library('taxize')
simplify
option for all functions that whose focus is to return information that could be encoded in taxon_name
, taxon_id
, taxon
, or taxon_rank
vectors, but all return other associated information in tables. If simplify = TRUE
the just the vector is returned, if simplify = FALSE
then the vector is the first column in a table containing the other information.temp <- gnr_resolve(names = c("Helianthos annus", "Homo saapiens")) head(temp)
The matched_name
could be a taxon_name
or taxon
vector and the data_source_title
could be encoded in its taxon_id
field.
mynames <- c("Helianthus annuus ssp. jaegeri", "Helianthus annuus ssp. lenticularis", "Helianthus annuus ssp. texanus") (tsn <- get_tsn(mynames, accepted = FALSE))
These could return taxon_id
vectors, which would store the database in their taxon_db
fields instead of using a class for the database.
The other attributes could remain the same or be put returned as columns in a table.
itis_acceptname(searchtsn = tsn)
The acceptedname
, acceptedtsn
, and author
columns could be converted to a taxon_name
vector column.
Alternativly, a vector of taxon
objects could be returned with the accepted as the first synonym and the query as the second.
specieslist <- c("Abies procera","Pinus contorta") classification(specieslist, db = 'itis')
This could return a classification
vector.
Would probably be replaced by the taxon_id
constructor to replicate the check = FALSE
behavior.
For the check = TRUE
behavior, perhaps taxon_id
class should have a validated
boolean field and then these functions could be replaced with a check_taxon_id
function that populates that field.
This would allow a vector of IDs from different databases to be validated.
downstream("Dasypodidae", downto = "Species", db = "col") downstream("Dasypodidae", downto = "Species", db = "col", intermediate = TRUE)
When intermediate = FALSE
, the return value could be a list of taxon_name
vectors or the columns with ids, names, ranks, and name status could be replaved with a taxon_name
vector.
When intermediate = TRUE
, the same as intermediate = FALSE
as described above could be used, or a list of taxonomy
could be returned.
children("Pinaceae", db = "ncbi")
Can also be list of taxon_name
or tables with taxon_name
as a column.
genbank2uid(id = 'AJ748748')
Can return taxon_id
vector.
x = apgOrders() head(x)
Can return a taxon
vector so synonyms can be included.
apg_lookup(taxa = "Hyacinthaceae", rank = "family") apg_lookup(taxa = "Asteraceae", rank = "family")
Can return a taxon_name
with the the db set to apg
as.data.frame(as.boldid(c("1973","101009","98597"), check=FALSE))
This functionality could mostly be handled by as.data.frame.taxon_id
, except for the multiple_matches
pattern_match
columns.
Perhaps these functions can call as.data.frame.taxon_id
and add on those columns
bold_search(name=c("Apis","Puma concolor")) bold_search(id=c(88899, 88899), dataTypes="all") bold_search(id=c(88899, 88899), dataTypes="stats") bold_search(id=c(88899, 88899), dataTypes="geo")
Can replace taxid
, taxon
, and tax_rank
columns with a taxon_name
column
Perhaps this could be modified to take taxonomy
class as input, since that could be the output of classifications
.
If so, it might make more sense to be in the taxa
package, or another focused on visluizing taxonomic info.
comm2sci(commnames='american black bear') comm2sci(commnames='american black bear') comm2sci(commnames='black bear', db='itis', simplify = FALSE)
Could return a list of taxon_name
vectors
x <- eol_search(terms='Homo') x
pageid, name, link columns could be replaced by taxon_name
vector.
eubon_search("Prionus")
A lot of these columns could be made into a taxon_name
vector or a taxon
vector if we want the synonyms to be incorperated.
fg_name_search(q = "Gymnopus")
A lot of these columns could be made into a taxon_name
vector or a taxon
vector if we want the synonyms to be incorperated.
id2name(19322, db = "itis")
Can return taxon_name
vector
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