Here in this article, we describe the data associated with
expowo package that are helpful to enhance performance
before and while mining the global diversity and distribution
data.
There are three associated data package, all of which can be accessed
and imported into the R environment by simply calling the
utils function data. Below, we explain how to
use the data package POWOcodes, angioData, and
botregions.
Setup
Install the latest development version of expowo from GitHub:
#install.packages("devtools")
devtools::install_github("DBOSlab/expowo")
POWOcodes - A complete list of vascular plant families
and associated URI addresses
The POWOcodes data is a dataframe containing a list of
families of vascular plants available in the POWO database. The
flowering plant families are according to APG IV’s classification. It
was produced by using the functions apgFamilies and
get_pow of the package taxize.
POWOcodes data is very useful when the purpose is to query
many plant families or all of them. In addition to the names of POWO’s
accepted plant families, which are required in any search with
expowo’s functions, this data package has the corresponding
family’s URI, which is used internally in the function for opening a
connection with each family page at Plants of The World Online. In
addition, plant families are classified into three groups: “angiosperm”,
“gymnosperm”, and “fern and lycophyte”.
To call this associated data to the R environment, use the code
below:
utils::data("POWOcodes")
angioData - A dataframe of Angiosperm species
The angioData is a dataframe-formatted list of species
of some families of flowering plants and associated data, as retrieved
from POWO database using the expowo’s function
powoSpecies. For publication purposes and package size
limitation, we selected some families to include in this associated data
and let the information easily available. Currently, there are species
from five plant families as listed in Table 1. The last update of this
data was at Nov 2022.
TABLE 1. The plant families and species number within
angioData.
| family | species_number | family | species_number |
|---|---|---|---|
| Lecythidaceae | 381 | Aristolochiaceae | 727 |
| Martyniaceae | 14 | Cabombaceae | 7 |
| Begoniaceae | 1993 |
In addition to all accepted species (excluding hybrid species) in the
families above, the angioData also contains the
publication, authorship, and global geographic distribution at country
or botanical level for each species. The global classification of
botanical divisions follows the World Geographical
Scheme for Recording Plant Distributions, which is already
associated with each taxon’s distribution in POWO.
The example below shows how to call angioData:
utils::data("angioData")
angioGenera - A data frame of Angiosperm genera
The angioGenera comprises the genera of some families of
flowering plants and associated data as mined from POWO database using
powoGenera. For publication purposes and package size
limitation, we selected some families to include in this associated data
and let the information easily available. Currently, there are six plant
families (Lecythidaceae, Aristolochiaceae, Begoniaceae, Martyniaceae,
Dipterocarpaceae, and Fagaceae) as listed in Table 2. The last update of
this data was at Nov 2022.
TABLE 2. The plant families and genera within
angioGenera.
| family | scientific_name | publication | species_number |
|---|---|---|---|
| Aristolochiaceae | Aristolochia L. | Sp. Pl.: 960 (1753) | 534 |
| Aristolochiaceae | Asarum L. | Sp. Pl.: 442 (1753) | 129 |
| Aristolochiaceae | Euglypha Chodat & Hassl. | Bull. Herb. Boissier, ser. 2, 6: 138 (1906) | 1 |
| Aristolochiaceae | Hydnora Thunb. | Kongl. Vetensk. Acad. Handl. 36: 69 (1775) | 7 |
| Aristolochiaceae | Lactoris Phil. | Verh. K. K. Zool.-Bot. Ges. Wien 15: 521 (1865) | 1 |
| Aristolochiaceae | Prosopanche de Bary | Abh. Naturf. Ges. Halle 10: 267 (1868) | 7 |
| Aristolochiaceae | Saruma Oliv. | Hooker's Icon. Pl. 19: t. 1895 (1889) | 1 |
| Aristolochiaceae | Thottea Rottb. | Nye Saml. Kongel. Danske Vidensk. Selsk. Skr. 2: 529 (1783) | 45 |
| Begoniaceae | Begonia L. | Sp. Pl.: 1056 (1753) | 1992 |
| Begoniaceae | Hillebrandia Oliv. | Trans. Linn. Soc. London 25: 361 (1866) | 1 |
| Martyniaceae | Craniolaria L. | Sp. Pl.: 618 (1753) | 2 |
| Martyniaceae | Holoregmia Nees | Flora 4: 300 (1821) | 1 |
| Martyniaceae | Ibicella (Stapf) Van Eselt. | Techn. Bull. New York Agric. Exp. Sta., Geneva 149: 31 (1929) | 2 |
| Martyniaceae | Martynia L. | Sp. Pl.: 618 (1753) | 2 |
| Martyniaceae | Proboscidea Schmidel | Icon. Pl. Anal., ed. Keller: 49 (1763) | 7 |
| Dipterocarpaceae | Anisoptera Korth. | Verh. Nat. Gesch. Ned. Bezitt., Bot.: 65 (1841) | 10 |
| Dipterocarpaceae | Cotylelobium Pierre | Fl. Forest. Cochinch.: t. 235 (1889) | 5 |
| Dipterocarpaceae | Dipterocarpus C.F.Gaertn. | Suppl. Carp. 3: 50 (1805) | 65 |
| Dipterocarpaceae | Dryobalanops C.F.Gaertn. | Suppl. Carp. 3: 49 (1805) | 7 |
| Dipterocarpaceae | Hopea Roxb. | Pl. Coromandel 3: 7 (1811), nom. cons. | 114 |
| Dipterocarpaceae | Marquesia Gilg | Bot. Jahrb. Syst. 40: 485 (1908) | 3 |
| Dipterocarpaceae | Monotes A.DC. | A.P.de Candolle, Prodr. 16(2): 623 (1868) | 23 |
| Dipterocarpaceae | Neobalanocarpus P.S.Ashton | Fl. Males. 9: 388 (1982) | 1 |
| Dipterocarpaceae | Parashorea Kurz | J. Asiat. Soc. Bengal, Pt. 2, Nat. Hist. 39: 65 (1870) | 13 |
| Dipterocarpaceae | Pseudomonotes A.C.Londoño, E.Alvarez & Forero | Brittonia 47: 230 (1995) | 1 |
| Dipterocarpaceae | Shorea Roxb. ex C.F.Gaertn. | Suppl. Carp.: 47 (1805) | 189 |
| Dipterocarpaceae | Stemonoporus Thwaites | Hooker's J. Bot. Kew Gard. Misc. 6: 67 (1854) | 26 |
| Dipterocarpaceae | Upuna Symington | Bull. Jard. Bot. Buitenzorg, ser. 3, 17: 88 (1941) | 1 |
| Dipterocarpaceae | Vateria L. | Sp. Pl.: 515 (1753) | 3 |
| Dipterocarpaceae | Vateriopsis F.Heim | Rech. Dipterocarp.: 94 (1892) | 1 |
| Dipterocarpaceae | Vatica L. | Mant. Pl. 2: 152 (1771) | 77 |
| Fagaceae | Castanea Mill. | Gard. Dict. Abr. ed. 4.: s.p. (1754) | 8 |
| Fagaceae | Castanopsis (D.Don) Spach | Hist. Nat. Veg. 11: 185 (1842), nom. cons. | 143 |
| Fagaceae | Chrysolepis Hjelmq. | Bot. Not. Suppl. 2, 1: 117 (1948) | 2 |
| Fagaceae | Fagus L. | Sp. Pl.: 997 (1753) | 12 |
| Fagaceae | Lithocarpus Blume | Bijdr. Fl. Ned. Ind.: 526 (1826) | 343 |
| Fagaceae | Notholithocarpus Manos, Cannon & S.H.Oh | Madrono 55: 188 (2008) | 1 |
| Fagaceae | Quercus L. | Sp. Pl.: 994 (1753) | 464 |
| Fagaceae | Trigonobalanus Forman | Taxon 11: 140 (1962) | 3 |
| Lecythidaceae | Allantoma Miers | Trans. Linn. Soc. London 30: 291 (1874) | 8 |
| Lecythidaceae | Asteranthos Desf. | Mem. Mus. Hist. Nat. 6: 9 (1820) | 1 |
| Lecythidaceae | Barringtonia J.R.Forst. & G.Forst. | Char. Gen. Pl.: 75 (1776), nom. cons. | 72 |
| Lecythidaceae | Bertholletia Bonpl. | F.W.H.A.von Humboldt & A.J.A.Bonpland, Pl. Aequinoct. 1: 122 (1807) | 1 |
| Lecythidaceae | Brazzeia Baill. | Bull. Mens. Soc. Linn. Paris 1: 609 (1886) | 3 |
| Lecythidaceae | Careya Roxb. | Fl. Ind. ed. 1832. 2: 636 (1832) | 3 |
| Lecythidaceae | Cariniana Casar. | Nov. Stirp. Bras. 4: 35 (1842) | 9 |
| Lecythidaceae | Chydenanthus Miers | Trans. Linn. Soc. London, Bot. 1: 111 (1875) | 1 |
| Lecythidaceae | Corythophora R.Knuth | H.G.A.Engler (ed.), Pflanzenr., IV, 219a: 50 (1939) | 4 |
| Lecythidaceae | Couratari Aubl. | Hist. Pl. Guiane 2: 723 (1775) | 19 |
| Lecythidaceae | Couroupita Aubl. | Hist. Pl. Guiane 2: 708 (1775) | 3 |
| Lecythidaceae | Crateranthus Baker f. | A.B.Rendle & al., Cat. Pl. Oban: 35 (1913) | 4 |
| Lecythidaceae | Eschweilera Mart. ex DC. | Prodr. 3: 293 (1828) | 99 |
| Lecythidaceae | Foetidia Comm. ex Lam. | Encycl. 2: 457 (1788) | 18 |
| Lecythidaceae | Grias L. | Syst. Nat. ed. 10. 2: 1075 (1759) | 12 |
| Lecythidaceae | Gustavia L. | Pl. Surin. 12: 17 (1775), nom. cons. | 46 |
| Lecythidaceae | Lecythis Loefl. | Iter Hispan.: 189 (1758) | 30 |
| Lecythidaceae | Napoleonaea P.Beauv. | Napoleone: 1 (1804) | 17 |
| Lecythidaceae | Oubanguia Baill. | Bull. Mens. Soc. Linn. Paris 2: 869 (1890) | 3 |
| Lecythidaceae | Petersianthus Merr. | Philipp. J. Sci., C 11: 200 (1916) | 2 |
| Lecythidaceae | Pierrina Engl. | Bot. Jahrb. Syst. 43: 374 (1909) | 1 |
| Lecythidaceae | Planchonia Blume | Fl. Serres Jard. Eur. 7: 24 (1851) | 8 |
| Lecythidaceae | Rhaptopetalum Oliv. | J. Linn. Soc., Bot. 8: 159 (1865) | 13 |
| Lecythidaceae | Scytopetalum Pierre ex Engl. | H.G.A.Engler & K.A.E.Prantl, Nat. Pflanzenfam., Nachtr. 1: 244 (1897) | 4 |
In addition to list all accepted genera in the above families, the
dataframe-formatted angioGenera also contains publication,
authorship, species number and global geographic distribution at country
or botanical level for each genus. The global classification of
botanical divisions follows the World Geographical
Scheme for Recording Plant Distributions, which is already
associated with each taxon’s distribution in POWO.
The example below shows how to call angioGenera:
utils::data("angioGenera")
botregions - Countries and associated classification of
botanical divisions
The botregions data package is a dataframe containing
all countries of the World and associated classification of botanical
divisions according to the World Geographical
Scheme for Recording Plant Distributions. It was built using a
custim script with specific functions from the packages
rgdal, ggplot2, broom,
sf and raster (original script can be made
available upon request). This dataset is useful when the purpose is to
query the distribution data by both divisions of the world and for the
expowo ’s functions convert the country names.
To call this associated data to your R environment, use the code
below:
utils::data("botregions")Reference
POWO (2019). “Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; http://www.plantsoftheworldonline.org/ Retrieved Nov 2022.”