I am working on a research project on killerwhales. My data are based on a 10 year photo ID monitoring program, based on opportunistic observation from fisheries (non regular time interval). I have temporary migration and I am consequently using a Robust design. Unfortunatly I have some issues with the data formating of individual time varying covariates. I want to add my level of marking as a covariates for p because it is is changing depending of the year ( new scarf on the dorsal fin for example).
I added it to my database before processing it. I obtain this database with different Mk for each individuals by occasion (Mk1, Mk2,....Mk102) ,following the trap dependance individual covariates example.
Then I prepare my database FD
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time.intervals<-c(0,3,0,0,5,0,0,0,5,0,0,8,0,0,5,0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,0,0,4,
0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,
M.proc<-process.data(FD,model="Robust", time.intervals=time.intervals)
design.p=list(time.varying=c("Mk"))
design.parameters=list(p=design.p)
M.ddl=make.design.data(M.proc,parameter=design.parameters)
p.effort2.ind<-list(formula=~Mk, share=TRUE)
model.2.ind=mark(M.proc,M.ddl, model = "Robust",
time.intervals=time.intervals,
design.parameters = design.parameters,
model.parameters=list(S=list(formula=~1),
GammaDoublePrime=list(formula=~1),
p=p.effort2.ind),threads=2)
And I got this erros message:
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Error in make.mark.model(data.proc, title = title, parameters = model.parameters, :
The following individual covariates are not allowed because they are factor variables: Mk1,Mk4,Mk9,Mk14,Mk22,Mk27,Mk28,Mk29,Mk32,Mk36,Mk37,Mk38,Mk39,Mk41,Mk43,Mk45
Error in mark(M.proc, M.ddl, model = "Robust", time.intervals = time.intervals, :
Misspecification of model or internal error in code
Indeed this number are used as session factors when I'm looking in M.design.
I was trying to change the indexation of Mk, but I didn't find any that is recognised when I run my model.
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Error in make.mark.model(data.proc, title = title, parameters = model.parameters, :
Error: Variable Mk used in formula is not defined in data
Error in mark(M.proc, M.ddl, model = "Robust", time.intervals = time.intervals, :
Misspecification of model or internal error in code
Do you have any idea of how I label my covariates to be able to run it ?
Regards