Code and most data associated with the Enyalius comparative phylogeography project. The README right now is just a file guide.
Directory and file guide:
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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
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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
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slim/
- experimenting with running spatial simulations in SLiM. These are modified from the Peter Ralph’s nebria github repo.
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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 packageprocessed_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
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R/
- R scripts used for analysismake_maps_fns.R
- functions to convert a raster to a SLiM map. Taken from Peter Ralph’snebria
repositoryadhoc/
- 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 becauserenv
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
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renv/
- folder to house R and Python package info. Don’t touch anything here.