Demographic analysis for article Hurricane-induced demographic changes in a nonhuman primate population
Hernández-Pacheco, Raisa et al. (2020), Demographic analysis for article Hurricane-induced demographic changes in a nonhuman primate population, Dryad, Dataset, https://doi.org/10.5061/dryad.5qfttdz2b
The demographic dataset of Cayo Santiago rhesus macaques was shared by the Caribbean Primate Research Center, University of Puerto Rico.
This folder contains all the required data and codes to reproduce the main study results. Codes were built in R version 3.5.1. These codes use packages “popbio”, “tidyverse”, “ggplot2”, “scales”, and “gamm4” for demographic data management and analysis. The data contains the following:
- Morcillo_et_al_nonhurricane_transitions.csv contains every individual transition during non-hurricane years; including age and stage at time t and fate or stage at time t+1.
- Morcillo_et_al_hurricane_transitions.csv contains every individual transition during hurricane years; including age and stage at time t and fate or stage at time t+1.
- Morcillo_et_al_nonhurricane_bootstrap.csv contains the bootstrap transition matrix for a non-hurricane year.
- Morcillo_et_al_hurricane_bootstrap.csv contains the bootstrap transition matrix for a hurricane year.
- Morcillo_et_al_annual_matrices.RData contains annual transition matrices from 1973 to 2018.
- Morcillo_et_al_gamm_model.RData contains the generalized additive mixed top model output
Specifically, the codes provide calculations for:
- Mean matrix populations models for non-hurricane and hurricane years from individual-level transition data.
- Eigen analysis for matrix models
- Life table response experiment
- Bootstrap and Kolmogorov-Smirnov test
- Generalized additive mixed model
National Institutes of Health, Award: 2 P40 OD012217