In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Notes on taxize integration

library('taxize')

General thoughts

• Add a 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.

gnr_resolve

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.

get_* functions

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.

accepted names functions

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.

classification

specieslist <- c("Abies procera","Pinus contorta")
classification(specieslist, db = 'itis')

This could return a classification vector.

as.*id functions

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

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

children("Pinaceae", db = "ncbi")

Can also be list of taxon_name or tables with taxon_name as a column.

genbank2uid

genbank2uid(id = 'AJ748748')

Can return taxon_id vector.

apgOrders and apgFamilies

x = apgOrders()
head(x)

Can return a taxon vector so synonyms can be included.

apg_lookup

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.*id

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

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

class2tree

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

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

eol_search

x <- eol_search(terms='Homo')
x

pageid, name, link columns could be replaced by taxon_name vector.

eubon_search

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

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

id2name(19322, db = "itis")

Can return taxon_name vector

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.