agaricales_updated: Sample data set of MyCoPortal records

In hjsimpso/fungarium: An R package for enabling the use of fungaria collection data in comprehensive trait analyses

Sample data set of MyCoPortal records

Description

Sample data set of fungal records downloaded from the MyCoPortal (https://mycoportal.org) on Dec 8, 2021. Downloaded as Darwin core tab-delimited file in UTF-8 encoding. Includes Agaricales records from the United States. Taxon names updated using fungarium::taxon_update. Records with name update error were removed. Records with species now classified outside of Agaricales were removed.

Usage

agaricales_updated

Format

A data frame with:

id

unique MyCoPortal ID for each record

institutionCode

code for the collection that houses the specimen, or digital observation

scientificName

canonical taxon name for each record

scientificNameAuthorship

authorship name(s) associated with the canonical name

recordedBy

name of collector(s)

eventDate

exact date of collection or observation

year

year in which the specimen was collected or observed

occurrenceRemarks

environmental metadata

habitat

environmental metadata

associatedTaxa

environmental metadata

country

country where specimen was collected or observed

stateProvince

state or province where specimen was collected or observed

county

county in which the specimen was observed or collected

decimalLatitude

latitude where the specimen was observed or collected

decimalLongitude

longitude where the specimen was observed or collected

references

link to MyCoPortal online record

query_full_name

exact string used in GBIF query

new_name

currently accepted canonical name (may be the same as the name originally listed in the input file, meaning that the orginal name is currently accepted)

new_author

authorship associated with the currently accepted scientific name

new_full_name

name and authorship combined into one character string. Represents the full scientific name.

new_kingdom

kingdom classification based on the new scientific name

new_phylum

phylum classification based on the new scientific name

new_class

class classification based on the new scientific name

new_order

order classification based on the new scientific name

new_family

family classification based on the new scientific name

new_genus

genus associated with the new scientific name

new_specific_epithet

specific epithet asscociated with the new scientific name

rank

taxonomic rank

new_species

canonical species name based on the new scientific name. This is useful for getting the species name for varieties or sub-species, which will have the full variety or subspecies names listed for "new_full_name".

taxon_conf

confidence score (0-100) for match quality of the full scientific name. Ex: "Trametes versicolor (L.) Lloyd" in sporocarp dataset matched with "Trametes versicolor (L.) Lloyd" in GBIF database would give a confidence score of 100.

taxon_matchtype

refers to match type of the canonical name. EXACT means a perfect match. Ex: "Trametes versicolor" in sporocarp dataset matched to "Trametes versicolor" in GBIF database. FUZZY means an imperfect match, likely due to spelling errors. Ex: "Trametes versacolor" in sporocarp dataset matched with "Trametes versicolor" in GBIF database.

error

error code for why a name could not be validated or updated

Source

https://mycoportal.org

hjsimpso/fungarium documentation built on Aug. 23, 2023, 3:59 p.m.