tr8 {TR8}R Documentation

tr8: a function for retrieving functional traits data from various databases.

Description

tr8 makes internally use of other functions provided by the TR8 package in order to query various databases and provide the user with a dataframe containing traits data for the species of interest. At the moment the following databeses are available:

The function can either be used in an interactive way (i.e. if the gui_config parameter is set to TRUE, a multi-panel html-GUI will ask users to choose among lists of available traits) or in a non-interactive way (providing the function with a vector containing the short codes of the trait which should be downloaded - in order to have an idea of the available traits and the associated codes to be used for the download_list, see the available_traits function).

When the HTML-GUI is being used, the user will have to select the traits of interest from the available lists and then click the "Send request" button and go back to the R console (NB: the browser web page will become inactive; the user will have to take care of closing it).

Usage

tr8(species_list, download_list = NULL, gui_config = FALSE,synonyms=FALSE,
        catminat_alternatives=FALSE, allow_persistent=NULL)

Arguments

species_list

a vector containing names of the plant species for which traits data want to be extracted.

download_list

a vector containing the short codes of traits which should be downlaoaded (to be used as an alternative to the GUI inerface)

gui_config

if set to TRUE a GUI for selecting traits of interest is shown (default is FALSE)

synonyms

if set to TRUE tr8 will use taxize to find synonyms for the species names provided with the species_list parameter and will return trait values for all those species; in that case the dataframe contained in the @results slot will have two additional columns called synonyms (which contains the synonyms found using tnrs) and another one called original_names which includes the original names provided with species_list (default is FALSE)

catminat_alternatives

if set to TRUE tr8 will search, within the Catminat traitbase, for entries which contain, in their names, the ones in the provided species_list; e.g. if "Myrtus communis" is included in the species_list, tr8 will query the following existing entries in Catminat: "Myrtus communis", "Myrtus communis v. communis" and "Myrtus communis v. leucocarpa". (default is FALSE)

allow_persistent

if set to TRUE, tr8 will store retrieved databases from LEDA and Ecoflora into local files to speed up future queries; if FALSE, the downloaded data will be store in a temp directory that will be cleaned up at the end of the session; when NULL (default value), the user will be prompted for a choice between the two options.

Details

Not all traitbases use the most updated accepted names, thus different traibases may use different names for the same biological entity; it is not easy to find an automatic way to solve this issue, thus users are urged to always check the results provided by the tr8 function. In order to help users, the new version of the function accepts two parameters, synonyms and catminat_alternative so that data will be retrieved also for species which are not directly requested, but may be of interest for the user (e.g. in Catminat currently there are not traits for "Myrtus communis" but there are some for its subspecies). In this case some careful manual work will be required later in order to select species and traits of interest.

Value

An object of class Tr8; the slots @results contains various traits data for the species of interest.

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

Please always use the following citations any time you use trait data retrieved with tr8

BiolFlor

Klotz, S., Kühn, I., Durka, W. (eds) (2002). BIOLFLOR - Eine Datenbank zu biologisch-ökologischen Merkmalen zur Flora von Deutschland. Schriftenreihe für Vegetationskunde *38*: 1-333. (Bundesamt für. Bonn, Bundesamt für Naturschutz)

Ecoflora

Fitter, A . H. and Peat , H. J. (1994). The Ecological Flora Database, J. Ecol., 82, 415-425. ‘⁠http://www.ecoflora.co.uk⁠’

LEDA traitbase Kleyer, M., Bekker, R.M., Knevel, I.C., Bakker, J.P, Thompson, K., Sonnenschein, M., Poschlod, P., Van Groenendael, J.M., Klimes, L., Klimesova, J., Klotz, S., Rusch, G.M., Hermy, M., Adriaens, D., Boedeltje, G., Bossuyt, B., Dannemann, A., Endels, P., Götzenberger, L., Hodgson, J.G., Jackel, A-K., Kühn, I., Kunzmann, D., Ozinga, W.A., Römermann, C., Stadler, M., Schlegelmilch, J., Steendam, H.J., Tackenberg, O., Wilmann, B., Cornelissen, J.H.C., Eriksson, O., Garnier, E., Peco, B. (2008). The LEDA Traitbase: A database of life-history traits of Northwest European flora. Journal of Ecology 96: 1266-1274.

Akhmetzhanova et al, 2012

Akhmetzhanova, A.A, Soudzilovskaia, N.A., Onipchenko, V.G., Cornwell, W. K., Agafonov, V. A., Selivanov, I.A., and Cornelissen, J. H. C. (2012): A rediscovered treasure: mycorrhizal intensity database for 3000 vascular plants species across the former Soviet Union. Ecology 93:689. ‘⁠http://esapubs.org/Archive/ecol/E093/059/default.htm⁠’

Pignatti et al., 2005

Pignatti, S., Menegoni, P., Pietrosanti, S. (2005). Biondicazione attraverso le piante vascolari. Valori di indicazione secondo Ellenberg (Zeigerwerte) per le specie della Flora d'Italia. Braun-Blanquetia 39, Camerino, pp. 97.

MycoFlor

Mycorrhizas in the Central European flora: relationships with plant life history traits and ecology Stefan Hempel, Lars Götzenberger, Ingolf Kühn, Stefan G. Michalski, Matthias C. Rillig, Martin Zobel, and Mari Moora Ecology 2013 94:6, 1389-1399

Catminat

Julve, P., 1998 ff. - Baseflor. Index botanique, écologique et chorologique de la flore de France. Version : 26 November 2014. http://perso.wanadoo.fr/philippe.julve/catminat.htm

BROT

Paula S, Arianoutsou M, Kazanis D, Tavsanoglu Ç, Lloret F, Buhk C, Ojeda F, Luna B, Moreno JM, Rodrigo A, Espelta JM, Palacio S, Fernández-Santos B, Fernandes PM, and Pausas JG. 2009. Fire-related traits for plant species of the Mediterranean Basin. Ecology 90: 1420.

AND

Paula S. & Pausas J.G. 2013. BROT: a plant trait database for Mediterranean Basin species. Version 2013.06. URL: http://www.uv.es/jgpausas/brot.htm

PLANTS

Green, W. (2009) USDA PLANTS Compilation, version 1, 09-02-02.

Pignatti S., Menegoni P., Pietrosanti S., 2005, Biondicazione attraverso le piante vascolari. Valori di indicazione secondo Ellenberg (Zeigerwerte) per le specie della Flora d'Italia. Braun-Blanquetia 39, Camerino, pp. 97.

See Also

bib()

Examples

## Not run: 
## download some trait data for Abies alba 
My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P"),allow_persistent=TRUE)

## End(Not run)
[Package TR8 version 0.9.22 Index]