taxon_id_pesi: Provide a taxon ID LSID to a taxon list.

In oggioniale/ReLTER: An Interface for the eLTER Community

Provide a taxon ID LSID to a taxon list.

Description

This function provide a taxon ID, usually a LSID, from a taxonomic list. The input of the function is a csv file with a list of taxa. The Taxon ID provided by this function is currently taken from Pan-European Species directories Infrastructure - PESI. This function takes advantage of taxize's eubon_search function https://docs.ropensci.org/taxize/ and the PESI RestAPI.

Usage

taxon_id_pesi(table, taxaColumn)

Arguments

table	A data.frame containing column with a taxa (e.g. Sphaerosoma seidlitzi, Malthinus, etc.).
taxaColumn	A numeric that identify the column containing taxa value.

Value

The output of the function is a tibble containing all the columns provided as input and new columns as: 'canonicalName', 'authorship', 'synonyms', 'LSID', 'url', 'accordingTo', 'checkStatus' gathered from PESI.

An example to export dataset obtained by this function is: datasetMerged <- dplyr::bind_rows(table) write.csv( datasetMerged, "table.csv", row.names = FALSE, fileEncoding = "UTF-8" )

Someone could have problems of characters encoding when CSV file is written. To resolve we suggest two different solutions:

Solution 1 -

1. Open the CSV in Notepad.

2. Click “File” and “Save As”.

3. In the new popup that displays, select “ANSI” from the “Encoding” field.

4. Click “Save”.

5. Now, you should be able to open the file in Excel and display the characters correctly.

Solution 2 -

1. Open Excel

2. Click “File” and “New”

3. Click on the “Data” tab

4. Click “From Text” and select the CSV file

5. Select “Delimited”

6. For “File origin”, select “65001 : Unicode (UTF-8)”

7. Click “Next”

8. Select “Comma”

9. Click “Finish”

10. Excel should now show you the CSV file and display the characters correctly.

Author(s)

Alessandro Oggioni, phD (2020) [e-mail]

References

\insertRef

taxizeR1ReLTER

\insertRef

taxizeR2ReLTER

\insertRef

dplyrRReLTER

Examples

## Not run: 
insects <- data.frame(
   taxonID = c(1, 2, 3, 4, 5, 6),
   family = c(
     "Alexiidae", "Anthicidae",
     "Anthribidae", "Anthribidae",
     "Biphyllidae", "Brentidae"
   ),
   scientificName = c(
     "Sphaerosoma seidlitzi", "Endomia tenuicollis tenuicollis",
     "Anthribus fasciatus", "Phaenotherion fasciculatum fasciculatum",
     "Diplocoelus fagi", "Holotrichapion (Apiops) pisi"
   )
)

output <- taxon_id_pesi(
  table = insects,
  taxaColumn = 3
)

# The annotated URIs of columns label are achieved by:
attributes(output)$uri


## End(Not run)

oggioniale/ReLTER documentation built on Jan. 4, 2024, 3:48 p.m.