To cite this code:
Connor M French, Laura D Bertola, Ana C Carnaval, Evan P Economo, Jamie M Kass, David J Lohman, Katharine A Marske, Rudolf Meier, Isaac Overcast, Andrew J. Rominger, Phillip Staniczenko, Michael J Hickerson. Global determinants of insect genetic diversity. https://github.com/connor-french/global-insect-macrogenetics/. 10.5281/zenodo.8125548. 2023.
Open access in Nature Communications:
Global determinants of insect genetic diversity
Connor M French, Laura D Bertola, Ana C Carnaval, Evan P Economo, Jamie M Kass, David J Lohman, Katharine A Marske, Rudolf Meier, Isaac Overcast, Andrew J. Rominger, Phillip Staniczenko, Michael J Hickerson Nature Communications 14, 5276 (2023); doi: https://doi.org/10.1038/s41467-023-40936-0
Where to find things:
All climate data is available online at the links provided in Supplementary Table 1 or meta/raster_list.csv. The BOLD insect data is available on figshare as bold_data_insects.txt, which belongs in the data/ folder.
The only data subfolders that come pre-populated are data/templates, which contains raster templates for aggregating raw climate data, and data/invasive, which contains spreadsheets with invasive species information for filtering out invasive species from the data set.
For the scripts to run, you need to create the following folders:
For raw climate:
data/climate_raw
Climate data aggregated for analysis:
data/climate_agg
Non-raster climate:
data/climate_poly
Folder to put output:
output/
- all necessary output subfolders will be generated by code
Metadata with information on predictor variables and invasive species lists is provided in the meta/ folder.
These are analysis notebooks containing annotated code. .ipynb are jupyter notebooks (open using python jupyter notebook), .Rmd are RMarkdown documents, and .qmd are Quarto documents (open .Rmd and .qmd in RStudio or VS Code). The links go to the readable jupyter notebook file or github markdown file so you don't have to download the repo to view the code. Below each link is the path to the raw report file.
Aggregating environmental data for analysis:
step-0_aggregate-rasters
reports/step-0_aggregate-rasters.ipynb
Filter and align sequence:
step-1_seq-filter-align-test
reports/step-1_seq-filter-align-test.ipynb
Calculate statistics from sequence:
step-2_seq-stats-test
reports/step-2_seq-stats-test.ipynb
Exploring, wrangling, and filtering data before modeling:
step-3_data-exploration
reports/step-3_data-exploration.Rmd
Modeling:
step-4-models
reports/step-4-models.qmd
Publication figures:
publication_figures
reports/publication_figures.Rmd
- I didn't optimize the plotting output for the report, so sorry for some unreadable plots
These are the reports necessary to regenerate the analyses for publication.
All helper R scrips are contained in the R/ folder. They are called in their respective report.