WNV_Mechanistic_Model

This repository is designed to be used with Kain and Bolker 2019: Predicting West Nile virus transmission in North American bird communities using phylogenetic mixed effects models and eBird citizen science data. (https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-019-3656-8)

All of the raw data (apart from eBird data) needed to run these models is present in this repository. eBird data can be obtained here (https://science.ebird.org/en/use-ebird-data)

This code can be run using two methods:

1. Clean eBird .zip file and run R code "manually" in two separate steps
   A) Run sh ebird_data_clean.sh in the command prompt once all eBird .zip files have been placed in the folder titled "ebird_zip_fresh"
   B) Open "top_level_script.R"
   i) Read the instructions at the top of this script
   ii) Adjust parameters and options as desired
   iii) Run the script as desired
   

2. Clean eBird .zip file and run R code in a single step
   A) Run sh ebird_bash_run.sh
   i) Will require some additional setup on the part of the user (see Step 4 in "ebird_bash_run.sh")
   ii) Cant be run if there are missing scientific names (see "saved_matching" below)
   

This repository contains a number of folders, many of which are empty. The folders are one of three types:

(1) Folders that need to have data placed in them prior to running the code. Data available as the supplementary material to Kain and Bolker 2019 at: URL HERE is organized in the appropriate folders
A) trees -- Contains phylogenetic tree data
B) ebird_zip_fresh -- Contains the .zip ebird file
C) data -- Contains all other data (bird responses, county data etc.)

(2) Folders that contain model components
A) stan -- Contains stan model definitions

(3) Folders that start empty but get filled as part of the automated workflow when output is saved to disk
A) ebird_data_for_R -- Will contain all of the eBird data once it is extracted
B) ebird_zip_dump -- Will contain .zip files after they get extracted
C) ebird_pieces -- One of two intermediate folders to momentarily house extracted eBird pieces
D) ebird_unzip -- Two of two intermediate folders to momentarily house extracted eBird pieces
E) saved_fits -- Contains intermediate fitted model results to expedite code in future runs
F) saved_matching -- Contains matched scientific names and bird body sizes
G) saved_output -- Contains all other fits including final "product"

Details for the purpose of each R script are in "top_level_script.R"