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ncba_stressor

Code for generating the the National Climate-Biodiversity Assessment multi-stressor map

Obejctive

Our chapter aims to assess the interaction between climate and other non-climatic stressors on biodiversity.

Instructions

Use data from O'Hara et al. (2021) to map out multi-stressors in the EEZs of USA, Canada and Mexico. Perhaps make a figure with panels with some combination of Fig 1 and Fig 2

• Code and data are available from the Knowledge Network for Biocomplexity - KNB

Also use Halpern's Cummulative Human Impact paper: https://www.nature.com/articles/s41598-019-47201-9 to create a USA-Mexico-Canada version of Figure 1.

• Available code on GitHub

Also use data from Pereira H., et al (2024). Global trends and scenarios for terrestrial biodiversity and ecosystem services from 1900 to 2050. All of the data in the paper is available publicly (see SM of paper for details). The code to produce each figure and the original model outputs are available.

• Check the zenodo repo for code. And the EBV datasets.

Time line

• Map draft for July 30

Data

Data and code: At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts

This work is dedicated to the public domain under the Creative Commons Universal 1.0 Public Domain Dedication. To view a copy of this dedication, visit https://creativecommons.org/publicdomain/zero/1.0/.

• bd_chi_master.zip, Zip file containing all code and generated data from Github repository: https://github.com/oharac/bd_chi. The README.md in the root directory describes the file structure and order of operations to replicate the results.

Data and code: Rate of change of Cumulative Human Impacts to the ocean

• All stressor, ecosystem, impact and cumulative impact data are available at knb and all code are at GitHub.

• (GitHub data)[https://github.com/OHI-Science/impact_acceleration/tree/master/paper]

  • eez_chi.csv, Comulative Human impact per EEZ
  • Fu=igures, rasters to make figure 1

Terrestrial biodiversity

Code for analysis is here Zenodo doce and the raw data in the following repos

• Alkemade, R., & Pereira, H. (2023). Global trends in ecosystem services (BES-SIM GLOBIO-ES) (Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/VQD4S4
• Baisero, D., Rondinini, C., & Pereira, H. (2023). Global trends in biodiversity (BES-SIM INSIGHTS) (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/H2EVR2
• Chaplin-Kramer, R., Sharp, R., & Pereira, H. (2023). Global trends in ecosystem services (BES-SIM InVEST) (Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/ZR4D27
• Haverd, V., & Pereira, H. (2023). Global trends in ecosystem services (BES-SIM CABLE POP) (Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/KTNB68
• Hill, S., Purvis, A., & Pereira, H. (2022). Global trends in biodiversity (BES-SIM PREDICTS) (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/VT7QK9
• Leclere, D., Obersteiner, M., & Pereira, H. (2022). Global trends in biodiversity (BES-SIM cSAR-IIASA) (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/HAQ7D4
• Martins, I., & Pereira, H. (2022). Global trends in biodiversity (BES-SIM cSAR-iDiv) (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/5ZMY41
• Ohashi, H., Hasegawa, T., & Pereira, H. (2023). Global trends in biodiversity (BES-SIM AIM) (Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/5WN357
• Poulter, B., Quesada, B., & Pereira, H. (2023). Global trends in ecosystem services (BES-SIM LPJ) (Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/XQ7A86
• Quesada, B., Anthoni, P., Arneth, A., & Pereira, H. (2023). Global trends in ecosystem services (BES-SIM LPJ-GUESS)(Version 2) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/Z5V9T2
• Schipper, A., Alkemade, R., & Pereira, H. (2023). Global trends in biodiversity (BES-SIM GLOBIO) (Version 1) [Dataset]. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. https://doi.org/10.25829/R7BT92

References

Casey C. O'Hara et al. ,At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts.Science372,84-87(2021).DOI:10.1126/science.abe6731

Note: This repository was cloned from oharac GitHub. The original ReadMe is below for reference

Files used / modified

• ms_figs/fig2_impact_intens_map_3panel.Rmd, this became ncba_fig2

At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts

Repository for code and generated data for "At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts" by Casey C. O'Hara, Melanie Frazier, Benjamin S. Halpern.

External data are freely available from:

• Species range maps: IUCN Red List of Threatened Species spatial data download
• Bird species range maps: BirdLife International Data Zone
• Species information: IUCN Red List API
• Stressor distributions: Recent pace of change in human impact on the world's ocean: Cumulative impacts. Knowledge Network for Biocomplexity

To replicate the analysis, download necessary data and set up an external directory for these datasets and large files generated during the analysis process.

Run all scripts in the _setup directory in numeric order. It will be necessary to point the scripts to the proper locations in your data directory. The common_fxns.R script may be helpful for setting filename objects to various data locations.

Run all scripts in the root project directory, in numeric order.

Finally, if you wish to generate the figures, run the appropriate scripts in the ms_figs directory.

Overview of file structure:

• _setup: scripts for pre-processing of data on threats, species range distributions, and stressor distributions.
• _raw: lookup tables created by the project team to facilitate the analysis.
• _data: data drawn from the IUCN API; note that the setup scripts also place larger IUCN files on the external data directory.
• _spatial: spatial data and maps generated in the setup scripts. Again, note that the setup scripts place larger spatial files on the external data directory.
• _output: all finalized datasets are stored here, including rasters of impacts, intensification, stressor footprints, and taxonomic species richness maps.
• figs: temporary figure storage
• ms_figs: code to generate figures for manuscript
• ms_tables: code to generate tables for manuscript