Analysis of seasonal habitat-use patterns of Aldabra giant tortoises of Aldabra Atoll (Aldabrachelys gigantea), Seychelles using temporary emigration models.
data/aldabra_tortoise_data_all.RData = data for running all veresions of models and predictions
*** Data here is representative just to make code running, not the actual data used in the analyses. ***
In all models lambda represents expected site-specific density and kept the same for all model versions:
lambda ~ island
We used availability probability part of the temporary emigration models (denoted as theta) as a proxy for habitat use. We assumed that when a tortoise was available to be detected in a specific habitat type, then it was using this site at that time of the year. Consequently, whereas a higher availability probability indicated higher habitat use, a lower availability probability indicated higher temporary emigration, meaning that the tortoise was not using the habitat when the transect counts were conducted. Therefore, we refer to theta as the habitat-use probability, and changed this component of the model to investigate different combination of season and habitat type.
To do so 5 different models were run:
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habitat_only = single effect of habitat type
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season_only = single effect of season
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habitat_season_additive(add) = additive effect of habitat type and season
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habitat_season_interaction(int) = interaction effect of habitat type and season
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habitat_season_interaction(int)_random_transect = interaction effect of habitat type and season together with random transect effect
In each folder, file order is the same, as an example inside the habitat_only folder:
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habitat_only_model_diags.R = code for running the habitat only model and its diagnostics
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habitat_only_pred.R = code for running predictions for the habitat only model
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L_I_T_H_Alt.txt = text file for the JAGS model
R version 4.2.1
JAGS (through R-package ‘jagsU’I)