Ecosphere-SRKW-modeling

Repo for Nelson et al. manuscript in Ecosphere

File descriptions

• "chinook_indices_ver_2.csv": PSC Chinook salmon indicies of abundance
• "fec_data.csv": Tablular data of births, by year, age and individual
• "ipm_data_ver_3.csv": Counts of live-captures by stage, by year, from 1962-1977
• "ipm_model_optim_func_ver_2.r": Primary R script for loading data files and executing JAGS models
• "ipm_survival_optim.r": R script for pre-processing the survival data
• "jags_ipm_optim_ver_2.r": JAGS model code
• "loo_script.r": R script for model selection criterion
• "mortality_data.csv": Tablular record of deaths, by age, sex, and year
• "nrkws.csv": NRKW abundance data (estimated and observed)
• "psc_sims.csv": Simulated PSC Chinook salmon abundance indicies
• "stage_data_ver_2.csv": SRKW annual abundance, by stage
• "stage_start_stop_ver_3.csv": Indexing file for execution of JAGS code
• "survival_age_to_stage.csv": Key that assigns sex-age combinations to stages for estimation of demographic survival rates