DEPART-SAM Model

This repository contains models and code to run the DEPART-SAM model. An explanation of the file structure is below:

1. scripts

• 00_data_clean.R
  • This script reads in all necessary data and formats the information consistently across sites
  • This includes filling small data gaps
• 01_model_prep.R
  • preps the data to be in the correct format for the Bayesian model
• 02_script_SAM.R
  • runs the DEPART-SAM model
• SAM_function.R
  • read in by 02_script_SAM.R
• check_convergence_function.R
  • read in by 02_script_SAM.R
• coda_functions.R
  • functions to help summarize JAGS coda output
• functions.R
  • helper functions, read in by various scripts

2. models

• Model_v3.R
  • combined DEPART-SAM model
• Model_split_v3.R
  • combined DEPART-SAM model, but splits the model to account for a large data gap at US-Vcp

3. input_data

• read into 00_data_clean.R

4. clean_data

• read into 01_model_prep.R and 02_script_SAM.R

5. output_dfs

• output data frames. Contains posterior means and uncertainty for variables of interest.