Multispecies IPM for South polar skua and Adelie penguin

Code and data for a multispecies IPM (integrated population model) on South polar skua and Adélie penguin.

Please contact me for any questionMail: [e-mail]: @LiseViollat

Code files : 

- multispeIPM_skua_adelie_CODE.txt: Code of the multispecies IPM (Bugs language)

- Parameter_init.txt : initialisation of the parameters used for the model

Bayesian posterior distributions of the multispecies IPM were approximated with Markov chain Monte Carlo (MCMC) algorithms. Two independent chains MCMC of 30 000 iterations were used, with a burn-in period of 10 000 iterations. Gelman-Rubin convergence diagnostics (Brooks and Gelman, 1998) were below 1.1 for each parameter and the mixing of the chains was satisfactory. The analyses were performed using JAGS (Plummer, 2003; version 4.3.0) and program R (R version 4.0.5).

Data files :

From 1988 to 2018

- Count_adelie.csv: Number of breeding pairs of Adelie Penguins and Chicks by year

- Count_skua.csv : Number of occupied sites, breeder, non breeder and chicks of South polar Skua by year

- Skua_matrix.txt: CMR data on South polar skua

  CMR code:     0 = non-observed

                1 = seen as non-breeder

                2 = seen as failed breeder

                3 = seen as successful breeder with one fledged chick

                4 = seen as successful breeder with two chicks fledged chicks

                5 = seen in a uncertain state

 The last column is if the individual as been seen dead (-1) or not (1)

- Climat_cova.txt: climatic covariables (Air temperature (AT), sea ice concentration (SIC), sea surface temperature anomalies (ssta),  and number of emperor penguin dead chicks

- N_immigrant: number of new individuals seen for the first time at the colony by year