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

[Colchero, Fernando]

Dear Fabiano,

   Thanks a lot for sending us your bug report. We found the problem and corrected it; it had nothing to do with your data but with the way BaSTA assigned column names to the matrix of estimates for the recapture probabilities. We just uploaded the latest version of BaSTA to CRAN (version 1.3). We hope it'll be available in the next couple of days. If you want to run it as soon as possible, you can try to install it from CRAN as binaries, I believe that should be available much sooner.

   Please let us know if you run into any additional problems. Best,

   Fernando


______________________________________________
 
Fernando Colchero

Max Planck Institute for Demographic Research
Konrad Zuse Str. 1, 18057, Rostock, Germany
Tel:  +49 (0) 381 2081 113
Fax: +49 (0) 381 2081 413
E-mail: Colchero at demogr.mpg.de
______________________________________________





On Jul 11, 2012, at 1:48 PM, Ezequiel Fabiano wrote:


	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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