Type: Package
Title: Taxonomic List Processing
Version: 0.0.148
Date: 2025-05-23
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Description: Taxonomic lists matching and merging, casting and melting scientific names, managing taxonomic lists from Global Biodiversity Information Facility 'GBIF' https://www.gbif.org/ or Integrated Taxonomic Information System 'ITIS', https://itis.gov/ harvesting names from Wikipedia and fuzzy matching.
License: CC0
Imports: taxize, wikitaxa, plyr, sqldf, stringr, stringdist, rmarkdown, stringi
Encoding: UTF-8
RoxygenNote: 7.3.2
BugReports: https://github.com/vijaybarve/taxotools/issues
NeedsCompilation: no
Packaged: 2025-05-24 00:01:06 UTC; barve
Author: Vijay Barve ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-27 09:40:05 UTC

taxotools: Taxonomic List Processing

Description

Taxonomic lists matching and merging, casting and melting scientific names, managing taxonomic lists from Global Biodiversity Information Facility 'GBIF' https://www.gbif.org/ or Integrated Taxonomic Information System 'ITIS', https://itis.gov/ harvesting names from Wikipedia and fuzzy matching.

Author(s)

Maintainer: Vijay Barve vijay.barve@gmail.com (ORCID)

See Also

Useful links:

Darwin Core to Taxolist format

Description

Converts a Darwin Core name list to taxolist format

Usage

DwC2taxo(namelist, statuslist = NA, source = NA)

Arguments

namelist

names list in Darwin Core format

statuslist

vector listing taxonomicStatus to be considered in the namelist. If Default value is NA, automatically uses list of

  • Accepted

  • Synonym

  • Valid

  • heterotypic Synonym

  • homotypic Synonym

  • doubtful,

  • proparte synonym

source

source of the namelist i.e. Global Biodiversity Information Facility 'GBIF' or Integrated Taxonomic Information System 'ITIS'. Default NA

Details

The name lists downloaded from 'GBIF' or 'ITIS' website in Darwin Core (DwC) format has all the required fields for taxolist. The list just needs to be converted to taxolist by renaming column names and and quality checked in terms of missing synonym to accepted name linkages at times.

Value

names list is taxolist format

See Also

Other List functions: cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


dwclist <- data.frame("taxonKey" = c("5129025","6224429","1896957"),
                      "scientificName" =  c("Charaxes solon Fabricius, 1793",
                                            "Papilio jason Linnaeus, 1767",
                                            "Charaxes jasius (Linnaeus, 1767)"),
                     "acceptedTaxonKey" = c("5129025","1896957","1896957"),
                     "acceptedScientificName" = c("Charaxes solon Fabricius, 1793",
                                                  "Charaxes jasius (Linnaeus, 1767)",
                                                  "Charaxes jasius (Linnaeus, 1767)"),
                     "taxonRank" = c("SPECIES","SPECIES","SPECIES"),
                     "taxonomicStatus" = c("ACCEPTED","SYNONYM","ACCEPTED"),
                     "family" = c("Nymphalidae","Nymphalidae","Nymphalidae"),
                     "order" = c("Lepidoptera","Lepidoptera","Lepidoptera"),
                     stringsAsFactors = FALSE)
                     
mytaxo <- DwC2taxo(dwclist)

Build genus level synonyms

Description

Build a genus level synonym list from master list.

Usage

build_gen_syn(dat)

Arguments

dat

master list

Details

This genus level synonym list is generated for passing on to get_accepted_names function as a parameter

Value

data frame with genus level synonyms with two columns viz. Valid_genus and Original_Genus

See Also

Other Name functions: cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


master <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                     "Hypochlorosis tenebrosa",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia ancharia",
                                     "Hypochlorosis ancharia tenebrosa",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c(0,1,1,0,0,0,0),
                     "source" = c("itis","itis","wiki","wiki","itis",
                                  "itis","itis"),
                     stringsAsFactors = FALSE)
 gen_syn <- build_gen_syn(master)

Construct canonical names

Description

Construct canonical names using Genus, Species and Subspecies fields. At times due to spaces or NAs in the data fields, it makes it tricky to generate canonical names.

Usage

cast_canonical(
  dat,
  canonical = "canonical",
  genus = "",
  species = "",
  subspecies = "",
  verbose = FALSE
)

Arguments

dat

data frame containing taxonomic list

canonical

field name for canonical names. Default 'canonical'

genus

field name for Genus field

species

field name for Species field

subspecies

field name for Subspecies field

verbose

verbose output, Default: FALSE

Value

a data frame containing Canonical names field added or repopulated using filed names for Genus, Species and Subspecies specified in parameters

See Also

Other Name functions: build_gen_syn(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


mylist <- data.frame("genus" = c("Acodon", "Akodon", "Abrothrix", "Abeomelomys"),
                     "species" = c("jelskii","longipilis","longipilis", "sevia"),
                     "subspecies" = c("pyrrhotis","castaneus","", NA))
cast_canonical(mylist,"canonical","genus","species","subspecies")

Build a character (comma) separated List within field

Description

Builds a character (comma) separated list within a field given a data frame with primary field repeating values and secondary field with values to be character separated in the same field (secondary)

Usage

cast_cs_field(
  data,
  pri,
  sec,
  duplicate = FALSE,
  sepchar = ",",
  verbose = FALSE
)

Arguments

data

data frame containing primary and secondary data columns

pri

Primary field name (repeating values)

sec

Secondary field (values would be added to same record, comma separated)

duplicate

If true, duplicate entries are allowed in secondary field

sepchar

Character separator between the data items. Default is comma

verbose

verbose output, Default: FALSE

Value

a data frame with two fields Primary and secondary (comma separated list)

See Also

Other List functions: DwC2taxo(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


SynList <- data.frame("canonical" = c("Abrothrix longipilis",
                                    "Abrothrix longipilis",
                                    "Abrothrix longipilis",
                                    "Abrothrix longipilis",
                                    "Abrothrix jelskii",
                                    "Abrothrix jelskii"),
                   "synonym" = c("Akodon longipilis",
                                 "Acodon hirtus",
                                 "Akodon longipilis apta",
                                 "Akodon longipilis castaneus",
                                 "Chroeomys jelskii",
                                 "Acodon jelskii pyrrhotis"),
                    stringsAsFactors = FALSE)
  cast_cs_field(SynList,"canonical","synonym")

Cast scientific name using taxonomic fields

Description

Combine scientific names using Genus, Species, Subspecies, Author etc.

Usage

cast_scientificname(
  dat = NULL,
  sciname = "scientificname",
  genus = "",
  subgenus = "",
  species = "",
  subspecies = "",
  author = "",
  verbose = FALSE
)

Arguments

dat

data frame containing taxonomic data

sciname

column name for scientific names, Default: 'scientificname'

genus

column name for genus, Default: 'genus'

subgenus

column name for subgenus, Default: ”

species

column name for species, Default: 'species'

subspecies

column name for subspecies, Default: 'subspecies'

author

column name for author, Default: 'author'

verbose

verbose output, Default: FALSE

Details

Helpful function to break down Scientific names into Genus, Subgenus, species, Subspecies, Author so that the names can be constructed into canonical names for matching

Value

data frame with additional columns for taxonomic fields

See Also

Other Name functions: build_gen_syn(), cast_canonical(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


mylist <- data.frame("id" = c(11,12,13,14,15,16,17,18,19),
                     "genus" = c("Hypochlorosis","Hypochlorosis","Hypochlorosis",
                                 "Myrina","Hypochlorosis","Hypochlorosis",
                                 "Hypochlorosis","Seuku","Sithon"),
                     "subgenus" = c("","","","","","","(Pseudonotis)","",""),
                     "species" = c("ancharia","ancharia","ancharia",
                                   "lorquinii","ancharia","ancharia",
                                   "metilia","emlongi","lorquinii"),
                     "subspecies" = c("","ancharia","humboldti",
                                      "","tenebrosa"," tenebrosa",
                                      "","",""),
                     "author" = c("(Hewitson, 1869)","(Hewitson, 1869)","Druce, 1894",
                                  "C. & R. Felder, 1865","Rothschild, 1915",
                                  "Rothschild, 1915","Fruhstorfer, 1908",
                                  "(Domning et al., 1986)",""),
                     stringsAsFactors = FALSE)

cast_scientificname(mylist,genus = "genus", subgenus = "subgenus",
                    species = "species", subspecies = "subspecies",
                    author = "author")

Parse and resolve a scientific name string

Description

Parse the name using Global Names Resolver 'GNR' and Global Biodiversity Information Facility 'GBIF' parse API to make sure the name is scientific name

Usage

check_scientific(name)

Arguments

name

scientific name string to be checked

Value

Resolved canonical name (NULL if not matched)

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


check_scientific("Akodon longipilis (Waterhouse, 1837)")
check_scientific("Mus longipilis Waterhouse, 1837")
check_scientific("Akodon hershkovitzi Patterson, Gallardo, and Freas, 1984")

compact id numbers

Description

Compacting and converting the id values to numeric if required to make sure dependent functions work well

Usage

compact_ids(dat, id = "id", accid = "accid", startid = 1, verbose = TRUE)

Arguments

dat

taxonomic list in a data frame with id and accid columns

id

column name for 'id'. Default 'id'

accid

column name for 'accid'. Default 'accid'

startid

starting id number for the list. Default 1

verbose

verbose output on the console

Details

Helper function to make sure values for ids are in right format and are compact

Value

returns data frame

See Also

Other List functions: DwC2taxo(), cast_cs_field(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


mylist <- data.frame("id" = c("1","2","3","4","5"),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", 
                                  "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c("0","1","1","0","0"),
                     "source" = c("itis","wiki","wiki","itis",
                                  "itis"),
                     stringsAsFactors = FALSE)

mylist_c <- compact_ids(mylist)

mylist_c <- compact_ids(mylist,startid=1001)

mylist <- data.frame("id" = c(11,12,13,14,15),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", 
                                  "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c(0,11,11,0,0),
                     "source" = c("itis","wiki","wiki","itis",
                                  "itis"),
                     stringsAsFactors = FALSE)
                     
mylist_c <- compact_ids(mylist)

Expands Scientific name

Description

At times the genus is specified with first character and '.' rather then repeating genus names every time. These are either synonyms or species of the same genus listed one bellow another. To convert these names to canonical names, we need to expand the genus name (typically) using previous entry in the list.

Usage

expand_name(fullname, shortname)

Arguments

fullname

full scientific name

shortname

scientific name with short form genus name to expand the Genus

Value

scientific name with Genus expanded using reference name provided as parameter

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples

expand_name("Addax gibbosa", "A. mytilopes")
expand_name("Oryx addax", "O. nasomaculatus")

get_accepted_names

Description

Match namelist with master and fetch the accepted names using the linkages provided within the data

Usage

get_accepted_names(
  namelist,
  master,
  gen_syn = NA,
  namelookup = NA,
  mastersource = NA,
  match_higher = FALSE,
  fuzzymatch = TRUE,
  fuzzydist = 2,
  canonical = NA,
  genus = NA,
  species = NA,
  subspecies = NA,
  prefix = "",
  verbose = TRUE
)

Arguments

namelist

data frame of the list of names to be resolved. Must contain either column canonical containing binomial or trinomial name without spp. and var. etc. or may contain columns for genus, species and subspecies (any sub-specific unit) and the names of the columns are passed as subsequent parameters.

master

data frame with required columns id, canonical and accid. Other columns like order, family are optional. Column id is typically running ids for each record and accid will contain 0 if the name is currently accepted name and id number of accepted name in case the name is a synonym. Column canonical contains binomial or trinomial without spp. var. etc.

gen_syn

data frame with columns Original_Genus and Valid_Genus where Original_genus is synonym and valid_genus is one present in the master. Default: NA when gen_syn is not used.

namelookup

Lookup data frame for names where some names might need manual lookup. The columns required are binomial and validname where binomial is new name and validname is present in the master. Default: NA when namelookup is not used.

mastersource

vector of sources to be used for assignment with priority

match_higher

match genus and family names present in canonical field

fuzzymatch

attempt fuzzy matching or not. Default: TRUE

fuzzydist

fuzzy distance while matching. Default : 2

canonical

column containing names to be resolved to accepted names , Default: NA when columns for genus and species are specified.

genus

column containing genus names to be resolved to accepted names and typically accompanied by species and subspecies columns, Default: NA when canonical parameter is supplied.

species

column containing species names to be resolved to accepted names and is accompanied by genus, Default: NA

subspecies

column containing species names to be resolved to accepted names and is accompanied by genus and species, Default: NA

prefix

to be added to all the return fields

verbose

display process messages, Default: TRUE

Details

Name resolution methods:

direct -

was a direct match with name or a synonym

direct2 -

was a direct match with name or a synonym in non mastersource

fuzzy -

used fuzzy matching

gensyn -

genus substitution with known genus level synonyms

lookup -

Manual lookup in earlier processing

sppdrop -

subspecies was dropped

sub2sp -

subspecies elevated to species

genus -

genus was matched

family -

family was matched

NA -

could not be resolved

Note: Make sure all the data frames have same character encoding to prevent errors.

Value

data frame containing all the original columns with following additional columns:

accepted_name -

Accepted name present in the master. NA is not resolved

method -

method used to resolve the name. See details for explanation of each method

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


master <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                    "Hypochlorosis tenebrosa",
                                    "Pseudonotis humboldti",
                                    "Myrina ancharia",
                                    "Hypochlorosis ancharia tenebrosa",
                                    "Hypochlorosis ancharia obiana",
                                    "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                    "accid" = c(0,1,1,1,0,0,0),
                    "source" = c("itis","itis","wiki","wiki","itis",
                                 "itis","itis"),
                    stringsAsFactors = FALSE)

mylist <- data.frame("id"= c(11,12,13,14,15,16,17,18,19),
                    "scname" = c("Hypochlorosis ancharia",
                                 "Hypochlorosis ancharii",
                                 "Hypochlorosis tenebrosa",
                                 "Pseudonotis humboldtii",
                                 "Abrothrix longipilis",
                                 "Myrinana anchariana",
                                 "Hypochlorosis ancharia ancharia",
                                 "Myrina lorquinii",
                                 "Sithon lorquinii"),
                    stringsAsFactors = FALSE)

res <- get_accepted_names(namelist = mylist,
                         master=master,
                         canonical = "scname")

gen_syn_list <- data.frame("Original_Genus"=c("Pseudonotis",
                                             "Myrina"),
                          "Valid_Genus"=c("Hypochlorosis",
                                          "Hypochlorosis"),
                          stringsAsFactors = FALSE)

res <- get_accepted_names(namelist = mylist,
                         master=master,
                         gen_syn = gen_syn_list,
                         canonical = "scname")

lookup_list <- data.frame("binomial"=c("Sithon lorquinii",
                                      "Hypochlorosis humboldti"),
                         "validname"=c("Hypochlorosis lorquinii",
                                       "Hypochlorosis lorquinii"),
                         stringsAsFactors = FALSE)

res <- get_accepted_names(namelist = mylist,
                         master=master,
                         gen_syn = gen_syn_list,
                         namelookup = lookup_list,
                         canonical = "scname")

mylist_s <- melt_canonical(mylist,canonical = "scname",
                          genus = "genus",
                          species = "species",
                          subspecies = "subspecies")

res <- get_accepted_names(namelist = mylist_s,
                         master=master,
                         gen_syn = gen_syn_list,
                         namelookup = lookup_list,
                         genus = "genus",
                         species = "species",
                         subspecies = "subspecies")

res <- get_accepted_names(namelist = mylist_s,
                         master=master,
                         gen_syn = gen_syn_list,
                         namelookup = lookup_list,
                         mastersource = c("itis"),
                         genus = "genus",
                         species = "species",
                         subspecies = "subspecies")

mylist <- data.frame("id"= c(11,12,13,14,15,16,17,18),
                    "scname" = c("Hypochlorosis ancharia",
                                 "Hypochlorosis ancharii",
                                 "Hypochlorosis",
                                 "Pseudonotis",
                                 "Lycaenidae",
                                 "Pseudonotis humboldtii",
                                 "Abrothrix longipilis",
                                 "Myrinana anchariana"),
                    stringsAsFactors = FALSE)

res <- get_accepted_names(namelist = mylist,
                         master=master,
                         match_higher = TRUE,
                         canonical = "scname")

Get Integrated Taxonomic Information System 'ITIS' Synonyms for a Scientific Name

Description

Fetch Synonyms using Integrated Taxonomic Information System 'ITIS' web service

Usage

get_itis_syn(scname)

Arguments

scname

Scientific Name

Value

a list containing synonyms

See Also

Other ITIS functions: list_itis_syn()

Examples

## Not run: 
get_itis_syn("Abrothrix longipilis")
get_itis_syn("Abditomys latidens")

## End(Not run)

get synonyms

Description

get all the synonyms from the master list for the names in the checklist

Usage

get_synonyms(master = NULL, checklist = NULL, commasep = FALSE, verbose = TRUE)

Arguments

master

master list of names (taxolist)

checklist

list of names to be processed (taxolist)

commasep

return list should be comma separated list or each synonym on its own row. Default false

verbose

verbose output on the console

Value

Data frame with names from the checklist and their synonyms present in the master list

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


master <- data.frame("id" = c(1,2,3,4,5),
                        "canonical" = c("Hypochlorosis ancharia",
                                        "Pseudonotis humboldti",
                                        "Myrina ancharia",
                                        "Hypochlorosis ancharia obiana",
                                        "Hypochlorosis lorquinii"),
                        "family" = c("Lycaenidae", "Lycaenidae", 
                                     "Lycaenidae", "Lycaenidae",
                                      "Lycaenidae"),
                        "accid" = c(0,1,1,0,0),
                        "source" = c("itis","wiki","wiki","itis",
                                     "itis"),
                        stringsAsFactors = FALSE)
checklist <- data.frame("id" = c(1,2,3),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Hypochlorosis tenebrosa",
                                     "Hypochlorosis ancharia tenebrosa"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae"),
                     "accid" = c(0,1,0),
                     "source" = c("itis","itis","itis"),
                     stringsAsFactors = FALSE)

get_synonyms(master,checklist,commasep=FALSE)
get_synonyms(master,checklist,commasep=TRUE)

Guess the taxonomic rank of Scientific Name

Description

Guesses the taxonomic rank i.e. Genus, Species or Subspecies based on number of words

Usage

guess_taxo_rank(name)

Arguments

name

scientific name string to be checked

Value

"Genus or above"

= single word

"Species"

= two words

"Subspecies"

= three words

"Unknown"

= zero or more than three words

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples

guess_taxo_rank("")
guess_taxo_rank("Akodon longipilis")
guess_taxo_rank("Akodon")
guess_taxo_rank("Abrocoma cinerea shistacea")
guess_taxo_rank("Abrocoma cinerea shistacea shistacea")

Get higher taxonomy data for list of names

Description

Retrieve higher taxonomy information (like Family and Order) for each record from the "Encyclopedia of Life" web API.

Usage

list_higher_taxo(
  indf,
  canonical,
  genus = FALSE,
  verbose = FALSE,
  progress = TRUE
)

Arguments

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.

Details

This function 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.

Value

data frame with added / updated columns

"Kingdom"

Kingdom of the Scientific name

"Phylum"

Phylum of the Scientific name

"Order_"

Order of the Scientific name

"Family"

Family of the Scientific name

"Genus"

Genus of the Scientific name

and also saves a local copy of taxonomy downloaded for future use in 'taxo.db' sqlite file

See Also

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()

Examples

## 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)

Get ITIS Synonyms for list of names

Description

Fetch Synonyms from Integrated Taxonomic Information System 'ITIS'

Usage

list_itis_syn(namelist)

Arguments

namelist

list of scientific names

Value

a data frame containing canonical names (passed) and synonyms

See Also

Other ITIS functions: get_itis_syn()

Examples

## Not run: 
list_itis_syn("Abrothrix longipilis")
list_itis_syn(c("Abditomys latidens", "Abeomelomys sevia", "Abrothrix jelskii" ))

## End(Not run)

Get Wikipedia Synonyms for list of names

Description

Fetch Synonyms from Wikipedia and clean them for use

Usage

list_wiki_syn(namelist, verbose = TRUE)

Arguments

namelist

list of scientific names

verbose

status output. Default TRUE

Value

a data frame containing names, synonyms and Canonical synonyms matched with is scientific name backbone taxonomy

Name

: Scientific name

WikiName

: Wikipedia page name

OrigSyn

: Original synonym returned by Wikipedia

Syn

: Synonym in canonical form, matched with GBIF

Examples


 list_wiki_syn("Abrothrix illutea")
 list_wiki_syn(c("Abditomys latidens", "Abeomelomys sevia",
                 "Abrocoma schistacea"))

match two taxonomic lists

Description

match two taxonomic lists using canonical names

Usage

match_lists(master, checklist, masterfld, checklistfld)

Arguments

master

master taxonomic list

checklist

match taxonomic list

masterfld

field name for canonical name in master list

checklistfld

field name for canonical name in match list

Value

a list with data frames containing matched records, records only in master and checklist and statistics about the records including Jaccard index

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


master <- data.frame("canonical" = c("Abrothrix longipilis",
                                    "Acodon hirtus",
                                    "Akodon longipilis apta",
                                    "Akodon longipilis castaneus",
                                    "Chroeomys jelskii",
                                    "Acodon jelskii pyrrhotis"),
                    stringsAsFactors = FALSE)
checklist <- data.frame("canonical" = c("Abrothrix longipilis",
                                    "Akodon longipilis apta",
                                    "Akodon longipilis castaneus",
                                    "Abrothrix jelskii",
                                    "Acodon jelskii pyrrhotis"),
                    stringsAsFactors = FALSE)
match_lists(master,checklist,"canonical","canonical")

Deconstruct canonical names

Description

Deconstruct canonical names into Genus, Species and Subspecies fields

Usage

melt_canonical(
  dat,
  canonical = "",
  genus = "",
  species = "",
  subspecies = "",
  verbose = FALSE
)

Arguments

dat

data frame containing taxonomic list

canonical

field name for canonical names

genus

field name for Genus

species

field name for Species

subspecies

field name for Subspecies

verbose

verbose output, Default: FALSE

Value

a data frame containing Genus, Species and Subspecies fields added or repopulated using data in canonical name field. If unable to parse the name Genus, Species and Subspecies fields will have NA.

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_scientificname(), resolve_names(), taxo_fuzzy_match()

Examples


mylist <- data.frame("canonical" = c("Abrothrix longipilis",
                                    "Acodon hirtus",
                                    "Akodon longipilis apta",
                                    "AKODON LONGIPILIS CASTANEUS",
                                    "Chroeomys jelskii",
                                    "Acodon jelskii pyrrhotis"),
                    stringsAsFactors = FALSE)
melt_canonical(mylist,"canonical","genus","species","subspecies")

Generate a list melting character (comma) separated field values into multiple records

Description

Builds a list, melting character (comma) separated field values given a data frame with a field with repeating values

Usage

melt_cs_field(data, melt, sepchar = ",", verbose = FALSE)

Arguments

data

data frame containing a data columns with character(comma) separated values

melt

Field name with character(comma) separated values

sepchar

Character separator between the data items. Default is comma

verbose

verbose output, Default: FALSE

Value

a data frame with separate records for each value in field specified

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples

## Not run: 
  scnames <- c("Abrothrix longipilis", "Abrothrix jelskii")
  syn_list <- list_itis_syn(scnames)
  cs_syn_list <- cast_cs_field(syn_list ,"Name","Syn")
  syn_list_new <- melt_cs_field(cs_syn_list,"Syn")

## End(Not run)

Melt scientific name into fields

Description

Parse scientific names into Genus, Species, Subspecies, Author etc.

Usage

melt_scientificname(
  dat,
  sciname = "",
  genus = "genus",
  subgenus = "subgenus",
  species = "species",
  subspecies = "subspecies",
  author = "author",
  verbose = FALSE
)

Arguments

dat

data frame containing scientific names

sciname

column name for scientific names, Default: ”

genus

column name for genus, Default: 'genus'

subgenus

column name for subgenus, Default: 'subgenus'

species

column name for species, Default: 'species'

subspecies

column name for subspecies, Default: 'subspecies'

author

column name for author, Default: 'author'

verbose

verbose output, Default: FALSE

Details

Helpful function to break down Scientific names into Genus, Subgenus, species, Subspecies, Author so that the names can be constructed into canonical names for matching

Value

data frame with additional columns for taxonomic fields

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), resolve_names(), taxo_fuzzy_match()

Examples


mylist <- data.frame("id"= c(11,12,13,14,15,16,17,18,19),
                     "scname" = c("Hypochlorosis ancharia (Hewitson, 1869)",
                                  "Hypochlorosis ancharia ssp. ancharia (Hewitson, 1869)",
                                  "Hypochlorosis ancharia ssp. humboldti Druce, 1894",
                                  "Myrina lorquinii C. & R. Felder, 1865",
                                  "Hypochlorosis ancharia tenebrosa Rothschild, 1915",
                                  "Hypochlorosis ancharia  tenebrosa Rothschild, 1915",
                                  "Hypochlorosis (Pseudonotis) metilia Fruhstorfer, 1908",
                                  "Seuku emlongi (Domning et al., 1986)",
                                  "Sithon lorquinii"),
                     stringsAsFactors = FALSE)

melt_scientificname(mylist, sciname="scname", genus="genus",
                    subgenus="subgenus", species="species",subspecies="subspecies",
                    author="author")

merge two lists of names

Description

Useful in generating a master list of names from multiple sources

Usage

merge_lists(master = NULL, checklist = NULL, output = "all", verbose = TRUE)

Arguments

master

master list of names

checklist

list to be merged

output

data returned by the function, one of the five options all, onlyadd, add, merged, new or multi. Default all

verbose

verbose output on the console

Details

Matches names is checklist with names on master and returns following data:

all

= orig + add + new + multi: all the data

onlyadd

= add : returns records from checklist that match with master

add

= orig + add : returns all records from master + matched records from checklist

merged

= orig + add + new : returns all records from master + matched records from checklist + new taxon from checklist

new

= returns only new taxon entities that did not match with master

multi

= taxon from checklist for which two synonyms matched with two different accepted names in master

Value

Data frame with addition column merge_tag. The merge_tag contains four possible values.

orig -

names in the master

add -

checklist names that matched using synonym linkages including direct matches

new -

checklist names that did NOT match with master. Potentially new taxa

multi -

taxon from checklist for which two synonyms matched with two different accepted names in master

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


master <- data.frame("id" = c(1,2,3),
                     "canonical" = c("Hypochlorosis ancharia",
                                     "Hypochlorosis tenebrosa",
                                     "Hypochlorosis ancharia tenebrosa"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae"),
                     "accid" = c(0,1,0),
                     "source" = c("itis","itis","itis"),
                     stringsAsFactors = FALSE)

checklist <- data.frame("id" = c(1,2,3,4,5),
                        "canonical" = c("Hypochlorosis ancharia",
                                        "Pseudonotis humboldti",
                                        "Myrina ancharia",
                                        "Hypochlorosis ancharia obiana",
                                        "Hypochlorosis lorquinii"),
                        "family" = c("Lycaenidae", "Lycaenidae", 
                                     "Lycaenidae", "Lycaenidae",
                                      "Lycaenidae"),
                        "accid" = c(0,1,1,0,0),
                        "source" = c("itis","wiki","wiki","itis",
                                     "itis"),
                        stringsAsFactors = FALSE)
merged_all <- merge_lists(master,checklist,output="all")
new_taxa <- merge_lists(master,checklist,output="new")
merged_with_new <- merge_lists(master,checklist,output="merged")
merged_add <- merge_lists(master,checklist,output="add")
multi_linked <- merge_lists(master,checklist,output="multi")

Resolve canonical names against GNA

Description

Resolve names against Global Names Architecture (GNA) to make sure the name exists

Usage

resolve_names(
  taxolist,
  sciname = "canonical",
  score_threshold = 0.98,
  best_match_only = TRUE,
  add_fields = NA,
  verbose = TRUE
)

Arguments

taxolist

(data frame) taxonomic list

sciname

() column name for scientific names

score_threshold

(numeric) to make sure names match as desired. Default (0.98) Higher value indicates best match, lower values would return matches at genus level

best_match_only

(logical) If TRUE, best match only returned else return all records returned by GNA. Default: TRUE

add_fields

(character) One of NA (default) , minimal or all. NA adds a logical column 'resolved', Minimal gives back just four fields, whereas all gives all fields back.

verbose

(logical) verbose output, Default: FALSE

Value

(data frame) names list resolves

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), taxo_fuzzy_match()

Examples


mylist <- data.frame("canonical" = c("Abrothrix longipilis",
                                     "Acodon hirtus",
                                     "Akodon longipilis apta",
                                     "AKODON LONGIPILIS CASTANEUS",
                                     "Chroeomys jelskii",
                                     "Acodon jelskii pyrrhotis"),
                     stringsAsFactors = FALSE)
test <- resolve_names(mylist)
test1 <- resolve_names(mylist,add_fields = "minimal")
test2 <- resolve_names(mylist,best_match_only = FALSE,add_fields = "minimal")
test3 <- resolve_names(mylist,best_match_only = FALSE,add_fields = "all")

Synonym list to taxolist

Description

Converts a Synonym list with Accepted Names and Synonym columns to taxolist format

Usage

syn2taxo(
  synlist,
  canonical = "canonical",
  synonym = "synonym",
  verbose = FALSE
)

Arguments

synlist

Synonym list with Accepted name (canonical) and Synonym columns

canonical

Accepted names column name, Default: 'canonical'

synonym

Synonym column name , Default: 'synonym'

verbose

verbose output on the console

Details

Converts a synonyms list to taxolist format. If order and family fields are present, then they are carried forward else NAs are populated. Duplicate synomyms with same source are removed but with different sources are retained.

Value

returns a data frame in taxolist format with all the names in canonical column and accepted names linked to synonyms using id and accid fields. Order, family and (guessed) taxonlevel are added if missing. Genus, species and subspecies fields are added by melting the canonical names.

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


 synlist <- data.frame("id" = c(1,2,3),
                       "canonical" = c("Hypochlorosis ancharia",
                                       "Hypochlorosis ancharia",
                                       "Hypochlorosis ancharia"),
                       "synonym" = c( "Hypochlorosis tenebrosa",
                                      "Pseudonotis humboldti",
                                      "Myrina ancharia"),
                       "family" = c("Lycaenidae", "Lycaenidae", 
                                    "Lycaenidae"),
                       "source" = c("itis","wiki","wiki"),
                       stringsAsFactors = FALSE)
                       
 mytaxo <- syn2taxo(synlist)

Convert all subspecies into synonyms of the species

Description

used in generating master lists

Usage

synonymize_subspecies(master, return_unmatched = FALSE, verbose = TRUE)

Arguments

master

List of names with a field named canonical

return_unmatched

If the return values should be unmatched (orphan) subspecies records. Default: FALSE

verbose

display process messages, Default: TRUE

Details

While dealing with taxonomic names only at species level, to take advantage of sub-specific names already available in the lists are sometimes treated as synonyms of the names at species rank. To convert all the subspecies names as synonyms this function is very handy. This function will add id, accid and taxonrank columns ro return data if missing from original data.

Value

Same list of names with id and accid fields added (or data updated the fields exists) with all subspecies linked to the species names as synonyms

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), taxo2DwC(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


master <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                     "Hypochlorosis tenebrosa",
                                     "Pseudonotis humboldti",
                                     "Myrina ancharia ancharia",
                                     "Hypochlorosis ancharia tenebrosa",
                                     "Hypochlorosis ancharia obiana",
                                     "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                     "accid" = c(0,1,1,0,0,0,0),
                     "source" = c("itis","itis","wiki","wiki","itis",
                                  "itis","itis"),
                     stringsAsFactors = FALSE)

synonymize_subspecies(master)
synonymize_subspecies(master,return_unmatched = TRUE)

Taxolist to Darwin Core (DwC)

Description

Converts a taxolist to Darwin Core format

Usage

taxo2DwC(taxolist, verbose = TRUE)

Arguments

taxolist

taxolist

verbose

verbose output, Default: TRUE

Details

Converts a taxolist to Darwin Core format

Value

returns a taxonomic list in DwC format

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2doc(), taxo2syn(), wiki2taxo()

Examples


mytaxo <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                    "Hypochlorosis tenebrosa",
                                    "Pseudonotis humboldti",
                                    "Myrina ancharia",
                                    "Hypochlorosis ancharia tenebrosa",
                                    "Hypochlorosis ancharia obiana",
                                    "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                    "accid" = c(0,1,1,1,0,0,0),
                    "source" = c("itis","itis","wiki","wiki","itis",
                                 "itis","itis"),
                    stringsAsFactors = FALSE)
mysynlst <- taxo2DwC(mytaxo)

Taxolist to document

Description

Converts a taxolist to a formatted document in html, pdf or word document

Usage

taxo2doc(
  taxolist = NULL,
  genus = NA,
  family = NA,
  title = "",
  addsource = TRUE,
  mastersource = "",
  duplicatesyn = TRUE,
  sourcecol = c("black", "blue"),
  outformat = "html_document",
  outdir = tempdir(),
  outfile = "taxolist.html"
)

Arguments

taxolist

taxolist

genus

only process for specific genus. Default("") implying process all

family

only process for specific family. Default("") implying process all

title

List title you want to print in output header

addsource

boolean If the source tag should be displayed. Default TRUE

mastersource

source string for the master list

duplicatesyn

boolean if synonyms should to displayed in their alphabetical sorted position too. Default TRUE

sourcecol

vector of text color values for each source value

outformat

output format one of "html_document", "word_document", "odt_document", "rtf_document", "pdf_document". Default ("html_document")

outdir

output directory for the document. Default temporary directory.

outfile

output file name. Default ("taxolist.html")

Details

Converts a taxolist to a formatted document in html, pdf or word document making it easy for taxonomist to read through the data

Value

NULL Saves a document file

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2syn(), wiki2taxo()

Examples


mytaxo <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                    "Hypochlorosis tenebrosa",
                                    "Pseudonotis humboldti",
                                    "Myrina ancharia",
                                    "Hypochlorosis ancharia tenebrosa",
                                    "Hypochlorosis ancharia obiana",
                                    "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                    "accid" = c(0,1,1,1,0,0,0),
                    "source" = c("itis","itis","wiki","wiki","itis",
                                 "itis","itis"),
                    stringsAsFactors = FALSE)
taxo2doc(mytaxo)
taxo2doc(mytaxo,source="My list")

Taxolist to Synonym list

Description

Converts a taxolist to Synonym list with Accepted Names and Synonym columns format

Usage

taxo2syn(
  taxolist,
  canonical = "canonical",
  synonym = "synonym",
  duplicate = FALSE,
  sepchar = ","
)

Arguments

taxolist

taxolist

canonical

names column name, Default: 'canonical'

synonym

Synonym column name to be created, Default: 'synonym'

duplicate

If true, duplicate entries are allowed in secondary field

sepchar

Character separator between the data items. Default is comma

Details

Converts a taxolist to synonyms list

Value

returns a synonym list all the names in same column and accepted names linked to synonyms with id and accid fields

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), wiki2taxo()

Examples


mytaxo <- data.frame("id" = c(1,2,3,4,5,6,7),
                    "canonical" = c("Hypochlorosis ancharia",
                                    "Hypochlorosis tenebrosa",
                                    "Pseudonotis humboldti",
                                    "Myrina ancharia",
                                    "Hypochlorosis ancharia tenebrosa",
                                    "Hypochlorosis ancharia obiana",
                                    "Hypochlorosis lorquinii"),
                     "family" = c("Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae", "Lycaenidae", "Lycaenidae",
                                  "Lycaenidae"),
                    "accid" = c(0,1,1,1,0,0,0),
                    "source" = c("itis","itis","wiki","wiki","itis",
                                 "itis","itis"),
                    stringsAsFactors = FALSE)
mysynlst <- taxo2syn(mytaxo)

taxo_fuzzy_match

Description

Fuzzy matching with names

Usage

taxo_fuzzy_match(name, master, dist = 2)

Arguments

name

Name to search

master

List of names

dist

Distance tolerance, Default: 2

Details

Fuzzy matching with names in the master list and return best match.

Value

Matched name, string distance and original name. Null if not found.

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), resolve_names()

Examples


master <- data.frame("canonical" = c("Abrothrix longipilis",
                                    "Acodon hirtus",
                                    "Akodon longipilis apta",
                                    "Akodon longipilis castaneus",
                                    "Chroeomys jelskii",
                                    "Acodon jelskii pyrrhotis"),
                    stringsAsFactors = FALSE)
 taxo_fuzzy_match("Acodon hirta",master)

Wikipedia list to taxo

Description

Converts the output of list_wiki_syn function to taxolist format of taxotools package

Usage

wiki2taxo(wikisyn)

Arguments

wikisyn

Wikipedia synonyms list

Details

Output of list_wiki_syn function has different format than taxolist. This function converts it making sure to add additional fields and maintain the synonym linkages.

Value

taxolist

See Also

Other List functions: DwC2taxo(), cast_cs_field(), compact_ids(), get_synonyms(), match_lists(), melt_cs_field(), merge_lists(), syn2taxo(), synonymize_subspecies(), taxo2DwC(), taxo2doc(), taxo2syn()

Examples


 wikilist <- data.frame("Name" = c("Abrothrix illutea",
                                   "Abrothrix illutea"),
                        "WikiName" = c("Abrothrix illuteus",
                                       "Abrothrix illuteus"),
                        "OrigSyn" = c("Akodon illuteus",
                                      "Abrothrix illuteus"),
                        "Syn" = c("Akodon illuteus",
                                  "Abrothrix illuteus"))
 wiki2taxo(wikilist)