View source: R/list_higher_taxo.R
list_higher_taxo | R Documentation |
Retrieve higher taxonomy information (like Family and Order) for each record from the "Encyclopedia of Life" web API.
list_higher_taxo(
indf,
canonical,
genus = FALSE,
verbose = FALSE,
progress = TRUE
)
indf |
input data frame containing taxonomic list |
canonical |
field name containing scientific names |
genus |
If TRUE, use only genus level data to get taxonomy |
verbose |
If TRUE, displays each name string for which the higher taxonomy is sought |
progress |
If TRUE prints progress bar and messages on the console. |
This function makes use of certain functions in the taxize
package. It scans and retrieves the taxonomic hierarchy for each scientific
name (or just genus name) in the data set. When new data are retrieved, they
are stored in a local sqlite database, taxo.db, for faster further access.
data frame with added / updated columns
Kingdom of the Scientific name
Phylum of the Scientific name
Order of the Scientific name
Family of the Scientific name
Genus of the Scientific name
and also saves a local copy of taxonomy downloaded for future use in 'taxo.db' sqlite file
Other Name functions:
build_gen_syn()
,
cast_canonical()
,
cast_scientificname()
,
check_scientific()
,
expand_name()
,
get_accepted_names()
,
guess_taxo_rank()
,
melt_canonical()
,
melt_scientificname()
,
resolve_names()
,
taxo_fuzzy_match()
## Not run:
mylist <- data.frame("canonical" = c("Abrothrix longipilis",
"Mus longipilis",
"Abrothrix jelskii",
"Cardinalis cardinalis",
"Danaus plexippus"),
stringsAsFactors = FALSE)
my_taxo_list <- list_higher_taxo(mylist,"canonical")
## End(Not run)
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