A Tool 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 publicly available databases (Biolflor, The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity databases, Catminat, BROT, PLANTS, Jepson Flora Project). The TR8 name, inspired by "car plates" jokes, was chosen since it both reminds of the main object of the package and is extremely short to type.


News

leda_fc

New function which allows to download Mean Floating Capacity data from LEDA

synonyms and alternative names

Now tr8() accepts two new arguments:

  • 'synonyms': when it is set to TRUE the function will use 'tnrs' function from the package 'taxize' to search for synonyms of the provided species list and search trait data for them as well.

  • 'catminat_alternatives': when TRUE tr8() searches - within the Catminat traitbase - also for species names which "contain" the names of the ones of interest (subspecies in Catminat are usually written in the form "Galium ver. halophilum" instead of "Galium verum subsp. halophilum"; cleaning this format in an automatic way is trickier than expected because for some entries we only have subspecies - thus automatically correcting the Genus is not always possible).

Fixes

  • LEDA is now using "https"
  • Cleaner requests to Ecoflora

Catminat database

Thanks to the `readxl` package, now the dataset (which is in
`xlsx` format) can be read without external dependencies
(i.e. users do not have to worry about installing `perl`)

BROT, PLANTS and Ecological Flora of California traitbases

 Three new databases are added as sources of data: BROT (mainly related to mediterranean
 species), PLANTS and Ecological Flora of California (from USA).

Reference manual

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install.packages("TR8")

0.9.21 by Gionata Bocci, 5 months ago


https://github.com/GioBo/TR8


Report a bug at https://github.com/GioBo/TR8/issues


Browse source code at https://github.com/cran/TR8


Authors: Gionata Bocci <[email protected]>


Documentation:   PDF Manual  


GPL (>= 2) license


Imports RCurl, XML, plyr, reshape, rappdirs, readxl, shiny, taxize

Depends on methods


See at CRAN