(in scripts/ subdirectory)
abc.R: run approximate Bayesian computation for demographic inference
bedassle.R: run BEDASSLE to estimate relative impact of environment on genetic differentiation
genotype_analysis.R: handle .vcf files and prepare for plotting; run PCA etc.
quality_control.R: visualize sequencing results (readcount by spp.)
scarab_analysis_notebook.Rmd: Rmarkdown digital notebook file for all assembly and analyses
scarab_analysis_notebook.md: knit digital notebook file, with images
snp_filtering.sh: SNP filtering parameters
stats.R: calculate summary statistics and mixed models
(in data/ subdirectory)
fst_dist_species.csv: pairwise FST by geographic distance data
genotypes.df.csv: genotype PCA and sample data
growth.csv: posterior distribution of parameters from ABC "growth" model
master.theta.df: etsimtates of theta across elevation
melted.bayes.csv: Bayes factor data from ABC
melted.coancestry.df.csv: fineRADstructure results
scarab_spp_master.csv: full sample and locality data
(in dDocent/ subdirectory)
*_config.file: species-specific dDocent assembly parameters
*_rename.txt: name manipulations to meet program reqs
(in bedassle/ subdirectory)
*.Robj: BEDASSLE output for each species