R/lcvp_group_search.R
lcvp_group_search.RdSearch all plant taxa names listed in the "Leipzig Catalogue of Vascular Plants" (LCVP) by order, family, genus or author.
lcvp_group_search(
group_names,
search_by,
max_distance = 0.2,
bind_result = TRUE,
status = c("accepted", "synonym", "unresolved", "external")
)A character vector specifying the taxa or author names.
This includes names of orders, families, genus or authors. Only valid
characters are allowed (see validEnc).
A character indicating whether to search by "Order", "Family", "Genus" or "Author".
It represents the maximum string distance allowed for a match when comparing the submitted name with the closest name matches in the LCVP. The distance used is a generalized Levenshtein distance that indicates the total number of insertions, deletions, and substitutions allowed to match the two names. It can be expressed as an integer or as the fraction of the binomial name. For example, a name with length 10, and a max_distance = 0.1, allow only one change (insertion, deletion, or substitution). A max_distance = 2, allows two changes.
If TRUE the function will return one data.frame (default). If False, the function will return a list of separate data.frames for each input group.
A character vector indicating what taxa status should be included in the results: "accepted", "synonym", "unresolved", "external".
The "unresolved" rank means that the status of the plant name could be either valid or synonym, but the information available does not allow a definitive decision. "external" is an extra rank that lists names outside the scope of this publication but useful to keep on this updated list.
A data.frame or a list of data.frames (if bind_result = FALSE)
with the following columns for all species of the matched groups:
The fixed species id of the input taxon in the Leipzig Catalogue of Vascular Plants (LCVP).
A character vector. The input genus of the corresponding vascular plant species name listed in LCVP.
A character vector. The input epitheton of the corresponding vascular plant species name listed in LCVP.
A character vector. The taxonomic rank ("species", subspecies: "subsp.", variety: "var.", subvariety: "subvar.", "forma", or subforma: "subf.") of the corresponding vascular plant species name listed in LCVP.
A character vector. If the indicated rank is below species, the subspecies epitheton input of the corresponding vascular plant species name listed in LCVP. If the rank is "species", the input is "nil".
A character vector. The taxonomic authority input of the corresponding vascular plant species name listed in LCVP.
A character vector. description if a taxon is classified as ‘valid’, ‘synonym’, ‘unresolved’, ‘external’ or ‘blanks’. The ‘unresolved’ rank means that the status of the plant name could be either valid or synonym, but the information available does not allow a definitive decision. ‘External’ in an extra rank which lists names outside the scope of this publication but useful to keep on this updated list. ‘Blanks’ means that the respective name exists in bibliography but it is neither clear where it came from valid, synonym or unresolved. (see the main text Freiberg et al. for more details)
The fixed species id of the output taxon in LCVP.
A character vector. The list of the accepted plant taxa names according to the LCVP.
A character vector. The corresponding family name of the Input.Taxon, staying empty if the Status is unresolved.
A character vector. The corresponding order name of the Input.Taxon, staying empty if the Status is unresolved.
A character vector. The bibliography used.
A character vector. Further taxonomic comments.
See LCVP:tab_lcvp for more details.
If no match is found for all searched names the function will return NULL and a warning message.
The algorithm will look for all the plant taxa names listed in the "Leipzig
Catalogue of Vascular Plants" (LCVP) based on a user-specified list of
orders, families, genus, or authors names. If no match is found, it will try
to find the closest name given the maximum distance defined in max_distance.
If more than one name is fuzzy matched, only the first will be returned.
Freiberg, M., Winter, M., Gentile, A. et al. LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants. Sci Data 7, 416 (2020). https://doi.org/10.1038/s41597-020-00702-z
# Ensure that LCVP package is available before running the example.
# If it is not, see the `lcvplants` package vignette for details
# on installing the required data package.
if (requireNamespace("LCVP", quietly = TRUE)) { # Do not run this
# Search by Genus
lcvp_group_search(c("AA", "Adansonia"), search_by = "Genus")
# Search by Author and keep only accepted names
lcvp_group_search("Schltr.", search_by = "Author", status = "accepted")
}