Man pages for jBernardADFG/ChenaSalchaSR
Chena Salcha State-Space Spawner-Recruit Analysis
| age_hist | Escapement by Age Histogram |
| clean_chains | Convert chains to an easier to use format and burnin further... |
| extract_abundance_by_age | Extract estimates of total run abundance by age from Jags... |
| extract_abundance_estimates | Extract abundance estimates from Jags output |
| extract_age_at_maturity | Extract estimates of total run abundance by age from Jags... |
| extract_sr_params | Extract biological reference points and parameters estimates... |
| format.paired | Format the data to run a paired analysis |
| format.standalone | Format the data to run a paired analysis |
| get_initial_values | Get a set of initial values for alpha and beta (the initial... |
| get_jags_data | Reads in and formats data so that it can be crammed into JAGS... |
| get_new_inits | Extracts and formats end values of chains so that they can be... |
| get_params | Retrieves the appropriate parameters to monitor |
| horsetail_plot | Horsetail Plot |
| profile_plot | Optimal Yield, Overfishing, and Optimal Recruitment... |
| residual_plot | Plot residuals of a model - need to implement for all models,... |
| save_jags_model | Save .jags version of a JAGS module Modified JAGS modules... |
| save_run_info | Add entry to log book # |
| set_model_specifications | Specify how the model should be run and document your... |
| source_directory | Source all files in a directory |
| sy_plot | Sustainable Yield Plot |
| trace_params | Get desired parameters for traceplots |
| write_jags_model.base | basic Ricker model |
| write_jags_model.base_ar | AR(1) term added to base Ricker |
| write_jags_model.base_tvm | Time varying age-at-maturity added to base Ricker |
| write_jags_model.base_tvm_ar | Time varying age-at-maturity and AR(1) term added to base... |
| write_jags_model.base_tvm_ar_tvp | Time varying age-at-maturity and AR(1) term added to base... |
