Status of coral reef monitoring: An assessment of methods and data at the national level

This repository contains code used for the production of the report:

Prasil Delaval, N., Wicquart, J., Staub, F., Planes, S. (eds.). Status of coral reef monitoring: an assessment of methods and data at the national level. Global Coral Reef Monitoring Network (GCRMN)/International Coral Reefs Initiative (ICRI), 2021.

1. How to download this project?

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

2. Description of the project

2.1 Datasets description

The figures and tables presented in this report were made using the seven following datasets:

• Background maps. The background maps data of land, minor islands and atolls as 1:10 m shapefiles (v. 4.1.0) were obtained from Natural Earth Data (Natural Earth Data, 2018).

• Economic Exclusive Zone (EEZ). The EEZ shapefile (v.11) was obtained from the Flanders Marine Institute, 2019.

• Coral reefs distribution. The distribution of coral reefs of the world shapefile was obtained from the WRI (Institute for Marine Remote Sensing - University of South Florida (IMaRS-USF), Institut de Recherche pour le Développement (IRD), UNEP-WCMC, The WorldFish Center, & World Resources Institute, 2011). This dataset was used to ensure consistency with the GCRMN report Status of Coral Reefs of the World: 2020 (Souter et al., 2021), which also uses this dataset.

• Hard coral species richness. The number of hard coral species in each country was estimated based on the IUCN Red-List Database (IUCN, 2021).

• Coral reef fish species richness. The number of fish species associated with coral reefs in each country was estimated based on the Fishbase database (Froese & Pauly, 2020).

• Marine Protected Areas (MPA). Marine Protected Area shapefiles were obtained from the Marine Protection Atlas Database (Marine Conservation Institute, 2020). Marine Protection Atlas uses the World Database on Protected Areas (UNEP-WCMC & IUCN, 2020) as the starting point for its database, conducting an independent, third-party review of the data and making additions and corrections if necessary.

• 2020 GCRMN world report database. The database built for the 2020 GCRMN Report Status of Coral Reefs of the World: 2020 (Souter et al., 2021) was used to describe the monitoring within the different countries. Hundreds of raw datasets, provided by numerous contributors worldwide, were homogenized and aggregated based on a dedicated workflow presented in Wicquart et al, (2022), order to produce a unique and homogeneous database. Variables used in this database are presented in the Table 1.

Table 1. Variables selected for the benthic synthetic dataset. The icons for the variables categories (Cat.) represents 📝 = description variables, 🌐 = spatial variables, 📆 = temporal variables, 📏 = methodological variables, 🦀 = taxonomic variables, 📈 = metric variables.

	Variable	Cat.	Type	Unit	Description
1	DatasetID	📝	Factor		Dataset ID
2	Area	🌐	Factor		Biogeographic area
3	Country	🌐	Factor		Country
4	Archipelago	🌐	Factor		Archipelago
5	Location	🌐	Factor		Location or island within the country
6	Site	🌐	Factor		Site within the location
7	Replicate	🌐	Integer		Replicate ID
8	Quadrat	🌐	Integer		Replicate ID
8	Zone	🌐	Factor		Reef zone
9	Latitude	🌐	Numeric		Latitude of the site (decimal format)
10	Longitude	🌐	Numeric		Longitude of the site (decimal format)
11	Depth	🌐	Numeric	m	Mean depth
12	Year	📆	Integer		Year
13	Date	📆	Date		Date (YYYY-MM-DD)
14	Method	📏	Factor		Description of the method used
15	Observer	📏	Factor		Name of the diver
16	Category	🦀	Factor		See Table 2
17	Group	🦀	Factor		See Table 2
18	Family	🦀	Factor		Family
19	Genus	🦀	Factor		Genus
20	Species	🦀	Factor		Species
21	Cover	📈	Numeric	%	Cover percentage

2.2 Code description

• 00_data-cleaning.Rmd This code is used to calculate reef area per country, to associate EEZ to benthic cover monitoring data and to select the data for the 30 pilot countries.
• 01_analyses-maps.Rmd. This code is used to produce all the maps.
• 02_analyses-graphs.Rmd This code is used to produce all other graphical outputs.
• 03_analyses-hard-coral-species.Rmd. This code is used to estimate the number of hard corals within each countries.
• 04_analyses-fish-species.Rmd This code is used to estimate the number of coral reef fish species within each countries.
• 05_analyses-mpa.Rmd This code is used to estimate the total MPA area within each country.
• 06_data-contributors.R This code is used to create the list of data contributors.

3. How to report issues?

Please report any bugs or issues HERE.

4. Reproducibility parameters

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Hmisc_4.4-1         Formula_1.2-4       survival_3.2-7     
 [4] lattice_0.20-41     rfishbase_3.0.4     leaflet_2.0.3      
 [7] formattable_0.2.0.1 DT_0.16             lubridate_1.7.9    
[10] readxl_1.3.1        forcats_0.5.0       stringr_1.4.0      
[13] dplyr_1.0.2         purrr_0.3.4         readr_1.4.0        
[16] tidyr_1.1.2         tibble_3.0.4        ggplot2_3.3.2      
[19] tidyverse_1.3.0    

loaded via a namespace (and not attached):
 [1] httr_1.4.2          jsonlite_1.7.1      splines_4.0.3      
 [4] modelr_0.1.8        assertthat_0.2.1    latticeExtra_0.6-29
 [7] blob_1.2.1          cellranger_1.1.0    yaml_2.2.1         
[10] pillar_1.4.6        backports_1.1.10    glue_1.4.2         
[13] digest_0.6.25       checkmate_2.0.0     RColorBrewer_1.1-2 
[16] rvest_0.3.6         colorspace_1.4-1    htmltools_0.5.0    
[19] Matrix_1.2-18       pkgconfig_2.0.3     broom_0.7.2        
[22] haven_2.3.1         scales_1.1.1        jpeg_0.1-8.1       
[25] htmlTable_2.1.0     generics_0.0.2      ellipsis_0.3.1     
[28] withr_2.3.0         nnet_7.3-14         cli_2.1.0          
[31] magrittr_1.5        crayon_1.3.4        memoise_1.1.0      
[34] evaluate_0.14       fs_1.5.0            fansi_0.4.1        
[37] xml2_1.3.2          foreign_0.8-80      data.table_1.13.0  
[40] tools_4.0.3         gh_1.1.0            hms_0.5.3          
[43] lifecycle_0.2.0     munsell_0.5.0       reprex_0.3.0       
[46] cluster_2.1.0       compiler_4.0.3      rlang_0.4.8        
[49] grid_4.0.3          rstudioapi_0.11     htmlwidgets_1.5.2  
[52] crosstalk_1.1.0.1   base64enc_0.1-3     rmarkdown_2.4      
[55] gtable_0.3.0        DBI_1.1.0           R6_2.4.1           
[58] gridExtra_2.3       knitr_1.30          stringi_1.5.3      
[61] Rcpp_1.0.5          rpart_4.1-15        vctrs_0.3.4        
[64] png_0.1-7           dbplyr_1.4.4        tidyselect_1.1.0   
[67] xfun_0.18