# Associated data

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")

    library(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.”