Taxon usage names for a taxon concept can be divided into three categories: accepted names, basionyms and synonyms. Each single taxon concept may at least have an accepted name, while basionym and synonyms are optional.
The function accepted_name() retrieves the accepted names for the indicated
taxon concepts or for the whole taxlist object.
By using show_traits=TRUE, the respective taxon traits will be
displayed as well, providing an overview of taxa included in the object.
The replacement method for this function will set the respective usage name
IDs as accepted names for the respective taxon concept, provided that these
names are already set as synonyms in the respective concepts.
The function synonyms() is working in a similar way as accepted_name(),
but this function does not include taxon traits in the output.
Alternatives for inserting new synonyms into a taxon concept are either
moving synonyms from other taxa by using change_concept<- or
inserting new names in the object by using add_synonym().
The function basionym() is retrieving and setting basionyms in the
respective taxon concepts similarly to accepted_name, but this function
does not retrieve any information on taxon traits, either.
The fucntion change_concept<- replace a taxon usage name (argument
'UsageID') to a different taxonomic concept (argument 'value').
Usage
accepted_name(taxlist, ...)
# S3 method for taxlist
accepted_name(taxlist, ConceptID, show_traits = FALSE, ...)
accepted_name(taxlist, ...) <- value
# S3 method for taxlist
accepted_name(taxlist, ConceptID, ...) <- value
synonyms(taxlist, ...)
# S3 method for taxlist
synonyms(taxlist, ConceptID, ...)
basionym(taxlist, ...)
# S3 method for taxlist
basionym(taxlist, ConceptID, ...)
basionym(taxlist, ...) <- value
# S3 method for taxlist
basionym(taxlist, ConceptID, ...) <- value
change_concept(taxlist, ...) <- value
# S3 method for taxlist
change_concept(taxlist, UsageID, ...) <- valueArguments
- taxlist
An object of class taxlist.
- ...
Further arguments passed among methods.
- ConceptID
Integer containing concept IDs where to request or set names for one category.
- show_traits
Logical value, whether traits should be included in the output of
accepted_nameor not.- value
Integer containing usage IDs to be set to the respective category in the respective taxon concept.
- UsageID
Numeric vector with taxon usage IDs that will be changed to a different taxonomic concept.
Value
Most of the methods return information in data frames, while replacement methods do it as taxlist objects.
See also
add_synonym() change_concept<-
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Set a different accepted name for Cyclosorus interruptus
summary(Easplist, "Cyclosorus interruptus")
#> ------------------------------
#> concept ID: 50074
#> view ID: 1
#> level: species
#> parent: 55055 Cyclosorus Link
#>
#> # accepted name:
#> 50074 Cyclosorus interruptus (Willd.) H. Itô
#>
#> # synonyms (13):
#> 52002 Dryopteris gongylodes (Schkuhr) Kuntze
#> 52008 Thelypteris interrupta (Willd.) K. Iwats.
#> 52009 Cyclosorus striatus Ching
#> 53097 Pteris interrupta Willd.
#> 53098 Aspidium continuum Desv.
#> 53099 Aspidium ecklonii Kunze
#> 53100 Aspidium gongylodes Schkuhr
#> 53101 Aspidium obtusatum Sw.
#> 53102 Aspidium pteroides (Retz.) Sw.
#> 53103 Aspidium serra (Sw.) Sw.
#> 53104 Aspidium serratum Sw.
#> 53105 Aspidium unitum (L.) Sw.
#> 53106 Nephrodium propinquum R. Br.
#> ------------------------------
accepted_name(Easplist, 50074) <- 53097
summary(Easplist, 50074)
#> ------------------------------
#> concept ID: 50074
#> view ID: 1
#> level: species
#> parent: 55055 Cyclosorus Link
#>
#> # accepted name:
#> 53097 Pteris interrupta Willd.
#>
#> # synonyms (13):
#> 50074 Cyclosorus interruptus (Willd.) H. Itô
#> 52002 Dryopteris gongylodes (Schkuhr) Kuntze
#> 52008 Thelypteris interrupta (Willd.) K. Iwats.
#> 52009 Cyclosorus striatus Ching
#> 53098 Aspidium continuum Desv.
#> 53099 Aspidium ecklonii Kunze
#> 53100 Aspidium gongylodes Schkuhr
#> 53101 Aspidium obtusatum Sw.
#> 53102 Aspidium pteroides (Retz.) Sw.
#> 53103 Aspidium serra (Sw.) Sw.
#> 53104 Aspidium serratum Sw.
#> 53105 Aspidium unitum (L.) Sw.
#> 53106 Nephrodium propinquum R. Br.
#> ------------------------------
## Inserting a new name first
summary(Easplist, "Basella alba")
#> ------------------------------
#> concept ID: 68
#> view ID: 1
#> level: species
#> parent: 54790 Basella L.
#>
#> # accepted name:
#> 68 Basella alba L.
#> ------------------------------
Easplist <- add_synonym(taxlist = Easplist, ConceptID = 68,
TaxonName = "Basella cordifolia", AuthorName = "Lam.")
summary(Easplist, 68)
#> ------------------------------
#> concept ID: 68
#> view ID: 1
#> level: species
#> parent: 54790 Basella L.
#>
#> # accepted name:
#> 68 Basella alba L.
#>
#> # synonyms (1):
#> 56139 Basella cordifolia Lam.
#> ------------------------------
accepted_name(Easplist, 68) <- 56139
summary(Easplist, 68)
#> ------------------------------
#> concept ID: 68
#> view ID: 1
#> level: species
#> parent: 54790 Basella L.
#>
#> # accepted name:
#> 56139 Basella cordifolia Lam.
#>
#> # synonyms (1):
#> 68 Basella alba L.
#> ------------------------------
## Display synonyms
head(synonyms(taxlist = Easplist))
#> TaxonUsageID TaxonConceptID TaxonName AuthorName
#> 2 52313 1 Hibiscus esculentus L.
#> 5 50361 3 Pavonia patens (Andrews) Chiov.
#> 23 50001 20 Spilanthes mauritiana (A. Rich. ex Pers.) DC.
#> 25 50002 21 Spilanthes uliginosa Sw.
#> 29 50003 24 Podocarpus usambarensis Pilg.
#> 44 50004 38 Amaranthus cruentus L.
#> AcceptedName AuthorAcceptedName
#> 2 Abelmoschus esculentus (L.) Moench
#> 5 Abutilon mauritianum (Jacq.) Medik.
#> 23 Acmella caulirhiza Delile
#> 25 Acmella uliginosa (Sw.) Cass.
#> 29 Afrocarpus usambarensis (Pilg.) C. N. Page
#> 44 Amaranthus hybridus ssp. cruentus (L.) Thell.
## Synonyms for an specific concept
synonyms(taxlist = Easplist, ConceptID = 20)
#> TaxonUsageID TaxonConceptID TaxonName
#> 23 50001 20 Spilanthes mauritiana
#> 2889 52448 20 Spilanthes caulirhiza
#> 2890 52449 20 Acmella mauritiana
#> 2891 52450 20 Spilanthes africana
#> 2892 52451 20 Spilanthes abyssinica
#> 2893 52452 20 Eclipta filicaulis
#> 2894 52453 20 Spilanthes filicaulis
#> 2895 52454 20 Spilanthes acmella var. acmella
#> 2896 52455 20 Verbesina acmella
#> 2897 52456 20 Spilanthes acmella
#> 2898 52457 20 Blainvillea acmella
#> 2899 52458 20 Eclipta latifolia
#> 2900 52459 20 Blainvillea latifolia
#> 2901 52460 20 Blainvillea rhomboidea
#> 2902 52461 20 Blainvillea dalla-vedovae
#> 2903 52462 20 Verbesina dichotoma
#> 2904 52463 20 Blainvillea dichotoma
#> 2905 52464 20 Spilanthes caulirhiza var. madagascariensis
#> 2906 52465 20 Spilanthes mauritiana f. madagascariensis
#> AuthorName AcceptedName AuthorAcceptedName
#> 23 (A. Rich. ex Pers.) DC. Acmella caulirhiza Delile
#> 2889 (Delile) DC. Acmella caulirhiza Delile
#> 2890 A. Rich. ex Pers. Acmella caulirhiza Delile
#> 2891 DC. Acmella caulirhiza Delile
#> 2892 Sch. Bip. ex A. Rich. Acmella caulirhiza Delile
#> 2893 Schumach. & Thonn. Acmella caulirhiza Delile
#> 2894 (Schumach. & Thonn.) C. D. Adams Acmella caulirhiza Delile
#> 2895 (L.) Murray Acmella caulirhiza Delile
#> 2896 L. Acmella caulirhiza Delile
#> 2897 (L.) Murray Acmella caulirhiza Delile
#> 2898 (L.) Philipson Acmella caulirhiza Delile
#> 2899 L. f. Acmella caulirhiza Delile
#> 2900 (L. f.) DC. Acmella caulirhiza Delile
#> 2901 Cass. Acmella caulirhiza Delile
#> 2902 A. Terracc. Acmella caulirhiza Delile
#> 2903 Murray Acmella caulirhiza Delile
#> 2904 (Murray) Stewart Acmella caulirhiza Delile
#> 2905 DC. Acmella caulirhiza Delile
#> 2906 (DC.) A. H. Moore Acmella caulirhiza Delile
## Basionym for Cyclosrus interruptus
summary(Easplist, 50074)
#> ------------------------------
#> concept ID: 50074
#> view ID: 1
#> level: species
#> parent: 55055 Cyclosorus Link
#>
#> # accepted name:
#> 53097 Pteris interrupta Willd.
#>
#> # synonyms (13):
#> 50074 Cyclosorus interruptus (Willd.) H. Itô
#> 52002 Dryopteris gongylodes (Schkuhr) Kuntze
#> 52008 Thelypteris interrupta (Willd.) K. Iwats.
#> 52009 Cyclosorus striatus Ching
#> 53098 Aspidium continuum Desv.
#> 53099 Aspidium ecklonii Kunze
#> 53100 Aspidium gongylodes Schkuhr
#> 53101 Aspidium obtusatum Sw.
#> 53102 Aspidium pteroides (Retz.) Sw.
#> 53103 Aspidium serra (Sw.) Sw.
#> 53104 Aspidium serratum Sw.
#> 53105 Aspidium unitum (L.) Sw.
#> 53106 Nephrodium propinquum R. Br.
#> ------------------------------
basionym(Easplist, 50074) <- 53097
summary(Easplist, 50074)
#> ------------------------------
#> concept ID: 50074
#> view ID: 1
#> level: species
#> parent: 55055 Cyclosorus Link
#>
#> # accepted name:
#> 53097 Pteris interrupta Willd.
#>
#> # basionym:
#> numeric(0) character(0) character(0)
#>
#> # synonyms (13):
#> 50074 Cyclosorus interruptus (Willd.) H. Itô
#> 52002 Dryopteris gongylodes (Schkuhr) Kuntze
#> 52008 Thelypteris interrupta (Willd.) K. Iwats.
#> 52009 Cyclosorus striatus Ching
#> 53098 Aspidium continuum Desv.
#> 53099 Aspidium ecklonii Kunze
#> 53100 Aspidium gongylodes Schkuhr
#> 53101 Aspidium obtusatum Sw.
#> 53102 Aspidium pteroides (Retz.) Sw.
#> 53103 Aspidium serra (Sw.) Sw.
#> 53104 Aspidium serratum Sw.
#> 53105 Aspidium unitum (L.) Sw.
#> 53106 Nephrodium propinquum R. Br.
#> ------------------------------
basionym(Easplist, 50074)
#> TaxonConceptID Basionym BasionymName BasionymAuthor
#> 601 50074 53097 Pteris interrupta Willd.
## Move the name Typha aethiopica to concept 573 (T. latifolia)
summary(Easplist, c(50105, 573))
#> ------------------------------
#> concept ID: 50105
#> view ID: 1
#> level: species
#> parent: 55040 Typha L.
#>
#> # accepted name:
#> 50105 Typha domingensis Pers.
#>
#> # synonyms (9):
#> 51999 Typha australis Schumach.
#> 53124 Typha angustifolia ssp. australis (Schumach.) Graebn.
#> 53125 Typha aequalis Schnizl.
#> 53126 Typha angustata Bory & Chaub.
#> 53127 Typha angustifolia ssp. angustata (Bory & Chaub.) Briq.
#> 53128 Typha angustata var. abyssinica Graebn.
#> 53129 Typha angustata var. aethiopica Rohrb.
#> 53130 Typha aethiopica (Rohrb.) Kronfeldt
#> 53131 Typha schimperi Rohrb.
#> ------------------------------
#> concept ID: 573
#> view ID: 1
#> level: species
#> parent: 55040 Typha L.
#>
#> # accepted name:
#> 573 Typha latifolia L.
#> ------------------------------
change_concept(Easplist, 53130) <- 573
summary(Easplist, c(50105, 573))
#> ------------------------------
#> concept ID: 50105
#> view ID: 1
#> level: species
#> parent: 55040 Typha L.
#>
#> # accepted name:
#> 50105 Typha domingensis Pers.
#>
#> # synonyms (8):
#> 51999 Typha australis Schumach.
#> 53124 Typha angustifolia ssp. australis (Schumach.) Graebn.
#> 53125 Typha aequalis Schnizl.
#> 53126 Typha angustata Bory & Chaub.
#> 53127 Typha angustifolia ssp. angustata (Bory & Chaub.) Briq.
#> 53128 Typha angustata var. abyssinica Graebn.
#> 53129 Typha angustata var. aethiopica Rohrb.
#> 53131 Typha schimperi Rohrb.
#> ------------------------------
#> concept ID: 573
#> view ID: 1
#> level: species
#> parent: 55040 Typha L.
#>
#> # accepted name:
#> 573 Typha latifolia L.
#>
#> # synonyms (1):
#> 53130 Typha aethiopica (Rohrb.) Kronfeldt
#> ------------------------------