Integrating community science and agency-collected monitoring data to expand monitoring capacity at large spatial scales

Contents of this repository

1. Data Folder: Description text file with eBird data access query information and links to download site covariate data for use in ArcMap. Washington Department of Fish and Wildlife Common Loon observation data from 2017. SitesandCovs.csv data file with all sites and covariate information, including indicators for data source (eBird or WDFW). See DESCRIPTION.txt for more information and links to covariate data sources.

2. Scripts Folder: R scripts for filtering eBird data to map in ArcMap, formatting spatially filtered eBird data and WDFW data for use in the occupancy model, Nimble multi-state occupancy model script to run the model, and files to generate figures and parameter estimates

3. Figures Folder:Figures 1-4 from the manuscript, folder with posterior coefficient density plots from MCMC output

Scripts

1. EBird_Auk_filtering.R & WDFWformat.R

2. SPfilteredEBird.R & FormattedData.R

3. NimbleOccModel.R

4. PosteriorsandTables.R, PredictionsandFigs.R, & ConvergeDiag.R

Figures

Figures found in manuscript Folder with posterior estimates from coefficients and key parameters

Required Packages

nimble

auk

coda

ggplot2

devtools

dplyr

data.table

lubridate

bayesplot

cowplot