I wrote this function in R many years ago that returns the desired pairwise
interlandmarks distances for all individuals present in an array; a single
matrix configuration is allowed too ; put a vector 1:n with n the number of
landmarks to have them all. I think it could be improved in terms of speed.
Hack it at your convenience. The output is in column format.
All the best
Paolo
distlm<-function(array,vector){
if(is.matrix(array)==T){array<-array(array,dim=c(nrow(array),ncol(array),1))}
distot<-NULL
for(i in 1:dim(array)[3]){
disti<-dist(as.matrix(array[vector,,i]))
distot<-c(distot,list(disti))
}
names(distot)<-unlist(dimnames(array)[3])
distot
distotfin<-NULL
for(j in 1:length(distot)){
distotfinj<-matrix(as.vector(distot[[j]]),nrow=1)
distotfin<-rbind(distotfin,distotfinj)
}
distotfin
comb<-combn(vector,2)
mycolnames<-NULL
for(k in 1:ncol(comb)){
mycolnamesi<-paste(comb[1,k],comb[2,k],sep="_")
mycolnames<-append(mycolnames,mycolnamesi)
}
distotfin
colnames(distotfin)<-mycolnames
rownames(distotfin)<-unlist(dimnames(array)[3])
distotfin
}
Il giorno ven 7 ott 2022 alle ore 09:17 alcardini <[email protected]> ha
scritto:
> For interlandmark distances from the original raw coordinates (no need
> to superimpose and rescale), one can use the EDMA function of PAST.
> Julien also has a script in his book to compute ILDs pairwise and the
> old Morpheus et al. had a command to get specific ILDs (this was also
> an option in PAST 2 and probably later versions).
>
> Cheers
>
> Andrea
>
> On 06/10/2022, 'Ann Ross' via Morphmet <[email protected]> wrote:
> > Hello Paolo,
> > You can convert your coordinate data to ILDs. But I am not sure that you
> can
> > compare ILDs to coordinate data directly. You could compare results from
> > both. I apologize if I misunderstood the question.
> > Best Regards,
> > Ann
> >
> > Ann H. Ross, Ph.D., D-ABFA
> >
> >
> >> On Oct 6, 2022, at 9:47 AM, Pablo Fisichella <[email protected]
> >
> >> wrote:
> >>
> >>
> >> Dear Julien,
> >>
> >> Thank you very much for your response and explanations. Yes, I mean the
> >> inter-landmark distances obtained after a Procrustes superimposition.
> >>
> >> All best,
> >>
> >> Paolo
> >>
> >>> El jue, 6 oct 2022 a las 10:25, Julien Claude
> >>> (<[email protected]>) escribió:
> >>> Dear Paolo
> >>> I am not sure about what you mean by 'Procrustes distance between pairs
> >>> of landmarks'. If it is the euclidean distance between two landmarks
> >>> after superimposition you just have to multiply them by centroid size
> in
> >>> mm. It will give you the interlandmark distance in mm, provided that
> your
> >>> coordinates were scaled to unit centroid size during the
> superimposition
> >>> process (sometimes referred as "partial procrustes superimposition").
> >>>
> >>> Julien CLAUDE
> >>>
> >>> De: "Pablo Fisichella" <[email protected]>
> >>> À: "Morphmet" <[email protected]>
> >>> Envoyé: Jeudi 6 Octobre 2022 15:09:34
> >>> Objet: [MORPHMET2] How to transform Procrustes distances to mlilimeters
> >>> Hi all,
> >>>
> >>> I performed a 2D GM analysis. I obtained Procrustes distances between
> >>> pairs of landmarks and I want to compare such distances with linear
> >>> distances in mm. Does somebody know how I can transform my Procrustes
> >>> distances to mm? Thanks in advance.
> >>>
> >>> All the best,
> >>>
> >>> Paolo
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