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RBIEN SALVIAS Tutorial
Brian Maitner
February 17, 2017
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knitr::opts_chunk$set(echo = TRUE)

Setup


#If you haven't already installed BIEN, do so now.
install.packages(pkgs = "devtools",repos = "https://cloud.r-project.org")
library(devtools)

install_github(repo = "bmaitner/RBIEN/BIEN")
library(BIEN)

Downloading SALVIAS data with BIEN

Downloading the SALVIAS data with the BIEN package is done using the function BIEN_plot_datasource


salvias_data <- BIEN_plot_datasource("SALVIAS")

If you would like additional information than is included in the default query, there are a number of options, including:

  • Additional taxonomic information

  • Additonal plot metadata

  • Information on native status of species

  • Information on the political regions that a record falls in

See ?BIEN_plot_datasource for more information

To download the SALVIAS dataset with all of the additional information:


salvias_data_full <- BIEN_plot_datasource(datasource = "SALVIAS",cultivated = T,only.new.world = F,all.taxonomy = T,native.status = T,political.boundaries = T,all.metadata = T)


If you would additionally like the stem measurements associated with the SALVIAS database, use the function BIEN_stem_datasource.


salvias_stem_data <- BIEN_stem_datasource("SALVIAS")

As with the BIEN_plot_datasource there are a number of additional data available.

Note, however, that setting native.status or cultivated to TRUE will greatly increase the amount of time the query takes.


salvias_stem_data_full <- BIEN_stem_datasource(datasource = "SALVIAS",cultivated = T,only.new.world = F,all.taxonomy = T,native.status = T,political.boundaries = T,all.metadata = T)