The goal of elodea is to clean and standardise published GBIF checklists. With elodea you can prepare checklists on alien species to create a unified checklist.
To get started, see:
- Function reference: overview of all functions.
You can install the development version of elodea from GitHub with:
Install the development version from GitHub with:
# install.packages("pak")
pak::pak("onestop-project/elodea")With elodea you can get the taxonomic and distribution information of a published GBIF checklist.
Here we get the source taxa and distributions of the Global Register of Introduced and Invasive Species - Monaco.
library(elodea)
datasetKey <- "fbba79dc-ca5b-47ab-9a88-9bdf15a1d11f"
taxa <- get_taxa(datasetKey)
distributions <- get_distributions(datasetKey, taxa)Then you can filter/standardise both taxa and distributions with
filter_data(), which will return a list with three data frames:
taxa, distributions and notes. The first two data frames are the
filtered taxa and distributions, while the notes data frame contains
information on the filtering process. Check
filter_data()
for the filter details.
filter_data(taxa, distributions, establishment_means = "introduced")
#> $taxa
#> # A tibble: 11 × 6
#> taxonKey nubKey taxonID scientificName kingdom taxonRank
#> <int> <int> <chr> <chr> <chr> <chr>
#> 1 196397247 9752149 74020 Phasianus colchicus Linnaeus, 17… Animal… SPECIES
#> 2 196397252 5156102 74016 Leptoglossus occidentalis Heidem… Animal… SPECIES
#> 3 196397254 8001222 74019 Corythauma ayyari (Drake, 1933) Animal… SPECIES
#> 4 196397256 9302212 74017 Phenacoccus peruvianus Granara d… Animal… SPECIES
#> 5 196397257 2094171 74015 Crisicoccus pini (Kuwana, 1902) Animal… SPECIES
#> 6 6275970 1047502 74013 Dactylispa pallidipennis (Motsch… Animal… SPECIES
#> 7 5019579 8636797 74018 Xyleborus compactus Eichhoff, 18… Animal… SPECIES
#> 8 196397264 4292054 74014 Trachyphloeosoma advena Zimmerma… Animal… SPECIES
#> 9 196397267 1651430 74010 Aedes albopictus (Skuse, 1894) Animal… SPECIES
#> 10 196397273 2643093 74012 Caulerpa racemosa (Forssk.) J.Ag… Plantae SPECIES
#> 11 196397274 2643172 74011 Caulerpa taxifolia (M.Vahl) C.Ag… Plantae SPECIES
#>
#> $distributions
#> # A tibble: 11 × 9
#> taxonKey nubKey countryCode occurrenceStatus establishmentMeans
#> <int> <int> <chr> <chr> <chr>
#> 1 196397247 9752149 MC present introduced
#> 2 196397252 5156102 MC present introduced
#> 3 196397254 8001222 MC present introduced
#> 4 196397256 9302212 MC present introduced
#> 5 196397257 2094171 MC present introduced
#> 6 6275970 1047502 MC present introduced
#> 7 5019579 8636797 MC present introduced
#> 8 196397264 4292054 MC present introduced
#> 9 196397267 1651430 MC present introduced
#> 10 196397273 2643093 MC present introduced
#> 11 196397274 2643172 MC present introduced
#> # ℹ 4 more variables: degreeOfEstablishment <chr>, pathway <chr>,
#> # eventDate <chr>, source <chr>
#>
#> $notes
#> # A tibble: 3 × 6
#> taxonID taxonKey scientificName action acceptedKey acceptedName
#> <chr> <int> <chr> <chr> <int> <chr>
#> 1 74013 196397261 Acanthoscelides pallidipenn… merge… 6275970 Dactylispa …
#> 2 74018 196397263 Xylosandrus compactus Eichh… merge… 5019579 Xyleborus c…
#> 3 74010 196397267 Aedes albopictus Skuse, 1894 scien… 1651430 Aedes albop…The notes can help improve the source checklist. The standardised taxa and distribution data can be used to build unified checklists by combining multiple checklists into a single checklist.
- We welcome contributions including bug reports.
- License: MIT
- Get citation
information
for elodea in R doing
citation("elodea"). - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.