https://doi.org/10.5061/dryad.kkwh70s89

The data provided here is to support the GEB study: "Geography, taxonomy, extinction risk, and exposure of fully migratory birds to droughts and cyclones"
Submitted to GEB April 2023

We provide information to allow readers to replicate our results and explore outputs in more depth.

Supporting Information:
These are additional outputs and data from our analysis. SI 2, 4, 5, 6 & 7 are required in order to replicate our results.

Additional Data Sources:
Several data sources cannot be attached as they are not the property of the authors. In order to fully replicate our methodology and results, you will need to see the notes, the methods section of the manuscript, and download the data from the sources provided

This repository contains the following folders and files:

Description of the data and file structure

CODE

This folder contains the following files and sub folders:

"CreateMainFigures.R"
Uses main input files and creates figures for main manuscript of exposure to cyclones and droughts

"ProduceSummaryStats.R"
Uses main drought and cyclone input files to generate summary statistics on exposure.

"ScriptFunctions.R"
Additional script functions used by other code files. Does not need to be opened or modified

"SupplementaryMaps.R"
Uses main input files and creates figures and tables for supplementary information of exposure to cyclones and droughts

INPUT DATA

This folder contains the following files and sub folders:
"specieslist_final.csv"
The full list of all species used in the final analyses

Cyclones

"AllSpecies_areascore_breeding.csv"
Area of exposure scores to cyclones for all species during the breeding season.
Scores are a proportion, ranging from 0 to 100%

"AllSpecies_areascore_wintering.csv"
Area of exposure scores to cyclones for all species during the wintering season.
Scores are a proportion, ranging from 0 to 100%

"AllSpecies_cumulscore.csv"
Cumulative exposure scores to cyclones for all species (for both seasons)
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. Plan.Exp.Score column is the cumulative exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. For a full description on how this metric is calculated please see the main manuscript.

"number_cyclones_raster.tif"
Output raster, showing all cyclones globally for the study period. Grid cell value is the number of cyclones that have impacted a given grid cell during the study period

"Upper25cumul_breeding.csv"
Top 25 percentile species, those most cumulatively exposed to cyclones during the breeding season.
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. Plan.Exp.Score column is the cumulative exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. For a full description on how this metric is calculated please see the main manuscript.

"Upper25cumul_wintering.csv"
Top 25 percentile species, those most cumulatively exposed to cyclones during the wintering season.
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. Plan.Exp.Score column is the cumulative exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. For a full description on how this metric is calculated please see the main manuscript.

Droughts

"AllSpecies_areascore.csv"
Area of exposure scores to drought for all species (for both seasons)
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. presence_months columns refers to the months defined as the breeding or wintering season for that bird (dependent on the seasonal column), where 04 = April etc. Scores are a proportion, ranging from 0 to 100%.

"AllSpecies_cumulscore.csv"
Cumulative exposure scores to drought for all species (for both seasons)
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. GenLength indicates the generation length of each species, as defined in the manuscript. En columns is the raw exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. e_score column is the scaled exposure, where En is scaled by generation length to produce overall exposure score.

"GPCCBinary_SEVERE_sum2.tif"
Output summary raster, showing all droughts included is study, mapped globally. Grid cell value is the number of severe droughts that have impacted a given grid cell during the study period. See methods for more details on how drought was defined and measured.

"Upper25cumul_breeding.csv"
Top 25 percentile species, those most cumulatively exposed to drought during the wintering season.
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. GenLength indicates the generation length of each species, as defined in the manuscript. En columns is the raw exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. e_score column is the scaled exposure, where En is scaled by generation length to produce overall exposure score.

"Upper25cumul_wintering.csv"
Top 25 percentile species, those most cumulatively exposed to drought during the wintering season
Seasonal column refers to the BirdLife seasonal short-hand, "2" indicates the breeding season, "3" the wintering. GenLength indicates the generation length of each species, as defined in the manuscript. En columns is the raw exposure score, which ranges from 0 to infinity, where higher indicates higher exposure. e_score column is the scaled exposure, where En is scaled by generation length to produce overall exposure score.

Downloaded Data

Some data cannot be included in this repository as they are not the property of the authors.
The following files are not included as they are not the work of the authors and must be downloaded seperately:

Coastline shapefiles

To make publication figures, we use a set of background coastlines to make outlines clearer. These can be downloaded from:
https://www.naturalearthdata.com/downloads/
We used 50m resolution, v4.1.0

Species range polygons

There are BirdLife range polygons and should be directly from:
This file can be filtered using the species list
http://datazone.birdlife.org/species/requestdis
Our species list can be found in "specieslist_final.csv"

IUCN red list categories
This contains the redlist information for each species. It is used in the code to classify and analyse exposure scores. They should be stored in a file named:
"RedListCats_20+23.csv"
We provide an empty file with column headers (and descriptions) as a template. All information should be taken from the IUCN website: https://www.iucnredlist.org/
The redlist was initially checked in 2020, and then re-checked in 2023, hence why there are multiple ratings for each species in this file.

Species listed as affected by cyclones, according to IUCN data
This is a list of species where cyclones are listed as key threats by the IUCN, extracted in 2023. They should be stored in a file named:
"SpAffectedByCyclones_2023.csv"
We provide an empty file with column headers (and descriptions) as a template. All information should be taken from the IUCN website: https://www.iucnredlist.org/

Species listed as affected by drought, according to IUCN data
This is a list of species where droughts are listed as key threats by the IUCN, extracted in 2023. They should be stored in a file named:
"SpAffectedByDrought_2023.csv"
We provide an empty file with column headers (and descriptions) as a template. All information should be taken from the IUCN website: https://www.iucnredlist.org/

Outputs

This saves tables and figures from the code scripts. Our results are included here (with the exception of the "CreateMainFigures" folder, as these are included in the main manuscript), but can be regenerated by running the scripts in the "code" folder. The folder name corresponds to the R script used to generate the outputs

CreateMainFigures
All outputs from CreateMainFigures.R are stored here. This has been left empty, as figures are provided in the main manuscript, but can be recreated by running the relevant code

ProduceSummaryStats
All outputs from ProduceSummaryStats.R are stored here.

"AreaScores.csv"
This provides all the main statistics for area of exposure scores, across all seasons and events. Event column details the extreme climate event, whether that is cyclone, drought, both, or either (designated as "any"). Season column refers to when exposure occurs, in either the breeding, wintering, both or either season. Additional classifications are also included here, which are provided as full text, "Any Exposure" refers to species that experienced any amount of exposure to an event, all others are set on our threshold of "high exposure" (see manuscript for definitions of thresholds). Number column refers to the number of species that fall within a given category (e.g. 33 species have a high area of exposure in the breeding season to cyclones). Total column refers to the total number of species in our database. Perc refers to the percentage of all species in a given category (number/total)

"CumulScores.csv"
This provides all the main statistics for cumulative exposure scores, across all seasons and events. Column definitions are the same as for "AreaScores.csv".

"IUCNcycloneComparison.csv"
This provides a summary of statistical comparisons between the IUCN red list and our analyses, regarding species at risk from cylones. Event column states which climate event is under consideration. Score column refers to whether statistic refers to cumulative exposure metric, area of exposure metric or neither. Descrip column contains a basic description of the comparions being undertaken. "Species shared (altogether)" refers to a basic comparison of how many species are present in both our species list and in the IUCN list of species vulnerable to cyclones. All others refer to the type of comparison, along the following format: "high IUCN + low cumul scores" indicates the comparions is between whether the species is flagged as high vulnerability to cyclones, but received a low cumulative exposure score in our analysis (i.e. under the threshold set). Number column indicates the number of species that fall within a given category, and total column the total number of species in our analysis

"IUCNdroughtComparison.csv"
This provides a summary of statistical comparisons between the IUCN red list and our analyses, regarding species at risk from drought. All column definitions are the same as for IUCNcycloneComparison, but for drought.

SupplementaryMaps
All outputs from SupplementaryMaps.R are stored here. This has been left empty, as figures and tables are provided in the main manuscript, but can be recreated by running the relevant code.

Code/Software

All code is for R. Analysis was carried out in R version 4.0.3