README.md

In WCS-Marine/local-reef-pressures: Analysis of local human pressures on tropical coral reefs

local-reef-pressures

A global mapping analysis of 6 local reef potential pressure layers

Results from this analysis are available as a scientific article: Andrello, M., Darling, E. S., Wenger, A., Suárez-Castro, A. F., Gelfand, S., & Ahmadia, G. N. (2022). A global map of human pressures on tropical coral reefs. Conservation Letters, Early view, e12858. https://doi.org/10.1111/conl.12858

1. List of the contents of this repository

BCU Report cards/

Contains the individual report cards (pdf), one for each of the 83 refugia (aka Bioclimatic Units: BCUs).

data-raw/

Contains the original data layers.

data-raw/Read_layers.R Code to

• read the original data layers, perform the spatial processing and save the results in the data/allreefs layer.
• draw Figure S13 (Sensitivity of coastal population to buffer size)

You do not need to run this script if you are only interested in the final results or if you want to extract values for new sites.

data/

Contains the final GIS layers of the 6 local reef pressures and the global climatic scores of Beyer et al. (2018), in three different formats:

• ESRI Shapefile (.shp, to open with ArcGIS)
• .GPKG (to open with QGis)
• .sql (in .zip, to open with a PostGIS database)
• .RData (with R)

In R, type data(allreefs) to load the dataset.

key.xlsx contains correspondence between field names of the RData and GPKG files, on one hand, the the ESRI file, on the other hand

data/report-cards/:

Contains data to produce the individual report cards, one for each of the 83 refugia.

R/

Contains some scripts to generate the report cards and extract the data from the data layers giving point coordinates. In particular:

• extract_values.R. Function to extract pressure values for a set of coordinates provided by the user. This is useful if you want to know the values of the six pressures for new sites. To see the documentation for this function, please load the code with devtools::load_all() and then look at the help file via ?extract_values.

analysis/

Contains all the scripts needed to reproduce the results and the figures of the article.

Analysis.R. Code to:

• perform all the analyses of the article
• draw Figure 3 (Individual pressures: regional comparisons)
• draw Figure 4 (Density distribution of pressure percentiles and frequency of occurrence of top pressures in refugia vs non-refugia)
• draw Figure S1 (Density distribution of pressure raw values)
• draw Figure S9 (Comparison of frequency of occurrence of top pressures between regions)
• draw Figure S10 (Pressure intensity when top-ranked)
• draw Figure S14 (Correlation among pressures)

Analysis BCU medians.R. Code to:

• calculate top pressure for each refugium
• draw Figure S11 (Median pressure for each refugium)
• draw Figure S12 (Regional comparisons of median pressure of refugia)

Post-treatment.R. Code to:

• change top threat from number conding (e.g. "1") to string coding ("Fishing")

Plot Maps.R. Code to

• draw Figure 1 (map of top pressures)
• draw Figure 2 (map of cumulative impact score)
• Figure S2 to S7 (individual pressure maps)

Sednut.R. Code to

• draw Figure 15 (areas of high sediments and low nutrients, and vice-versa)

analysis/report-cards/ contains the code to produce the report cards, which are saved in BCU Report cards/.

2. How to use the content of this repository

2.1 Creating the final GIS layers from the original layers

Run data-raw/read_layers.R to create the final GIS layers in data/ from the six original layers stored in data-raw/. Beware that treatment of the raster layers (coastal population and tourism) takes a long time to run.

2.2 Reproducing the Figures and the results appearing in the paper

Figure | Script --- | --- Figure 1 | analysis/Plot Maps.R (first part) Figure 2 | analysis/Plot Maps.R (second part) Figure 3 | analysis/Analysis.R Figure 4 | analysis/Analysis.R Supplementary Figure 1 | analysis/Analysis.R Supplementary Figure 2 to 7 | analysis/Plot Maps.R (second part) Supplementary Figure 9 | analysis/Analysis.R Supplementary Figure 10 | analysis/Analysis.R Supplementary Figure 11 | analysis/Analysis BCU medians.R Supplementary Figure 12 | analysis/Analysis BCU medians.R Supplementary Figure 13 | data-raw/Read_layers.R Supplementary Figure 14 | analysis/Analysis.R Supplementary Figure 15 | analysis/Sednut.R

Please note that Supplementary Figure 8 was made with QGis and annotated in Power Point, there is no R code to produce it

2.3 Getting the list of climatic refugia with their top and second-top pressure

Run analysis/Analysis BCU medians.R.

2.4 Extracting pressure values for a given set of sites

Use the function extract_values.R on a list of points with longitude and latitude. To see the documentation for this function, please load the code with devtools::load_all() and then look at the help file via ?extract_values.

WCS-Marine/local-reef-pressures documentation built on Feb. 13, 2022, 9:26 a.m.