Pathogens & Planetary Change

This code is used to generate the figures for the review on biodiversity, climate & planetary change, and infectious disease, citation to come.

Note for reviewers: Please note that the revision will contain an updated version of figures with analyses rerun following taxonomic harmonization between the CLOVER/VIRION databases and the IUCN Red List.

For Users

We do not provide a __main.R file for you to run all of the analysis at once, but rather, each piece (denoted by the subfolders of the /src folder) are self-contained so you are able to reproduce each figure individually without having to run the (potentially) longer subsets of code that other figures might require. To reproduce a single figure please use the code in the associated /src sub-folder.

The code herein uses IUCN data, which takes the form of a large shapefile. Due to its size it can't be stored on GitHub, so it's currently stored on Google Drive. There's a file src/iucn-download.R that you should run to download that data.

All other data are provided, and the sources are noted in the subfolder README.md files.

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Please feel free to use and borrow from this code base according to the licence below!

Shield:

This work is licensed under a Creative Commons Attribution 4.0 International License.

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Accompanying information

This document contains a brief run-down of all the analysis-related figures in the main text of the pathogens & planetary change manuscript referenced in the root README. The code to generate each of the figures can be found in their respectively named subfolders in the src folder.

Figure 1

Figure 1 is the figure involving the most data generated in other publications. For details on how it was created, see ./data/recreation/README.md or Text S2 in the main text of the manuscript.

Figure 4

Figure 4 is based on data from GBIF exclusively. The download of those data are down directly in the assocatiated script. Note however that accessing GBIF to download the data anew is not just click & run, as it's specific to each GBIF user's profile, and a user would need to configure their R environment to handle the GBIF record pulling if you wanted a fresh version from online. We accessed our version for this paper on 07 July 2024.

Figure from Box 2

Box two discusses data opportunities and data gaps. The figure makes use of IUCN data and data from the Virion dataset, the IUCN data is mentioned above, and here we use a flat file version of Virion for consistency. Updated versions of Virion can be found here.

Packages used

We rely on a number of packages to do this analysis. Here are their citations:

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