xraynaud/TR8

R package for downloading functional traits data for plant species

TR8

R package for downloading functional traits data for plant species

Plant ecologists often need to collect "traits" data about plant species which are often scattered among various databases: TR8 contains a set of tools which take care of automatically retrieving some of those functional traits data for plant species from the following publicly available databases:

• Biolflor
• The Ecological Flora of the British Isles
• LEDA traitbase
• Ellenberg values for Italian Flora
• Mycorrhizal intensity database
• http://luirig.altervista.org/
• MycoFlor
• Catminat
• BROT
• PLANTS
• Ecological Flora of California

Install the package

You can either install the stable relase of the package using the version available on CRAN:

install.packages(TR8,dependencies=TRUE)

Or, if you want to try the devel version of the package hosted here, you will need devtools:

## install the package
install.packages("devtools")
## load it
library(devtools)
## activate dev_mode
dev_mode(on=T)
## install TR8
install_github("GioBo/TR8")
## load TR8
library(TR8)
## you can now work with TR8 functions

## if you want to go back and use the CRAN version
## already installed, simply deactivate dev_mode
dev_mode(on=F)

Usage

The package comes with two vignettes aimed at helping users: the first one is a basic guide on how to use the package main function (tr8()); to browse it, simply type in the R console:

vignette("TR8")

The second one is a step-by-step description of what might be considered as a typical workflow for a plant ecologist who needs to collect traits' data and later analyze them; to view the vignette, write:

vignette("TR8_workflow")

Citation

Please use the following citation whenever you mention the package in a scientific journal:

"Bocci, G. (2015). TR8: an R package for easily retrieving plant species traits. Methods in Ecology and Evolution, 6(3), 347-350."

Or, if you use BibTeX:

  @Article{,
    author = {Bocci Gionata},
    title = {TR8: an R package for easily retrieving plant species traits},
    journal = {Methods in Ecology and Evolution},
    year = {2015},
    volume = {6},
    number = {3},
    pages = {347--350},
    url = {http://dx.doi.org/10.1111/2041-210X.12327},
  }

Users of the TR8 package should always cite the sources of information which provided the traits data: the correct citations to be used for the retrieved data can be obtained through the bib method; to learn how to use it, just type:

?bib

Changes from past versions

Important note: the new version of tr8() accepts the new argument 'synonyms': when set to true the function tnrs from the package taxize will be used to to search for synonyms of the provided species list and search trait data for them as well.

Please check NEWS file for other changes/updates from past versions of the package.