| Title: | A Tool for Downloading Functional Traits Data for Plant Species |
|---|---|
| Description: | 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 (The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg values for Italian Flora, Mycorrhizal intensity databases, 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. |
| Authors: | Gionata Bocci [aut, cre] |
| Maintainer: | Gionata Bocci <[email protected]> |
| License: | GPL (>=2) |
| Version: | 0.9.23 |
| Built: | 2024-11-21 05:21:28 UTC |
| Source: | https://github.com/giobo/tr8 |
This package provide a set of functions for extracting traits data for plant species from the following sources:
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
MycoFlor
‘http://luirig.altervista.org/’
‘http://perso.wanadoo.fr/philippe.julve/catminat.htm’
BROT ‘http://www.uv.es/jgpausas/brot.htm’
PLANTS ‘http://www.bricol.net/’
| Package: | TR8 |
| Type: | Package |
| Version: | 0.9.22 |
| Date: | 2020-10-08 |
| License: | GPL>=2 |
| Depends: | XML, RCurl, plyr, readxl |
The easiest way of using the package is through the
tr8() function, which accepts a vector of plant
species names and returns a data frame containg traits data
which have been found in the various sources.
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.
Gionata Bocci <[email protected]>
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’
Hempel et al, 2013
Hempel, S., Götzenberger, L., Kühn. I., Michalski, S.G., Rillig, M.C., Zobel, M., and Moora, M., 2013. Mycorrhizas in the Central European flora: relationships with plant life history traits and ecology. Ecology 94: 1389-1399.
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.
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.
bib()
## Not run: ## download some trait data for Abies alba My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P")) ## End(Not run)## Not run: ## download some trait data for Abies alba My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P")) ## End(Not run)
The available_tr8 dataframe can be used as a reference in order
to know which traits can be downloaded with the TR8 package.
data("available_tr8")data("available_tr8")
A data frame with the following variables:
short_codecontains the codes that should be used when
using the tr8() function
descriptioncontains a short description of the traits
dbindicates from which databases the traits will be downloaded
This dataframe can be viewed by those users who want to use the
tr8() function in a non-interactive way (i.e. not willing to
use the GUI for selecting traits to be retrieved). The users should
take note of the short_code used for the traits of interest,
since these are the codes that should be passed to tr8 in the
download_list parameter.
Gionata Bocci <[email protected]>
data(available_tr8) ## Not run: tr8(species_list=c("Salix alba","Populus nigra"),download_list=c("life_form_P")) ## End(Not run)data(available_tr8) ## Not run: tr8(species_list=c("Salix alba","Populus nigra"),download_list=c("life_form_P")) ## End(Not run)
The function is meant to help users in showing which traits (and from which databases) can be downloaded
available_traits()available_traits()
Users can call the function to see what data are available
for download and decide which one should be passed to the
tr8() function (in the download_list
argument); the codes to be used as the download_list
argument are those contained short_code column.
a data frame
Gionata Bocci <[email protected]>
tr8
## available_traits() ## If the traits \code{Maximum area} and \code{Leaf area} from ## Ecoflora are needed for the species Salix alba and Populus nigra, type ## Not run: tr8(species_list=c("Salix alba","Populus nigra"),download_list=c("life_form_P")) ## End(Not run)## available_traits() ## If the traits \code{Maximum area} and \code{Leaf area} from ## Ecoflora are needed for the species Salix alba and Populus nigra, type ## Not run: tr8(species_list=c("Salix alba","Populus nigra"),download_list=c("life_form_P")) ## End(Not run)
This dataframe is used to retrieve species URLs from the BiolFlor website (‘http://www.ufz.de/biolflor/index.jsp’).
biolflor_lookupbiolflor_lookup
A data frame with 3688 observations on the following 8 variables.
a character vector containing the original species' names as used in BiolFlor
a character vector containing the
acceptedanme according to the tnrs function
a character vector; all the names are checked against
the iPlant\_TNRS database
a character vector expressing the score for matching
submitted and accepted names
name matched by the tnrs function
a character vector
a character vector
url of the BiolFlor web page for the species of interest
Please use the follow citation ay time you use data derived from Biolflor: BIOLFLOR - Eine Datenbank zu biologisch-ökologischen Merkmalen zur Flora von Deutschland. Schriftenreihe für Vegetationskunde 38: 1-333. (Bundesamt für. Bonn, Bundesamt für Naturschutz)
head(biolflor_lookup)head(biolflor_lookup)
A list containing a brief description of traits data
retrieved by the various databases; it's used as a hash table by some
internal tr8 functions.
Each element contains a key which express the short name for the
traits that TR8 can download and to each key a three-elements
vector is associated, which contains a shorter code for the trait, a long
description of the trait and the reference database
:c( "h_max","Maximum height","Ecoflora")
:c( "h_min","Minimum height","Ecoflora")
:c( "le_area","Leaf area","Ecoflora")
:c( "le_long","Leaf longevity","Ecoflora")
:c( "phot_path","Photosynthetic pathway","Ecoflora")
:c( "li_form","Life form","Ecoflora")
:c("reprod_meth","Vegetative reprod method","Ecoflora")
:c("flw_early","Flowering earliest month","Ecoflora")
:c( "flw_late","Flowering latest month","Ecoflora")
:c( "poll_vect","Pollen vector","Ecoflora")
:c( "seed_wght","Seed weight mean","Ecoflora")
:c( "propag","Method of propagation","Ecoflora")
:c( "ell_light_uk","Ellenberg light","Ecoflora")
:c( "ell_moist_uk","Ellenberg moisture","Ecoflora")
:c( "ell_pH_uk","Ellenberg pH","Ecoflora")
:c( "ell_N","Ellenberg nitrogen","Ecoflora")
:c( "ell_S","Ellenberg salt","Ecoflora")
:c( "age_first_flowering","Age of first flowering","LEDA")
:c( "branching","Branching","LEDA")
c( "bud_bank_seasonality_soil","Bud bank seasonality at soil level","LEDA")
:c( "buoyancy","Buoyancy","LEDA")
:c( "canopy_height","Mean canopy height","LEDA")
:c( "dispersal","Dispersal type","LEDA")
:c( "leaf_distribution","Leaf distribution along the stem","LEDA")
:c( "leaf_dmc","Leaf dry matter content ","LEDA")
:c( "leaf_mass","Leaf mass","LEDA")
:c( "leaf_size","Leaf size","LEDA")
:c( "dispersal_morphology","Dispersal morphology","LEDA")
:c( "growth_form","Growth form","LEDA")
:c( "life_span","Life span","LEDA")
:c( "releasing_height","Releasing height","LEDA")
:c( "sbank","Seed bank","LEDA")
:c( "seed_mass","Seed mass","LEDA")
:c( "shoot_growth_form","Shoot growth form","LEDA")
:c( "seed_number_per_shoot","Seed number per shoot","LEDA")
:c( "woodiness","Woodiness","LEDA")
:c( "terminal_velocity","Terminal velocity","LEDA")
:c( "li_form_B","Life form","BiolFlor")
:c( "li_span","Life span","BiolFlor")
:c( "ros","Rosettes","BiolFlor")
:c( "reprod_B","Type of reproduction","BiolFlor")
:c( "strategy","Strategy type","BiolFlor")
:c( "poll_vect_B","Pollen vector","BiolFlor")
:c( "ell_L_it","Ellenberg value for light in Italy","Pignatti")
:c( "ell_T_it","Ellenberg value for temperature in Italy","Pignatti")
:c( "ell_C_it","Ellenberg value for continentality in Italy","Pignatti")
:c( "ell_U_it","Ellenberg value for humidity in Italy","Pignatti")
:c( "ell_R_it","Ellenberg value for soil reaction in Italy","Pignatti")
:c( "ell_N_it","Ellenberg value for nitrogen in Italy","Pignatti")
:c( "ell_S_it","Ellenberg value for salinity in Italy","Pignatti")
:c( "life_form_P","Life form for Italian Flora","Pignatti")
:c( "distribution_p","Distributions of species for the Italian Flora","Pignatti")
:c( "IT_beg_flow","Beginning of flowering in Italy","Pignatti")
:c( "IT_end_flow","End of flowering in Italy","Pignatti")
:c( "Myco_infection","Infection of AMF according to Akhmetzhanova et al.","AMF")
:c( "MycoFlor","Infection of AMF according to MycoFlor","AMF")
:c( "inflorescence_fr","Type of inflorescence","Catminat")
:c( "sex_reprod_fr","Type of sexual reproduction","Catminat")
:c( "poll_vect_fr","Pollen vector","Catminat")
:c( "fruit_type_fr","Type of fruit","Catminat")
:c( "dissemination_fr","Type of dissemination","Catminat")
:c( "flower_colour_fr","Flower colour","Catminat")
:c( "ell_L_fr","Ellenberg values for Light","Catminat")
:c( "ell_T_fr","Ellenberg values for temperature","Catminat")
:c( "ell_C_fr","Ellenberg values for continentality","Catminat")
:c( "ell_U_atm_fr","Ellenberg values for atmospheric moisture","Catminat")
:c( "ell_U_fr","Ellenberg values for moisture","Catminat")
:c( "ell_R_fr","Ellenberg values for soil reaction","Catminat")
:c( "ell_N_fr","Ellenberg values for nitrogen","Catminat")
:c( "ell_S_fr","Ellenberg values for salt","Catminat")
:c( "Soil_texture_fr","Type of soil texture","Catminat")
:c( "organic_matter_fr","Organic matter in the soil","Catminat")
:c( "beg_flow_fr","Beginning of flowering (month)","Catminat")
:c( "end_flow_fr","End of flowering (month)","Catminat")
Gionata Bocci <[email protected]>
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. URL: 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.
Julve, 1998
Julve, P., 1998 ff. - Baseflor. Index botanique, écologique et chorologique de la flore de France. Version : 26 November 2014 . URL: 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
## inspect the structure of the list str(column_list)## inspect the structure of the list str(column_list)
This dataset is not ment to be directly accessed by the
final user. It is imported by the ecoflora()
function to extrapolate the correct URL for each
species of interest and download the corresponding
functional traits. This dataset is used as a lookup table
from the ecoflora() function.
A data frame containing URL for the species contained in the Ecoflora web database.
a vector containing the species names as defined on Ecoflora website
a character vector containing the URL of each species trait web page
a character vector containing the accepted name according to TNRS
a character vector containing the source used by the taxize::tnrs function
a numeric vector containing the score obtained by taxize::tnrs function
a character vector containing the matched names by taxize::tnrs
a character vector containing Ecoflora-URL for each species
Please alwasy cite the database according to:
Fitter, A . H. and Peat , H. J., 1994, The Ecological Flora Database, J. Ecol., 82, 415-425.
## observe the data for the first few species ## Not run: head(ECOFLORA_df) ## End(Not run)## observe the data for the first few species ## Not run: head(ECOFLORA_df) ## End(Not run)
imkerbond_check defines a list containg pairs in the form
original plant species names in the retrieved data =
corrected names.
This list is used from the tr8 function to correct the wrong
plant species names found in the original dataset retrieved from the
‘http://users.telenet.be/imkerbondzoersel/bijenplanten.html’ website.
The format is: a list of pairs of plant species names, each pair contains the original name and the corrected name.
‘http://users.telenet.be/imkerbondzoersel/bijenplanten.html’
## observe the sructure of the dataset str(imkerbond_check)## observe the sructure of the dataset str(imkerbond_check)
Allows the user to retrieve the data files from the LEDA
Traitbase website, merge them in a single R dataset
and store the result in a local file; this file could be
then used whenever the tr8() function is used in
order to speed up the process of retrieving traits data.
leda_download_to_local_directory(directory)leda_download_to_local_directory(directory)
directory |
is the directory where the downloaded data will be stored (in order to be used in future R sessions); default is NULL. |
The function uses a GUI created via the gWidgets
package, to let the user select a folder where the datasets
has to be stored.
The function save a local copy of LEDA data in a file
called leda_database.Rda
Gionata Bocci <[email protected]>
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., Corneliss n, 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. ‘ http://www.leda-traitbase.org/LEDAportal/data_files.jsp’
Downloads the mean floating capacity values from LEDA traitbase.
leda_fc(species_list)leda_fc(species_list)
species_list |
a vector of plant species names |
Returns a dataframe where for each plant species (row) mean values of Floating Capacity are reported - if present in the LEDA database - for each category of dispersal type.
Gionata Bocci <[email protected]>
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., Corneliss n, 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. ‘ http://www.leda-traitbase.org/LEDAportal/data_files.jsp’
tr8()
Contains useful references for the LEDA Traitbase: these
data are used by the TR8 package to find URLs of the different
.txt files containing the raw data.
data(leda_lookup)data(leda_lookup)
Each element contains a key which express the short name for the
traits of interest (to be retrieved from the LEDA Traitbase), to each key a four-elements
vector is associated, which contains the name of the .txt files
hosted at the LEDA website which containts the trait data, a
int which expresses the number of rows to be skipped when
reading the txt file, a longer code for the trait, a short code
for the trait.
‘http://www.leda-traitbase.org/LEDAportal/citation.jsp’
Please cite the following reference any time you use data retrieved from the 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.
head(leda_lookup)head(leda_lookup)
a vector containing traits that can be downloaded from Biolflor
A vector of plant traits
Gionata Bocci <[email protected]>
Please use the follow citation ay time you use data derived from 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)
## have a look at the first rows of the dataset ##head(list_of_traits_Biolflor)## have a look at the first rows of the dataset ##head(list_of_traits_Biolflor)
local_storage can download traits data from LEDA and Akhmetzhanova databases and store them in a local folder.
local_storage(db,directory)local_storage(db,directory)
db |
can contain the following values: "AMF" and "LEDA" depending on the database which should be downloaded |
directory |
the directory where the local Rda files will be stored |
Downloading data from the web is time consuming, thus a
local storage of some traits data will speed up future data
requests; this is possible for LEDA and Akhmetzhanova
databases. The function must be run only once (ideally
before running the tr8 function for the first time):
thanks to the rappdirs package, the downloaded data
will be stored in the directory commonly used for
user data (which depends on the Operatim System
where R is running). Users can change the
destination folder through the directory parameters,
passing the full path of the directory to be used by the
function.
nothing
Gionata Bocci <[email protected]>>
pignatti is a dataframe containing traits data for
italian species
Contains the following traits data about Italian Flora species
: species name in the original dataset
: numeric code
: numeric code
: scientific name with authors
: life form
: distribution of species
: Ellenberg value for light
: Ellenberg value for temperature
: Ellenberg value for continentality
: Ellenberg value for soil humidity
: Ellenberg value for soil pH
: Ellenberg value for Nutrients in the soil
: Ellenberg value for soil salinity
: species name according to tnrs
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.
## inspect the first rows of the dataset head(pignatti)## inspect the first rows of the dataset head(pignatti)
Contains species names without outhors which correspond to the ones in PLANTS traitbase.
data("ref_PLANTS")data("ref_PLANTS")
Scientific.Name: this is the name used in the original dataset
acceptednamethe accepted name of the species used
obtained using taxize::tnrs
score: score for the species names' matching, returned by taxize::tnrs
matchedname: the matched named returned by taxize::tnrs
authority: species authors' names
Symbol: code used in the original dataset
Synonym.Symbol: code used in the original dataset
This dataframe is not meant to be managed by users: it serves as a
lookup table for the tr8 function in order to speed-up data retrieval
‘http://www.bricol.net/’
‘http://www.bricol.net/’
data(ref_PLANTS)data(ref_PLANTS)
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)tr8(species_list, download_list = NULL, gui_config = FALSE,synonyms=FALSE, catminat_alternatives=FALSE, allow_persistent=NULL)
species_list |
a vector containing names of the plant species for which traits data want to be extracted. |
download_list |
a vector containing the |
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 |
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 |
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. |
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.
An object of class Tr8; the slots @results contains various traits data for the species
of interest.
Gionata Bocci <[email protected]>
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()
## 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)## 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)
tr8_config a GUI to configure TR8 package.This function will make a simple GUI appear which
contains a tab for each trait database: the user can choose
which traits should be downloaded by the tr8
function.
tr8_config()tr8_config()
Returns a list containing the selected traits for each source of information
Gionata Bocci <[email protected]>
tr8()
For some traitbases tr8 uses lookup-tables which contain URLs of the species of interest; some of the traitbases queried by tr8 are uploaded from time to time thus the function may be unable to retrieve traits data for the most recently uploaded species. This function allows the user to refresh some of these lookup tables. BEWARE: this function takes a long time to run (nearly 20 minutes are required - on a fast connection - for retrieving lookup tables for BiolFlor).
tr8_setup()tr8_setup()
At the moment BiolFlor and Ecoflora lookup tables are re-generated by this function.
The values does not return anythis useful for the user; it's used for
its side effects, i.e. it stores the retrieved lookup table in one
directory for later use from the tr8 function.
The function takes a lot to run; I suggest to run it just at your
first installation of the TR8 package.
Gionata Bocci <[email protected]>
## Not run: tr8_setup() ## End(Not run)## Not run: tr8_setup() ## End(Not run)
"Tr8"
Class Tr8 is used as a "containter" for all other functions and classes needed to download traits data from various databases
Objects can be created by calls of the form new("Tr8", ...).
species_list:Object of class "vector" list of species for which traits data are to be searched
results:Object of class "data.frame" dataframe containing scraped traits
not_valid:Object of class "vector" species whose name were not present in the Ecoflora database
double_names:Object of class "vector" species for which more than one name was found
signature(.Object = "Tr8"): method to get bibliographic references for the downloaded data
signature(.Object = "Tr8"): method to underline
'problematic' species
signature(object = "Tr8"): method to
extract the object@results dataframe from a Tr8 object
signature(.Object = "Tr8"): a method to show brief reference for the downloaded data
signature(.Object = "Tr8"): method to print
species names for which data retrieval was problematic
(e.g. double entries in remote databases).
Additional datasets may be added in future.
Gionata Bocci [email protected]
## Not run: ## the bib() methods let the user have the exact ## bibliographic citations to be used for the ## retrieved data ## download some trait data for Abies alba My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P")) ## See what citations should be used for the data ## bib(My_traits) ## to see a short explanation for the codes used to identify ## the traits use lookup() lookup(My_traits) ## End(Not run)## Not run: ## the bib() methods let the user have the exact ## bibliographic citations to be used for the ## retrieved data ## download some trait data for Abies alba My_traits<-tr8(species_list=c("Abies alba"),download_list=c("life_form_P")) ## See what citations should be used for the data ## bib(My_traits) ## to see a short explanation for the codes used to identify ## the traits use lookup() lookup(My_traits) ## End(Not run)
traits_eco defines a list containg pairs in the form
short_name_of_the_trait =
corresponding_code_in_Ecoflora At the moment the
package does not download all the traits available at
Ecoflora; curious users can expand the number of
downloadable traits simply extending the list with other
'pairs' (take care of using the right Ecoflora codes
as described in
‘http://www.ecoflora.org.uk/search_plantchar.php’).
The format is: a list of the following 17 elements, where each element is a pair of the form "traits":"code used in Ecoflora HTML code":
: num 3.05
: num 3.06
: num 3.17
: num 3.22
: num 4.02
: num 5.01
: num 5.05
: num 5.07
: num 5.08
: num 5.15
: num 5.34
: num 5.52
: num 7.14
: num 7.15
: num 7.16
: num 7.17
: num 7.18
Fitter, A . H. and Peat , H. J., 1994, The Ecological Flora Database, J. Ecol., 82, 415-425. ‘http://www.ecoflora.co.uk’
## Not run: data(traits_eco) ## End(Not run)## Not run: data(traits_eco) ## End(Not run)
a vector containing traits that can be downloaded from Biolflor
A vector of plant traits
Gionata Bocci <[email protected]>
Please use the follow citation ay time you use data derived from 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)
## Not run: #data(traits_pollen_Biolflor) ## End(Not run)## Not run: #data(traits_pollen_Biolflor) ## End(Not run)
a vector containing traits that can be downloaded from Biolflor
A vector of plant traits
Gionata Bocci <[email protected]>
Please use the follow citation ay time you use data derived from 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)
## Not run: #data(traits_special_Biolflor) ## End(Not run)## Not run: #data(traits_special_Biolflor) ## End(Not run)