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Match names that start or contain a specified text string

Usage

fuzzy_filter(
  name,
  by = c("scientificName", "vernacularName"),
  provider = getOption("taxadb_default_provider", "itis"),
  match = c("contains", "starts_with"),
  version = latest_version(),
  db = td_connect(),
  ignore_case = TRUE,
  collect = TRUE
)

Arguments

name

vector of names (scientific or common, see by) to be matched against.

by

a column name in the taxa_tbl (following Darwin Core Schema terms). The filtering join is executed with this column as the joining variable.

provider

from which provider should the hierarchy be returned? Default is 'itis', which can also be configured using options(default_taxadb_provider=..."). See [td_create] for a list of recognized providers.

match

should we match by names starting with the term or containing the term anywhere in the name?

version

Which version of the taxadb provider database should we use? defaults to latest. See tl_import for details.

db

a connection to the taxadb database. See details.

ignore_case

should we ignore case (capitalization) in matching names? Can be significantly slower to run.

collect

logical, default TRUE. Should we return an in-memory data.frame (default, usually the most convenient), or a reference to lazy-eval table on disk (useful for very large tables on which we may first perform subsequent filtering operations.)

Details

Note that fuzzy filter will be fast with an single or small number of names, but will be slower if given a very large vector of names to match, as unlike other filter_ commands, fuzzy matching requires separate SQL calls for each name. As fuzzy matches should all be confirmed manually in any event, e.g. not every common name containing "monkey" belongs to a primate species.

This method utilizes the database operation %like% to filter tables without loading into memory. Note that this does not support the use of regular expressions at this time.

Examples

# \donttest{

## match any common name containing:
name <- c("woodpecker", "monkey")
fuzzy_filter(name, "vernacularName")
#> # A tibble: 254 × 15
#>    taxonID     scientificName      taxonRank acceptedNameUsageID taxonomicStatus
#>    <chr>       <chr>               <chr>     <chr>               <chr>          
#>  1 ITIS:573055 Pygathrix bieti     species   ITIS:944259         synonym        
#>  2 ITIS:944191 Oreonax flavicauda  species   ITIS:572961         synonym        
#>  3 ITIS:944216 Chlorocebus cynosu… species   ITIS:944445         synonym        
#>  4 ITIS:944298 Simia beelzebub     species   ITIS:572935         synonym        
#>  5 ITIS:944300 Mycetes flavimanus  species   ITIS:572935         synonym        
#>  6 ITIS:944303 Mycetes niger       species   ITIS:572939         synonym        
#>  7 ITIS:944310 Nyctipithecus feli… species   ITIS:572951         synonym        
#>  8 ITIS:944315 Aotus senex         species   ITIS:572946         synonym        
#>  9 ITIS:944321 Ateles braccatus    species   ITIS:572954         synonym        
#> 10 ITIS:944349 Jacchus grandis     species   ITIS:612150         synonym        
#> # ℹ 244 more rows
#> # ℹ 10 more variables: update_date <lgl>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> #   vernacularName <chr>, infraspecificEpithet <lgl>

## match scientific name
fuzzy_filter("Chera", "scientificName",
             match = "starts_with")
#> # A tibble: 6 × 15
#>   taxonID      scientificName      taxonRank acceptedNameUsageID taxonomicStatus
#>   <chr>        <chr>               <chr>     <chr>               <chr>          
#> 1 ITIS:1025104 Cheracebus lugens   species   ITIS:1025104        accepted       
#> 2 ITIS:1025111 Cheracebus regulus  species   ITIS:1025111        accepted       
#> 3 ITIS:1025107 Cheracebus lucifer  species   ITIS:1025107        accepted       
#> 4 ITIS:1025110 Cheracebus purinus  species   ITIS:1025110        accepted       
#> 5 ITIS:1025106 Cheracebus torquat… species   ITIS:1025106        accepted       
#> 6 ITIS:1025105 Cheracebus medemi   species   ITIS:1025105        accepted       
#> # ℹ 10 more variables: update_date <lgl>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> #   vernacularName <chr>, infraspecificEpithet <lgl>
# }