Eleni Matechou, San Chye Cheng, Lindall R. Kidd, and Colin J. Garroway. 2015. Reproductive consequences of the timing of seasonal movements in a nonmigratory wild bird population. Ecology 96:16411649. http://dx.doi.org/10.1890/14-0886.1


Supplement

R and C code used for the analysis of the great tits data set and for the simulation study presented in Appendix B.
Ecological Archives E096-146-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Eleni Matechou
School of Mathematics, Statistics and Actuarial Science
University of Kent
Cornwallis Building
Canterbury
CT2 7NF UK
E-mail: e.matechou@kent.ac.uk

San Chye Cheng
Department of Statistics
University of Oxford
1 South Parks Road
Oxford OX1 3TG
E-mail: sanchye@yahoo.com.sg

Lindall Kidd
Edward Grey Institute of Ornithology, Department of Zoology
University of Oxford
Tinbergen Building, South Parks Road
Oxford OX1 3PS
E-mail: lindall.kidd@gmail.com

Colin J. Garroway
Edward Grey Institute of Ornithology, Department of Zoology
University of Oxford
Tinbergen Building, South Parks Road
Oxford OX1 3PS
E-mail: colin.garroway@gmail.com


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.