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Status and Trends of Coral Reefs of the Pacific: 1980-2023

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Status and Trends of Coral Reefs of the Pacific

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.
  • 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_)

  • a1_select_benthic-data.R Select gcrmndb_benthos data to use in the analyses.
  • a2_benthic_data_sources.R Extract data sources from gcrmndb_benthos.
  • a3_clean_eez.R Select and clean economic exclusive zones (EEZ) from marineregions.
  • a4_clean_land.R Clean Pacific land data (high spatial resolution) from Princeton University.
  • a5_clean_bathy.R Clean bathymetry data from Natural Earth Data.
  • a6_clean-reef-distribution.R Select Pacific coral reefs distribution from the Tropical Coral Reefs of the World World Resources Institute (WRI).
  • a7_reef-buffer.js Create 100 km reef buffer using Google Earth Engine (GEE).
  • a8_clean_cyclones.R Clean cyclone dataset from IBTrACS.
  • a9_extract_dhw-year.R Create TIFF files of maximum DHW per year using Coral Reef Watch data.

Extract indicators (except benthic cover) (b_)

  • b1_extract_indicator_land.js Extract total land area for each EEZ using GEE.
  • b2_extract_indicator_elevation.js Extract mean land elevation for each EEZ using GEE.
  • b3_extract_indicator_population.js Extract human population for each EEZ using GEE.
  • b4_extract_indicator_sst.R Extract SST on coral reefs for each EEZ.
  • b5_extract_indicator_cyclones.R Extract cyclones on coral reefs for each EEZ.

Models (benthic cover) (c_)

  • c1_select_pred-sites.js
  • c2_extract_predictor_gee.js
  • c3_extract_predictor_gravity.R
  • c4_extract_predictor_enso.R
  • c5_extract_predictor_cyclones.R
  • c6_extract_predictor_dhw-year.R
  • c7_model_data-preparation.R
  • c8_model_data-exploration.R
  • c9_model_tuning.R
  • c10_model_bootstrap.R

Figures and tables (d_)

  • d1_materials-and-methods.R
  • d2_pacific_map.R
  • d3_territories_map.R
  • d4_pacific_sst.R
  • d5_territories_sst.R
  • d6_pacific_cyclones.R
  • d7_territories_cyclones.R
  • d8_pacific_spatio-temporal.R
  • d9_territories_spatio-temporal.R
  • d10_benthic-cover_trends.R
  • d11_other-indicators.R
  • d12_case-studies.R

3. Reproducibility parameters

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24 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     2024-07-04
 pandoc   3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version    date (UTC) lib source
 askpass         1.2.0      2023-09-03 [1] CRAN (R 4.4.0)
 backports       1.5.0      2024-05-23 [1] CRAN (R 4.4.0)
 base64enc       0.1-3      2015-07-28 [1] CRAN (R 4.4.0)
 bit             4.0.5      2022-11-15 [1] CRAN (R 4.4.0)
 bit64           4.0.5      2020-08-30 [1] CRAN (R 4.4.0)
 blob            1.2.4      2023-03-17 [1] CRAN (R 4.4.0)
 broom           1.0.6      2024-05-17 [1] CRAN (R 4.4.0)
 bslib           0.7.0      2024-03-29 [1] CRAN (R 4.4.0)
 cachem          1.1.0      2024-05-16 [1] CRAN (R 4.4.0)
 callr           3.7.6      2024-03-25 [1] CRAN (R 4.4.0)
 cellranger      1.1.0      2016-07-27 [1] CRAN (R 4.4.0)
 class           7.3-22     2023-05-03 [1] CRAN (R 4.4.0)
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 cli             3.6.2      2023-12-11 [1] CRAN (R 4.4.0)
 clipr           0.8.0      2022-02-22 [1] CRAN (R 4.4.0)
 clock           0.7.0      2023-05-15 [1] CRAN (R 4.4.0)
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 conflicted      1.2.0      2023-02-01 [1] CRAN (R 4.4.0)
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 curl            5.2.1      2024-03-01 [1] CRAN (R 4.4.0)
 data.table      1.15.4     2024-03-30 [1] CRAN (R 4.4.0)
 DBI             1.2.3      2024-06-02 [1] CRAN (R 4.4.0)
 dbplyr          2.5.0      2024-03-19 [1] CRAN (R 4.4.0)
 diagram         1.6.5      2020-09-30 [1] CRAN (R 4.4.0)
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 ellipsis        0.3.2      2021-04-29 [1] CRAN (R 4.4.0)
 evaluate        0.23       2023-11-01 [1] CRAN (R 4.4.0)
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Status and Trends of Coral Reefs of the Pacific: 1980-2023

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