Setup

Install the latest development version of expowo from GitHub:

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

library(expowo)

Mining all accepted genera for any angiosperm family

The function powoGenera returns a dataframe or saves a CSV file listing all genera with associated number of accepted species and their global geographic distribution at country or botanical level. 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.

ABM <- powoGenera(family = c("Aristolochiaceae", "Begoniaceae", "Martyniaceae"),
                  verbose = FALSE,
                  save = FALSE,
                  dir = "results_powoGenera/",
                  filename = "Arist_Begon_Martyniaceae_search")

Mining all accepted genera for all angiosperm families

To mine a global genus checklist with associated species number and distribution for all families of flowering plants, we recommend to load the dataframe-formatted data object called POWOcodes that comes associated with the expowo package. Because the POWOcodes data object already contains the URI addresses for all angiosperms families recognized in the POWO database, you just need to run the code below.

The example below shows how to mine a global checklist of all accepted genera of flowering plants by using the vector of all angiosperm families and associated URI addresses stored in the POWOcodes object.

data(POWOcodes)

ALL_gen <- powoGenera(POWOcodes$family,
                      verbose = TRUE,
                      save = FALSE,
                      dir = "results_powoGenera/",
                      filename = "all_angiosperm_genera")

Narrowing down the powoGenera search based on a specified country vector

You can also narrow down the search for all accepted genera of any family so as to focus on just a particular country or a list of countries. You just need to define a vector of country names in the argument country. In the example below, see that we have originally searched for the genera within the families Aristolochiaceae, Lecythidaceae, Fagaceae, and Dipterocarpaceae, but the function only returned a list of genera of Aristolochiaceae and Lecythidaceae, because the remaining families do not have any genera recorded in the list of countries of interest, i.e. Argentina, Brazil or French Guiana.

ADFL <- powoGenera(family = 
                     c("Aristolochiaceae", "Dipterocarpaceae", "Fagaceae", "Lecythidaceae"),
                   country = c("Argentina", "Brazil", "French Guiana"),
                   verbose = FALSE,
                   save = FALSE,
                   dir = "results_powoGenera/",
                   filename = "country_constrained_search")
  

Narrowing down the powoGenera search based on a specified genus vector

You may want to retrieve information for just one or a list of accepted genera from a given country (or from a list of countries). Just like before, you only need to define a vector of genus names in the argument genus and a vector of country names in the argument country. In the example below, see that we have again searched for just the genera Asarum and Bertholletia of the families Aristolochiaceae and Lecythidaceae, but the function only returned the Lecythidaceae genus Bertholletia, because Asarum does not occur in any of the provided list of countries, i.e. Brazil or French Guiana.

AL <- powoGenera(family = c("Aristolochiaceae", "Lecythidaceae"), 
                 genus = c("Asarum", "Bertholletia"),
                 country = c("Brazil", "French Guiana"),
                 verbose = TRUE,
                 save = FALSE,
                 dir = "results_powoGenera/",
                 filename = "genus_country_constrained_search")