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I am running a "count" detector with differences in usage between sessions and occasions. Usage is characterized as the distance searched by scat detecting dogs in each grid cell. Therefore, it is not a 0 or 1, but instead a 0 or some other positive integer (eg. 8, 125, 16, etc.). It would seem that when creating the capture history object I need to set binary.usage = FALSE. When I invoke the usage(traps()) or summary(traps()) commands, the usage is evident. My question is whether or not the usage information is automatically used in any models run with the capture history object or if I need to explicitly tell the model to consider usage in some manner? In addition, should I be using the hazard function (detectfn=1) for detection and the Poisson model for counts (binomN = 0)?
Thanks

#Create capture history object
coy <- read.capthist("Capt_Coy.txt",c("NP_Trap_Coy09.txt","MR_Trap_Coy10.txt","NP_Trap_Coy10.txt",
"MR_Trap_Coy11.txt","NP_Trap_Coy11.txt","MR_Trap_Coy12.txt",
"NP_Trap_Coy12.txt"),detector="count",fmt="trapID",
noccasions=NULL,covnames="Sex",binary.usage=FALSE)

#Create masks for each session
NPcoy09 <- read.traps(file="NP_Trap_Coy09.txt",detector="count",binary.usage=FALSE)
NPcoy09 <- make.mask(NPcoy09,buffer=3000,spacing=5000,type="trapbuffer")
MRcoy10 <- read.traps(file="MR_Trap_Coy10.txt",detector="count",binary.usage=FALSE)
MRcoy10 <- make.mask(MRcoy10,buffer=3000,spacing=5000,type="trapbuffer")
NPcoy10 <- read.traps(file="NP_Trap_Coy10.txt",detector="count",binary.usage=FALSE)
NPcoy10 <- make.mask(NPcoy10,buffer=3000,spacing=5000,type="trapbuffer")
MRcoy11 <- read.traps(file="MR_Trap_Coy11.txt",detector="count",binary.usage=FALSE)
MRcoy11 <- make.mask(MRcoy11,buffer=3000,spacing=5000,type="trapbuffer")
NPcoy11 <- read.traps(file="NP_Trap_Coy11.txt",detector="count",binary.usage=FALSE)
NPcoy11 <- make.mask(NPcoy11,buffer=3000,spacing=5000,type="trapbuffer")
MRcoy12 <- read.traps(file="MR_Trap_Coy12.txt",detector="count",binary.usage=FALSE)
MRcoy12 <- make.mask(MRcoy12,buffer=3000,spacing=5000,type="trapbuffer")
NPcoy12 <- read.traps(file="NP_Trap_Coy12.txt",detector="count",binary.usage=FALSE)
NPcoy12 <- make.mask(NPcoy12,buffer=3000,spacing=5000,type="trapbuffer")

#Run null model
coy_n0 <- secr.fit(coy,model=list(D~1,g0~1,sigma~1),
mask=list(NPcoy09,MRcoy10,NPcoy10,MRcoy11,NPcoy11,MRcoy12,NPcoy12),
detectfn=0,trace=FALSE,ncores=2,CL=FALSE,groups="Sex")

Hi mttmmm (?)

Once you populate the 'usage' attribute it is used by default unless you suppress it with the 'ignore.usage' details argument (see ?details). The default model for count detectors is Poisson, so strictly you do not need to specify binomN = 0, but go ahead if you want to be sure (this should show in the header printed for the fitted secr model).

You seem to have got to grips with most of the issues. Use whatever detection functions you like (I don't recommend hazard-rate detectfn = 1, but that's up to you, and independent of usage issues; detectfn = 'HHN' is perhaps more mainstream).

Murray

...that should be ignoreusage, sorry

Thanks Murray!

Matt Mumma
Postdoctoral Scholar
University of Northern British Columbia
mttmmm@hotmail.com
610-212-9590