Coral reefs benthic monitoring: spatio-temporal distribution, methods and stakeholders

This repository contains code associated to the article:

Wicquart, J., Prasil-Delaval, N., Obura, D., Gudka, M., Logan, M., Souter, D., Staub, F., Towle, E.K., Burt, J.A., Padovani Ferreira, B., Kimura, T., Chan, S., Tun, K., Ibrahim, N., Amer, M., Reyes Bonilla, H., Smith, F., GCRMN Consortium, Planes, S. (2022). Coral reefs benthic monitoring: spatio-temporal distribution, methods and stakeholders. in prep.

1. Abstract

2. How to download this project?

On the project main page on GitHub, click on the green button Code and then click on Download ZIP

3. Context

[To be completed]

4. Description of the project

4.1 Project organization

📂 R
- 📂 functions Functions used in the two main scripts
  - graphical_par.R Graphical parameters
  - theme_graph.R Theme for graphs
  - theme_map.R Theme for maps (primary)
  - theme_map2.R Theme for maps (secondary)
- 01_reefs-ecoregion.R Filter ecoregions containing coral reefs
- 02_analysis.Rmd Main analysis script

4.2 Data description

Four datasets were used for the analyses:

Base map datasets downloaded on Natural Earth Data.
Marine Ecoregions of the World (MEOW) dataset from Spalding et al, 2007.
Distribution of coral reefs of the world from UNEP-WCMC.
Synthetic dataset used for the Status of Coral Reefs of the World: 2020 report.

5. How to report issues?

Please report any bugs or issues HERE.

6. Reproducibility parameters

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31 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     2023-12-19
 pandoc   3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version    date (UTC) lib source
 abind           1.4-5      2016-07-21 [1] CRAN (R 4.3.1)
 askpass         1.2.0      2023-09-03 [1] CRAN (R 4.3.2)
 backports       1.4.1      2021-12-13 [1] CRAN (R 4.3.1)
 base64enc       0.1-3      2015-07-28 [1] CRAN (R 4.3.1)
 bit             4.0.5      2022-11-15 [1] CRAN (R 4.3.2)
 bit64           4.0.5      2020-08-30 [1] CRAN (R 4.3.2)
 blob            1.2.4      2023-03-17 [1] CRAN (R 4.3.2)
 boot            1.3-28.1   2022-11-22 [1] CRAN (R 4.3.2)
 brio            1.1.4      2023-12-10 [1] CRAN (R 4.3.2)
 broom           1.0.5      2023-06-09 [1] CRAN (R 4.3.2)
 bslib           0.6.1      2023-11-28 [1] CRAN (R 4.3.2)
 cachem          1.0.8      2023-05-01 [1] CRAN (R 4.3.2)
 callr           3.7.3      2022-11-02 [1] CRAN (R 4.3.2)
 car             3.1-2      2023-03-30 [1] CRAN (R 4.3.2)
 carData         3.0-5      2022-01-06 [1] CRAN (R 4.3.2)
 cellranger      1.1.0      2016-07-27 [1] CRAN (R 4.3.2)
 class           7.3-22     2023-05-03 [1] CRAN (R 4.3.2)
 classInt        0.4-10     2023-09-05 [1] CRAN (R 4.3.2)
 cli             3.6.2      2023-12-11 [1] CRAN (R 4.3.2)
 clipr           0.8.0      2022-02-22 [1] CRAN (R 4.3.2)
 cluster         2.1.4      2022-08-22 [1] CRAN (R 4.3.2)
 colorspace      2.1-0      2023-01-23 [1] CRAN (R 4.3.2)
 commonmark      1.9.0      2023-03-17 [1] CRAN (R 4.3.2)
 conflicted      1.2.0      2023-02-01 [1] CRAN (R 4.3.2)
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 DBI             1.1.3      2022-06-18 [1] CRAN (R 4.3.2)
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 ragg            1.2.7      2023-12-11 [1] CRAN (R 4.3.2)
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 [1] C:/Users/jwicquart/AppData/Local/Programs/R/R-4.3.2/library

──────────────────────────────────────────────────────────────────────────────

Name		Name	Last commit message	Last commit date
Latest commit History 76 Commits
R		R
.gitignore		.gitignore
README.Rmd		README.Rmd
README.md		README.md
monitoring_reefs.Rproj		monitoring_reefs.Rproj

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Coral reefs benthic monitoring: spatio-temporal distribution, methods and stakeholders

1. Abstract

2. How to download this project?

3. Context

4. Description of the project

4.1 Project organization

4.2 Data description

5. How to report issues?

6. Reproducibility parameters

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Coral reefs benthic monitoring: spatio-temporal distribution, methods and stakeholders

1. Abstract

2. How to download this project?

3. Context

4. Description of the project

4.1 Project organization

4.2 Data description

5. How to report issues?

6. Reproducibility parameters

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