limited time varying capture recapture probabilities

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limited time varying capture recapture probabilities

Postby equallen » Thu Jul 21, 2022 7:45 pm

Hello,

I am new to transitioning from MARK to RMARK and am having difficulty with the model notation. I would like to run a robust design model such that capture and recapture probabilities only vary on day 1, but are constant for every day of trapping within a session after day 1. In MARK, this would like like p=c(1,2) but I am having trouble figuring out how to create a valid formula for this in RMARK.
equallen
 
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Re: limited time varying capture recapture probabilities

Postby jlaake » Wed Aug 10, 2022 4:38 pm

I just noticed that this post never got a reply. Sorry about that. Essentially you need to add design data that creates a factor variable which pools the days after day1 or just by having a numeric variable that is 1 for day 1 an 0 for all other days. Below is an example but if that is not what you intended you'll have to provide more information. --jeff

Here is an examples using the robust data in RMark

Code: Select all
data(robust)
# data from Robust.dbf with MARK
# 5 primary sessions with secondary sessions of length 2,2,4,5,2
#
time.intervals=c(0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0)
rb.proc=process.data(robust,model="Robust",time.intervals=time.intervals)
rb.ddl=make.design.data(rb.proc)

# create variable in p design data which is 1 for day (time) 1 and 0 otherwise
rb.ddl$p$day1=ifelse(rb.ddl$p$time==1,1,0)
# need to add the same variable to c because we are sharing p/c - in this case day1=0 because c is only for occasions past day1
rb.ddl$c$day1=0

S.time=list(formula=~time)
# p varies by day1 for each session and by session for other days but constant across those days within session
p.time.session=list(formula=~-1+session:day1+session,share=TRUE)

mark(rb.proc,rb.ddl,model.parameters=list(S=S.time,p=p.time.session))


Here is beginning of output.
Output summary for Robust model
Name : S(~time)Gamma''(~1)Gamma'(~1)p(~-1 + session:day1 + session)c()f0(~session)

Npar : 21
-2lnL: -18057.08
AICc : -18014.92

Beta
estimate se lcl ucl
S:(Intercept) 2.0771695 0.1325296 1.8174115 2.3369276
S:time2 -0.1977186 0.2091827 -0.6077167 0.2122794
S:time3 -0.9472555 0.1654696 -1.2715759 -0.6229351
S:time4 -0.8406458 0.3081152 -1.4445515 -0.2367400
GammaDoublePrime:(Intercept) -1.9649189 0.0995623 -2.1600611 -1.7697767
GammaPrime:(Intercept) -2.1762911 0.5102500 -3.1763811 -1.1762011
p:session1 0.5996324 0.0795988 0.4436187 0.7556461
p:session2 0.3431816 0.0803888 0.1856196 0.5007436
p:session3 0.5910726 0.0491665 0.4947064 0.6874389
p:session4 0.4682220 0.0471904 0.3757288 0.5607153
p:session5 -0.1260259 0.1436539 -0.4075875 0.1555357
p:session1:day1 0.1835033 0.0948776 -0.0024569 0.3694634
p:session2:day1 0.2275862 0.1031532 0.0254059 0.4297666
p:session3:day1 -0.6412770 0.0893858 -0.8164733 -0.4660808
p:session4:day1 -0.1575436 0.1007473 -0.3550082 0.0399210
p:session5:day1 0.0803370 0.1417940 -0.1975793 0.3582534
f0:(Intercept) 4.7123162 0.1427475 4.4325311 4.9921012
f0:session2 0.0771959 0.1972439 -0.3094020 0.4637939
f0:session3 -1.9772190 0.3179338 -2.6003694 -1.3540687
f0:session4 -3.2746265 0.5575347 -4.3673946 -2.1818584
f0:session5 -0.0291131 0.2471420 -0.5135114 0.4552852

jlaake
 
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