Taxon name resolution service (tnrs) applied to a vector of names by batches

Usage

tnrs_match(input, reference_taxonomy, tip, ...)

# S3 method for default
tnrs_match(input, reference_taxonomy = "ott", ...)

# S3 method for phylo
tnrs_match(input, reference_taxonomy = "ott", tip = NULL, ...)

Arguments

input

A character vector of taxon names, or a phylo object with tip names, to be matched to taxonomy.

reference_taxonomy

A character vector specifying the reference taxonomy to use for TNRS. Options are "ott", "ncbi", "gbif" or "irmng". The function defaults to "ott".

tip

A vector of mode numeric or character specifying the tips to match. If left empty all tips will be matched.

...

Arguments passed on to rotl::tnrs_match_names

context_name: name of the taxonomic context to be searched (length-one character vector or NULL). Must match (case sensitive) one of the values returned by tnrs_contexts. Default to "All life".
do_approximate_matching: A logical indicating whether or not to perform approximate string (a.k.a. “fuzzy”) matching. Using FALSE will greatly improve speed. Default, however, is TRUE.
ids: A vector of ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length.
include_suppressed: Ordinarily, some quasi-taxa, such as incertae sedis buckets and other non-OTUs, are suppressed from TNRS results. If this parameter is true, these quasi-taxa are allowed as possible TNRS results.

Value

An object of class data frame or phylo, with the added class match_names.

NULL

Details

There is no limit to the number of names that can be queried and matched.

The output will preserve all elements from original input phylo object and will add

phy$mapped: A character vector indicating the state of mapping of phy$tip.labels:
phy$original.tip.label: A character vector preserving all original labels.
phy$ott_ids: A numeric vector with ott id numbers of matched tips. Unmatched and original tips will be NaN.

if tips are duplicated, tnrs will only be run once (avoiding increases in function running time) but the result will be applied to all duplicated tip labels

Examples

tnrs_match(input = c("Mus"))
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#> 
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#>   search_string                  unique_name approximate_match  ott_id
#> 1           mus Mus (genus in Deuterostomia)             FALSE 1068778
#>   is_synonym          flags number_matches
#> 1      FALSE SIBLING_HIGHER              3
tnrs_match(input = c("Mus", "Mus musculus"))
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#> 
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#>   search_string                  unique_name approximate_match  ott_id
#> 1           mus Mus (genus in Deuterostomia)             FALSE 1068778
#> 2  mus musculus                 Mus musculus             FALSE  542509
#>   is_synonym          flags number_matches
#> 1      FALSE SIBLING_HIGHER              3
#> 2      FALSE                             1
tnrs_match(input = c("Mus", "Echinus", "Hommo", "Mus"))
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#> 
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#>     search_string                     unique_name approximate_match  ott_id
#> 1             mus    Mus (genus in Deuterostomia)             FALSE 1068778
#> 2         echinus Echinus (genus in Opisthokonta)             FALSE  616574
#> 3           hommo                            Homo              TRUE  770309
#> 1.1           mus    Mus (genus in Deuterostomia)             FALSE 1068778
#>     is_synonym          flags number_matches
#> 1        FALSE SIBLING_HIGHER              3
#> 2        FALSE sibling_higher              4
#> 3        FALSE sibling_higher              1
#> 1.1      FALSE SIBLING_HIGHER              3