DOI: 10.5061/dryad.2rbnzs7tc
title: Antarctic fur seal abundance at South Georgia

description: Data sets for the abundance analysis of Antarctic fur seal data at South
 Georgia. Data were obtained from helicopter surveys in 2007–09 and
 long-term studies at the Special Study Beach of Bird Island, South
 Georgia, from 1994 to 2022.
description: Helicopter survey and hand-held digital SLR cameras. South
 Georgia, SW Atlantic. Antarctic fur seal long-term
 demographic and genetic studies at Bird Island, South Georgia.
 See manuscript for detail: Article Title:
 Ninety years of change, from commercial extinction to recovery, range
 expansion and decline for Antarctic fur seals at South
 Georgia<br>Article DH_ID: 17818825<br>Article DOI:
 10.1111/gcb.16947<br>Journal Code: GCB<br>Institution/Funder
 Name: British Antarctic Survey
description: Data requires R software. It has two scripts (*.r) for RStudio
 for fitting integrated population models (IPM) models with R and JAGS; one
 for female and another for male Antarctic fur seal count and
 mark-recapture data. The scripts reproduce the results in the the
 published article. Data files for using the R scripts
 are in R software Rds format. The best use of the
 scripts and data files is described in detail in the Readme
 file.
description: # Antarctic fur seal abundance at South Georgia Published article: Ninety
 years of change, from commercial extinction to recovery, range expansion
 and decline for Antarctic fur seals at South Georgia Jaume Forcada(1),
 Joseph I. Hoffman(2,1), Olivier Gimenez(3), Iain J. Staniland(4), Pete
 Bucktrout(1), Andrew G. Wood(1) 1\. British Antarctic Survey\, Natural
 Environment Research Council\, UKRI\, Cambridge\, UK 2\. Department of
 Animal Behavior\, University of Bielefeld\, Postfach 10 01 31\, 33615
 Bielefeld\, Germany 3\. CEFE\, CNRS\, Univ Montpellier\, EPHE\, IRD\,
 Montpellier\, France 4\. International Whaling Commission\, Impington\, UK
 Contact Information Dr Jaume Forcada; tel. +44 (0)1223 221326; Email:
 jfor@bas.ac.uk; https://orcid.org/0000-0002-2115-0150 ## Description of
 the data and file structure Data and R script files: 1\.
 'SouthGeorgiaSurveyCounts\.csv' Aerial photo-counts of pups,
 breeding females and territorial males of Antarctic fur seal at South
 Georgia. There are columns for: day in December, year and latitude and
 longitude for each count.   2\. Two scripts for R software \(with
 extension ‘\*\.r’\) to fit the integral projection models for females and
 males separately\. These are executable from program ‘RStudio’ and require
 installation of several R packages\, including ‘jagsUI’ and ‘rjags’\. The
 scripts also require the installation of program ‘jags’ for MCMC
 analysis\. Each script call data files in ‘\*\.Rds’ format\, from R\. For
 reproducibility\, closely follow instructions specified in the \*\.r
 scripts\. Ideally one wants to declare a working directory \(as specified
 in the scripts\)\, and all the specific \*\.rds data files\, contained in
 zipped files\, should be extracted in the working directory\.   2.1. File
 'SSBFemaleIPM20012022.r' R script for R Studio to reproduce the
 integrated population model for Antarctic fur seal females at the Special
 Study Beach of Bird Island, South Georgia. Calls the following \*.Rds data
 files (‘femaleRds.zip’).   2.1.1 "rCH1.Rds" Capture-recapture
 histories of females pit-tagged at birth. Matrix of integers (values 1 to
 4) of 2760 rows and 22 columns. 2.1.2 "rCH2.Rds"
 Capture-recapture histories of females sampled as breeders. Matrix of
 integers (values 1 to 3) of 902 rows and 22 columns. 2.1.3
 "prod.Rds" numerical vector of 22 annual total pup productions
 observed at the Special Study Beach of Bird Island. 2.1.4
 "pFem.Rds" numerical vector of 22 annual proportions of female
 pups observed at the Special Study Beach of Bird Island. 2.1.5
 "f1.Rds" vector of 2760 integers with values from 1 to 21
 denoting in which capture occasion each pup was PIT-tagged. 2.1.6
 "f2.Rds" vector of 902 integers with values from 1 to 22
 denoting in which capture occasion each breeding female was first
 captured. 2.1.7 "phi0.Rds" vector of 22 numerical values
 corresponding to the mean estimates of survival from 0 to 1.5 months used
 as priors for this parameter. 2.1.8 "yy.Rds" vector of 70
 integers corresponding to the total daily counts of mature females at the
 Special Study Beach of Bird Island, to fit GAMM models. 2.1.9
 "nn.Rds" number of days (integer) to indicate sample size to fit
 GAMM models. 2.1.10 "X.Rds" matrix of 70 rows and 10 columns
 with prior estimates to fit the GAMM models. 2.1.11 "z1.Rds"
 matrix of 2760 rows and 22 columns containing initial values (integers
 representing latent states from 2 to 9) for the latent states in the
 state-process of the capture-recapture likelihood for the PIT-tagged pups.
   2.2. File 'SSBMaleIPM19942022.r’ R script for R Studio to reproduce
 the integrated population model for Antarctic fur seal males at the
 Special Study Beach of Bird Island, South Georgia. Calls the following
 \*.Rds data files (‘maleRds.zip’).   2.2.1 "N1m.Rds" numerical
 vector of size 11 containing the 11 annual initial population values to
 initialise the state-space model. 2.2.2 "aBeta.Rds" vector of 6
 numerical values corresponding to the shape parameter 1 to generate priors
 for beta distributions of the recruitment parameters. 2.2.3
 "bBeta.Rds" vector of 6 numerical values corresponding to the
 shape parameter 2 to generate priors for beta distributions of the
 recruitment parameters. 2.2.4 "pMal.Rds" numerical vector of 28
 annual proportions of male pups observed at the Special Study Beach of
 Bird Island. 2.2.5 "np.Rds" numerical vector of 14 annual total
 pup productions observed at the Special Study Beach of Bird Island. 2.2.6
 "alphaS.Rds” vector of 28 numerical values corresponding to the shape
 parameter 1 to generate priors for beta distributions of the survival
 parameters from birth to 1.5 months of age. 2.2.7 "betasS.Rds” vector
 of 28 numerical values corresponding to the shape parameter 2 to generate
 priors for beta distributions of the survival parameters from birth to 1.5
 months of age. 2.2.8 "surAlpha.Rds” vector of 11 numerical values
 corresponding to the shape parameter 1 to generate priors for beta
 distributions of the survival at age (1 to 11) parameters for
 pre-territorial males. 2.2.9 "surBeta.Rds” vector of 11 numerical
 values corresponding to the shape parameter 2 to generate priors for beta
 distributions of the survival at age (1 to 11) parameters for
 pre-territorial males. 2.2.10 "CH.ms.Rds" Capture-recapture
 histories of genetically sampled territorial males at the Special Study
 Beach of Bird Island. Matrix of 1221 rows (individuals) and 14 columns
 (annual periods) of integer values 1 and 2. 2.2.11 "yy2.Rds"
 vector of 60 integers corresponding to the total daily counts of mature
 males at the Special Study Beach of Bird Island, to fit GAMM models.
 2.2.12 "nn2.Rds" number of days (integer) to indicate sample
 size to fit GAMM models. 2.2.13 "X2.Rds" matrix of 60 rows and
 10 columns with prior estimates to fit the GAMM models.