[Basta-users] Question on survivorship for pre-emergence

[Rebke, Maren]

Hi Fabiano,
 
Could it be that the starting year of your study is 1988 and not 1987
since you specified 1988 as the starting year in the model that runs? 
 
Best wishes,
Maren
 
 

________________________________

From: basta-users-bounces at lists.r-forge.r-project.org
[mailto:basta-users-bounces at lists.r-forge.r-project.org] On Behalf Of
Ezequiel Fabiano
Sent: Mittwoch, 11. Juli 2012 13:49
To: Basta-users at lists.r-forge.r-project.org
Subject: Re: [Basta-users] Question on survivorship for pre-emergence


Hi all,
 
I am trying to run analyse a data set with BaSTA but running to a
problem whenever I tried to constrain recapture probabilities and or run
more than one simulation. It runs perfectly when either is not included.
I would appreciate any help.
 
Histories<- read.csv("Histories1.csv", header = TRUE)

newData<-DataCheck(Histories,studyStart=1988, studyEnd=2000,
autofix=rep(1,7), silent = TRUE) #checking for errors

rawCovMat<- read.csv("SexAndFarmType.csv", header = TRUE) #inputting
covariates

covMat <- MakeCovMat(x = c("sex", "farm"), data = rawCovMat)
#constructing the covariate matrix for BaSTA, 
 
inputMat <- as.data.frame(cbind(Histories, covMat[, -1]))   #merging
capture histories with covariates

out<-basta(object=inputMat,studyStart=1988,studyEnd=2000) #model runs
perfectly
 
As soon as I add recaptTrans or try multiple simulations then I get an
error message:
the error message says: Error in `colnames<-`(`*tmp*`, value =
"pi[1987]") : 
  length of 'dimnames' [2] not equal to array extent
 
out<-basta(object=inputMat,studyStart=1987,studyEnd=2000, model = "WE",
shape = "simple", minAge = 1, recaptTrans = c(1987, 1995)) # error
message

out <- basta(object = inputMat, studyStart = 1987, studyEnd = 2000,
recaptTrans = c(1987, 1995), model = "GO", shape = "simple", niter =
1000, burnin = 100, thinning = 10, nsim = 2) # error message
 
No problems were detected with the data. # data check 
 
Best,
Fabiano


 
2012/4/3 Ezequiel Fabiano <chimbioputo at gmail.com>


	Hi all, 

	I am busy sorting out my data to run with BaSTA. I have a
question. In most cases no data in available for pre-emergence litters.
How does BaSTA handles this? Or is it similar to ways previously used
like in life-tables?

	Thanks
	
	Fabiano





-- 

Ezequiel C. Fabiano, MEnvDev
PhD student at Pontificia Universidade Catolica do Rio Grande do Sul,
Brazil
Senior Research Assistant at Cheetah Conservation Fund, Namibia


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