Supplementary data archive for Rates of passerine body plan evolution in time and space

Supplementary Data Archive This record provides the data directory used in the analyses for 'Rates of passerine body plan evolution in time and space', to be published in Nature Ecology & Evolution. This archive is intended to be used with the companion code repository for the same release/version:https://github.com/jakeberv/passerine-bodyplan-evolution This code repository is separately archived at Zenodo here: https://doi.org/10.5281/zenodo.19211076 After downloading and extracting the code archive, download this data archive and place the data folder at the code repository's root. Most of the individual files in this archive are .RDS files, which are serialized R data files. These files store precomputed R objects exactly as they were saved in the analysis workflow and can be loaded in R with readRDS() for direct reuse in the companion scripts. Contents data/temporal/: Contains core empirical inputs, cached rate-shift search outputs, simulation outputs, false-negative analyses, and a paleoclimate reference workbook used in the temporal analyses. data/spatial/: Contains cached taxonomy-matching results, processed range objects, gridded climate summaries, and temporal-to-spatial bridge inputs used in the spatial analyses. Included processed data products data/temporal/01_core_inputs/: Core empirical inputs for the temporal workflow, including the main multivariate trait objects and the time-calibrated passerine tree data/temporal/02_shift_search/: Cached outputs from multiregime rate-shift searches across alternative information-criterion thresholds data/temporal/03_simulations/: Cached simulation outputs used to evaluate method performance and shift-recovery behavior data/temporal/04_false_negative_outputs/: Cached analyses used to assess false-negative behavior and corresponding corrected variants data/temporal/05_climate_reference/: Paleoclimate reference workbook used for temporal figure overlays and contextual plotting data/spatial/01_taxonomy_matching/: Cached species-name matching outputs linking the phylogeny and trait data to spatial range data data/spatial/02_ranges_and_filters/: Cleaned, merged, filtered, and simplified polygon products used in downstream spatial analyses data/spatial/03_grid_climate_weights/: Precomputed gridded climate summary objects and spatial weighting inputs used in regression and mapping workflows data/spatial/04_temporal_bridge_inputs/: Cached objects that connect temporal rate estimates to the spatial analysis pipeline Notes on excluded raw-source inputs Some upstream raw-source inputs are documented in place but are not redistributed in this archive due to licensing restrictions. The original BirdLife range source object is not included. See data/spatial/00_raw_range_source/README.md. The original WorldClim 2.1 bioclim GeoTIFF rasters are not included. See data/spatial/05_bioclim_rasters/wc2.1_5m_bio/README.md. These local README files explain the exclusions and point readers to the processed products provided in this archive. Reproducibility note This archive is designed for use with the released cached-mode workflow in the companion code repository. Most computationally intensive steps are represented here by cached intermediate and result objects. A full rerun of the earliest raw-input spatial preprocessing steps would require separately obtaining the excluded upstream source files from their original providers. The authors can provide guidance on expected inputs and workflow. Use and citation Please cite the associated manuscript together with the versioned code and data archives used in your analysis. Some contents reflect third-party source datasets used in the analyses, and the reuse of those underlying materials may remain subject to provider-specific terms.