# Code and data associated with Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA
# email: tyson.wepprich@gmail.com

R files numbered 0*_* contain the analysis of abundance trends starting from raw data in order of analysis.
Bulk of the paper's results come from 05_Abundance_trends.R, which sources needed data files
Population indices needed to reproduce analysis of trends are in allpops.csv
Raw data can be requested from the North American Butterfly Monitoring network (www.thebutterflynetwork.org)
Sample raw data for Cabbage Whites included for testing
Phylogenetic tree was produced using custom Python scripts in phylogeny/ directory

01_Data_prep.R 		Loads data, option to plot temperature trends
02_Fit_gam.R		Fits a generalized additive model for each species raw counts to estimate phenology patterns
03_Plot_gam.R		Visualizes results of GAM
04_Siteyear_popindex.R	Uses GAM to interpolate missing surveys, then estimate a population index for each species x site x year
05_Abundance_trends.R	Main analysis, estimates trends with population indices. Code to plot figures (Fig 2-4) of trends
06_Species_traits.R	Linear models of species traits effects on trends
07_Phylogenetic.R	Phylogenetic GLS models of species traits effects on trends (Fig 5)
08_Sitemap.R		Plots map of sites (Fig 1)
Utils.R			Functions used in other scripts

data/
allpops.csv		Processed data, needed to replicate paper's analysis, resulting from 04_siteyear_popindex of species x site x year population estimates
dailyDD2016.csv		Daily temperature and degree-days used for GAM phenology models (from Daymet)
OHbflyID.csv		Identifiers for genetic sequences for each species used to produce phylogenetic tree
OHsites2018update.txt	Geographic coordinates and names of monitoring sites
RAxML_*.nex		Phylogenetic tree from phylogeny/ workflow used in 07_Phylogenetic.R trait analysis
sample_rawdata.csv	Sample raw data from Ohio Lepidopterists butterfly monitoring for Cabbage Whites
sampling_covariates.csv	List-length and survey duration used as covariates
spain.csv		Annual index of total abundance from Catalonia BMS (citation in paper)
species_names.csv	Species common and scientific names
speciestraits.csv	Species traits collected from various sources and authors' knowledge (metadata below)
speciestraits_meta.txt	Metadata explaining species trait variables
speciesTrends.csv	Intermediate product output by 05_abundance_trends.R, used in 06_Species_traits.R
trend_models.rds	Intermediate product of 81 species model results
ukbms_country.csv	Annual collated index of UKBMS countryside species (citation in paper)
ukbms_special.csv	Annual collated index of UKBMS specialist species (citation in paper)
unique_surveys.csv	Dates and locations for all surveys, combined with other data in analysis	

phylogeny/analysis_pipeline
code/			Python scripts used to construct trees
rax10k_constrainedA_*/	Results from tree constrained by families hypothesized in Espeland et al. 2018
rax10k_unconstrainedA/	Results from unconstrained tree
analysis_pipeline.sh	Commands used for constructing phylogenetic tree