----- Forwarded message from Dean Adams -----
Date: Tue, 26 Jun 2012 13:26:54 -0400
From: Dean Adams
Reply-To: Dean Adams
Subject: Re: reading nts file format in R: addendum
To: morphmet@morphometrics.org
Folks,
Sorry. Neglected to include a second function required by my
readland.nts file. Both functions are below.
Dean
--
Dr. Dean C. Adams
Associate Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
Ames, Iowa
50011
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
#function required by readland.nts
arrayspecs<-function(A,p,k,byLand=T){
names<-rownames(A)
n<-length(unlist(A))/(p*k)
if(byLand==T){
n.m<-NULL
for(i in 1:n){
temp<-as.matrix(A[((1+(i-1)*p):(i*p)),1:k])
n.m<-cbind(n.m,temp)}
specimens<-array(n.m,dim=c(p,k,n))
}
if(byLand==F){
n.m<-NULL
for(i in 1:n){
temp<- matrix(A[i,],ncol=k,byrow=T)
n.m<-cbind(n.m,temp)}
specimens<-array(n.m,dim=c(p,k,n))
}
dimnames(specimens)[[3]]<-names
return(specimens)
}
#read landmark data from NTS file
readland.nts<-function(file){
ntsfile<-scan(file=file,what="char",quote="",sep="\n",strip.white=T,comment.char="\"",quiet=T)
header<-unlist(strsplit(ntsfile[1]," "))
if(header[1]!=1){
stop("NTS file not a rectangular matrix. First value in parameter
line must be '1'.") }
header<-casefold(header,upper=T)
dimval<-unlist(grep("DIM=",header))
if(length(dimval)==0){
stop("Header does not contain 'DIM=' designator.") }
labval<-unlist(grep("L",header))
r.lab<-ifelse(is.element("2",labval)==T,T,F)
c.lab<-ifelse(is.element("3",labval)==T,T,F)
header<-sub("L","",header)
header<-as.numeric(sub("DIM=","",header))
missdata<-ifelse(header[4]!=0,T,F)
if(missdata==T){missval<-ifelse(dimval==6,header[5],header[6]) }
n<-header[2];k<-header[dimval];p<-header[3]/k;
tmp<-gsub("\\t"," ",ntsfile[-1]) #replace tabs with spaces
tmp<-unlist(strsplit(tmp,split=" +"))
speclab<-NULL;
if(r.lab==T){
speclab<-tmp[1:n]
tmp<-tmp[-(1:length(speclab))] }
if(c.lab==T){ tmp<-tmp[-(1:(p*k))] }
if(missdata==T){tmp<-sub(missval,"-999",tmp)}
landdata<-matrix(as.numeric(tmp),ncol=k,byrow=T)
coords<-arrayspecs(landdata,p,k,byLand=T)
dimnames(coords)[[3]]<-speclab
return(coords=coords)
}
On 6/26/2012 11:35 AM, morphmet_modera...@morphometrics.org wrote:
> ----- Forwarded message from ppi...@uniroma3.it -----
>
> Date: Tue, 19 Jun 2012 06:42:52 -0400
> From: ppi...@uniroma3.it
> Reply-To: ppi...@uniroma3.it
> Subject: reading nts file format in R
> To: morphmet@morphometrics.org
>
> Hi folks,
> someones knows if exists a code to read nts files in R?
> Thankyou
> Paolo
>
----- End forwarded message -----
