tr8: a function for retrieving functional traits data from various
databases.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:
Biolflor http://www.ufz.de/biolflor/index.jsp
Ecological Flora of the British Isles http://www.ecoflora.co.uk/
LEDA traitbase http://www.leda-traitbase.org/LEDAportal/
Ellenberg values for Italian Flora
Mycorrhizal intensity database http://esapubs.org/Archive/ecol/E093/059/default.htm
MycoFlor http://www.esajournals.org/doi/abs/10.1890/12-1700.1
Catminat http://philippe.julve.pagesperso-orange.fr/catminat.htm
BROT http://www.uv.es/jgpausas/brot.htm
PLANTS http://www.bricol.net/
Imkerbond Zoersel http://users.telenet.be/imkerbondzoersel/
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).
tr8(species_list, download_list = NULL, gui_config = FALSE,synonyms=FALSE,
catminat_alternatives=FALSE, allow_persistent=NULL)An object of class Tr8; the slots @results contains various traits data for the species
of interest.
a vector containing names of the plant species for which traits data want to be extracted.
a vector containing the short codes of
traits which should be downlaoaded (to be used as an alternative
to the GUI inerface)
if set to TRUE a GUI for selecting traits of interest is shown (default is FALSE)
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)
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)
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.
Gionata Bocci <boccigionata@gmail.com>
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.
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.
bib()
if (FALSE) {
## download some trait data for Abies alba
My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P"),allow_persistent=TRUE)
}
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