README

Enyalius project

Code and most data associated with the Enyalius comparative phylogeography project. The README right now is just a file guide.

Directory and file guide:

• analysis/- where I house all analysis-related files. It’s organized into subfolders:

  • data/- mostly raw data files used for analysis

  • atlantic_forest/atlantic_forest.geojson- shapefile of the Atlantic Forest boundaries. I should figure out the provenance of this file- I don’t remember where I got it.

  • brazil_clim/- bioclimate variables (.tif rasters) refined for Brazil, from Ramoni-Perazzi et al. 2022. Downloaded on 2022-02-25.

  • chelsa_trace21k/- CHELSA bioclimatic variables from the LGM

  • forest_cover/- forest cover rasters (classes 1-4) from Tuanmu and Jetz 2014. The data was housed at earthenv.org/landcover. Downloaded on 2022-02-26.

  • enyalius_locs.csv- table of enyalius localities and metadata

  • Laura_ALL_ms_FINAL_80complete.snps.phy- SNPs file I’m using until I finalize my own assemblies of the data

  • output/- output files from analyses. This folder is labile, so will change regularly.

    • cropped_predictors/- cropped bioclims and forest cover variables for SDMs

    • sdm_models/- SDM models for each Enyalius species

    • sdm_projections/- SDM projections for each species

    • sdm_response_curves/- response curves for environmental variables used in the SDMs

    • thinned_localities/- localites for each species after spatial thinning. Saved as geojson files

  • reports/- Rmarkdown and Quarto reports for each analysis

    • assembly_exploration.Rmd- interactive document to explore assembly statistics. Runs on shiny.

    • exploratory_phylogenetic_analysis.Rmd- some quick trees to investigate if any individuals don’t map to their species or are otherwise wonky

    • explore-slim-output.qmd- exploring SLiM output of spatial simulations that I’m toying around with. I used them for the 2022 Evolution meeting

    • slim_map_small.qmd- short script to aggregate and convert SDM rasters to SLiM’s format. They are at a lower resolution to facilitate speed

    • species_distribution_modeling.Rmd- species distribution models of each species with some post-processing

    • spatial_thin_log.txt- log file produced when running spThin to spatially thin localities

    • recap/- msprime recapitation output that gets generated when processing SLiM output

    • *_files/- static files that get generated when rendering .qmd reports

  • slim/- experimenting with running spatial simulations in SLiM. These are modified from the Peter Ralph’s nebria github repo.

• assembly/- files related to Enyalius RADseq assembly. This is going to be modified soon * man/- folder to house documentation of functions if I turn this into a package

  • processed_localities/- spreadsheets containing data about samples with locality data that were processed from the original raw CSV.
    • locs_nobad.csv- all individuals that had poor sequencing or otherwise had something wrong with them removed

• R/- R scripts used for analysis

  • make_maps_fns.R- functions to convert a raster to a SLiM map. Taken from Peter Ralph’s nebria repository

  • adhoc/ - functions used for a specific/single use that aren’t needed to reproduce results

    • conda_setup.R - script I used to setup a conda environment for python package management. Users don’t need it because renv tracks python packages after initializing the conda repo. They just need to install miniconda or anaconda

    • evolution_2022_figures.R- code I used to generate figures for the 2022 Evolution Conference in Cleveland

• renv/- folder to house R and Python package info. Don’t touch anything here.