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Rphylip.R
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## calls threshml from PHYLIP (Felsenstein 2013)
## written by Liam J. Revell 2013, 2015
Rthreshml<-function(tree,X,types=NULL,path=NULL,...){
if(is.null(path)) path<-findPath("threshml")
if(is.null(path)) stop("No path provided and was not able to find path to threshml")
if(class(tree)!="phylo") stop("tree should be an object of class 'phylo'")
if(is.null(types)){
types<-sapply(X,class)
types[types=="numeric"]<-"continuous"
types[types%in%c("factor","character")]<-"discrete"
}
types<-crop(types)
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","intree","outfile"))==0) return(NULL)
tree$tip.label<-sapply(tree$tip.label,function(x,y) which(x==y)[1],y=rownames(X))
## this is for the current idiosyncratic tree input file requirement of threshml
text<-write.tree(tree)
text<-strsplit(text,"")[[1]]
text<-paste(paste(text[1:(length(text)-1)],collapse=""),"0.00000000;\n",sep="")
write(text,file="intree")
if(any(types=="c")) write.continuous(X[,types=="c"])
if(any(types=="d")) write.dna(apply(as.matrix(X[,types=="d"]),2,to.integers),append=any(types=="c"))
## start populating arguments
oo<-c("r")
if(!any(types=="d")) oo<-c(oo,"d")
if(any(types=="c")) oo<-c(oo,"c")
if(hasArg(burnin)){
burnin<-list(...)$burnin
oo<-c(oo,"b",burnin)
}
if(hasArg(nchain)){
nchain<-list(...)$nchain
oo<-c(oo,"n",nchain)
}
if(hasArg(ngen)){
ngen<-list(...)$ngen
oo<-c(oo,"s",ngen)
}
if(hasArg(proposal)){
proposal<-list(...)$proposal
oo<-c(oo,"p",proposal)
}
if(hasArg(lrtest)) lrtest<-list(...)$lrtest
else lrtest<-FALSE
if(lrtest){
# oo<-c(oo,"t")
cat("/nLR-test does not seem to work yet: ignoring argument lrtest.\n\n")
}
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y",sample(seq(1,99999,by=2),1))
system("touch outfile")
system(paste(path,"/threshml",sep=""),input=oo,show.output.on.console=(!quiet))
temp<-readLines("outfile")
cc<-which(types=="c")
dd<-which(types=="d")
## parse covariance matrix
ii<-grep("Covariance matrix",temp)
if(temp[ii]==" Covariance matrix of continuous characters"||temp[ii]==" Covariance matrix of liabilities of discrete characters"){
if(temp[ii+1]==" and liabilities of discrete characters"||temp[ii+1]==" and liability of the discrete character") ii<-ii+5
else ii<-ii+3
} else ii<-ii+5
Covariance_matrix<-matrix(NA,ncol(X),ncol(X))
for(i in 1:ncol(X)){
x<-strsplit(temp[i+ii]," ")[[1]]
Covariance_matrix[i,]<-as.numeric(x[x!=""])[1:ncol(X)+1]
}
jj<-order(c(cc,dd))
Covariance_matrix<-Covariance_matrix[jj,jj]
rownames(Covariance_matrix)<-colnames(Covariance_matrix)<-colnames(X)
## parse transform matrix 1
ii<-grep("Transform from independent variables",temp)+4
Transform_indepvar_liab<-matrix(NA,ncol(X),ncol(X))
for(i in 1:ncol(X)){
x<-strsplit(temp[i+ii]," ")[[1]]
Transform_indepvar_liab[i,]<-as.numeric(x[x!=""])[1:ncol(X)+1]
}
Transform_indepvar_liab<-Transform_indepvar_liab[jj,jj]
rownames(Transform_indepvar_liab)<-colnames(Transform_indepvar_liab)<-colnames(X)
## parse variances of change
ii<-grep("its change",temp)+1
Var_change<-vector()
for(i in 1:ncol(X)){
x<-strsplit(temp[i+ii]," ")[[1]]
Var_change[i]<-as.numeric(x[x!=""])[2]
}
Var_change<-Var_change[jj]
names(Var_change)<-colnames(X)
## parse transform matrix 2
ii<-grep("Transform from liabilities or characters",temp)+4
Transform_liab_cont<-matrix(NA,ncol(X),ncol(X))
for(i in 1:ncol(X)){
x<-strsplit(temp[i+ii]," ")[[1]]
Transform_liab_cont[i,]<-as.numeric(x[x!=""])[1:ncol(X)+1]
}
Transform_liab_cont<-Transform_liab_cont[jj,jj]
rownames(Transform_liab_cont)<-colnames(Transform_liab_cont)<-colnames(X)
## done parsing
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup) cleanFiles(c("infile","intree","outfile"))
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
return(list(Covariance_matrix=Covariance_matrix,
Transform_indepvar_liab=Transform_indepvar_liab,
Var_change=Var_change,
Transform_liab_cont=Transform_liab_cont))
}
## internal function read.multi.dna
## written by Liam J. Revell 2014
read.multi.dna<-function(file,N,n){
FF<-readLines(file)
skip<-grep(pattern=paste(" ",n,sep=""),FF)-1
X<-lapply(skip,read.dna,file=file,format="sequential")
return(X)
}
## internal function read.multi.phylip.data
## written by Liam J. Revell 2014
read.multi.phylip.data<-function(file,N,n){
FF<-readLines(file)
skip<-grep(pattern=paste(" ",n,sep=""),FF)-1
X<-lapply(skip,read.phylip.data,file=file,format="sequential")
return(X)
}
## internal function read.multi.rest.data
## written by Liam J. Revell 2014
read.multi.rest.data<-function(file,N,n){
FF<-readLines(file)
skip<-grep(pattern=paste(" ",n,sep=""),FF)-1
X<-lapply(skip,read.rest.data,file=file)
return(X)
}
## read.phylip.data
## written by Liam J. Revell 2014
read.phylip.data<-function(file,format="interleaved",skip=0,nlines=0,comment.char="#",as.character=FALSE){
X<-read.dna(file,format,skip,nlines,comment.char,as.character=TRUE)
class(X)<-"phylip.data"
X
}
## read.rest.data
## written by Liam J. Revell 2014
read.rest.data<-function(file,skip=0){
X<-readLines(file)
nn<-strsplit(X[skip+1]," ")[[1]]
nn<-as.numeric(nn[nn!=""])
X<-X[1:(nn[1]*ceiling(nn[2]/50))+1]
X<-sapply(1:nn[1],function(i,x,nn) paste(x[1:ceiling(nn[2]/50)+(i-1)*ceiling(nn[2]/50)],collapse=""),x=X,nn=nn)
X<-strsplit(X,"")
labels<-sapply(lapply(X,function(x) x[1:10]),function(x) x[1:max(setdiff(1:10,which(x==" ")))])
X<-lapply(lapply(X,function(x) x[11:length(x)]),function(x) x<-x[x!=" "])
names(X)<-labels
attr(X,"nenzymes")<-nn[3]
attr(X,"nsites")<-nn[2]
class(X)<-"rest.data"
X
}
## calls seqboot from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rseqboot<-function(X,path=NULL,...){
if(is.null(path)) path<-findPath("seqboot")
if(is.null(path)) stop("No path provided and was not able to find path to seqboot")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet){
files<-c("ancestors","categories","infile","mixture","outancestors","outcategories","outfile",
"outmixture","weights")
if(file.warn(files)==0) return(NULL)
}
oo<-vector()
if(hasArg(type)){
type<-list(...)$type
type<-tolower(type)
} else {
if(class(X)=="DNAbin"||class(X)=="proseq") type<-"sequence"
else if(class(X)=="phylip.data") type<-"morph"
else if(class(X)=="rest.data") type="rest"
else if(class(X)=="matrix") type="gene.freq"
}
if(type=="morph") oo<-c(oo,"d")
else if(type=="rest") oo<-c(oo,rep("d",2),"e")
else if(type=="gene.freq") oo<-c(oo,rep("d",3))
if(hasArg(method)) method<-list(...)$method
else method<-"bootstrap"
method<-tolower(method)
if(method=="jacknife") oo<-c(oo,"j")
else if(method=="permute") oo<-c(oo,rep("j",2))
if(hasArg(percentage)) percentage<-list(...)$percentage
else percentage<-100
if(percentage!=100) oo<-c(oo,"%",percentage)
if(hasArg(block.size)) block.size<-list(...)$block.size
else block.size<-1
if(block.size!=1) oo<-c(oo,"b",block.size)
if(hasArg(replicates)) replicates<-list(...)$replicates
else replicates<-100
if(replicates!=100) oo<-c(oo,"r",replicates)
if(hasArg(weights)){
weights<-list(...)$weights
oo<-c(oo,"w")
write(paste(weights,collapse=""),file="weights")
} else weights<-NULL
if(hasArg(rate.categories)&&type=="sequence"){
rate.categories<-list(...)$rate.categories
write(paste(rate.categories,collapse=""),file="categories")
oo<-c(oo,"c")
} else rate.categories<-NULL
if(hasArg(mixture)&&type=="morph"){
mixture<-list(...)$mixture
oo<-c(oo,"x")
mixture<-toupper(mixture)
write(paste(mixture,collapse=""),file="mixture")
} else mixture<-NULL
if(hasArg(ancestors)&&type=="morph"){
ancestors<-list(...)$ancestors
oo<-c(oo,"n")
ancestors<-toupper(ancestors)
write(paste(ancestors,collapse=""),file="ancestors")
} else ancestors<-NULL
if(quiet) oo<-c(oo,2)
oo<-c(oo,"i","y",sample(seq(1,99999,by=2),1),"r")
if(type=="sequence"||type=="morph") write.dna(X)
else if(type=="rest") write.rest.data(X)
else if(type=="gene.freq") write.continuous(X)
system("touch outfile")
if(!is.null(ancestors)){
system("touch outancestors")
oo<-c(oo,"r")
}
if(!is.null(mixture)){
system("touch outmixture")
oo<-c(oo,"r")
}
if(!is.null(rate.categories)){
system("touch outcategories")
oo<-c(oo,"r")
}
system(paste(path,"/seqboot",sep=""),input=oo,show.output.on.console=(!quiet))
if(type=="sequence") XX<-read.multi.dna(file="outfile",N=replicates,n=nrow(X))
if(type=="morph") XX<-read.multi.phylip.data(file="outfile",N=replicates,n=nrow(X))
if(type=="rest") XX<-read.multi.rest.data(file="outfile",N=replicates,n=length(X))
if(class(X)=="proseq") XX<-lapply(XX,function(x){ class(x)<-"proseq"; x })
if(type=="sequence"||type=="morph") X<-lapply(XX,function(x,y){ rownames(x)<-y; x },y=rownames(X))
else if(type=="rest") X<-lapply(XX,function(x,y){ names(x)<-y; x },y=names(X))
if(!is.null(ancestors)){
A<-readLines("outancestors")
A<-strsplit(paste(A,collapse=""),"")[[1]]
A<-A[A!=" "]
m<-length(A)/replicates
A<-lapply(1:replicates,function(i,m,x) x[1:m+(i-1)*m],m=m,x=A)
}
if(!is.null(mixture)){
M<-readLines("outmixture")
M<-strsplit(paste(M,collapse=""),"")[[1]]
M<-M[M!=" "]
m<-length(M)/replicates
M<-lapply(1:replicates,function(i,m,x) x[1:m+(i-1)*m],m=m,x=M)
}
if(!is.null(rate.categories)){
R<-readLines("outcategories")
R<-strsplit(paste(R,collapse=""),"")[[1]]
R<-R[R!=" "]
m<-length(R)/replicates
R<-lapply(1:replicates,function(i,m,x) as.numeric(x[1:m+(i-1)*m]),m=m,x=R)
}
if(!is.null(ancestors)){
if(is.null(mixture)) X<-mapply(function(x,y) list(data=x,ancestors=y),x=X,y=A,SIMPLIFY=FALSE)
else X<-mapply(function(x,y,z) list(data=x,ancestors=y,mixture=z),x=X,y=A,z=M,SIMPLIFY=FALSE)
} else if(!is.null(mixture)) X<-mapply(function(x,y) list(data=x,mixture=y),x=X,y=M,SIMPLIFY=FALSE)
if(!is.null(rate.categories)) X<-mapply(function(x,y) list(data=x,categories=y),x=X,y=R,SIMPLIFY=FALSE)
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile")
if(!is.null(weights)) files<-c(files,"weights")
if(!is.null(ancestors)) files<-c(files,"ancestors","outancestors")
if(!is.null(rate.categories)) files<-c(files,"categories","outcategories")
if(!is.null(mixture)) files<-c(files,"mixture","outmixture")
cleanFiles(files)
}
return(X)
}
## calls clique from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rclique<-function(X,path=NULL,...){
if(class(X)=="DNAbin") stop("you should be using Rdnacomp for DNA data.\n\n")
if(is.vector(X)&&!is.list(X)) X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
if(is.list(X)){
if(all(sapply(X,length)!=1)) X<-t(sapply(X,function(x) x))
else X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
}
if(is.data.frame(X)) X<-as.matrix(X)
if(is.null(path)) path<-findPath("clique")
if(is.null(path)) stop("No path provided and was not able to find path to clique")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("ancestors","infile","outfile","outtree","weights"))==0) return(NULL)
oo<-c("r","r")
if(hasArg(ancestral)){
oo<-c(oo,"a")
write(paste(ancestral,collapse=""),file="ancestors")
} else ancestral<-NULL
if(hasArg(weights)){
oo<-c(oo,"w")
write(paste(weights,collapse=""),file="weights")
} else weights<-NULL
if(hasArg(minimum.clique)) minimum.clique<-list(...)$minimum.clique
else minimum.clique<-NULL
if(!is.null(minimum.clique)) oo<-c(oo,"c",minimum.clique)
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y")
write.dna(X)
system("touch outtree")
system("touch outfile")
system(paste(path,"/clique",sep=""),input=oo,show.output.on.console=(!quiet))
tree<-read.tree("outtree")
temp<-readLines("outfile")
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
if(!quiet){
cat("Translation table\n")
cat("-----------------\n")
temp<-lapply(1:nrow(X),function(x,y) cat(paste("\t",paste(x,y[x],sep="\t"),"\n",sep="")),y=rownames(X))
cat("\n")
}
if(class(tree)=="phylo") tree$tip.label<-rownames(X)[as.numeric(tree$tip.label)]
else if(class(tree)=="multiPhylo"){
foo<-function(x,y){
x$tip.label<-y[as.numeric(x$tip.label)]
x
}
tree<-lapply(tree,foo,y=rownames(X))
class(tree)<-"multiPhylo"
}
if(hasArg(outgroup)){
outgroup<-list(...)$outgroup
tree<-outgroup.root(tree,outgroup,quiet)
}
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile","outtree")
if(!is.null(ancestral)) files<-c(files,"ancestors")
if(!is.null(weights)) files<-c(files,"weights")
cleanFiles(files)
}
return(tree)
}
## calls restml from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rrestml<-function(X,path=NULL,...){
if(is.null(path)) path<-findPath("restml")
if(is.null(path)) stop(paste("No path provided and was not able to find path to restml"))
if(class(X)!="rest.data") stop("X should be an object of class 'rest.data'")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","intree","outfile","outtree"))==0) return(NULL)
oo<-c("r")
if(hasArg(tree)){
oo<-c(oo,"u")
tree<-list(...)$tree
tree$tip.label<-sapply(tree$tip.label,function(x,y) which(x==y),y=rownames(X))
write.tree(tree,"intree")
intree<-TRUE
} else intree<-FALSE
if(hasArg(all.sites)) all.sites<-list(...)$all.sites
else all.sites<-FALSE
if(all.sites) oo<-c(oo,"a")
if(hasArg(speedier)) speedier<-list(...)$speedier
else speedier<-FALSE
if((!speedier)) oo<-c(oo,"s")
if(hasArg(global)) global<-list(...)$global
else global<-TRUE
if(global) oo<-c(oo,"g")
if(hasArg(random.order)) random.order<-list(...)$random.order
else random.order<-TRUE
if(random.order){
if(hasArg(random.addition)) random.addition<-list(...)$random.addition
else random.addition<-10
oo<-c(oo,"j",sample(seq(1,99999,by=2),1),random.addition)
}
if(hasArg(site.length)) site.length<-list(...)$site.length
else site.length<-6
if(site.length!=6) oo<-c(oo,"l",site.length)
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y","r")
write.rest.data(X)
system("touch outtree")
system("touch outfile")
temp<-system(paste(path,"/restml",sep=""),input=oo,show.output.on.console=(!quiet))
tree<-read.tree("outtree")
temp<-readLines("outfile")
logLik<-as.numeric(strsplit(temp[grep("Ln Likelihood",temp)],"=")[[1]][2])
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
if(!quiet){
cat("Translation table\n")
cat("-----------------\n")
temp<-lapply(1:length(X),function(x,y) cat(paste("\t",paste(x,y[x],sep="\t"),"\n",sep="")),y=names(X))
cat("\n")
}
tree$tip.label<-names(X)[as.numeric(tree$tip.label)]
if(hasArg(outgroup)){
outgroup<-list(...)$outgroup
tree<-outgroup.root(tree,outgroup,quiet)
}
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile","outtree")
if(intree) files<-c(files,"intree")
cleanFiles(files)
}
tree$logLik<-logLik
return(tree)
}
## function converts string or matrix to object of class "rest.data"
## written by Liam J. Revell 2014
as.rest.data<-function(x,...){
if(is.data.frame(x)){
if(ncol(x)==1) x<-setNames(as.vector(t(X)),rownames(X))
else {
X<-as.data.frame(t(x))
class(X)<-"rest.data"
}
}
if(is.vector(x)){
X<-sapply(x,strsplit,split="")
X<-as.data.frame(X)
class(X)<-"rest.data"
}
if(is.matrix(x)){
X<-as.data.frame(apply(x,1,factor))
class(X)<-"rest.data"
}
attr(X,"row.names")<-NULL
if(hasArg(nenzymes)) nenzymes<-list(...)$nenzymes
else nenzymes<-1
attr(X,"nenzymes")<-nenzymes
nsites<-sapply(X,length)
if(any(nsites!=max(nsites))) stop("All species should have the same number of sites scored.")
attr(X,"nsites")<-min(nsites)
return(X)
}
## S3 print method for "rest.data"
## written by Liam J. Revell 2014
print.rest.data<-function(x,printlen=6,digits=3,...){
cat(paste(attr(x,"nsites")," restriction site scores for ",length(x)," species stored in a object of class \"rest.data\".\n\n",sep=""))
cat(paste("All sequences of same length:",attr(x,"nsites"),"\n\n"))
cat(paste("Number of restriction enzymes used to generate the data:",attr(x,"nenzymes"),"\n\n"))
if(printlen<length(x))
cat(paste("Labels:",paste(names(x)[1:min(printlen,length(x))],collapse=" "),"...\n\n"))
else
cat(paste("Labels:",paste(names(x)[1:min(printlen,length(x))],collapse=" "),"\n\n"))
}
## function writes rest.data to file in PHYLIP format with numbers as labels
## written by Liam J. Revell 2014
write.rest.data<-function(X,append=FALSE){
write(paste(" ",length(X)," ",attr(X,"nsites")," ",attr(X,"nenzymes"),sep=""),file="infile",append=append)
for(i in 1:length(X)){
sp<-as.character(i)
sp<-paste(sp,paste(rep(" ",11-nchar(sp)),collapse=""),collapse="")
tt<-paste(sp,paste(X[[i]],collapse=""),collapse=" ")
write(tt,append=TRUE,file="infile")
}
}
## calls restdist from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rrestdist<-function(X,path=NULL,...){
if(is.null(path)) path<-findPath("restdist")
if(is.null(path)) stop("No path provided and was not able to find path to restdist")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","outfile"))==0) return(NULL)
oo<-c("r"); ee<-vector()
if(hasArg(data)) data<-list(...)$data
else data<-"sites"
data<-tolower(data)
if(data=="fragments") oo<-c(oo,"r")
if(hasArg(method)) method<-list(...)$method
else method<-"modified"
method<-tolower(method)
if(method=="nei/li") oo<-c(oo,"n")
if(hasArg(gamma)){
gamma<-list(...)$gamma
oo<-c(oo,"g")
ee<-c(ee,1/sqrt(gamma))
}
if(hasArg(kappa)){
kappa<-list(...)$kappa
oo<-c(oo,"t",kappa)
}## calls gendist from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rgendist<-function(X,path=NULL,...){
if(is.null(path)) path<-findPath("gendist")
if(is.null(path)) stop("No path provided and was not able to find path to gendist")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","outfile"))==0) return(NULL)
if(is.matrix(X)){
## assumes X is a matrix of continuous character data
N<-nrow(X)
tips<-rownames(X)
if(hasArg(nalleles)) nalleles<-list(...)$nalleles
else nalleles<-rep(2,ncol(X))
write(paste(" ",nrow(X)," ",ncol(X),sep=""),file="infile")
write(paste(nalleles,collapse=" "),file="infile",append=TRUE)
for(i in 1:nrow(X)){
sp<-as.character(i)
sp<-paste(sp,paste(rep(" ",11-nchar(sp)),collapse=""),collapse="")
tt<-paste(sp,paste(X[i,],collapse=" "),collapse=" ")
write(tt,append=TRUE,file="infile")
}
} else if(is.list(X)){
## assumes X is a list of matrices containing gene frequency data
N<-nrow(X[[1]])
tips<-rownames(X[[1]])
X<-lapply(X,function(x,tips) x[tips,],tips=tips)
write(paste(" ",nrow(X[[1]])," ",length(X),sep=""),file="infile")
nalleles<-sapply(X,ncol)
write(paste(nalleles,collapse=" "),file="infile",append=TRUE)
## verify that all rows of all X sum to 1.0
temp<-sapply(X,rowSums)
if(!all(round(temp,2)==1)) stop("Some of the rows of X do not sum to 1.0")
for(i in 1:length(tips)){
sp<-as.character(i)
sp<-paste(sp,paste(rep(" ",11-nchar(sp)),collapse=""),collapse="")
dd<-vector()
for(j in 1:length(X)) dd<-c(dd,X[[j]][i,])
tt<-paste(sp,paste(dd,collapse=" "),collapse=" ")
write(tt,append=TRUE,file="infile")
}
} else stop("X should be a matrix (for continuous characters) or a list (for gene frequencies)")
oo<-c("r"); ee<-vector()
if(hasArg(method)) method<-list(...)$method
else method<-"nei"
method<-tolower(method)
if(method=="nei") oo<-c(oo,"n")
else if(method=="cavalli-sforza") oo<-c(oo,"c")
else if(method=="reynolds") oo<-c(oo,"r")
else {
cat(paste("Warning:\n don't recognize method of type",method,".\n"))
cat(" setting method to default type.\n\n")
oo<-c(oo,"n")
}
oo<-c(oo,"y")
system("touch outfile")
system(paste(path,"/gendist",sep=""),input=oo,show.output.on.console=(!quiet))
temp<-readLines("outfile")
xx<-strsplit(paste(temp,collapse=" ")," ")[[1]]
xx<-xx[xx!=""]
D<-matrix(NA,N,N)
for(i in 1:N) D[i,]<-as.numeric(xx[1:N+(i-1)*(N+1)+2])
rownames(D)<-colnames(D)<-tips
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile")
cleanFiles(files)
}
return(as.dist(D))
}
if(hasArg(site.length)) site.length<-list(...)$site.length
else site.length<-6
if(site.length!=6) oo<-c(oo,"l",site.length)
oo<-c(oo,ee,"y")
write.rest.data(X)
system("touch outfile")
system(paste(path,"/restdist",sep=""),input=oo,show.output.on.console=(!quiet))
temp<-readLines("outfile")
xx<-strsplit(paste(temp,collapse=" ")," ")[[1]]
xx<-xx[xx!=""]
N<-length(X)
D<-matrix(NA,N,N)
for(i in 1:N) D[i,]<-as.numeric(xx[1:N+(i-1)*(N+1)+2])
rownames(D)<-colnames(D)<-names(X)
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile")
cleanFiles(files)
}
return(as.dist(D))
}
## calls kitsch from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rkitsch<-function(D,path=NULL,...){
if(class(D)=="dist"||class(D)=="data.frame") D<-as.matrix(D)
D<-D[rownames(D),rownames(D)]
if(is.null(path)) path<-findPath("kitsch")
if(is.null(path)) stop("No path provided and was not able to find path to kitsch")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","intree","outfile","outtree"))==0) return(NULL)
oo<-c("r")
if(hasArg(method)) method<-list(...)$method
else method<-"fm"
if(method=="FM"||method=="fm") method<-"fm"
else if(method=="ME"||method=="me"){
method<-"me"
oo<-c(oo,"d")
} else if(method=="LS"||method=="ls") method<-"ls"
else {
cat("\nWarning:\n method not recognized - using method=\"FM\"\n")
method="fm"
}
if(hasArg(tree)){
oo<-c(oo,"u")
tree<-list(...)$tree
tree$tip.label<-sapply(tree$tip.label,function(x,y) which(x==y),y=rownames(D))
write.tree(tree,"intree")
intree<-TRUE
} else intree<-FALSE
if(hasArg(power)){
power<-list(...)$power
oo<-c(oo,"p",power)
} else if(method=="ls") oo<-c(oo,"p",0)
if(hasArg(negative)) negative<-list(...)$negative
else negative<-FALSE
if(!negative) oo<-c(oo,"-")
if(hasArg(random.order)) random.order<-list(...)$random.order
else random.order<-TRUE
if(random.order){
if(hasArg(random.addition)) random.addition<-list(...)$random.addition
else random.addition<-10
oo<-c(oo,"j",sample(seq(1,99999,by=2),1),random.addition)
}
if(hasArg(subreplicate)) subreplicate<-list(...)$subreplicate
else subreplicate<-FALSE
if(subreplicate) oo<-c(oo,"s")
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y","r")
write.distances(D)
system("touch outtree")
system("touch outfile")
system(paste(path,"/kitsch",sep=""),input=oo,show.output.on.console=(!quiet))
tree<-read.tree("outtree")
temp<-readLines("outfile")
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
if(!quiet){
cat("Translation table\n")
cat("-----------------\n")
temp<-lapply(1:nrow(D),function(x,y) cat(paste("\t",paste(x,y[x],sep="\t"),"\n",sep="")),y=rownames(D))
cat("\n")
}
tree$tip.label<-rownames(D)[as.numeric(tree$tip.label)]
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile","outtree")
if(intree) files<-c(files,"intree")
cleanFiles(files)
}
return(tree)
}
## calls gendist from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rgendist<-function(X,path=NULL,...){
if(is.null(path)) path<-findPath("gendist")
if(is.null(path)) stop("No path provided and was not able to find path to gendist")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("infile","outfile"))==0) return(NULL)
if(is.matrix(X)){
## assumes X is a matrix of continuous character data
N<-nrow(X)
tips<-rownames(X)
if(hasArg(nalleles)) nalleles<-list(...)$nalleles
else nalleles<-rep(2,ncol(X))
write(paste(" ",nrow(X)," ",ncol(X),sep=""),file="infile")
write(paste(nalleles,collapse=" "),file="infile",append=TRUE)
for(i in 1:nrow(X)){
sp<-as.character(i)
sp<-paste(sp,paste(rep(" ",11-nchar(sp)),collapse=""),collapse="")
tt<-paste(sp,paste(X[i,],collapse=" "),collapse=" ")
write(tt,append=TRUE,file="infile")
}
} else if(is.list(X)){
## assumes X is a list of matrices containing gene frequency data
N<-nrow(X[[1]])
tips<-rownames(X[[1]])
X<-lapply(X,function(x,tips) x[tips,],tips=tips)
write(paste(" ",nrow(X[[1]])," ",length(X),sep=""),file="infile")
nalleles<-sapply(X,ncol)
write(paste(nalleles,collapse=" "),file="infile",append=TRUE)
## verify that all rows of all X sum to 1.0
temp<-sapply(X,rowSums)
if(!all(round(temp,2)==1)) stop("Some of the rows of X do not sum to 1.0")
for(i in 1:length(tips)){
sp<-as.character(i)
sp<-paste(sp,paste(rep(" ",11-nchar(sp)),collapse=""),collapse="")
dd<-vector()
for(j in 1:length(X)) dd<-c(dd,X[[j]][i,])
tt<-paste(sp,paste(dd,collapse=" "),collapse=" ")
write(tt,append=TRUE,file="infile")
}
} else stop("X should be a matrix (for continuous characters) or a list (for gene frequencies)")
oo<-c("r"); ee<-vector()
if(hasArg(method)) method<-list(...)$method
else method<-"nei"
method<-tolower(method)
if(method=="nei") oo<-c(oo,"n")
else if(method=="cavalli-sforza") oo<-c(oo,"c")
else if(method=="reynolds") oo<-c(oo,"r")
else {
cat(paste("Warning:\n don't recognize method of type",method,".\n"))
cat(" setting method to default type.\n\n")
oo<-c(oo,"n")
}
oo<-c(oo,"y")
system("touch outfile")
system(paste(path,"/gendist",sep=""),input=oo,show.output.on.console=(!quiet))
temp<-readLines("outfile")
xx<-strsplit(paste(temp,collapse=" ")," ")[[1]]
xx<-xx[xx!=""]
D<-matrix(NA,N,N)
for(i in 1:N) D[i,]<-as.numeric(xx[1:N+(i-1)*(N+1)+2])
rownames(D)<-colnames(D)<-tips
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile")
cleanFiles(files)
}
return(as.dist(D))
}
## calls dolpenny from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rdolpenny<-function(X,path=NULL,...){
if(is.vector(X)&&!is.list(X)) X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
if(is.list(X)){
if(all(sapply(X,length)!=1)) X<-t(sapply(X,function(x) x))
else X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
}
if(is.data.frame(X)) X<-as.matrix(X)
if(is.null(path)) path<-findPath("dolpenny")
if(is.null(path)) stop("No path provided and was not able to find path to dolpenny")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("ancestors","infile","outfile","outtree","weights"))==0) return(NULL)
oo<-c("r")
if(hasArg(method)) method<-list(...)$method
else method<-"dollo"
method<-tolower(method)
if(method=="polymorphism") oo<-c(oo,"p")
if(hasArg(groups)){
groups<-list(...)$groups
oo<-c(oo,"h",groups)
}
if(hasArg(report)){
report<-list(...)$report
oo<-c(oo,"f",report)
}
if(hasArg(simple)) simple<-list(...)$simple
else simple<-TRUE
if(!simple) oo<-c(oo,"s")
if(hasArg(threshold)) threshold<-list(...)$threshold
else threshold<-0
if(threshold!=0) oo<-c(oo,"t",threshold)
if(hasArg(ancestral)){
oo<-c(oo,"a")
ancestral<-toupper(ancestral)
write(paste(ancestral,collapse=""),file="ancestors")
} else ancestral<-NULL
if(hasArg(weights)){
weights<-list(...)$weights
if(!any(sapply(weights,"%in%",c(0,1)))){
cat("\n\nWarning:\n only weights of 0 & 1 are permitted\n\n")
weights<-NULL
} else {
oo<-c(oo,"w")
write(paste(weights,collapse=""),file="weights")
}
} else weights<-NULL
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y","r")
write.dna(X)
system("touch outtree")
system("touch outfile")
system(paste(path,"/dolpenny",sep=""),input=oo,show.output.on.console=(!quiet))
tree<-read.tree("outtree")
temp<-readLines("outfile")
ii<-grep("requires a total of",temp)
xx<-strsplit(temp[ii]," ")[[1]]
if(class(tree)=="multiPhylo") for(i in 1:length(tree)) tree[[i]]$pscore<-as.numeric(xx[length(xx)])
else tree$pscore<-as.numeric(xx[length(xx)])
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
if(!quiet){
cat("Translation table\n")
cat("-----------------\n")
temp<-lapply(1:nrow(X),function(x,y) cat(paste("\t",paste(x,y[x],sep="\t"),"\n",sep="")),y=rownames(X))
cat("\n")
}
if(class(tree)=="phylo") tree$tip.label<-rownames(X)[as.numeric(tree$tip.label)]
else if(class(tree)=="multiPhylo"){
foo<-function(x,y){
x$tip.label<-y[as.numeric(x$tip.label)]
x
}
tree<-lapply(tree,foo,y=rownames(X))
class(tree)<-"multiPhylo"
}
if(hasArg(outgroup)){
outgroup<-list(...)$outgroup
tree<-outgroup.root(tree,outgroup,quiet)
}
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile","outtree")
if(!is.null(weights)) files<-c(files,"weights")
if(!is.null(ancestral)) files<-c(files,"ancestors")
cleanFiles(files)
}
return(tree)
}
## calls dollop from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2014
Rdollop<-function(X,path=NULL,...){
if(is.vector(X)&&!is.list(X)) X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
if(is.list(X)){
if(all(sapply(X,length)!=1)) X<-t(sapply(X,function(x) x))
else X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
}
if(is.data.frame(X)) X<-as.matrix(X)
if(is.null(path)) path<-findPath("dollop")
if(is.null(path)) stop("No path provided and was not able to find path to dollop")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("ancestors","infile","intree","outfile","outtree","weights"))==0) return(NULL)
oo<-c("r")
if(hasArg(tree)){
oo<-c(oo,"u")
tree<-list(...)$tree
tree$tip.label<-sapply(tree$tip.label,function(x,y) which(x==y),y=rownames(X))
write.tree(tree,"intree")
intree<-TRUE
} else intree<-FALSE
if(hasArg(method)) method<-list(...)$method
else method<-"dollo"
method<-tolower(method)
if(method=="polymorphism") oo<-c(oo,"p")
if(hasArg(random.order)) random.order<-list(...)$random.order
else random.order<-TRUE
if(random.order){
if(hasArg(random.addition)) random.addition<-list(...)$random.addition
else random.addition<-10
oo<-c(oo,"j",sample(seq(1,99999,by=2),1),random.addition)
}
if(hasArg(threshold)) threshold<-list(...)$threshold
else threshold<-0
if(threshold!=0) oo<-c(oo,"t",threshold)
if(hasArg(ancestral)){
oo<-c(oo,"a")
ancestral<-toupper(ancestral)
write(paste(ancestral,collapse=""),file="ancestors")
} else ancestral<-NULL
if(hasArg(weights)){
oo<-c(oo,"w")
write(paste(weights,collapse=""),file="weights")
} else weights<-NULL
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y","r")
write.dna(X)
system("touch outtree")
system("touch outfile")
system(paste(path,"/dollop",sep=""),input=oo,show.output.on.console=(!quiet))
tree<-read.tree("outtree")
temp<-readLines("outfile")
ii<-grep("requires a total of",temp)
xx<-strsplit(temp[ii]," ")[[1]]
if(class(tree)=="multiPhylo") for(i in 1:length(tree)) tree[[i]]$pscore<-as.numeric(xx[length(xx)])
else tree$pscore<-as.numeric(xx[length(xx)])
if(!quiet) temp<-lapply(temp,function(x) { cat(x); cat("\n") })
if(!quiet){
cat("Translation table\n")
cat("-----------------\n")
temp<-lapply(1:nrow(X),function(x,y) cat(paste("\t",paste(x,y[x],sep="\t"),"\n",sep="")),y=rownames(X))
cat("\n")
}
if(class(tree)=="phylo") tree$tip.label<-rownames(X)[as.numeric(tree$tip.label)]
else if(class(tree)=="multiPhylo"){
foo<-function(x,y){
x$tip.label<-y[as.numeric(x$tip.label)]
x
}
tree<-lapply(tree,foo,y=rownames(X))
class(tree)<-"multiPhylo"
}
if(hasArg(outgroup)){
outgroup<-list(...)$outgroup
tree<-outgroup.root(tree,outgroup,quiet)
}
if(hasArg(cleanup)) cleanup<-list(...)$cleanup
else cleanup<-TRUE
if(cleanup){
files<-c("infile","outfile","outtree")
if(!is.null(intree)) files<-c(files,"intree")
if(!is.null(weights)) files<-c(files,"weights")
if(!is.null(ancestral)) files<-c(files,"ancestors")
cleanFiles(files)
}
return(tree)
}
## calls penny from PHYLIP 3.695 (Felsenstein 2013)
## written by Liam J. Revell 2013
Rpenny<-function(X,path=NULL,...){
if(is.vector(X)&&!is.list(X)) X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
if(is.list(X)){
if(all(sapply(X,length)!=1)) X<-t(sapply(X,function(x) x))
else X<-t(sapply(X,function(x) strsplit(x,split="")[[1]]))
}
if(is.data.frame(X)) X<-as.matrix(X)
if(is.null(path)) path<-findPath("penny")
if(is.null(path)) stop("No path provided and was not able to find path to penny")
if(hasArg(quiet)) quiet<-list(...)$quiet
else quiet<-FALSE
if(!quiet) if(file.warn(c("ancestors","infile","mixture","outfile","outtree","weights"))==0) return(NULL)
oo<-c("r")
if(hasArg(mixture)){
oo<-c(oo,"x")
mixture<-toupper(mixture)
write(paste(mixture,collapse=""),file="mixture")
} else mixture<-NULL
if(hasArg(method)) method<-list(...)$method
else {
if(!is.null(mixture)) method<-"wagner"
else method<-"mixed"
}
method<-tolower(method)
if((method=="camin-sokal"||method=="wagner")&&!is.null(mixture)){
cat("Warning: mixture provided for mixed method.\n")
cat(" using method=\"mixed\"\n\n")
method<-"mixed"
}
if(method=="camin-sokal") oo<-c(oo,"p")
if(hasArg(groups)){
groups<-list(...)$groups
oo<-c(oo,"h",groups)
}
if(hasArg(report)){
report<-list(...)$report
oo<-c(oo,"f",report)
}
if(hasArg(simple)) simple<-list(...)$simple
else simple<-TRUE
if(!simple) oo<-c(oo,"s")
if(hasArg(threshold)) threshold<-list(...)$threshold
else threshold<-0
if(threshold!=0) oo<-c(oo,"t",threshold)
if(hasArg(ancestral)){
oo<-c(oo,"a")
ancestral<-toupper(ancestral)
write(paste(ancestral,collapse=""),file="ancestors")
} else ancestral<-NULL
if(hasArg(weights)){
weights<-list(...)$weights
if(!any(sapply(weights,"%in%",c(0,1)))){
cat("\n\nWarning:\n only weights of 0 & 1 are permitted\n\n")
weights<-NULL
} else {
oo<-c(oo,"w")
write(paste(weights,collapse=""),file="weights")
}
} else weights<-NULL
if(quiet) oo<-c(oo,2)
oo<-c(oo,"y","r")