Status and Trends of Caribbean Coral Reefs: 1970-2024

1. Introduction

2. Code

Functions

• data_descriptors.R Get number of sites, surveys, datasets, first and last year of monitoring.
• graphical_par.R Graphical parameters, including colors and fonts.
• plot_region.R Regional background map.
• theme_graph.R Main ggplot theme for the plots of the reports.
• theme_map.R Main ggplot theme for the maps of the reports.

Cleaning and selection (a_)

• a01_select_benthic-data.R
• a03_clean_shp.R
• a07_reef-buffer.js
• a08_clean_cyclones.R
• a09_extract_dhw-year.R

Extract indicators (b_)

• b05_extract_indicator_cyclones

Models (benthic cover) (c_)

Models (fish biomass) (d_)

Figures and tables (e_)

• e02_region_map.R
• e03_territories_map.R
• e06_region_cyclones.R
• e07_territories_cyclones.R
• e11_other-indicators.R

3. Reproducibility parameters

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 10 x64 (build 18363)
 system   x86_64, mingw32
 ui       RTerm
 language (EN)
 collate  French_France.utf8
 ctype    French_France.utf8
 tz       Europe/Paris
 date     2024-07-18
 pandoc   3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version    date (UTC) lib source
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 [1] C:/Users/jwicquart/AppData/Local/Programs/R/R-4.4.1/library

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