In DBOSlab/expowo: An R package for mining global plant diversity and distribution data

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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`.\

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## Setup

Install the latest development version of __expowo__ from 
[GitHub](https://github.com/):

``` r
#install.packages("devtools")
devtools::install_github("DBOSlab/expowo")

library(expowo)

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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")

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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 | | |

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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")

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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.\

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TABLE 2. The plant families and genera within angioGenera.\

utils::data("angioGenera")
df <- angioGenera

knitr::kable(df[-c(2, 3, 7, 8, 9, 10, 11, 12, 13)],
             row.names = FALSE)

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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")

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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")

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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."

DBOSlab/expowo documentation built on Oct. 29, 2024, 6:27 p.m.