Supplement 1. R and C code used for the analysis of the great tits data set and for the simulation study presented in Appendix B.

File List AllFunctions.R (MD5: d3120c7372ab36b802dd9f0c01138f1a) Functions needed to fit the models presented in the paper. AllFits.R (MD5: f7caa2c394d6c710195c1bca762d1851) R code for fitting the models to the data set of great tits. Simulations.R (MD5: d3a8a230b93a10bc74420f6694b6e8b1) R code for performing the simulation study presented in Appendix B. PMdata.csv (MD5: 6fa6abb6c8240ba8eb0100c8031182ae) The data set of already marked female great tits. PUdata.csv (MD5: 19f72c2afdc3736b87c8956dd9c94a3e) The data set of previously unmarked female great tits. Effort.csv (MD5: 95b7da2637fd9b08b9818832e23cb7f5) Data on sampling effort. WithBreeding.dll MD5: ffe47405123db8b78289af44f4e050d3) The log-likelihood in compiled C code. C.zip (MD5: 9452e29327a86ce7bc2ab968bdd720dc) The original C code containing the log-likelihood. Description All of the functions needed to fit the models presented in the paper are in AllFunctions.R. The log-likelihood function is evaluated in C via R and is contained in the WithBreeding.dll file. The original C file is in the folder C.zip. The analysis of the great tits data set (PMdata.csv is the data set of already marked birds and PUdata.csv is the data set of previously unmarked birds) presented in the paper was performed using the functions in AllFits.R while the simulation study presented in Appendix B was performed using Simulations.R. Information on capture and resight effort (number of sites visited etc) is in effort.csv.