inst/doc/mining_accepted_genera.R

In expowo: An R Package for Mining Global Plant Diversity and Distribution Data

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----package load, message=FALSE, warning=FALSE-------------------------------
library(expowo)

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

## ----echo = FALSE, warning = FALSE--------------------------------------------
utils::data("angioGenera")
fam <- c("Aristolochiaceae", "Begoniaceae", "Martyniaceae")
df <- angioGenera[angioGenera$family %in% fam, ]

knitr::kable(df[-c(7, 8, 9, 10, 11, 12)],
             row.names = FALSE,
             caption = "TABLE 1. A general `powoGenera` search for mining all 
             accepted genera for some specific families.")

## ----eval = FALSE-------------------------------------------------------------
# data(POWOcodes)
# 
# ALL_gen <- powoGenera(POWOcodes$family,
#                       hybrid = TRUE,
#                       verbose = TRUE,
#                       save = FALSE,
#                       dir = "results_powoGenera",
#                       filename = "all_plant_genera")

## ----eval = FALSE-------------------------------------------------------------
# data(POWOcodes)
# 
# ALL_gen <- powoGenera(POWOcodes$family,
#                       hybrid = TRUE,
#                       verbose = TRUE,
#                       rerun = TRUE,
#                       save = FALSE,
#                       dir = "results_powoGenera",
#                       filename = "all_plant_genera")

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

## ----echo = FALSE, warning = FALSE--------------------------------------------
utils::data("angioGenera")
fam <- c("Aristolochiaceae", "Dipterocarpaceae", 
         "Fagaceae", "Lecythidaceae")
df <- angioGenera[angioGenera$family %in% fam, ]

country <- c("Argentina", "Brazil", "French Guiana")
pattern <- paste(country, collapse = "|")
df <- df[grepl(pattern, df$native_to_country), ]

knitr::kable(df[-c(7, 8, 9, 10, 11, 12, 13)],
             row.names = FALSE,
             caption = "TABLE 2. A `powoGenera` search based on a specified 
             country vector.")

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

## ----echo = FALSE, warning = FALSE--------------------------------------------
utils::data("angioGenera")
genus <- c("Asarum", "Bertholletia")
df <- angioGenera[angioGenera$genus %in% genus, ]

country <- c("Brazil", "French Guiana")
pattern <- paste(country, collapse = "|")
df <- df[grepl(pattern, df$native_to_country), ]

knitr::kable(df[-c(8, 9, 10, 11, 12)],
             row.names = FALSE,
             caption = "TABLE 3. A `powoGenera` search based on specified genus 
             and country vectors.")