Package 'Binomen'

Package ‘binomen’ April 26, 2017 Title 'Taxonomic' Specification and Parsing Methods Description Includes functions for working with taxonomic data, including functions for combining, separating, and filtering taxonomic groups by any rank or name. Allows standard ('SE') and non-standard evaluation ('NSE'). Version 0.1.2 License MIT + file LICENSE URL https://github.com/ropensci/binomen BugReports https://github.com/ropensci/binomen/issues LazyLoad yes LazyData yes VignetteBuilder knitr Imports methods, stats, jsonlite, lazyeval, dplyr Suggests roxygen2 (>= 6.0.1), testthat, knitr, taxize, covr RoxygenNote 6.0.1 NeedsCompilation no Author Scott Chamberlain [aut, cre] Maintainer Scott Chamberlain Repository CRAN Date/Publication 2017-04-25 22:11:47 UTC

R topics documented:

binomen-package ...... 2 binomial ...... 3 gethier ...... 3 grouping ...... 4 make_taxon ...... 6 make_taxon_fromclass ...... 7 parts ...... 7

1 2 binomen-package

pick ...... 9 pop ...... 10 rank_table ...... 11 scatter ...... 11 span...... 12 strain ...... 13 taxa ...... 14 taxon ...... 14 taxonref ...... 15 taxonrefs ...... 16 taxon_classes ...... 16 taxon_df ...... 17

Index 18

binomen-package Taxonomic class speciﬁcation and parsing methods

Description Taxonomic class speciﬁcation and parsing methods

Author(s) Scott Chamberlain

Examples library("binomen")

# operating on `taxon` objects out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua') # get single name out %>% pick(family) out %>% pick(genus) out %>% pick(species) out %>% pick(species) %>% name() out %>% pick(species) %>% uri() # get range of names out %>% span(kingdom, genus)

# operating on taxonomic data.frames df <- data.frame(class=c('Magnoliopsida','Magnoliopsida','Magnoliopsida', 'Magnoliopsida','Magnoliopsida','Magnoliopsida'), order=c('Asterales','Asterales','Fagales','Poales','Poales','Poales'), family=c('Asteraceae','Asteraceae','Fagaceae','Poaceae','Poaceae','Poaceae'), genus=c('Helianthus','Helianthus','Quercus','Poa','Festuca','Holodiscus'), stringsAsFactors = FALSE) (df2 <- taxon_df(df)) binomial 3

## select single taxonomic class df2 %>% pick(order) df2 %>% pick(family, genus)

## filter to get a range of classes df2 %>% span(order, genus) df2 %>% span(family, genus)

binomial A class to represent a taxonomic binomial

Description A class to represent a taxonomic binomial

Usage binomial(genus = NULL, epithet = NULL, canonical = NULL, species = NULL, authority = NULL)

Arguments genus A genus name epithet A speciﬁc epithet name canonical Canonical name species Species, genus plus epithet authority Authority name

Examples binomial("Poa") binomial("Poa", "annua", authority="L.")

gethier Get hierarchy as a data.frame

Description Get hierarchy as a data.frame

Usage gethier(x) 4 grouping

Arguments x An object of class taxon

Examples bin <- binomial("Poa", "annua", authority="L.") class <- grouping(kingdom=taxonref("kingdom", "Plantae"), species=taxonref("family", "Poaceae")) out <- taxon(bin, class) # get hierarchy as data.frame gethier(out)

grouping A class to represent a taxonomic classiﬁcation

Description A class to represent a taxonomic classiﬁcation

Usage grouping(kingdom = NULL, subkingdom = NULL, infrakingdom = NULL, division = NULL, phylum = NULL, subdivision = NULL, infradavision = NULL, superclass = NULL, clazz = NULL, subclass = NULL, infraclass = NULL, superorder = NULL, order = NULL, suborder = NULL, infraorder = NULL, superfamily = NULL, family = NULL, subfamily = NULL, tribe = NULL, subtribe = NULL, genus = NULL, subgenus = NULL, section = NULL, subsection = NULL, species = NULL, subspecies = NULL, variety = NULL, race = NULL, subvariety = NULL, stirp = NULL, morph = NULL, form = NULL, aberration = NULL, subform = NULL, unspecified = NULL)

Arguments kingdom A kingdom name subkingdom A subkingdom name infrakingdom A infrakingdom name division A division name phylum A phylum name subdivision A subdivision name infradavision A infradavision name superclass A superclass name clazz A clazz name subclass A subclass name grouping 5

infraclass A infraclass name superorder A superorder name order A order name suborder A suborder name infraorder A infraorder name superfamily A superfamily name family A family name subfamily A subfamily name tribe A tribe name subtribe A subtribe name genus A genus name subgenus A subgenus name section A section name subsection A subsection name species A species name subspecies A subspecies name variety A variety name race A race name subvariety A subvariety name stirp A stirp name morph A morph name form A form name aberration A aberration name subform A subform name unspecified A unspeciﬁed name

Examples

grouping(kingdom=taxonref("kingdom", "Animalia"), species=taxonref("species", "Homo sapiens")) 6 make_taxon

make_taxon Make taxon from class

Description Make taxon from class

Usage make_taxon(genus = "none", epithet = "none", authority = "none", ...)

Arguments genus Genus name, e.g., Homo (in Homo sapiens) epithet Speciﬁc epithet, e.g., sapiens (in Homo sapiens) authority Taxonomic authority ... Further args.

Examples (out <- make_taxon(genus="Poa")) (out <- make_taxon(genus="Poa", epithet="annua", authority="L.")) (out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua')) out$binomial out$binomial$canonical out$binomial$species out$binomial$authority out$grouping out$grouping$family out %>% pick(family) # get a single rank out %>% span(kingdom, family) # get a range of ranks gethier(out) # get hierarchy as data.frame

# Using dplyr df <- data.frame(class=c('Magnoliopsida','Magnoliopsida','Magnoliopsida', 'Magnoliopsida','Magnoliopsida','Magnoliopsida'), order=c('Asterales','Asterales','Fagales','Poales','Poales','Poales'), family=c('Asteraceae','Asteraceae','Fagaceae','Poaceae','Poaceae','Poaceae'), genus=c('Helianthus','Helianthus','Quercus','Poa','Festuca','Holodiscus'), species=c('annuus','petrus','kellog','annua','arundinaceae','fava'), stringsAsFactors = FALSE)

library(dplyr) xx <- df %>% rowwise() xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < family)) %>% .[[1]] xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < genus)) %>% .[[1]] xx %>% do(i = strain(make_taxon(.$species, genus = .$genus), . < species)) %>% .[[1]] make_taxon_fromclass 7

make_taxon_fromclass Make taxon from class

Description Make taxon from class

Usage make_taxon_fromclass(data, authority = "none")

Arguments data A data.frame authority Taxonomic authority

Examples df <- data.frame(rank=c('family','tribe','subtribe','genus','subgenus','species'), name=c('Helianthi','Helianthi','Helianthi','Poa','Festuci','Poa annua'), id=c(1,2,3,4,5,6), stringsAsFactors = FALSE) apply(df, 1, make_taxon_fromclass)

parts Pick out parts by name

Description This suite of functions act on taxon or taxonref objects, and pick out object elements by the name of the function.

Usage name(x, unname = TRUE)

## S3 method for class 'taxon' name(x, unname = TRUE)

## S3 method for class 'taxonref' name(x, unname = TRUE)

uri(x, unname = TRUE)

## S3 method for class 'taxon' uri(x, unname = TRUE) 8 parts

## S3 method for class 'taxonref' uri(x, unname = TRUE)

rank(x, unname = TRUE)

## S3 method for class 'taxon' rank(x, unname = TRUE)

## S3 method for class 'taxonref' rank(x, unname = TRUE)

taxonid(x, unname = TRUE)

## S3 method for class 'taxon' taxonid(x, unname = TRUE)

## S3 method for class 'taxonref' taxonid(x, unname = TRUE)

Arguments x Input, object of class taxon or taxonref unname (logical) Unname output elements? Ignored when input is of class taxonref. Default: TRUE

Value For taxon inputs, gives back a taxonref object. For taxondf inputs, gives back taxondf.

Examples # operating on `taxon` objects out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua')

out %>% name() out %>% uri() out %>% rank() out %>% taxonid()

## or don't unname the output out %>% name(unname = FALSE)

# operating on `taxonref` objects res <- taxonref("genus", "Poa", 56, "http://scottchamberlain.info/") res %>% name() res %>% uri() res %>% rank() res %>% taxonid() pick 9

pick Pick names

Description Pick names

Usage pick(.data, ...)

Arguments .data Input, object of class taxon ... Further unnamed args, see examples

Value For taxon inputs, gives back a taxonref object. For taxondf inputs, gives back taxondf.

Examples # operating on `taxon` objects out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua') out %>% pick(family) out %>% pick(genus) out %>% pick(species, genus) out %>% pick(species) %>% name() out %>% pick(species) %>% uri()

## select single or many taxonomic classes df2 %>% pick(order) df2 %>% pick(family, genus)

# From taxa object df2 %>% scatter %>% pick(family) df2 %>% scatter %>% pick(family, species) df2 %>% scatter %>% pick(family, species, genus) 10 pop

pop Pop names out

Description That is, drop them

Usage pop(.data, ...)

Arguments .data Input, object of class taxon ... Further unnamed args, see examples

Value For taxon inputs gives back a taxon object. For taxa inputs gives back a taxa object. For taxondf inputs, gives back a taxondf object.

Examples # operating on `taxon` objects out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua') ## single taxonomic group out %>% pop(family) out %>% pop(genus) out %>% pop(species) ## many taxonomic groups out %>% pop(family, genus, species)

## pop out a single taxonomic group df2 %>% pop(order) df2 %>% pop(family) df2 %>% pop(genus)

## pop out many taxonomic groups df2 %>% pop(order, family) rank_table 11

df2 %>% pop(order, genus)

# From taxa object df2 %>% scatter %>% pop(family) df2 %>% scatter %>% pop(family, species) df2 %>% scatter %>% pop(family, species, genus)

rank_table Lookup-table for IDs of taxonomic ranks

Description Lookup-table for IDs of taxonomic ranks

Value data.frame with two columns and 34 rows. The two columns: • rankid integer; smaller numbers are higher ranks. • ranks character; rank name. Some rows have more than one name, in which the names are considered of equal height.

scatter Scatter each taxon in a taxondf to a taxon object

Description Scatter each taxon in a taxondf to a taxon object

Usage scatter(x, ...)

assemble(x, ...)

## S3 method for class 'taxa' assemble(x, ...)

Arguments x A taxonomic data.frame ... Further args, ignored for now

Details Right now, assemble may not give back the identical data.frame that one would pass to scatter. 12 span

Value

Gives a taxa object, with each individual component a row from your data.frame, and of class taxon

Examples

## scatter each taxon into a taxon class df2 %>% scatter()

## re-assemble df2 df2 %>% scatter() df2 %>% scatter() %>% assemble

span Parse taxon or taxondf objects by a range of names

Description

Parse taxon or taxondf objects by a range of names

Usage

span(.data, ...)

Arguments

.data Input, object of class taxon ... Pass in two unquoted taxonomic rank names, and only two. May make this more ﬂexible in the future.

Value

A single or list of taxon class objects strain 13

## filter to get a range of classes df2 %>% span(order, genus) df2 %>% span(family, genus)

## from taxa object df2 %>% scatter %>% span(family, species)

strain Parse taxon or taxondf objects by a range of names

Description Parse taxon or taxondf objects by a range of names

Usage strain(.data, ...)

Arguments .data Input, object of class taxon ... Logical predicates. Multiple conditions are combined with &. See Details.

Details Example predicates: • . > family = Get all taxa greater than family • . < family = Get all taxa less than family • . == family = Get all taxa equal to family • . != family = Get all taxa not equal to family • genus < order = Get all taxa between genus and order • genus .. family = Get all taxa between genus and order 14 taxon

Value A single or list of taxon class objects

Examples # operating on `taxon` objects out <- make_taxon(genus="Poa", epithet="annua", authority="L.", family='Poaceae', clazz='Poales', kingdom='Plantae', variety='annua') out %>% strain(. < family) out %>% strain(. < genus) out %>% strain(. > family) out %>% strain(. < family)

taxa A class to represent a list of taxa

Description A class to represent a list of taxa

Usage taxa(...)

Arguments ... An object of class taxon

Examples bin <- binomial("Poa", "annua", authority="L.") class <- grouping(kingdom=taxonref("kingdom", "Plantae"), species=taxonref("family", "Poaceae")) taxa(taxon(bin, class), taxon(bin, class))

taxon A class to represent a single taxon

Description A class to represent a single taxon

Usage taxon(binomial, grouping) taxonref 15

Arguments binomial A binomial name grouping A grouping object

Examples bin <- binomial("Poa", "annua", authority="L.") class <- grouping(kingdom=taxonref("kingdom", "Plantae"), species=taxonref("family", "Poaceae")) taxon(bin, class)

# many names input splist <- c('Litsea bindoniana', 'Rubus ghanakantae', 'Desmanthus palmeri', 'Leptinella longipes', 'Asarum sakawanum', 'Cistanche compacta', 'Ormosia nanningensis', 'Claoxylon physocarpum', 'Hedycarya arborea', 'Hypnum gracile') lapply(splist, binomial)

taxonref A class to represent a taxonomic reference

Description A class to represent a taxonomic reference

Usage taxonref(rank = "none", name = "none", id = "none", uri = "none")

Arguments rank (character) Taxonomic rank name (character) A name id (character,numeric) Identiﬁer uri (character) Source of name

Examples taxonref("genus", "Poa", 56, "http://scottchamberlain.info/")

taxonrefs A class to represent a list of taxonomic references

Description A class to represent a list of taxonomic references

Usage taxonrefs(...)

Arguments ... One or more taxonref objects

Examples

a <- taxonref("genus", "Poa", 56, "http://scottchamberlain.info/") b <- taxonref("genus", "Quercus", 32343, "http://scottchamberlain.info/") taxonrefs(a, b)

taxon_classes Taxonomic class methods

Description Taxonomic class methods

Details The taxonomic classes:

• binomial - A binomial, via binomial • taxonref - A single taxonref, via taxonref • taxonrefs - A list of taxonrefs, via taxonrefs • grouping - A grouping (classiﬁcation) object, via grouping • taxon - A taxon, via taxon • taxa - List of taxon objects, via taxa taxon_df 17

taxon_df Taxon data.frame

Description Taxon data.frame

Usage taxon_df(x)

Arguments x A data.frame of taxa

Examples # subset data.frame using taxonomy df <- data.frame(family=c('Asteraceae','Asteraceae','Asteraceae','Poaceae','Poaceae','Poaceae'), tribe=c('Helianthi','Helianthi','Helianthi','Poaeae','Festuci','Poaeae'), genus=c('Helianthus','Helianthus','Madia','Poa','Festuca','Holodiscus'), stringsAsFactors = FALSE) df2 <- taxon_df(df) df2 %>% pick(family) df2 %>% pick(genus, tribe) Index

∗Topic data rank_table, 11 ∗Topic package binomen-package,2 assemble (scatter), 11 binomen (binomen-package),2 binomen-package,2 binomial,3, 16 gethier,3 grouping,4, 16 make_taxon,6 make_taxon_fromclass,7 name (parts),7 parts,7 pick,9 pop, 10 rank (parts),7 rank_table, 11 scatter, 11 span, 12 strain, 13 taxa, 14, 16 taxon, 14, 16 taxon_classes, 16 taxon_df, 17 taxonid (parts),7 taxonref, 15, 16 taxonrefs, 16, 16 uri (parts),7