DOI: 10.5061/dryad.v6wwpzh1g
title: Code from: The relative influence of climate extremes and species richness on the temporal variability of bird communities

description: Understanding the relationship between biodiversity and ecological
 stability is increasingly urgent as rapid species extinction continues.
 Though evidence of positive diversity-stability relationships is
 accumulating, empirical results are inconsistent and effect sizes tend to
 be small, raising questions about relative contributions of intrinsic
 (i.e., species composition/interactions) and extrinsic (i.e.,
 environmental) drivers of stability. Community stability may be more
 strongly influenced by environmental conditions than by community
 diversity in some contexts, yet little is known about the comparative
 importance of diversity and climate means, extremes, and variability in
 regulating stability. We used a half-century of continental-scale bird
 data to quantify avian community temporal variability (a metric often used
 to approximate ecological stability) at 1,379 sites and compared relative
 effects of climatic variables and species richness. We found that extreme
 heat and extremely low precipitation at decadal scales are associated with
 high bird community variability and these climate variables outperformed
 species richness in terms of variance explained and magnitude of effect.
 This provides empirical support for the theoretical concept that, at a
 continental, decadal scale, environmental conditions can play a larger
 role than intrinsic factors in determining community stability. Our
 findings also increase understanding of how climate extremes cause diverse
 ecological responses.
description: # Code from: The relative influence of climate extremes and species
 richness on the temporal variability of bird communities Date: Mar 30,
 2023 Lead author contact: Samantha M. Cady, University of Nebraska-Lincoln
 ([samantha.cady@unl.edu](mailto:samantha.cady@unl.edu)) Additional
 authors/cooperators: Samuel D. Fuhlendorf (Oklahoma State University),
 Craig A. Davis (Oklahoma State University), Barney Luttbeg (Oklahoma State
 University), Caleb P. Roberts (University of Arkansas), and Scott R. Loss
 (Oklahoma State University) ## DATA User must download 5 open-source
 datasets and 1 dataset from Cady et al. (2023) on Dryad before running the
 accompanying R Code. Open Source Data: Datasets 1-3: Breeding Bird Survey
 2019 Release, state-level data 1966-2018, weather.csv, and coords.csv. All
 three datasets are available online: Pardieck, K.L., Ziolkowski, D.J.,
 Lutmerding, M., Aponte, V.I. & Hudson, M.-A.R. (2019). North American
 Breeding Bird Survey Dataset 1966-2018 (ver. 2018.0). Accessed Aug, 2019
 from [https://www.pwrc.usgs.gov/bbs/](https://www.pwrc.usgs.gov/bbs/)
 (North America Breeding Bird Survey data) Dataset 4: US EPA Level III
 ecoregions. Open-source shapefile available at:
 [https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states](https://www.epa.gov/eco-research/level-iii-and-iv-ecoregions-continental-united-states) Dataset 5: PRISM climate--Climate data extracted from PRISM rasterized data. Raw PRISM data are publicly available at: [https://prism.oregonstate.edu/ ](https://prism.oregonstate.edu/)Each row should be a BBS route ID and each column monthly data for precip, tmed, tmax, and tmin extracted at each BBS route start point for temporal extent of study (1967-2018). PRISM Climate Group, Oregon State University. (2018). Accessed Aug, 2019 from [https://prism.oregonstate.edu/](https://prism.oregonstate.edu/) (climate data) Metadata: Points.RTENO= unique BBS route identifier Columns 2:2497= weather variables (maximum temperature, mean temperature, minimum temperature, total precipitation) for each month and year between 1967-2018. Naming convention retained from PRISM rasters Manuscript-specific Data: Dataset 6: SpeciesList.csv --dataframe available on Dryad to inform which species to exclude from analysis (waterbirds, raptors, etc.) Metadata: AOU=original AOU code for bird species; AOU2=new AOU code for lumped subspecies (i.e., all subspecies given the same AOU code under AOU2); Columns 3:5 and 8:11 are species taxonomic information; Unid= binary value: if 1 species ID was uncertain and species was removed if 0 ID observaton was highly confident and species was retained; Remove= binary value: if 1 species was removed if 0 species was retained ## CODE Source code format: R Filename: R_Code_Cady_etAl_Community_Stability2024.R Dependencies: tidyverse; sp; raster; rgdal; lme4; bbmle; reshape2; stringr; vegan