This repository contains all code related to case study 2 in which we develop an integrated community model to quantify relative abundance trends in ten open-habit-associated butterfly species in the Midwestern U.S. from 2008-2017 using data from five volunteer-based monitoring programs. The directory is split into the following structure. Each sub-directory contains its own README file with details on each of the files in that specific sub-directory.
code: contains all scripts for data processing, running the integrated community model inspAbundance, and processing of the results. Contains custom code for running the integrated community model inStan. Also contains code for data generation and model fitting for a simulated data analysis.data: contains data for fitting the model. Note this only contains data from three of the five data sources, as two of the data sources (North American Butterfly Association (NABA) and Ohio Lepidopterists) are propietary. For access to the NABA data, please contact NABA directly (www.naba.org). A simulated data set is also contained within this directory. The simulated data set has the same structure as the case study data, and allows for direct fitting of the model using the exact form described in the manuscript.results: directory containing model results files used to generate Figure 3 in the manuscript.