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<!-- README.md is generated from README.Rmd. Please edit that file -->mermaidr
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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: 19 × 15
#> id name countries num_sites tags notes status data_policy_beltfish
#> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 02e6915c-1… TWP … Indonesia 14 "WCS… "" Open Private
#> 2 170e7182-7… 2018… Fiji 10 "WCS… "Thi… Open Private
#> 3 173c2353-3… Copy… Fiji 8 "WCS… "Nam… Open Public Summary
#> 4 1fbdb9ea-9… a2 Canada, … 9 "WWF… "Nam… Open Private
#> 5 2c0c9857-b… Shar… Canada, … 27 "" "dhf… Open Public Summary
#> 6 2d6cee25-c… WCS … Mozambiq… 74 "WCS… "Dat… Open Private
#> 7 3a9ecb7c-f… Aceh… Indonesia 18 "WCS… "" Open Private
#> 8 4080679f-1… Mada… Madagasc… 74 "WCS… "MAC… Open Private
#> 9 4d23d2a1-7… Mada… Madagasc… 16 "WCS… "Mon… Open Public Summary
#> 10 507d1af9-e… Kari… Indonesia 43 "WCS… "" Open Private
#> 11 5679ef3d-b… Mada… Madagasc… 33 "WCS… "" Open Public Summary
#> 12 5f13e6dc-4… Copy… Indonesia 43 "WCS… "" Open Public Summary
#> 13 75ef7a5a-c… Kubu… Fiji 78 "WCS… "" Open Private
#> 14 7a6bfd69-6… Copy… Belize 31 "WCS… "" Open Public Summary
#> 15 9de82789-c… XPDC… Indonesia 37 "" "XPD… Open Private
#> 16 a1b7ff1f-8… Grea… Fiji 76 "Uni… "" Open Private
#> 17 bacd3529-e… Beli… Belize, … 35 "WCS… "" Open Public Summary
#> 18 d065cba4-e… 2019… Fiji 31 "WCS… "Ble… Open Private
#> 19 e1efb1e0-0… 2016… Fiji 8 "WCS… "Nam… Open Private
#> # ℹ 7 more variables: data_policy_benthiclit <chr>,
#> # data_policy_benthicpit <chr>, data_policy_benthicpqt <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: 79 × 91
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 2 WCS Mozambique Co… WCS … Mozamb… Baby… -11.0 40.7 fringing fore reef
#> 3 WCS Mozambique Co… WCS … Mozamb… Balu… -22.0 35.5 patch fore reef
#> 4 WCS Mozambique Co… WCS … Mozamb… Barr… -26.0 32.9 barrier back reef
#> 5 WCS Mozambique Co… WCS … Mozamb… Barr… -26.1 32.9 barrier back reef
#> 6 WCS Mozambique Co… WCS … Mozamb… Bunt… -12.6 40.6 fringing fore reef
#> 7 WCS Mozambique Co… WCS … Mozamb… Bunt… -12.6 40.6 fringing fore reef
#> 8 WCS Mozambique Co… WCS … Mozamb… Chec… -26.8 32.9 patch fore reef
#> 9 WCS Mozambique Co… WCS … Mozamb… Coli… -12.6 40.6 fringing fore reef
#> 10 WCS Mozambique Co… WCS … Mozamb… Dogt… -12.5 40.6 fringing crest
#> # ℹ 69 more rows
#> # ℹ 83 more variables: reef_exposure <chr>, tide <lgl>, current <lgl>,
#> # visibility <lgl>, management <chr>, management_secondary <lgl>,
#> # management_est_year <dbl>, management_size <dbl>, management_parties <chr>,
#> # management_compliance <chr>, management_rules <chr>, sample_date <date>,
#> # depth_avg <dbl>, depth_sd <dbl>, biomass_kgha_avg <dbl>,
#> # biomass_kgha_sd <dbl>, biomass_kgha_trophic_group_avg_piscivore <dbl>, …
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: 108 × 70
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 2 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 3 WCS Mozambique Co… WCS … Mozamb… Baby… -11.0 40.7 fringing fore reef
#> 4 WCS Mozambique Co… WCS … Mozamb… Balu… -22.0 35.5 patch fore reef
#> 5 WCS Mozambique Co… WCS … Mozamb… Barr… -26.0 32.9 barrier back reef
#> 6 WCS Mozambique Co… WCS … Mozamb… Barr… -26.0 32.9 barrier back reef
#> 7 WCS Mozambique Co… WCS … Mozamb… Barr… -26.1 32.9 barrier back reef
#> 8 WCS Mozambique Co… WCS … Mozamb… Barr… -26.1 32.9 barrier back reef
#> 9 WCS Mozambique Co… WCS … Mozamb… Bunt… -12.6 40.6 fringing fore reef
#> 10 WCS Mozambique Co… WCS … Mozamb… Bunt… -12.6 40.6 fringing fore reef
#> # ℹ 98 more rows
#> # ℹ 62 more variables: reef_exposure <chr>, reef_slope <lgl>, tide <lgl>,
#> # current <lgl>, visibility <lgl>, relative_depth <lgl>, management <chr>,
#> # management_secondary <lgl>, management_est_year <dbl>,
#> # management_size <dbl>, management_parties <chr>,
#> # management_compliance <chr>, management_rules <chr>, sample_date <date>,
#> # sample_time <time>, depth <dbl>, transect_number <dbl>, label <dbl>, …
And raw observations are available by changing it to “observations”:
wcs_mozambique %>%
mermaid_get_project_data(method = "fishbelt", data = "observations")
#> # A tibble: 2,637 × 52
#> project tags country site latitude longitude reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 2 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 3 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 4 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 5 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 6 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 7 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 8 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 9 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> 10 WCS Mozambique Co… WCS … Mozamb… Aqua… -21.8 35.5 barrier back reef
#> # ℹ 2,627 more rows
#> # ℹ 44 more variables: reef_exposure <chr>, reef_slope <lgl>, tide <lgl>,
#> # current <lgl>, visibility <lgl>, relative_depth <lgl>, management <chr>,
#> # management_secondary <lgl>, management_est_year <dbl>,
#> # management_size <dbl>, management_parties <chr>,
#> # management_compliance <chr>, management_rules <chr>, sample_date <date>,
#> # sample_time <time>, depth <dbl>, transect_length <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: 161 × 9
#> id name status biomass_constant_a biomass_constant_b biomass_constant_c
#> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 0091bb… Kyph… Open 0.0193 3.03 0.986
#> 2 00b644… Mugi… Open 0.0166 2.94 0.974
#> 3 00f427… Zena… Open 0.00427 3.02 1
#> 4 02268a… Sphy… Open 0.00448 3.11 1
#> 5 0880aa… Labr… Open 0.0120 3.04 0.997
#> 6 0aff09… Scom… Open 0.0111 3.03 0.988
#> 7 0b69f2… Ophi… Open 0.00139 2.93 1
#> 8 0d9904… Albu… Open 0.0105 2.99 1
#> 9 0e5b1d… Hemi… Open 0.0373 3.16 0.99
#> 10 151384… Serr… Open 0.0136 3.03 0.997
#> # ℹ 151 more rows
#> # ℹ 3 more variables: regions <chr>, 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: 170 × 15
#> id name countries num_sites tags notes status data_policy_beltfish
#> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 00673bdf-b… TPK … "Indones… 15 "WCS… "" Open Private
#> 2 01bbe407-f… Mada… "Madagas… 12 "WCS… "Sur… Open Private
#> 3 02e6915c-1… TWP … "Indones… 14 "WCS… "" Open Private
#> 4 07df6a50-6… Cend… "Indones… 37 "TNC… "" Open Private
#> 5 0b39fe6c-0… Open… "Indones… 2 "WCS… "Thi… Open Private
#> 6 0c000a00-f… 2019… "Fiji" 18 "WCS… "" Open Private
#> 7 0c16681c-6… REEF… "" 0 "" "" Open Public Summary
#> 8 0de6f1fc-1… Copy… "Fiji" 9 "WWF… "Dat… Open Public Summary
#> 9 0f17035f-0… what "" 0 "" "" Open Public Summary
#> 10 124b9142-3… Sam "" 0 "" "" Open Private
#> # ℹ 160 more rows
#> # ℹ 7 more variables: data_policy_benthiclit <chr>,
#> # data_policy_benthicpit <chr>, data_policy_benthicpqt <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: 2,725 × 13
#> id name notes project latitude longitude country reef_type reef_zone
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 0415d9e5-… mysi… <NA> 2c56b9… -1 -1 Bangla… atoll back reef
#> 2 6cd334f9-… meli… <NA> ea4751… 49 -110 Canada atoll back reef
#> 3 afe4dac0-… meli… <NA> ea4751… 49 -110 Canada atoll back reef
#> 4 02355d6c-… BA09 <NA> a1b7ff… -17.4 178. Fiji atoll back reef
#> 5 03e5576e-… BA03 <NA> 89f2d4… -17.4 178. Fiji atoll back reef
#> 6 0879390b-… BA16 <NA> a1b7ff… -17.2 178. Fiji atoll back reef
#> 7 18f09a09-… BA06 <NA> 0de6f1… -17.4 178. Fiji atoll back reef
#> 8 19258ea5-… BA15 <NA> a1b7ff… -17.2 178. Fiji atoll back reef
#> 9 19e60884-… YA02 <NA> a1b7ff… -17.0 177. Fiji atoll back reef
#> 10 20aeb13f-… BA11 <NA> a1b7ff… -17.3 178. Fiji atoll back reef
#> # ℹ 2,715 more rows
#> # ℹ 4 more variables: exposure <chr>, predecessor <chr>, created_on <chr>,
#> # updated_on <chr>
And all managements:
mermaid_get_managements()
#> # A tibble: 1,344 × 17
#> id name name_secondary est_year size parties compliance open_access
#> <chr> <chr> <chr> <int> <dbl> <chr> <chr> <lgl>
#> 1 0031d438-… Mata… Fish Habitat … 2018 25 commun… full FALSE
#> 2 00c920d6-… Lape… Special Manag… 2017 198 commun… full FALSE
#> 3 02479d18-… Prot… Zona Perlindu… 2015 NA commun… full FALSE
#> 4 029852d5-… Haaf… Fish Habitat … 2007 139 commun… full FALSE
#> 5 02cd9d54-… Kaib… <NA> 2017 NA commun… full FALSE
#> 6 02e546ac-… VIR3 <NA> 2012 NA commun… full FALSE
#> 7 03bab6aa-… VIR9 <NA> 2016 NA commun… full FALSE
#> 8 04286cba-… Test… <NA> 2018 NA govern… full FALSE
#> 9 044c6e26-… Fono… Fish Habitat … 2017 191 commun… full FALSE
#> 10 05227cee-… Test… <NA> 2018 5 <NA> full FALSE
#> # ℹ 1,334 more rows
#> # ℹ 9 more variables: no_take <lgl>, access_restriction <lgl>,
#> # periodic_closure <lgl>, size_limits <lgl>, gear_restriction <lgl>,
#> # species_restriction <lgl>, notes <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.