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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
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```{css, echo=FALSE} .table{ width: auto; font-size: 14px; } .table caption { font-size: 1em; }

Here in this article, we show how to use the package's function `powoFam` 
for mining the species number for any family of angiosperms, gymnosperms and 
pteridophytes. By providing a family name or a vector of family names, 
the `powoFam` function visits each POWO page of the genera within the queried 
family(ies) to extract the accepted species number. Then, it sums these values 
to deliver the total species number within each plant family.\

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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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Mining the total species number for any plant family

The function powoFam returns a data frame or saves a CSV file listing the total species number (excluding hybrid species) for the queried plant families.\

The example below shows how to mine the total species number by defining a vector of three families: Cabombaceae, Lecythidaceae, and Martyniaceae. The resulting output (TABLE 1) is also saved directly in the specified directory results_powoFam.\

CLM <- powoFam(family = c("Cabombaceae", "Lecythidaceae", "Martyniaceae"),
               verbose = TRUE,
               save = FALSE,
               dir = "results_powoFam",
               filename = "Camb_Lecy_Martyniaceae_diversity")

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utils::data("angioData")
utils::data("POWOcodes")
family <- c("Cabombaceae", "Lecythidaceae", "Martyniaceae")
fams <- angioData$family[angioData$family %in% family]
sp_nbr <- as.data.frame(table(fams))
powo_uri <- gsub("^http", "https", POWOcodes$uri[POWOcodes$family %in% family])
kew_id <- gsub(".+[:]", "", powo_uri)
species_number <- sp_nbr$Freq
res <- data.frame(family, species_number, kew_id, powo_uri)

knitr::kable(res,
             row.names = FALSE,
             align = 'c',
             caption = "TABLE 1. A general `powoFam` search for mining the total species number of three angiosperm families.")

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Mining species number accross all plant families

To mine the species number of all families of vascular plants, we recommend to load the dataframe-formatted 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 the R environment.\

The example below shows how to mine the species number of all vascular plant families by using the vector of all plant families and associated URI addresses stored in the POWOcodes object.\

utils::data(POWOcodes)

ALL_fam <- powoFam(POWOcodes$family,
                   verbose = TRUE,
                   save = FALSE,
                   dir = "results_powoFam",
                   filename = "all_plants_species_number")

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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 April 2023."

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