Message-ID: <bd084d8969c147d49ce75c2b7ef0d974@ES-SDC-EMR-03.es.govt.state.ma.us>
Date: 2019-07-17T16:54:29Z
From: Nelson, Gary (FWE )
Subject: Question concerning nlme
I work in the field of fisheries. We sample fish using gears that collect individual in clusters, so any analyses done using such sample have to be corrected for intra-cluster correlation. This has been shown in many papers in my field.
I am trying to compare growth curves between two sexes using the nlme function. The individuals were collected via cluster sampling. I have been trying to use the nlme function but am having trouble understanding how to specify the correct formulation.
My growth model is:
vonBert<-deriv(~Linf*(1-exp(-K*(x-t0))),c("Linf","K","t0"),function(x,Linf,K,t0){})
and I created grouped data with cluster as the grouping variable
vbdata<-groupedData(lens~age|cluster,data=catchdata,labels=list(x="age",y="length"))
and the mixed model I have is
vbfull<--nlme(lens~vonBert(age,Linf,K,t0),data=vbdata,fixed=list(Linf~1,K~1,t0~1),random=Linf+K+t0~1,start=c(Linf=c(270),
K=c(0.7),t0=c(0.1)),control=nlmeControl(maxIter=100000,msMaxIter=100000))
My question is how do I incorporate sexes? I've tried assuming sex is nested within a cluster where
vbdata<-groupedData(lens~age|cluster/sex,data=catchdata,labels=list(x="age",y="length")) but am unsure if this is correct.
Any help would be appreciated.
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Gary A. Nelson, Ph. D
Massachusetts Division of Marine Fisheries
Annisquam River Field Station
30 Emerson Avenue
Gloucester, MA 01930
email: gary.nelson @state.ma.us
phone: 978-282-0308 x114
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