Looking for the taxonomic status of a scientific name for a plant based on the database from The Plant List Website.
Arguments
- species
A vector of character strings representing the scientific names of species
- exact
Logical, Wheter the exactly matching search will be applied.
- spell_error_max
Integer, represents the number of spelling errors. Only effective when exact = FALSE.
- detail
Logical, implicate whether detailed version of the results will be displayed, including ID for the names being searched.
Value
The function will reture a data frame containing the following columns
- SCIENTIFIC_NAME
The scientifc name matched
- AUTHOR
the authorship for SCIENTIFIC_NAME
- STATUS
status of this matched scientific name
- FAMILY
The family provided by the plantlist website
- ACCEPTED_ID
the accepted ID for the matched scientific name
- ACCEPTED_SPECIES
The accepted species
- ACCEPTED_AUTHOR
The authorship for the accepted species
Details
The scientific names will be formatted before being processed, including: The first letter of the scientific name will be changed to upper case while the rest will be in lower case; multiple whites paces will be replaced by one, and the white space at the beginning or the end will be removed. The scientific name will then be parsed to GENUS, SPECIES, AUTHOR_OF_SPECIES, INFRASPECIFIC_RANK, INFRASPECIFIC_EPITHET, AUTHOR_OF_INFRASPECIFIC_RANK, respectively. However, only GENUS, SPECIES, INFRASPECIFIC_RANK, INFRASPECIFIC_EPITHET will be used for searching against the embedded TPL database. Please note the authorship will not be used in searching, therefore the same scientific name with different authorship should result in multiple entries.
Since 'f.' is also used in the authorship,please do not provide the author name for the species when it is a form.Eg. the name "Hypoxishirsuta (L.) Coville f. vollosissima Fernald". should be provided as "Hypoxis hirsuta f. vollosissima Fernald" or "Hypoxis hirsuta f. vollosissima".
if exact = TRUE, the function only show the species that perfectly matching the "keywords". If exact = FALSE, the function use the general expression(function grep()) and will return all the species containting the "keywords".
The function also allows Approximate String Matching (Fuzzy Matching) using agrep(), when exact = FALSE and spell_error_max > 0. But it will be much more slower.
References
The Plantlist Website http://www.theplantlist.org/
The embedded database is available at http://pan.baidu.com/s/1hqHrW9I
See also
See Also TPL for family of each genus
Author
Jinlong Zhang jinlongzhang01@gmail.com
Examples
sp <- c( "Elaeocarpus decipiens",
"Syzygium buxifolium",
"Daphniphyllum oldhamii",
"Loropetalum chinense",
"Rhododendron latoucheae",
"Rhododendron ovatum",
"Vaccinium carlesii",
"Schima superba")
status(sp)
#> [1] "8 name(s) to process."
#> [1] "Checking the status for species: 1 Elaeocarpus decipiens"
#> [1] "Checking the status for species: 5 Rhododendron latoucheae"
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY
#> 1 Elaeocarpus decipiens F.B.Forbes & Hemsl. Synonym Elaeocarpaceae
#> 2 Syzygium buxifolium Hook. & Arn. Accepted Myrtaceae
#> 3 Daphniphyllum oldhamii (Hemsl.) K.Rosenthal Synonym Daphniphyllaceae
#> 4 Loropetalum chinense (R. Br.) Oliv. Accepted Hamamelidaceae
#> 5 Rhododendron latoucheae Franch. Accepted Ericaceae
#> 6 Rhododendron ovatum (Lindl.) Planch. ex Maxim. Accepted Ericaceae
#> 7 Vaccinium carlesii Dunn Accepted Ericaceae
#> 8 Schima superba Gardner & Champ. Accepted Theaceae
#> ACCEPTED_SPECIES ACCEPTED_AUTHOR
#> 1 Elaeocarpus sylvestris (Lour.) Poir.
#> 2 Syzygium buxifolium Hook. & Arn.
#> 3 Daphniphyllum pentandrum Hayata
#> 4 Loropetalum chinense (R. Br.) Oliv.
#> 5 Rhododendron latoucheae Franch.
#> 6 Rhododendron ovatum (Lindl.) Planch. ex Maxim.
#> 7 Vaccinium carlesii Dunn
#> 8 Schima superba Gardner & Champ.
status(sp, detail = TRUE)
#> [1] "8 name(s) to process."
#> [1] "Checking the status for species: 1 Elaeocarpus decipiens"
#> [1] "Checking the status for species: 5 Rhododendron latoucheae"
#> SEARCH ID FAMILY
#> 273157 Elaeocarpus decipiens kew-2785478 Elaeocarpaceae
#> 375018 Syzygium buxifolium kew-199335 Myrtaceae
#> 262599 Daphniphyllum oldhamii kew-56437 Daphniphyllaceae
#> 254595 Loropetalum chinense tro-15100094 Hamamelidaceae
#> 224358 Rhododendron latoucheae tro-50060696 Ericaceae
#> 224484 Rhododendron ovatum tro-50060643 Ericaceae
#> 224971 Vaccinium carlesii tro-12304517 Ericaceae
#> 571205 Schima superba tro-31600253 Theaceae
#> SCIENTIFIC_NAME AUTHOR STATUS ACCEPTED_ID
#> 273157 Elaeocarpus decipiens F.B.Forbes & Hemsl. Synonym kew-2786062
#> 375018 Syzygium buxifolium Hook. & Arn. Accepted kew-199335
#> 262599 Daphniphyllum oldhamii (Hemsl.) K.Rosenthal Synonym kew-56446
#> 254595 Loropetalum chinense (R. Br.) Oliv. Accepted tro-15100094
#> 224358 Rhododendron latoucheae Franch. Accepted tro-50060696
#> 224484 Rhododendron ovatum (Lindl.) Planch. ex Maxim. Accepted tro-50060643
#> 224971 Vaccinium carlesii Dunn Accepted tro-12304517
#> 571205 Schima superba Gardner & Champ. Accepted tro-31600253
#> ACCEPTED_SPECIES ACCEPTED_AUTHOR
#> 273157 Elaeocarpus sylvestris (Lour.) Poir.
#> 375018 Syzygium buxifolium Hook. & Arn.
#> 262599 Daphniphyllum pentandrum Hayata
#> 254595 Loropetalum chinense (R. Br.) Oliv.
#> 224358 Rhododendron latoucheae Franch.
#> 224484 Rhododendron ovatum (Lindl.) Planch. ex Maxim.
#> 224971 Vaccinium carlesii Dunn
#> 571205 Schima superba Gardner & Champ.
status("Myrica rubra")
#> [1] "1 name(s) to process."
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY ACCEPTED_SPECIES
#> 1 Myrica rubra (Lour.) Siebold & Zucc. Accepted Myricaceae Myrica rubra
#> ACCEPTED_AUTHOR
#> 1 (Lour.) Siebold & Zucc.
status(c("Myrica rubra", "Adinandra millettii",
"Machilus thunbergii", "Ranunculus japonicus",
"Cyclobalanopsis neglecta" ))
#> [1] "5 name(s) to process."
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY
#> 1 Myrica rubra (Lour.) Siebold & Zucc. Accepted Myricaceae
#> 2 Adinandra millettii <NA> <NA> <NA>
#> 3 Machilus thunbergii Siebold & Zucc. Accepted Lauraceae
#> 4 Ranunculus japonicus Thunb. Accepted Ranunculaceae
#> 5 Cyclobalanopsis neglecta Schottky Synonym Fagaceae
#> ACCEPTED_SPECIES ACCEPTED_AUTHOR
#> 1 Myrica rubra (Lour.) Siebold & Zucc.
#> 2 <NA> <NA>
#> 3 Machilus thunbergii Siebold & Zucc.
#> 4 Ranunculus japonicus Thunb.
#> 5 Quercus myrsinifolia Blume
status("Adinandra millettii")
#> [1] "1 name(s) to process."
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY ACCEPTED_SPECIES ACCEPTED_AUTHOR
#> 1 Adinandra millettii <NA> NA NA NA <NA>
status("cyclobalanopsis neglecta")
#> [1] "1 name(s) to process."
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY ACCEPTED_SPECIES
#> 1 Cyclobalanopsis neglecta Schottky Synonym Fagaceae Quercus myrsinifolia
#> ACCEPTED_AUTHOR
#> 1 Blume
status("Lirianthe henryi")
#> [1] "1 name(s) to process."
#> SCIENTIFIC_NAME AUTHOR STATUS FAMILY
#> 1 Lirianthe henryi (Dunn) N.H.Xia & C.Y.Wu Synonym Magnoliaceae
#> ACCEPTED_SPECIES ACCEPTED_AUTHOR
#> 1 Magnolia henryi Dunn