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jclbrooks / MD_Stream_Salamanders

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MD_Stream_Salamanders

Main repository for Jacey Brooks thesis project and analyses examining the effect of AMD stream remediation on stream-breeding salamanders.

Files

Regional Occupancy Models

Each species will be modeled individually because of discrete range boundaries creating challenges for a multi-species model and not that many species for random effects any way.

Folder: Code/

  1. combine_obs_data.R - formats and organizes occupancy data before being organized in prep_occ.R

  2. query_climate.R - get the daymet climate data averaged by catchment from USGS Conte SHEDS db - also gets landscape and huc data

  3. format_landscape_data.R - format and organize the landscape data

  4. prep_occ.R - organize data for modeling (not sure if necessary)

  5. dynamic_occ_jags.R - run the MCMC and save results

  6. check_mcmc.R - check posteriors

  7. summarize_results.R - make tables and figures of results

Western MD Abundance Modeling

data_exploration.R - code for making summary tables and figures of the raw data

run_jags.R - script for running JAGS N-mixture model

run_glm.R - script for running GLM, maybe GLMM??