## $AICc.obs.pmm
## [1] 265.648
##
## $AICc.constrained.pmm
## [1] 385.6354
##
## $optimmessage.pmm
## [1] "Optimization has converged."