Northern royal albatross demography, JAGS model

Files necessary to run the Bayesian multi-state capture-recapture model to analyse the demography of northern royal albatross at Taiaroa Head, New Zealand. The model is used for the article at peerj.com/preprints/712/, submitted for peer-reviewed publication. The files consist of: - model.bug - the Bayesian multi-state capture-recapture model, written in the BUG language, - data.txt - Data, in R raw format (readable in R using the source function), - inits.txt - Initialisation values for the model, - jags.cmd - JAGS command file to run the model, containing the names of the parameters to monitor, and to specify the length of the burnin period and of the total number of iterations.

To run the model, assuming that JAGS is installed, simply run "jags jags.cmd". The data consist of 11 objects: - age : matrix of 355 x 23 values being the age in years for all 355 individuals and 23 years. - atcol : matrix of 355 x 23 values, with 1 indicating that an individual was at the colony, 0 otherwise, in each of the 23 years. - bsucc : matrix of 355 x 23 values, with 2 if an individual produced a fledgling, 1 otherwise, for each of the 23 years. - firstcap: vector of 355 values, representing the first year each individual was seen during the studied period, with 1 being the start of the period (1988-89). - k.R : minimum recruitment age, single value. - k.B : minimum age at first reproduction, single value. - N : number of individuals, single value. - sex : vector of 355 values, containing the gender of each individual: 1 for female, 2 for male, NA for unknown. - state : matrix of 355 x 23 values, being the state of each individual each year: 1: breeding adult, 2: non-breeding adult, 3: pre-breeder, 4: juvenile, 5: dead, NA: unknown. - T : number of years considered in the dataset, single value. - Tstar : maximum individual age in the dataset, single value.