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Mining the top richest genera of vascular plants

Source: vignettes/mining_toprichest_genera.Rmd
mining_toprichest_genera.Rmd

Here in this article, we show how to use the package’s function topGen for mining the top most species rich genera for any family of vascular plants.


Setup

Install the latest development version of expowo from GitHub:

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


Mining the top richest genera for any vascular plant family

The function topGen is relatively similar to the megaGen, but instead of using a specific threshold of species number to be considered a big genera, it saves a CSV file listing the top most species-rich genera of any target vascular plant family, and their associated number of accepted species based on an integer number set in the argument limit. In the example below, we used the default to search for the top ten richest genera (i.e., when the argument limit is set as NULL, the function searches for the 10 most diverse genera within a plant family). Some columns were omitted to display the results, and the rows show the top ten of the three chosen angiosperm families: Bignoniaceae, Solanaceae and Lecythidaceae. Note that the table does not have 30 rows, what would be expected if we multiply each family (n = 3) by ten. It is not an error, since some plant families do not have many genera, which is the case of Begoniaceae with 2 genera.

ABL_top <- topGen(family = c("Aristolochiaceae", "Begoniaceae", "Lecythidaceae"),
                  limit = NULL,
                  verbose = TRUE,
                  save = FALSE,
                  dir = "results_topGen",
                  filename = "Aristo_Bego_Lecythidaceae_search")


TABLE 1. A general topGen search to mining the top most species rich genera for some specific angiosperm families.
family genus species_number
Aristolochiaceae Aristolochia 534
Aristolochiaceae Asarum 129
Aristolochiaceae Thottea 45
Aristolochiaceae Hydnora 7
Aristolochiaceae Prosopanche 7
Aristolochiaceae Euglypha 1
Aristolochiaceae Lactoris 1
Aristolochiaceae Saruma 1
Begoniaceae Begonia 1992
Begoniaceae Hillebrandia 1
Lecythidaceae Eschweilera 99
Lecythidaceae Barringtonia 72
Lecythidaceae Gustavia 46
Lecythidaceae Lecythis 30
Lecythidaceae Couratari 19
Lecythidaceae Foetidia 18
Lecythidaceae Napoleonaea 17
Lecythidaceae Rhaptopetalum 13
Lecythidaceae Grias 12
Lecythidaceae Cariniana 9


Mining the top richest genera accross all vascular plant families

To mine a global checklist of the top species-richest genera for all families of vascular plants, including their associated species number, we recommend to load the dataframe-formatted data object called POWOcodes that comes associated with the expowo package. The POWOcodes data object already contains the URI addresses for all plant families recognized in the POWO database, so you just need to call it to your R environment.

The example below shows how to mine all top most species-rich genera of vascular plants by using the vector of all plant families, the associated URI addresses stored in the POWOcodes object and the limit of 10 genera for each family.

data(POWOcodes)

ALL_top <- topGen(POWOcodes$family,
                  limit = 10,
                  verbose = TRUE,
                  save = FALSE,
                  dir = "results_topGen",
                  filename = "all_toprichest_plant_genera")


Reference

POWO (2019). “Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; http://www.plantsoftheworldonline.org/ Retrieved April 2023.”