This repository contains code to assess the relationship between environmental variability and pace of life across the world's resident bird species.
This repository contains code to assess the relationship between environmental variability and pace of life across the world's resident bird species. The project is part of the Institute for Biodiversity, Ecology, Evolution, and Macrosystems (IBEEM) at Michigan State University, and led by IBEEM Postdoctoral Fellows. The research uses data from open access biodiversity repositories to evaluate how patterns of environmental variability within a year (i.e., seasons) and between years affect species' life histories. The analysis investigates environmental variability within and between years across the ranges of 7,477 non-migratory and non-marine avian species in order to evaluate the impacts of temporal environmental variability on species' pace of life. Environmental data are from the ERA5 climate reanalysis, bird trait and distribution data are from AVONET, BirdTree, and BirdLife databases as well as previously published research. Environmental variability values were extracted across individual species' ranges in order to quantify how environmental change has affected avian species' pace of life around the world. For more on the project see the project research summary and the publications linked below.
Funding is provided by a Michigan State University Strategic Partnership Grant for the Institute for Biodiversity, Ecology, Evolution, and Macrosystems (IBEEM).
Youngflesh, C, K Kapsar, A Uscanga, PJ Williams, JW Doser, L Kounta, PL Zarnetske. Environmental variation shapes life history of the world’s birds. In Review
Youngflesh, C., K. Kapsar, A. Uscanga, P.J. Williams, J.W. Doser, L. Kounta, and P.L. Zarnetske. 2024. Inter- and intra-annual temperature and precipitation variability (1950-2022) across the ranges of non-migratory birds and their association with generation length ver 2. Environmental Data Initiative. https://doi.org/10.6073/pasta/fc057e288924cb09fc3eb5092856d99c (Accessed 2024-09-11).
Software used to analyze data includes: R version 4.3.2
The workflow for this repository follows the guidelines set out by the Environmental Data Initiative (EDI). Briefly, this involves aligning with FAIR data practices, and employing a workflow that uses different levels for harmonization and derived data products. Data are read in as raw data at Level 0 (L0). Level 1 (L1) data represent cleaned L0 data. Level 2 data are data merged or otherwise derived from two or more L1 data, etc.
Repository structure:
Note: Scripts are designed to be run in sequence from 0-XXXX.R -> 1-XXXX.R -> ...
Scripts/
0-config.R - congfiguration file specifying location of data directory and model run date0-csv-to-tif.R - convert csv files back into geospatial format (tif) for analysis 1-clean-data/1a-clean-Bird-et-al.R - clean and combine gen time data from Bird et al. 20201b-process-ncdf.R - create time series of env data, yearly averages for specified months, and sd across specified months (seasonality)1b-process-ncdf.slurm - slurm script to submit job1c-taxonomic-harmonization.R - sort out naming differences and save individual range maps for birds1d-uncertainty-gl.R - calculate gen length uncertainty2-env-metrics/2a-env-metrics.R - calculate env variability metrics2b-env-merge.R - merge env metrics2c-env-var-time.R - explore trend in env variation over time3-extract-species-env/ - extract env var data from species range3a-split-sp-ids-birdtree.R - generate sets of bird ids for parallel processing3b-extract-avg-within-range-birdtree.R - extract environmental covariates from species ranges3b-extract-compile-birdtree.sh - bash script to iterate through all pieces of data and run 3b-extract-birdtree.sbatch3b-extract-birdtree.sbatch - bash script to load one piece of data and run 3b-extract-avg-within-range-birdtree.R on HPCC3c-get-master-file-birdtree.R - generate master file with rows for species and columns for environmental and life history data3c-get-master-file-birdtree.sbatch - bash script to run 3c-get-master-file-birdtree.R3d-env-var-range.R - explore spatial variation in environmental variation across species ranges4-phylo-cor - get phylogenetic correlation matrix4a-bird-get-con-tree-pieces.R - calculate consensus trees for 10 chunks of 100 phylogenies for birds4b-bird-get-cor-matrix.R - calculate final consensus tree and phylo cor matrix for birds 5-model/5-gl-phylo-vint-berk-oe.R - fit gl ~ env var6-rasterize - rasterize ranges6a-create-rasters.R - create .tif files birds6a-raster-comile.sh - bash script to iterate through all pieces of data and run 6a-raster.sbatch6a-raster.sbatch - bash script to load one piece of data and run 6a-create-rasters.R on HPCC6b-stack-rasters.R - script to stack rasters and produce main .tif7-figures - figuresModel_files/ - Stan model filesData/ (ignored)
L0/ - raw dataclimate/era5/ - raw ERA5 reanalysis dataranges/BOTW.gdb - BirdLife range mapstrait/ - raw trait dataL1/climate/era5/ - ERA data averaged over specified months (one value per cell/year)
ERA5-1_2_3_4_5_6_7_8_9_10_11_12.csv - yearly average over all months and sd across months (seasonality) for temp and (sqrt root transform of) preciprange/ - bird rangestrait/ - processed bird traitsL2/climate/era5/ - env variability metrics per cell
Env-var-1_2_3_4_5_6_7_8_9_10_11_12.csv - variability for all monthsEnv-main.csv - main env datarange-env-pieces/ - IDs for speciesrange-raster/ - rasterized ranges (tifs) with gen length and delta metrics (relative abiotic change) as layersL3/ - main data filesmain-bird-data.csv - merged bird dataraster-gl-dT-dP-nsp.tif - raster of median and sd of gen length and delta metrics (relative abiotic change), as well as number of species in each cell (5 layers)bird-phylo-cor-matrix.rda - bird phylogenetic correlation matrixbird-consensus-tree.rda - bird consensus treefinal-bird-data-for-archival.csv - archival version of main-bird-data.csvenv_var.csv - archival environmental variability grid datadelta.csv - archival $\delta_T$ and $\delta_P$ grid data Casey Youngflesh - cyoungf@clemson.edu