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elodea

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:

Installation

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")

Usage

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.

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