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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.”