This function enables the user to search the Family/Genus/Order for higher plants under modern Classification Systems. Genus/Families relationship came from the Plant list Website.
Value
A data frame containing Genus (parsed from the string), Family (For Angiosperms: APGIII, For Gymnosperms: Christenhusz 2011, For lycophytes and ferns: Christenhusz 2011) orders.
Details
This function search the Family, Family Number and Order for (1) Species (2) Genus (3) Family.
Note
Please also pay attention to the following family names:
Palmae= Arecaceae
Gramineae= Poaceae
Leguminosae= Fabaceae
Guttiferae= Clusiaceae
Cruciferae= Brassicaceae
Labiatae= Lamiaceae
Compositae= Asteraceae
Umbelliferae= Apiaceae
A small proportion of genus has been divided into several genera, even being placed into different families, this will lead to multiple entries for one enquiry. Pay attention to these issues. Users need to check the acceptance based on their own experiences or knowledge. They are:
Acanthocladium, Acanthodium, Acetosella, Acosta, Adelia, Agropogon,
Alliaria, Amblytropis, Amelasorbus, Ammocalamagrostis, Anacampseros,
Argyrautia, Arthraxon, Asplenosorus, Asteriscium, Atomostigma, Balbisia,
Banalia, Bartonia, Bassia, Benthamia, Blechum, Blyttia, Bonapartea,
Brachyloma, Brassocattleya, Bridgesia, Brocchia, Brodiaea, Brugmansia,
Bruguiera, Brya, Bubbia, Bulbostylis, Burnettia, Calophyllum, Candollea,
Carduocirsium, Cedrus, Cephalopactis, Cladocolea, Coelidium, Condalia,
Corynotheca, Craspedophyllum, Crepidophyllum, Ctenium, Cuspidaria, Cycnia,
Cynoctonum, Cyrtanthus, Dactyloglossum, Darcya, Dianthera, Distichia,
Ditrichum, Donax, Drummondia, Dryopteris, Dudleveria, Dunalia, Dusenia,
Duvalia, Eria, Eriosonia, Erucaria, Esenbeckia, Euchresta, Eucodonopsis,
Eustegia, Filicula, Flemingia, Froelichia, Gastrochilus, Gerardia,
Gertrudia, Gilibertia, Goeppertia, Griffithia, Grimaldia, Guidonia,
Gymnotheca, Gymnotraunsteinera, Haemanthus, Harveya, Hedwigia, Heeria,
Helicophyllum, Heliohebe, Hepatica, Heteroneurum, Holboellia, Honckenya,
Hornschuchia, Humboldtia, Hutchinsonia, Hygrophila, Hymenolepis,
Hypopterygium, Isoloma, Joannesia, Jonesia, Kaulfussia, Laeliocattleya,
Lamprophyllum, Lasia, Laxmannia, Lepidostemon, Leptopyrum, Lichtensteinia,
Lightfootia, Limnobium, Lophiocarpus, Lopholepis, Lumnitzera, Malacocarpus,
Mammea, Manettia, Mannia, Massularia, Mastigophora, Meeboldia, Mertensia,
Meyenia, Micranthus, Micromitrium, Miltonidium, Mnium, Mollia, Moniera,
Myconia, Myrmecophila, Myzorrhiza, Neesia, Nivenia, Odontitella, Omalanthus,
Onychium, Orchidactyla, Orchigymnadenia, Orchiserapias, Oreocallis,
Ornithocidium, Oxymitra, Pachyneurum, Pachypodium, Pachyveria, Pancovia,
Panzeria, Parmentiera, Parsonsia, Petagnia, Phalangium, Piquetia,
Pityromeria, Platyloma, Pleuridium, Polypodiopsis, Pseudadenia, Pseudinium,
Pseuditella, Pseudogaltonia, Pseudorhiza, Rauia, Razoumofskya, Reinwardtia,
Rhacoma, Rhynchocarpa, Richardia, Richea, Roemeria, Roscoea, Rostellaria,
Roylea, Schmidtia, Schrebera, Sebastiania, Serapicamptis, Silvia, Solena,
Solenopsis, Solmsia, Sorbaronia, Sorbopyrus, Spiranthera, Spirostachys,
Stipularia, Swartzia, Thomandersia, Tillandsia, Trichocyclus, Tricholepis,
Trisetokoeleria, Triticale, Triticosecale, Tulasnea, Uncaria, Urtica,
Usteria, Vandopsis, Wahlenbergia, Waitzia, Washingtonia, Webera, Wedelia,
Welwitschia, Wettsteinia, Wiborgia, Wilhelmsia, Zappania, Zieria, Ziziphus
References
Bremer, Birgitta, K. Bremer, Mark Chase, Mike Fay, James Reveal, Douglas Soltis, Pamella Soltis and Peter Stevens. (2009) "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III." Botanical Journal of the Linnean Society.
Christenhusz, M., Zhang, X. C., and Schneider, H. (2011). A linear sequence of extant families and genera of lycophytes and ferns. Phytotaxa. 19:7-54
Christenhusz, M., Reveal, J., Farjon, A., Gardner, M. F., Mill, R. R., and Chase, M. W. (2011). A new classification and linear sequence of extant gymnosperms. Phytotaxa. 19:55-70
Haston, E., Richardson, J. E., Stevens, P. F., Chase, M. W. and Harris, D. J. (2009). The Linear Angiosperm Phylogeny Group (LAPG) III: a linear sequence of the families in APG III. Botanical Journal of the Linnean Society, 161(2), 128-131.
Liu Bing, Ye Jianfei , Liu Su, Wang Yuan, Yang Yong, Lai Yangjun, Zeng Gang and Lin Qinwen(2015). Families and genera of Chinese angiosperms: a synoptic classification based on APG III. Biodiversity Science. 23(2), 225-231.
Checklist of Genera of Higher Plants at the Plant List Website: http://www.theplantlist.org/1.1/browse/-/-/
See also
taxa.table, for generating taxa table for Phylomatic.
Author
Jinlong Zhang jinlongzhang01@gmail.com
Examples
TPL("Carex")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Carex Carex Cyperaceae APGIII_099 Poales Angiosperms
TPL("Apple")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Apple Apple <NA> <NA> <NA> <NA>
splist <- c( "Ranunculus japonicus",
"Solanum nigrum",
"Punica sp.",
"Machilus", "Today", "####" )
res <- TPL(splist)
taxa.table(res)
#> [1] "Ranunculaceae/Ranunculus/Ranunculus_japonicus"
#> [2] "Solanaceae/Solanum/Solanum_nigrum"
#> [3] "Lythraceae/Punica/Punica_sp."
#> [4] "Lauraceae/Machilus/Machilus"
#> [5] "NA/Today/Today"
#> [6] "NA/####/####"
TPL("Arecaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Arecaceae Arecaceae Arecaceae APGIII_076 Arecales Angiosperms
TPL("Palmae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Palmae Palmae Arecaceae APGIII_076 Arecales Angiosperms
TPL("Poaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Poaceae Poaceae Poaceae APGIII_106 Poales Angiosperms
TPL("Gramineae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Gramineae Gramineae Poaceae APGIII_106 Poales Angiosperms
TPL("Fabaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Fabaceae Fabaceae Fabaceae APGIII_144 Fabales Angiosperms
TPL("Leguminosae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Leguminosae Leguminosae Fabaceae APGIII_144 Fabales Angiosperms
TPL("Clusiaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Clusiaceae Clusiaceae Clusiaceae APGIII_211 Malpighiales Angiosperms
TPL("Guttiferae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Guttiferae Guttiferae Clusiaceae APGIII_211 Malpighiales Angiosperms
TPL("Brassicaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER
#> 1 Brassicaceae Brassicaceae Brassicaceae APGIII_273 Brassicales
#> GROUP
#> 1 Angiosperms
TPL("Cruciferae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Cruciferae Cruciferae Brassicaceae APGIII_273 Brassicales Angiosperms
TPL("Lamiaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Lamiaceae Lamiaceae Lamiaceae APGIII_373 Lamiales Angiosperms
TPL("Labiatae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Labiatae Labiatae Lamiaceae APGIII_373 Lamiales Angiosperms
TPL("Asteraceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Asteraceae Asteraceae Asteraceae APGIII_400 Asterales Angiosperms
TPL("Compositae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Compositae Compositae Asteraceae APGIII_400 Asterales Angiosperms
TPL("Apiaceae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Apiaceae Apiaceae Apiaceae APGIII_413 Apiales Angiosperms
TPL("Umbelliferae")
#> YOUR_SEARCH POSSIBLE_GENUS FAMILY FAMILY_NUMBER ORDER GROUP
#> 1 Umbelliferae Umbelliferae Apiaceae APGIII_413 Apiales Angiosperms