LGR_SimulationStudy

Simulation study related to estimating escapement past Lower Granite Dam

File descriptions

• SimFunc.R: functions that simulate fish crossing over Lower Granite Dam, and generate "observed" datasets on a weekly time-scale
• SimScenarios: folder containing the R script for each scenario. Each script generates 500 similar simulations, and saves the resulting estimates from the ISEMP and SCOBI models.
• SimulationFits: folder to store the results of simulations and estimates
• Run_AllSims.R: run all the scenario scripts, and save outputs
• SummariseResults.Rmd: summarise the results of the simulations with tables and figures
• SCOBI: contains the R functions to run the SCOBI model (the TAC estimate)

JAGS models

• LGR_TotalEscape_JAGS.txt: JAGS model file to estimate wild escapement
• LGR_TotalEscape_AllOrigins.txt: JAGS model file to estimate wild, hatchery and hatchery no-clip escapement
• LGR_TotalEscape_NB2.txt: JAGS model file with extra over-dispersion parameter for the negative binomial, to help estimate the mean-variance relationship. Currently not tested or used.

Outdated scripts

• RunSims.R: run multiple simulations and save the resulting estimates and truth (based on the simulations). Focus is on wild fish only
• RunSims_AllOrigins.R: same as above, but this model includes estimates of natural origin, hatchery origin and hatchery no-clip fish
• EvaluateSims.R: pre-cursor to SummarizeResults.Rmd