Source code and data

The package provides Matlab code for the individual based model and approximate Bayesian computation based inference introduced in article "Assessing the dynamics of natural populations by fitting individual based models with approximate Bayesian computation" by Jukka Sirén, Luc Lens, Laurence Cousseau and Otso Ovaskainen accepted for publication in Methods in Ecology and Evolution. The package includes also the White-starred robin data analyzed in the article

PG_genepop9loc

This genepop file contains the genetic data (9 microsatellites) used in most genetic analyses: Effective sizes, STRUCTURE, DiyABC, Bottleneck, BIMr (adults). The file is divided by forest fragments (MB:Mbololo,NG:Ngangao,FU:Fururu,ND:Ndiwenyi,CH:Chawia) and period (1 and 2)

Phyllastrephus_cabanisi_microsatellites

Microsatellites data: 10 loci; RING = individual ID; FRAG: Forest fragment; PERIOD: 1 (1996-2000) and 2 (2006-2010); followed by 10 loci (one column per allele): Ase18, Indigo41, Ls1, Ls2, Mcyu4, Pca3, Pca4, Pfi04, Pfl54, WBSW2

CMR_data

This folder contains all minimally necessary information to run the Jolly-Seber models with program MARK (White, Gary C., and Kenneth P. Burnham. Program MARK: survival estimation from populations of marked animals. Bird study 46.S1 (1999): S120-S139) as mentioned in the main paper. There are 10 input files for program MARK, two for each of the five fragments (MB:Mbololo,NG:Ngangao,FU:Fururu,ND:Ndiwenyi,CH:Chawia) that represent periods 1 & 2 respectively. Additionally, another 10 auxiliary datasets are provided to adjust for unequal interval lengths between sampling occasions within each fragment (see program MARK documentation). Each input data file is a tab-separated text file (.txt) in which the first column represents an encounter history of an individual, for a given fragment and time period (columns 2 and 3). Each auxiliary data file is a tab-separated text file (.txt) with interval id, starting date of interval, interval length (in days) and interval length (in fraction of a year)

PG_BIMr_nestlings_fledglings

Dataset used to estimate recent migration rates (BIMr software: Faubet & Gaggiotti 2008) from nestlings and recent fledglings (second period only)