DOI: 10.5281/zenodo.13766320
title: Supporting Data for Crawford et al. 2024, Effects of Cropland Abandonment on Biodiversity

description: This archive contains derived and supporting data products to support:

Crawford CL*, Wiebe RA, Yin H, Radeloff VC, and Wilcove DS. 2024. Effects of cropland abandonment on biodiversity. Nature Sustainability. In press.

*Contact Christopher L. Crawford at ccrawford@alumni.princeton.edu with any questions.

A public Zenodo archive of the Github repository containing analysis scripts developed for this project (https://github.com/chriscra/biodiversity_abandonment) can be found here: 10.5281/zenodo.13777205

This analysis builds on: Crawford, C. L., Yin, H., Radeloff, V. C. & Wilcove, D. S. Rural land abandonment is too ephemeral to provide major benefits for biodiversity and climate. Science Advances 8, 1–13 (2022). Data and scripts from Crawford et al. 2022 are archived and publicly available at Zenodo (https://doi.org/10.1126/sciadv.abm8999).

The annual land cover maps (1987-2017, 30 meter resolution) that underlie our analysis were developed on Google Earth Engine using publicly available Landsat satellite imagery (Yin et al. 2020, Remote Sensing of Environment, https://doi.org/10.1016/j.rse.2020.111873).These annual land cover maps, along with other derived data that were produced by Crawford et al. 2022, are archived and publicly available at Zenodo (https://doi.org/10.5281/zenodo.5348287).

This archive includes important derived data products created for Crawford et al. 2024. Note that these and other project data are described in detail in **util/_util_files.R** (https://github.com/chriscra/biodiversity_abandonment). This is a convenience script that loads many of the relevant input and derived data that are used throughout the project. The primary required data files for reproducing this work are archived here, but "_util_files.R" also includes information about where additional files can be accessed (if external, e.g., https://doi.org/10.5281/zenodo.5348287) or created across the various .R and .Rmd files in this repository (e.g., "habitats.Rmd" chunk {r land-cover-of-abn-pixels}).

Naming conventions for sites and raster files follow Crawford et al. 2022, as described here: https://doi.org/10.5281/zenodo.5348287

Site file names correspond to the following geographic locations:belarus = Vitebsk, Belarus / Smolensk, Russiabosnia_herzegovina = Bosnia & Herzegovinachongqing = Chongqing, Chinagoias = Goiás, Braziliraq = Iraqmato_grosso = Mato Grosso, Brazilnebraska = Nebraska / Wyoming, USAorenburg = Orenburg, Russia / Uralsk, Kazakhstanshaanxi = Shaanxi/Shanxi, Chinavolgograd = Volgograd, Russiawisconsin = Wisconsin, USA

This archive includes the following files:



site_df.csv

crop_to_abn_iucn_observed.zip

crop_to_abn_iucn_potential.zip

max_abn_lcc_iucn.zip

max_abn_lcc_iucn_potential.zip

lcc_iucn_habitat.zip

lcc_iucn_habitat_potential.zip

frag_df.csv

frag_hypo_no_abn_2017_df.csv

iucn_lc_crosswalk.csv

habitat_age_req_coded.csv

centroids_df.csv

aoh_l.parquet

aoh_feols.parquet

aoh_start_end_l.parquet

aoh_change_df.parquet

aoh_est_change_tmp_all.csv

aoh_obs_change_tmp_all.csv

taxonomy_df.parquet

final_species_list.csv

trait_mod_df_modx1.rds


site_df.csv

A list of site names and related metadata describing our study sites, taken from https://zenodo.org/records/5348287

Derived habitat rasters:

crop_to_abn_iucn_observed.zip (Calculation 1a)crop_to_abn_iucn_potential.zip (Calculation 1b)max_abn_lcc_iucn.zip (Calculation 2a)max_abn_lcc_iucn_potential.zip (Calculation 2b)lcc_iucn_habitat.zip (Calculation 3a)lcc_iucn_habitat_potential.zip (Calculation 3b)

These maps show IUCN Level 2 habitat types (Jung et al. 2020) interpolated onto the land cover classes in the Yin et al. (2020) abandonment maps at multiple spatial and temporal extents, which serve as inputs for the three primary calculations in our manuscript. Accompanying each calculation is a corresponding map for a scenarios in which no abandoned croplands were recultivated over the course of the time series (marked as "potential"). Each .zip file contains maps for each of 11 sites.

Calculation 1. This calculation isolates the direct effect of abandonment on habitat availability, by comparing the habitat provided before and after abandonment. These "crop_to_abn_iucn" maps show IUCN Level 2 habitats in cropland pixels that experienced abandonment, including the abandonment period as well as the immediately preceding period of cultivation (to allow for a proper before and after comparison). As a result, these maps show only habitat provided by croplands when they were actively cultivated, abandoned, or, where appropriate, recultivated, which allows for a proper before and after comparison. These maps are created in the script "cluster/noncrop_precrop_mask.R".

Calculation 2. This calculation considered changes in habitat that took place exclusively in pixels that experienced abandonment at some point during the time series (following Calculation 1), but expanded to track changes across our entire time series, from 1987 through 2017, in order to account for any land cover that was cleared for agriculture prior to abandonment. These "max_abn_lcc_iucn" maps therefore show IUCN Level 2 habitat types for each pixel that was abandoned at any point during the time series, across the full time series. These maps were created in the script "habitats.Rmd" code chunks {r mask-lcc-iucn-habitat-to-abn} and {r *potential_max}. 

Calculation 3. This calculation tracks habitat area provided by every pixel throughout the entire spatial and temporal extent (1987-2017), in order to place abandonment into the context of broader land-cover change dynamics like ongoing cropland expansion taking place alongside of abandonment. These "lcc_iucn" maps therefore show the IUCN Level 2 habitat types for each pixel at each site in each year of our time series. These maps were created in the script "habitats.Rmd" code chunks {r lcc-iucn-habitat-composite} and {r *potential-lcc-full} and the script "cluster/potential_full_iucn.R".

Some analyses require these .tif files (manipulated as SpatRasters using {terra}, https://rspatial.org/terra/) to be converted to tabular format (data.tables, via {data.table} (https://rdatatable.gitlab.io/data.table/) and saved as .parquet files (via {arrow}, https://arrow.apache.org/docs/r/). This can be accomplished via scripts "cluster/save_spatraster_as_dt.R" and "cluster/save_parquet.R."

frag_df.csvfrag_hypo_no_abn_2017_df.csv

These tabular files contain derived fragmentation statistics calculated using the {landscapemetrics} R package (https://r-spatialecology.github.io/landscapemetrics/). The second file contains metrics for a scenario in which no croplands were abandoned through the year 2017, in order to assess the effect cropland abandonment on landscape configuration. Each file contains 11 columns: 



"layer" -- the spatial raster layer for which the metric is calculated, corresponding to a year.

"level" -- the level at which the metric is calculated, in our case, the land cover "class."

"class" -- corresponding the to land cover class for which the metric is calculated (1 = non-vegetation, 2 = woody vegetation [i.e., forest], 3 = cropland, and 4 = herbaceous vegetation [i.e., grassland]).

"id" -- An unused field containing NA values.

"metric" -- the specific term used for each metric by {landscapemetrics} ("area_mn", "clumpy", or "para_mn").

"value" -- the numerical value of the statistic.

"name" -- the name of the landscape metric being calculated ("patch area," "clumpiness index," or "perimeter-area ratio").

"type" -- the broad type of metric being calculated ("area and edge metric," "aggregation metric," or "shape metric").

"function_name" -- the name of the {landscapemetrics} function used to calculate the statistic.

"site" -- the site (out of 11 study sites) for which this statistic was calculated.

"year" -- the year corresponding to the metric statistic, between 1987-2017 (including 1986-2018 for Nebraska and 1987-2018 for Wisconsin)Additional details on these metrics can be found at https://r-spatialecology.github.io/landscapemetrics/.


The spatial IUCN data underlying our analyses (species range maps) are available upon request from BirdLife International (http://datazone.birdlife.org/species/requestdis) and IUCN (https://www.iucnredlist.org/resources/spatial-data-download). Tabular species assessment data (including habitat and elevation preferences) are freely available from IUCN (https://www.iucnredlist.org/). Here we share three IUCN-related data files that serve as important inputs throughout our analyses:

iucn_lc_crosswalk.csv

This tabular file outlines the crosswalk between the 4 land cover classes in Yin et al. 2020 and the IUCN Level 2 habitat types mapped by Jung et al. 2020. It contains five columns:



"map_code" -- the habitat code corresponding to Jung et al. (2020).

"Coarse_Name" -- the broad Level 1 habitat grouping.

"lc" -- the corresponding land cover type from Yin et al. (2020) (1 = non-vegetation, 2 = woody vegetation [i.e., forest], 3 = cropland, and 4 = herbaceous vegetation [i.e., grassland]).

"IUCNLevel" -- the full IUCN Level 2 habitat type name. 

"code" -- the IUCN Level 2 habitat code. 


habitat_age_req_coded.csv

This tabular file lists whether each species was determined (by R. Alex Wiebe [AW] and Christopher L. Crawford [CLC]) to be a "mature forest obligate" (i.e., requiring forest older than 30 years, our time series length) or not. Species determined to be "mature forest obligate" species were excluded from our final analysis. The file includes 11 columns: 



"vert_class" -- Vertebrate class ("bird" or "mam" [mammal])

"binomial" -- Species' binomial scientific name containing genus and species.

"common_names" -- Species' common names listed by IUCN.

"mature_forest_obl" -- Whether a species is determined to be a "mature forest obligate" species (1) or not (0). Some species are marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty, but these were rounded to the nearest integer for the final analysis.

"water_obl" -- Whether a species is determined to be a "water obligate" species (1) or not (0). Some species were marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty. Note: this field was not used in the analysis.

"habitat" -- The description of the species' habitat, drawn from individual IUCN assessments (see https://www.iucnredlist.org/).

"site_presence" -- Where each species is present across our 11 study sites.

"suitable_habitats" -- A list of IUCN Level 2 habitat types consider suitable habitat by each species.

"major_habitats" -- A list of IUCN Level 2 habitat types listed as having "Major Importance" for that species.

"coder" -- The author that assigned the mature forest obligate and water obligate codes ("AW" = R. Alex Wiebe, "CLC" = Christopher L. Crawford).

"Chris_notes" -- A text field contains notes on coding process.


centroids_df.csv

This is a simple tabular dataset containing the longitude and latitude of the centroid of each bird and mammal species' range that overlaps with one of my sites. Columns include "binomial," which lists each species binomial scientific name, "centroid_longitude," and centroid_latitude." Centroid positions were calculated in QGIS using species range files from IUCN and BirdLife International.

aoh_l.parquet

This tabular file contains the raw AOH results produced using the script "cluster/aoh.R." This file contains the area of each suitable IUCN Level 2 habitat for each bird and mammal species at each site in each year of our time series (1987-2017), calculated across a range of calculations and scenarios. This file includes the primary data that serve as inputs for much of the rest of the analysis. The overall area of habitat for each species in each year at each site (a tabular data file named "aoh") summed across suitable habitat types and filtered to include or exclude passage areas for migratory birds, is calculated from "aoh_l" in the "AOH.Rmd" script in code chunks "filter-aoh-suitability-by-season" and "**calculate-aoh" (similarly to other derived datasets that serve as inputs for various parts of the analysis). This "aoh" file provides input data for the linear models used to extract AOH trends and test for significance. "aoh_l.parquet" includes 20 columns: 



"aoh_type" -- A label indicating the temporal and spatial scale at which AOH is calculated: "crop_abn_iucn" (Calc. 1a), "crop_abn_potential_iucn" (Calc. 1b), "max_abn_iucn" (Calc. 2a), "max_potential_abn_iucn" (Calc. 2b), "full_iucn" (Calc. 3a), and "full_potential_iucn" (Calc. 3b). "abn_iucn" and "potential_abn_iucn" correspond to calculations that only capture habitat following abandonment (i.e., not including habitat provided by croplands prior to abandonment); these calculations are not included in our final analysis.

"vert_class" -- Vertebrate class ("amp," amphibians; "bird," birds; or "mam," mammals). Note that only birds and mammals were included in our final analysis.

"site" -- One of our 11 study sites (see above).

"binomial" -- Species binomial scientific name.

"year" -- Year for which AOH is calculated (1987-2017).

"map_code" -- Code indicating the IUCN Level 2 habitat associated with the area statistic. See "iucn_lc_crosswalk.csv."

"season" -- Seasonal code indicating the season in which a species considers the habitat to be suitable, drawn from IUCN. Codes are: 1 ("Resident"), 2 ("Breeding") (2), "Non-breeding Season" (3), Passage (4), and Seasonal Occurrence Uncertain (5)

"area" -- Area of Habitat, in hectares (ha).

"mature_forest_obl" -- Whether a species is determined to be a "mature forest obligate" species (1) or not (0), drawn directly from "habitat_age_req_coded.csv" (see above). Some species are marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty, but these were rounded to the nearest integer for the final analysis.

"redlistCategory" -- IUCN Red List Category: "Extinct," "Extinct in the Wild," "Critically Endangered," "Endangered," "Vulnerable," "Near Threatened," "Least Concern," "Data Deficient," or "Not Evaluated."

"IUCN_aoh_ha" -- [Unused] A preliminary summation of all habitat area for each species in each year, prior to filtering. We did not use this field in our analysis. Our final AOH calculation involved first filtering out mismatched season and habitat suitability combinations.

"time" -- The time required for the area of habitat calculation (in seconds).

"className" -- Vertebrate class: "AMPHIBIA," "AVES," or "MAMMALIA."

"category" -- Duplicate field for IUCN Red List Category, unused.

"core_index" -- An index used to assign specific AOH calculations to run in parallel across multiple computing cores on Princeton's High-Performance Computing Cluster.

"total_range_area" -- The species total range area, in square kilometers (km^2), calculated across all range polygons for each species provided by IUCN and BirdLife International. See "cluster/calc_range_area.R."

"range_size_quantile" -- A numerical index representing global species range size quantiles, within each class. Values range from 0 (the smallest global range within a class) to 1 (the largest global range within a class). These quantiles are used to define "small-ranged species," as species with global range sizes smaller than the median global range size in their class. See "cluster/calc_range_area.R."

"water_obl" -- Whether a species is determined to be a "water obligate" species (1) or not (0). Some species were marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty. Note: this field was not used in the analysis. Drawn directly from "habitat_age_req_coded.csv" (see above).

"coder" -- The author that assigned the mature forest obligate and water obligate codes ("AW" = R. Alex Wiebe, "CLC" = Christopher L. Crawford). Drawn directly from "habitat_age_req_coded.csv" (see above).

"common_names" -- Species' common names listed by IUCN, drawn directly from "habitat_age_req_coded.csv" (see above).


aoh_feols.parquet

This tabular data contains the results of linear regressions predicting area of habitat as a function of time. We parameterized models for each species in each site for each of the 6 AOH calculation types described above and in Crawford et al. 2024 (Calculations 1a, 1b, 2a, 2b, 3a, and 3b). We used the R package {fixest} to parameterize these ordinary least squares (OLS) linear regressions, using the Newey-West estimator to calculate standard errors. We used the R package {broom} to extract ("tidy") the model coefficient estimates and statistics. See "AOH.Rmd" chunk {r **feols}. This file includes 20 columns:



"term" -- The name of the regression term: "(Intercept)" or slope ("year0").

"estimate" -- The estimated value of the regression term.

"std.error" -- The standard error of the regression term.

"statistic" -- The value of a T-statistic to use in a hypothesis that the regression term is non-zero.

"p.value" -- The two-sided p-value associated with the observed statistic.

"conf.low" -- Lower bound on the confidence interval for the estimate (in our case 5%).

"conf.high" -- Upper bound on the confidence interval for the estimate (in our case, 95%).

"aoh_type" -- A label indicating the temporal and spatial scale at which AOH is calculated: "crop_abn_iucn" (Calc. 1a), "crop_abn_potential_iucn" (Calc. 1b), "max_abn_iucn" (Calc. 2a), "max_potential_abn_iucn" (Calc. 2b), "full_iucn" (Calc. 3a), and "full_potential_iucn" (Calc. 3b). "abn_iucn" and "potential_abn_iucn" correspond to calculations that only capture habitat following abandonment (i.e., not including habitat provided by croplands prior to abandonment); these calculations are not included in our final analysis.

"run_index" -- An index used to easily pull observations for each model run. There is one index for each unique species at each site, in each of the aoh_types, calculated including and excluding passage areas.

"vert_class" -- Vertebrate class ("amp," amphibians; "bird," birds; or "mam," mammals). Note that only birds and mammals were included in our final analysis.

"site" -- One of our 11 study sites (see above).

"binomial" -- Species binomial scientific name.

"n_obs" -- The number of observations included in the model run.

"n_unique_obs" -- The number of unique observations included in the model run (used to exclude species with constant AOH).

"redlistCategory" -- IUCN Red List Category: "Extinct," "Extinct in the Wild," "Critically Endangered," "Endangered," "Vulnerable," "Near Threatened," "Least Concern," "Data Deficient," or "Not Evaluated."

"mature_forest_obl" -- Whether a species is determined to be a "mature forest obligate" species (1) or not (0), drawn directly from "habitat_age_req_coded.csv" (see above). Some species are marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty, but these were rounded to the nearest integer for the final analysis.

"common_names" -- Species' common names listed by IUCN, drawn directly from "habitat_age_req_coded.csv" (see above).

"start_year" -- The first year for which this species has area of habitat at this site (i.e., the first observation included in the model).

"end_year" -- The last year for which this species has area of habitat at this site (i.e., the last observation included in the model).

"passage_type" -- Whether a model run includes passage areas ("include_passage") or does not include passage areas ("exclude_passage") when calculating area of habitat (AOH) for migratory birds.


Two files contain model effect sizes for AOH models:

aoh_start_end_l.parquet

This tabular data file contains observed effect sizes: the observed change in AOH for each species at each site, in each calculation, derived directly from observations from the start and end of the time series. These data are calculated in "AOH.Rmd" chunk: {r observed-change-in-aoh-by-window-size}. This data serves as direct input for the file "aoh_obs_change_tmp_all" (see below), which is the primary input for the traits linear models in our analysis (see "traits.Rmd", "_util_files.R").  This file contains 24 columns:



"run_index" -- An index used to easily pull observations for each model run. There is one index for each unique species at each site, in each of the aoh_types, calculated including and excluding passage areas.

"start" -- The mean area of habitat (AOH), in hectares (ha), at the "start" of the time series, as calculated across the number of years specified in "window_size."

"start_year" -- The year of the first AOH observation.

"end" -- The mean area of habitat (AOH), in hectares (ha), at the "end" of the time series, as calculated across the number of years specified in "window_size."

"end_year" -- The year of the last AOH observation.

"window_size" -- The number of years across which "start" and "end" AOH values are averaged (e.g., if "window_size" is 5, "start" is then the mean AOH across the first 5 years of observations, and "end" is the mean AOH across the last 5 years of observations).

"abs_change" -- The absolute change in AOH, calculated as the difference between the mean AOH at the end of the time series and the mean AOH at the start of the time series (i.e., end - start).

"prop_change" -- The proportional change in AOH, calculated as the absolute change in AOH divided by the AOH value at the start of the time series (i.e., abs_change/start).

"percent_change" -- The percent change in AOH, calculated as 100 times the proportional change in AOH (i.e., 100 * prop_change).

"ratio" -- The ratio of the mean AOH at the end of the time series to the mean AOH at the start of the time series (i.e., end/start).

"ratio_mod" -- A modified ratio of the ending AOH to the starting AOH, for which ratio values less than 1 are replaced by additive inverse of the reciprocal value (i.e., 1/ratio * -1). Ratios greater than 1 are left the same.

"abs_change_as_prop_site_area" -- The absolute change in AOH as a proportion of site area (i.e., abs_change / total_site_area_ha_2017).

"aoh_type" -- A label indicating the temporal and spatial scale at which AOH is calculated: "crop_abn_iucn" (Calc. 1a), "crop_abn_potential_iucn" (Calc. 1b), "max_abn_iucn" (Calc. 2a), "max_potential_abn_iucn" (Calc. 2b), "full_iucn" (Calc. 3a), and "full_potential_iucn" (Calc. 3b). "abn_iucn" and "potential_abn_iucn" correspond to calculations that only capture habitat following abandonment (i.e., not including habitat provided by croplands prior to abandonment); these calculations are not included in our final analysis.

"vert_class" -- Vertebrate class ("amp," amphibians; "bird," birds; or "mam," mammals). Note that only birds and mammals were included in our final analysis.

"site" -- One of our 11 study sites (see above).

"binomial" -- Species binomial scientific name.

"passage_type" -- Whether a model run includes passage areas ("include_passage") or does not include passage areas ("exclude_passage") when calculating area of habitat (AOH) for migratory birds.

"common_names" -- Species' common names listed by IUCN, drawn directly from "habitat_age_req_coded.csv" (see above).

"redlistCategory" -- IUCN Red List Category: "Extinct," "Extinct in the Wild," "Critically Endangered," "Endangered," "Vulnerable," "Near Threatened," "Least Concern," "Data Deficient," or "Not Evaluated."

"mature_forest_obl" -- Whether a species is determined to be a "mature forest obligate" species (1) or not (0), drawn directly from "habitat_age_req_coded.csv" (see above). Some species are marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty, but these were rounded to the nearest integer for the final analysis.

"total_site_area_ha_2017" -- The total site area (ha) in 2017. (Drawn directly from "area_summary_df," from https://zenodo.org/records/5348287)

"area_ever_abn_ha" -- The total area of those pixels that were abandoned at least once during the time series (corresponding to the area of potential abandonment, as of 2017). (Drawn directly from "area_summary_df," from https://zenodo.org/records/5348287)

"trend" -- The overall trend in AOH ("gain," "loss," or "no trend"), determined by the sign of slope coefficients and statistical significance at p < 0.05.

"factor_change" -- The factor change in AOH, calculated as either the proportional change in AOH (i.e., prop_change) for values greater than 0, or as the reciprocal of the proportional change in AOH (i.e., 1/prop_change) for values greater than 0.


aoh_change_df.parquet

This tabular data file contains effect sizes estimated from linear regression coefficients (i.e., slopes and intercepts), calculated in "AOH.Rmd" chunk {r estimated-changes-aoh-change-df}. This file contains 29 columns:



"run_index" -- An index used to easily pull observations for each model run. There is one index for each unique species at each site, in each of the aoh_types, calculated including and excluding passage areas.

"est_type" -- The estimate type, whether the estimated model slope ("estimate") or the lower ("conf.low") or upper ("conf.high") bounds of the 95% confidence interval around the slope estimate.

"vert_class" -- Vertebrate class ("amp," amphibians; "bird," birds; or "mam," mammals). Note that only birds and mammals were included in our final analysis.

"site" -- One of our 11 study sites (see above).

"start_year" -- The year of the first AOH observation.

"end_year" -- The year of the last AOH observation.

"slope" -- The model estimated slope value.

"intercept" -- The model estimated intercept value.

"aoh_type" -- A label indicating the temporal and spatial scale at which AOH is calculated: "crop_abn_iucn" (Calc. 1a), "crop_abn_potential_iucn" (Calc. 1b), "max_abn_iucn" (Calc. 2a), "max_potential_abn_iucn" (Calc. 2b), "full_iucn" (Calc. 3a), and "full_potential_iucn" (Calc. 3b). "abn_iucn" and "potential_abn_iucn" correspond to calculations that only capture habitat following abandonment (i.e., not including habitat provided by croplands prior to abandonment); these calculations are not included in our final analysis.

"passage_type" -- Whether a model run includes passage areas ("include_passage") or does not include passage areas ("exclude_passage") when calculating area of habitat (AOH) for migratory birds.

"binomial" -- Species binomial scientific name.

"mature_forest_obl" -- Whether a species is determined to be a "mature forest obligate" species (1) or not (0), drawn directly from "habitat_age_req_coded.csv" (see above). Some species are marked as 0.9, 0.75, 0.25, or 0.1 as an indication of some uncertainty, but these were rounded to the nearest integer for the final analysis.

"total_site_area_ha_2017" -- The total site area (ha) in 2017. (Drawn directly from "area_summary_df," from https://zenodo.org/records/5348287)

"area_ever_abn_ha" -- The total area of those pixels that were abandoned at least once during the time series (corresponding to the area of potential abandonment, as of 2017). (Drawn directly from "area_summary_df," from https://zenodo.org/records/5348287)

"trend" -- The trend in AOH experienced by the species at this site for this aoh_type calculation ("gain," "loss," or "no trend"), determined by the sign of slope coefficients and assigning statistical significance when p < 0.05.

"n_trends" -- The number of distinct trends in AOH experienced by the species across all of the sites overlapping with its range, including this site.

"trend_types" -- The types of trends in AOH experienced by this species across all sites overlapping with its range (some combination of "gain", "loss", and/or "no trend").

"overall_trend" -- The overall trend in AOH experienced by this species across all sites overlapping with its range ("gain" - experiencing "gain" trends at all occurring sites; "loss" - experiencing "loss" trends at all occurring sites; "no trend" - experiencing "no trend" at all occurring sites; "weak gain" - experiencing "gain" trends at some sites and "no trend" at others; "weak loss" - experiencing "loss" trends at some sites and "no trend" at others; or "context dependent" - experienced "gain" trends at some sites and "loss" trends at other sites [referred to as "mixed" effects in Crawford et al. 2024])

"trend_direction" -- The general direction of the trend in AOH for the species across all occurring sites ("gain" when overall_trend is either "gain" or "weak_gain"; "loss" when overall_trend is either "loss" or "weak_loss"; "context dependent" when overall_trend is "context dependent" [i.e., "mixed" effects]; and "no trend" when overall_trend is "no trend").

"trend_consistency" -- An indication of how consistent the trend in AOH is across all occurring sites ("consistent" if overall_trend is "gain" or "loss"; "weak" if "weak_gain" or "weak_loss"; and "opposite" if "context dependent" [i.e., "mixed" effects]).

"time_range" -- The number of years for which the species has AOH observations at this site for this aoh_type calculations.

"aoh_start_est" -- The estimated AOH at the start of the time series, calculated from linear regression slope and intercept coefficients.

"aoh_end_est" -- The estimated AOH at the end of the time series, calculated from linear regression slope and intercept coefficients.

"abs_change" -- The absolute change in estimated AOH over the course of the time series (i.e., aoh_end_est - aoh_start_est).

"abs_change_as_prop_site_area" -- The absolute change in estimated AOH as a proportion of site area (i.e., abs_change / total_site_area_ha_2017).

"ratio_change" -- The ratio of the estimated AOH at the end of the time series to the estimated AOH at the start of the time series (i.e., aoh_end_est / aoh_start_est).

"prop_change" -- The proportional change in estimated AOH, calculated as the absolute change in estimated AOH divided by the estimated AOH value at the start of the time series (i.e., abs_change / aoh_start_est).

"factor_change" -- The factor change in estimated AOH, calculated as either the proportional change in estimated AOH (i.e., prop_change) for values greater than 0, or as the reciprocal of the proportional change in estimated AOH (i.e., 1/prop_change) for values greater than 0.

"percent_change" -- The percent change in estimated AOH, calculated as 100 times the proportional change in estimated AOH (i.e., 100 * prop_change).


taxonomy_df.parquet

This tabular data file contains basic taxonomic information used in the analysis, including 10 columns:



"vert_class" -- Vertebrate class ("bird," birds; or "mam," mammals).

"binomial" -- Species binomial scientific name, drawn from IUCN or BirdLife International.

"redlistCategory" -- IUCN Red List Category: "Extinct," "Extinct in the Wild," "Critically Endangered," "Endangered," "Vulnerable," "Near Threatened," "Least Concern," "Data Deficient," or "Not Evaluated."

"order" -- Taxonomic order.

"family" -- Taxonomic family.

"n_sp_in_family_sample" -- The number of species contained in the family included in our analysis.

"order_common" -- A common name to refer to the order.

"family_common" -- A common name to refer to the family.

"n_in_family" -- The total number of species contained in the family globally.

"threatened" -- Whether a species is considered threatened with extinction (i.e., is listed as "Critically Endangered," "Endangered," or "Vulnerable" on the IUCN Red List).


aoh_obs_change_tmp_all.csvaoh_est_change_tmp_all.csv

These two tabular data files contain data used as inputs for the linear models involved in our traits analysis exploring how species' responses to cropland abandonment are affected by habitat suitabilities and other traits. The key variables are the response variables for our models ("binary_gain_v_loss", "abs_change_percent_site", and "log(ratio)") and predictor variables c("forest_occ", "savanna_occ", "shrubland_occ", "grassland_occ", "wetlands_occ", "rocky_occ", "caves_occ", "desert_occ", "urban_occ", "arable_occ", "n_suitable_habitats_lvl2", "vert_class", "threatened", "Trophic_level", "log10(Body_mass_g)", "log10(total_range_area)", "abs(centroid_latitude)", and "max_abn_ext_percent_site"). Further details are contained in "traits.Rmd"

These two files are developed from "aoh_start_end_l" and "aoh_change_df," but filtered to include only birds and mammals, to exclude passage areas from AOH calculations, to exclude mature forest obligate species, and to use only a window_size of 5 years (for "aoh_obs_change_tmp_all") and model estimates (rather than 95% confidence interval bounds, for "aoh_est_change_tmp_all"). 

aoh_obs_change_tmp_all.csv contains 63 columns.



Columns 1-24 match "aoh_start_end_l". 

Columns 25-31 match "taxonomy_df" columns 3 through 10.

Columns 32-34: "Body_mass_g" (species body mass, in grams), "Trophic_level" (whether a species is a "Carnivore", a "Herbivore," or an "Omnivore"), and "Habitat_breadth_IUCN" (the number of IUCN Level 2 habitats a species can occupy) were taken from from Etard et al. 2020 (https://doi.org/10.1111/geb.13184)

Column 35: "total_range_area" -- drawn from "aoh_l," see above

Columns 36-37: "centroid_longitude" and "centroid_latitude" are drawn from "centroids_df," see above.

Columns 38-50 are Boolean variables that indicate whether a species can occupy a specific IUCN Level 1 habitat type (i.e., whether IUCN lists that Level 1 habitat as suitable for the species). These variables are as follows, with the IUCN Level 1 habitat code listed in brackets: "forest_occ" [1], "savanna_occ" [2], "shrubland_occ" [3], "grassland_occ" [4], "wetlands_occ" [5], "rocky_occ" [6], "caves_occ" [7], "desert_occ" [8], "marine_intertidal_occ"[12], "marine_coastal_occ" [13], "artificial_terrestrial_occ" [14], "artificial_aquatic_occ" [15], and "introduced_occ" [16].

Columns 51-52 represent the number of IUCN Level 1 ("n_suitable_habitats") and IUCN Level 2 ("n_suitable_habitats_lvl2") habitats a species has listed as suitable habitats by IUCN, respectively.

Columns 53-56 are Boolean variables indicating whether a species can occupy a subset of IUCN Level 2 habitats, which are listed in brackets: "arable_occ" [14.1 Arable Land]; "farmland_occ" [14.1 Arable Land, 14.2 Pastureland, or 14.4 Rural Gardens]; "ag_occ" (duplicate of "farmland_occ"); "urban_occ" [14.5 Urban Areas].

Columns 57-58 represent the maximum spatial extent of abandonment at a give site (i.e., the area of all lands that were abandoned at least once during the time series), whether divided by site area ("max_abn_extent_div_site_area," i.e,. area_ever_abn_ha / total_site_area_ha_2017) or as a percent of site area ("max_abn_ext_percent_site").

Column 59 is "abs_change_percent_site," calculated as 100 * abs_change_as_prop_site_area.

Columns 60-63 are binary values (1 or 0) indicating the whether the species experienced statistically significant gains in AOH ("binary_trend_gain"), statistically significant losses in AOH ("binary_trend_loss"), no trend in AOH ("binary_trend_no_trend"). Column 63 ("binary_gain_v_loss") is a binary value assigning a value of 1 for gains, 0 for losses, and NA for other values.


aoh_est_change_tmp_all.csv contains 70 columns:



Columns 1-29 match "aoh_change_df".

Columns 30-37 match "taxonomy_df" columns 3 through 10.

Columns 38-40: "Body_mass_g" (species body mass, in grams), "Trophic_level" (whether a species is a "Carnivore", a "Herbivore," or an "Omnivore"), and "Habitat_breadth_IUCN" (the number of IUCN Level 2 habitats a species can occupy) were taken from from Etard et al. 2020 (https://doi.org/10.1111/geb.13184)

Column 41: "total_range_area" -- drawn from "aoh_l," see above

Columns 42-43: "centroid_longitude" and "centroid_latitude" are drawn from "centroids_df," see above.

Columns 44-56 are Boolean variables that indicate whether a species can occupy a specific IUCN Level 1 habitat type (i.e., whether IUCN lists that Level 1 habitat as suitable for the species). These variables are as follows, with the IUCN Level 1 habitat code listed in brackets: "forest_occ" [1], "savanna_occ" [2], "shrubland_occ" [3], "grassland_occ" [4], "wetlands_occ" [5], "rocky_occ" [6], "caves_occ" [7], "desert_occ" [8], "marine_intertidal_occ"[12], "marine_coastal_occ" [13], "artificial_terrestrial_occ" [14], "artificial_aquatic_occ" [15], and "introduced_occ" [16].

Columns 57-58 represent the number of IUCN Level 1 ("n_suitable_habitats") and IUCN Level 2 ("n_suitable_habitats_lvl2") habitats a species has listed as suitable habitats by IUCN, respectively.

Columns 59-62 are Boolean variables indicating whether a species can occupy a subset of IUCN Level 2 habitats, which are listed in brackets: "arable_occ" [14.1 Arable Land]; "farmland_occ" [14.1 Arable Land, 14.2 Pastureland, or 14.4 Rural Gardens]; "ag_occ" (duplicate of "farmland_occ"); "urban_occ" [14.5 Urban Areas].

Columns 63-64 represent the maximum spatial extent of abandonment at a give site (i.e., the area of all lands that were abandoned at least once during the time series), whether divided by site area ("max_abn_extent_div_site_area," i.e,. area_ever_abn_ha / total_site_area_ha_2017) or as a percent of site area ("max_abn_ext_percent_site").

Columns 65-68 are binary values (1 or 0) indicating the whether the species experienced statistically significant gains in AOH ("binary_trend_gain"), statistically significant losses in AOH ("binary_trend_loss"), no trend in AOH ("binary_trend_no_trend"). Column 63 ("binary_gain_v_loss") is a binary value assigning a value of 1 for gains, 0 for losses, and NA for other values.

Column 69, "slope_prop_site", is the estimated linear regression coefficient, or slope, as a proportion of site area, calculated as slope / total_site_area_ha_2017. 

Column 70 is "abs_change_percent_site," calculated as 100 * abs_change_as_prop_site_area.


final_species_list.csv

The final list of bird and mammal species included in our analysis, including the vertebrate class ("vert_class") and binomial species scientific name ("binomial") along with the overall response to cropland abandonment ("overall_trend"), the sites where that species had AOH affected by cropland abandonment ("sites"), the IUCN Red List Category ("redlistCategory"), the "obligate_type" (i.e., whether a species is a mature forest obligate, or not), the "range_size_quantile" (ranking species by global geographic range size), and "common_names". Note that mature forest obligates were excluded from our final results. These columns match the definitions included above.

trait_mod_df_modx1.rds

This R data file contains the results of our regression models run in "traits.Rmd" code chunk "*many-models", which is where our three traits linear regression models are run. These data are contained in the form of a nested tibble, or a set of tibbles nested within columns of a tibble (see: https://tidyr.tidyverse.org/articles/nest.html). These data include the input data ("data"), resulting models ("model"), model coefficients ("tidy"), regression tables ("gt"), and diagnostic statistics ("glance") for our many model runs across different response variables ("response") and AOH calculations ("aoh_type"). See  "traits.Rmd" code chunk "*many-models" for more information.