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Enrich and certify a list of species names by comparing with WoRMS.

Source: R/taxon_id_worms.R
taxon_id_worms.Rd

[Stable] This function provide tibble object with all the columns of input table of taxa plus new columns such as valid_name, valid_authority, valid_AphiaID, status, synonyms, LSID, url, matchType, nOfWormsRecords, wormsRecords obtained from Word Register of Marine Species WoRMS rest API.

Usage

taxon_id_worms(input, taxaColumn = 1, verbose = TRUE, refine = FALSE)

Arguments

input

A tibble. The table that contain the species names list to be checked.

taxaColumn

A numeric. The cardinal number of the column where species list is. Default is 1.

verbose

A logical. Whit this selection, the function returns a message with number of record(s) that don't match with any Worms names and the number of record(s) that match with more that one Worms name. Default is TRUE.

refine

A logical. With this selection, the function allows to refine the result(s) that match with more Worms records. By a interactive use of the terminal, the user can chose the result. Default is FALSE.

Value

The output of the function is a tibble with the columns provided and new columns such as: valid_name, valid_authority, valid_AphiaID, status, synonyms, LSID, url, matchType, nOfWormsRecords, wormsRecords obtained by Worms rest API. The function also return, if verbose is TRUE, the list of records that don't match with Worms name species.

Most of the labels of the columns are the terms of Darwin Core terms. The columns labels are annotate with the link (URI) of the Darwin Core terms as attributes of the tibble.

See also

worrms::wm_records_names()

Author

Alessandro Oggioni, phD (2021) oggioni.a@irea.cnr.it

Paolo Tagliolato, phD (2021) tagliolato.p@irea.cnr.it

Examples

phytoplankton <- tibble::tibble(
   ID = c(1, 2, 3, 4, 5, 6, 7),
   species = c(
   "Asterionella formosa", "Chrysococcus sp.",
   "Cryptomonas rostrata", "Dinobryon divergens",
   "Mallomonas akrokomos", "Melosira varians",
   "Cryptomonas rostrata"
 )
)
table <- taxon_id_worms(
  input = phytoplankton,
  taxaColumn = 2,
  verbose = TRUE,
  refine = TRUE
)
#> 
#> After the finding operation the number of record(s) that don't match
#> with any Worms names are:
#> *--- 0 on 7 examined ---*
#> please verify the species name provided and run again this
#> function. The record(s) that match with more that one Worms name are:
#> *--- 7 on 7 examined ---*
#> please use the function taxon_id_worms_refine for specify wich
#> is the exact corrispondence with your given species name.
#> This is the taxa name provided by you:
#> Cryptomonas rostrata
#> Worms don't contain a unique records that match with this name.
#> The Worms records most similar are:
#> 
#> 1:  Cryptomonas rostrata (Skuja, 1948)
#>     Worms status: accepted
#>     Unaccept reason: NA
#>     Match type: exact
#>     Modified: 2015-06-26T12:14:04.327Z
#> 2:  Cryptomonas rostrata (O.V.Troitzkaja, 1922)
#>     Worms status: unaccepted
#>     Unaccept reason: synonym
#>     Match type: exact
#>     Modified: 2021-08-27T06:27:33.180Z
#> 
#> ----
#> Please select the record that you think
#> most similar to the taxa name that you have provided.
#> Insert the number of record:
#> This is the taxa name provided by you:
#> Cryptomonas rostrata
#> Worms don't contain a unique records that match with this name.
#> The Worms records most similar are:
#> 
#> 1:  Cryptomonas rostrata (Skuja, 1948)
#>     Worms status: accepted
#>     Unaccept reason: NA
#>     Match type: exact
#>     Modified: 2015-06-26T12:14:04.327Z
#> 2:  Cryptomonas rostrata (O.V.Troitzkaja, 1922)
#>     Worms status: unaccepted
#>     Unaccept reason: synonym
#>     Match type: exact
#>     Modified: 2021-08-27T06:27:33.180Z
#> 
#> ----
#> Please select the record that you think
#> most similar to the taxa name that you have provided.
#> Insert the number of record:
table
#> # A tibble: 7 × 17
#>      ID originalNameUsage    scientificName       scientificNameAuthor…¹ taxonID
#>   <dbl> <chr>                <chr>                <chr>                    <int>
#> 1     1 Asterionella formosa Asterionella formosa Hassall, 1850           148954
#> 2     2 Chrysococcus sp.     NA                   NA                          NA
#> 3     3 Cryptomonas rostrata NA                   NA                          NA
#> 4     4 Dinobryon divergens  Dinobryon divergens  O.E.Imhof, 1887         157248
#> 5     5 Mallomonas akrokomos Mallomonas akrokomos Ruttner, 1913           249722
#> 6     6 Melosira varians     Melosira varians     C.Agardh, 1827          149043
#> 7     7 Cryptomonas rostrata NA                   NA                          NA
#> # ℹ abbreviated name: ¹​scientificNameAuthorship
#> # ℹ 12 more variables: taxonomicStatus <chr>, synonyms <chr>, taxonRank <chr>,
#> #   kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> #   genus <chr>, scientificNameID <chr>, nOfWormsResults <dbl>,
#> #   wormsRecords <list>

# The annotated URIs of columns label are achieved by:
attributes(table)$uri
#>  [1] ""                                                     
#>  [2] "http://rs.tdwg.org/dwc/terms/originalNameUsage"       
#>  [3] "http://rs.tdwg.org/dwc/terms/scientificName"          
#>  [4] "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship"
#>  [5] "http://rs.tdwg.org/dwc/terms/taxonID"                 
#>  [6] "http://rs.tdwg.org/dwc/terms/taxonomicStatus"         
#>  [7] ""                                                     
#>  [8] "http://rs.tdwg.org/dwc/terms/taxonRank"               
#>  [9] "http://rs.tdwg.org/dwc/terms/kingdom"                 
#> [10] "http://rs.tdwg.org/dwc/terms/phylum"                  
#> [11] "http://rs.tdwg.org/dwc/terms/class"                   
#> [12] "http://rs.tdwg.org/dwc/terms/order"                   
#> [13] "http://rs.tdwg.org/dwc/terms/family"                  
#> [14] "http://rs.tdwg.org/dwc/terms/genus"                   
#> [15] "http://rs.tdwg.org/dwc/terms/scientificNameID"        
#> [16] ""                                                     
#> [17] ""