mermaidr is an R package that enables you to access data from MERMAID, an open-source data platform developed to help you collect, analyze, and share coral reef monitoring data. Through mermaidr you can access data from MERMAID directly in R.
For more information and detailed instructions on usage, please visit the package website.
If you are new to the R programming language, our new R users guide is a great place to start! If you find yourself stuck, please don’t hesitate to ask for help.
Installation
You can install mermaidr from GitHub with:
# install.packages("remotes")
remotes::install_github("data-mermaid/mermaidr")Usage
Through mermaidr, you can access aggregated data from your coral reef surveys. To do this, first load the package and access your MERMAID projects:
library(mermaidr)
projects <- mermaid_get_my_projects()At this point, you will have to authenticate to the Collect app. R will help you do this automatically by opening a browser window for you to log in to Collect, either via Google sign-in or username and password - however you normally do! Once you’ve logged in, come back to R. Your login credentials will be stored for a day, until they expire, and you will need to log in again. The package handles the expiration for you, so just log in again when prompted.
This function gives us information on your projects, including project countries, the number of sites, tags, data policies, and more:
projects
#> # A tibble: 12 × 14
#> id name countries num_sites tags notes status data_policy_bel…
#> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 02e691… TWP Gi… Indonesia 14 "WCS In… "" Open Private
#> 2 170e71… 2018_V… Fiji 10 "WCS Fi… "This i… Open Private
#> 3 2d6cee… WCS Mo… Mozambiq… 74 "WCS Mo… "Databa… Open Private
#> 4 3a9ecb… Aceh J… Indonesia 18 "Vibran… "" Open Private
#> 5 408067… Madaga… Madagasc… 74 "WCS Ma… "MACMON… Open Private
#> 6 4d23d2… Madaga… Madagasc… 16 "WCS Ma… "Monito… Open Public Summary
#> 7 507d1a… Karimu… Indonesia 43 "Vibran… "" Open Private
#> 8 5679ef… Madaga… Madagasc… 33 "WCS Ma… "" Open Public Summary
#> 9 75ef7a… Kubula… Fiji 78 "WCS Fi… "" Open Private
#> 10 9de827… XPDC K… Indonesia 37 "" "XPDC K… Open Private
#> 11 a1b7ff… Great … Fiji 76 "Fiji M… "" Open Private
#> 12 e1efb1… 2016_N… Fiji 8 "WCS Fi… "Namena… Open Private
#> # … with 6 more variables: data_policy_benthiclit <chr>,
#> # data_policy_benthicpit <chr>, data_policy_habitatcomplexity <chr>,
#> # data_policy_bleachingqc <chr>, created_on <chr>, updated_on <chr>To focus on just one or a few projects, you can filter by fields like the project name, country, or tags using the dplyr package. For example, I’ll narrow in on the WCS Mozambique Coral Reef Monitoring project.
library(dplyr)
wcs_mozambique <- projects %>%
filter(name == "WCS Mozambique Coral Reef Monitoring")You can access data collected on fishbelt, benthic LIT, benthic PIT, bleaching, or habitat complexity - the main function to pull data related to your project is mermaid_get_project_data():
wcs_mozambique_fishbelt_samples <- wcs_mozambique %>%
mermaid_get_project_data(method = "fishbelt", data = "sampleevents")The data = "sampleevents" argument specifies that I’d like to pull data summarised to the level of a sample event, which is a site and date - we can see that this pulls information about the site and date of samples, along with aggregations like the total biomass of that site/date, and broken down by trophic group and fish family.
wcs_mozambique_fishbelt_samples
#> # A tibble: 80 × 75
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambiq… WCS Mo… Mozamb… Aquarium -21.8 35.5 barrier back reef
#> 2 WCS Mozambiq… WCS Mo… Mozamb… Babylon -11.0 40.7 fringing fore reef
#> 3 WCS Mozambiq… WCS Mo… Mozamb… Baluba -22.0 35.5 patch fore reef
#> 4 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.0 32.9 barrier back reef
#> 5 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.1 32.9 barrier back reef
#> 6 WCS Mozambiq… WCS Mo… Mozamb… Bunting… -12.6 40.6 fringing fore reef
#> 7 WCS Mozambiq… WCS Mo… Mozamb… Bunting… -12.6 40.6 fringing fore reef
#> 8 WCS Mozambiq… WCS Mo… Mozamb… Checkers -26.8 32.9 patch fore reef
#> 9 WCS Mozambiq… WCS Mo… Mozamb… Coliseum -12.6 40.6 fringing fore reef
#> 10 WCS Mozambiq… WCS Mo… Mozamb… Dogtooth -12.5 40.6 fringing crest
#> # … with 70 more rows, and 67 more variables: reef_exposure <chr>, tide <lgl>,
#> # current <lgl>, visibility <lgl>, aca_geomorphic <chr>, aca_benthic <chr>,
#> # andrello_grav_nc <dbl>, andrello_sediment <dbl>, andrello_nutrient <dbl>,
#> # andrello_pop_count <dbl>, andrello_num_ports <dbl>,
#> # andrello_reef_value <dbl>, andrello_cumul_score <dbl>, beyer_score <dbl>,
#> # beyer_scorecn <dbl>, beyer_scorecy <dbl>, beyer_scorepfc <dbl>,
#> # beyer_scoreth <dbl>, beyer_scoretr <dbl>, management <chr>, …If you’d like data related to the units of survey (for example, to transects or quadrats), it’s just a matter of changing data to “sampleunits”:
wcs_mozambique %>%
mermaid_get_project_data(method = "fishbelt", data = "sampleunits")
#> # A tibble: 111 × 85
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambiq… WCS Mo… Mozamb… Aquarium -21.8 35.5 barrier back reef
#> 2 WCS Mozambiq… WCS Mo… Mozamb… Aquarium -21.8 35.5 barrier back reef
#> 3 WCS Mozambiq… WCS Mo… Mozamb… Babylon -11.0 40.7 fringing fore reef
#> 4 WCS Mozambiq… WCS Mo… Mozamb… Baluba -22.0 35.5 patch fore reef
#> 5 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.0 32.9 barrier back reef
#> 6 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.0 32.9 barrier back reef
#> 7 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.1 32.9 barrier back reef
#> 8 WCS Mozambiq… WCS Mo… Mozamb… Barreir… -26.1 32.9 barrier back reef
#> 9 WCS Mozambiq… WCS Mo… Mozamb… Bunting… -12.6 40.6 fringing fore reef
#> 10 WCS Mozambiq… WCS Mo… Mozamb… Bunting… -12.6 40.6 fringing fore reef
#> # … with 101 more rows, and 77 more variables: reef_exposure <chr>,
#> # reef_slope <lgl>, tide <lgl>, current <lgl>, visibility <lgl>,
#> # relative_depth <lgl>, aca_geomorphic <chr>, aca_benthic <chr>,
#> # andrello_grav_nc <dbl>, andrello_sediment <dbl>, andrello_nutrient <dbl>,
#> # andrello_pop_count <dbl>, andrello_num_ports <dbl>,
#> # andrello_reef_value <dbl>, andrello_cumul_score <dbl>, beyer_score <dbl>,
#> # beyer_scorecn <dbl>, beyer_scorecy <dbl>, beyer_scorepfc <dbl>, …And raw observations are available by changing it to “observations”:
wcs_mozambique %>%
mermaid_get_project_data(method = "fishbelt", data = "observations")
#> # A tibble: 2,714 × 65
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 2 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 3 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 4 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 5 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 6 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 7 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 8 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 9 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 10 WCS Mozambique… WCS Moz… Mozamb… Aqua… -21.8 35.5 barrier back reef
#> # … with 2,704 more rows, and 57 more variables: reef_exposure <chr>,
#> # reef_slope <lgl>, tide <lgl>, current <lgl>, visibility <lgl>,
#> # relative_depth <lgl>, aca_geomorphic <chr>, aca_benthic <chr>,
#> # andrello_grav_nc <dbl>, andrello_sediment <dbl>, andrello_nutrient <dbl>,
#> # andrello_pop_count <dbl>, andrello_num_ports <dbl>,
#> # andrello_reef_value <dbl>, andrello_cumul_score <dbl>, beyer_score <dbl>,
#> # beyer_scorecn <dbl>, beyer_scorecy <dbl>, beyer_scorepfc <dbl>, …For more details on accessing project data, please see the Accessing Project Data article.
You may also want to access data that is not related to projects. To access this data, you do not need to authenticate R with MERMAID.
For example, you can pull reference data (the names and information of the fish and benthic attributes you can choose in MERMAID), using mermaid_get_reference():
mermaid_get_reference(reference = "fishfamilies")
#> # A tibble: 162 × 9
#> id name status biomass_constan… biomass_constan… biomass_constan… regions
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 0091… Kyph… Open 0.0193 3.03 0.986 Easter…
#> 2 00b6… Mugi… Open 0.0166 2.94 0.974 Easter…
#> 3 00f4… Zena… Open 0.00427 3.02 1 Easter…
#> 4 0226… Sphy… Open 0.00448 3.11 1 Easter…
#> 5 0880… Labr… Open 0.0120 3.04 0.997 Easter…
#> 6 0aff… Scom… Open 0.0111 3.03 0.988 Easter…
#> 7 0b69… Ophi… Open 0.00139 2.93 1 Easter…
#> 8 0d99… Albu… Open 0.0105 2.99 1 Tropic…
#> 9 0e5b… Hemi… Open 0.0373 3.16 0.99 Easter…
#> 10 1513… Serr… Open 0.0136 3.03 0.997 Easter…
#> # … with 152 more rows, and 2 more variables: created_on <chr>,
#> # updated_on <chr>Using this function, you can access the fish family, fish genera, fish species, and benthic attributes references by changing the reference argument.
You can also get a list of all projects (not just your own):
mermaid_get_projects()
#> # A tibble: 129 × 14
#> id name countries num_sites tags notes status data_policy_bel…
#> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 00673b… TPK Gi… "Indonesi… 15 "WCS I… "" Open Private
#> 2 01bbe4… Madaga… "Madagasc… 12 "WCS M… "Survey… Open Private
#> 3 02e691… TWP Gi… "Indonesi… 14 "WCS I… "" Open Private
#> 4 07df6a… Cender… "Indonesi… 36 "Cende… "" Open Private
#> 5 0b39fe… Open C… "Indonesi… 2 "WCS I… "This i… Open Private
#> 6 0c000a… 2019_O… "Fiji" 18 "WCS F… "" Open Private
#> 7 0c1668… REEFol… "" 0 "" "" Open Public Summary
#> 8 0f1703… what "" 0 "" "" Open Public Summary
#> 9 124b91… Sam "" 0 "" "" Open Private
#> 10 1277ef… Taka B… "Indonesi… 39 "WCS I… "" Open Public Summary
#> # … with 119 more rows, and 6 more variables: data_policy_benthiclit <chr>,
#> # data_policy_benthicpit <chr>, data_policy_habitatcomplexity <chr>,
#> # data_policy_bleachingqc <chr>, created_on <chr>, updated_on <chr>As well as all sites:
mermaid_get_sites()
#> # A tibble: 2,543 × 13
#> id name notes project latitude longitude country reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 02355d6… BA09 "" a1b7ff1f… -17.4 178. Fiji atoll back reef
#> 2 03e5576… BA03 "" 89f2d43e… -17.4 178. Fiji atoll back reef
#> 3 0879390… BA16 "" a1b7ff1f… -17.2 178. Fiji atoll back reef
#> 4 19258ea… BA15 "" a1b7ff1f… -17.2 178. Fiji atoll back reef
#> 5 19e6088… YA02 "" a1b7ff1f… -17.0 177. Fiji atoll back reef
#> 6 20aeb13… BA11 "" a1b7ff1f… -17.3 178. Fiji atoll back reef
#> 7 2831d61… BA06 "" 89f2d43e… -17.4 178. Fiji atoll back reef
#> 8 2a4625f… BA04 "" 89f2d43e… -17.4 178. Fiji atoll back reef
#> 9 2af472d… BA12 "" a1b7ff1f… -17.3 178. Fiji atoll back reef
#> 10 2c31d8c… BA05 "" 89f2d43e… -17.4 178. Fiji atoll back reef
#> # … with 2,533 more rows, and 4 more variables: exposure <chr>,
#> # predecessor <chr>, created_on <chr>, updated_on <chr>And all managements:
mermaid_get_managements()
#> # A tibble: 695 × 17
#> id name name_secondary rules notes est_year no_take periodic_closure
#> <chr> <chr> <chr> <chr> <chr> <int> <lgl> <lgl>
#> 1 0031d4… Matafo… "Fish Habitat … No T… "" 2018 TRUE FALSE
#> 2 004bb2… Pulau … "" No T… "" NA TRUE FALSE
#> 3 00c920… Lape B… "Special Manag… Peri… "" 2017 FALSE TRUE
#> 4 0118e3… Sustai… "Perikanan Ber… Gear… "" 2020 FALSE FALSE
#> 5 02479d… Protec… "Zona Perlindu… No T… "" 2015 TRUE FALSE
#> 6 02600e… Dawa_L… "" Acce… "" NA FALSE FALSE
#> 7 029852… Haafev… "Fish Habitat … No T… "" 2007 TRUE FALSE
#> 8 02cd9d… Kaibu_… "" Peri… "" 2017 FALSE TRUE
#> 9 02e546… VIR3 "" No T… "" 2012 TRUE FALSE
#> 10 03bab6… VIR9 "" No T… "" 2016 TRUE FALSE
#> # … with 685 more rows, and 9 more variables: open_access <lgl>,
#> # size_limits <lgl>, gear_restriction <lgl>, species_restriction <lgl>,
#> # compliance <chr>, predecessor <chr>, parties <chr>, created_on <chr>,
#> # updated_on <chr>There is additional data available from the MERMAID API, both related to specific projects and not. If you think you’ll need to use these, please see mermaid_get_endpoint() and mermaid_get_project_endpoint().
This is a small sample of the wealth of data that’s available on your MERMAID projects, and on the ecosystem as a whole! Please explore the package website for more.
