Type: Package
Title: A Tool for Downloading Functional Traits Data for Plant Species
Version: 0.9.23
Date: 2024-09-19
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.
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
LazyData: true
Encoding: UTF-8
URL: https://github.com/GioBo/TR8
BugReports: https://github.com/GioBo/TR8/issues
Depends: R (≥ 3.5.0), methods, stats, utils
Imports: RCurl, XML, dplyr, plyr, reshape, rappdirs, readxl, shiny,
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2024-09-22 07:16:12 UTC; gionata
Author: Gionata Bocci [aut, cre]
Maintainer: Gionata Bocci <boccigionata@gmail.com>
Repository: CRAN
Date/Publication: 2024-09-22 07:40:02 UTC

TR8: a tool for retrieving functional traits data for plant species.

Description

This package provide a set of functions for extracting traits data for plant species from the following sources:

Details

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.

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’

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.

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"))

## End(Not run)

ECOFLORA_df: local lookup table for Ecoflora species' url(s)

Description

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.

Format

A data frame containing URL for the species contained in the Ecoflora web database.

species

a vector containing the species names as defined on Ecoflora website

web_link

a character vector containing the URL of each species trait web page

acceptedname

a character vector containing the accepted name according to TNRS

sourceid

a character vector containing the source used by the taxize::tnrs function

score

a numeric vector containing the score obtained by taxize::tnrs function

matchedname

a character vector containing the matched names by taxize::tnrs

uri

a character vector containing Ecoflora-URL for each species

References

Please alwasy cite the database according to:

Fitter, A . H. and Peat , H. J., 1994, The Ecological Flora Database, J. Ecol., 82, 415-425.

Examples

## observe the data for the first few species
## Not run: 
head(ECOFLORA_df)

## End(Not run)

Class "Tr8"

Description

Class Tr8 is used as a "containter" for all other functions and classes needed to download traits data from various databases

Objects from the Class

Objects can be created by calls of the form new("Tr8", ...).

Slots

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

Methods

bib

signature(.Object = "Tr8"): method to get bibliographic references for the downloaded data

issues

signature(.Object = "Tr8"): method to underline 'problematic' species

extract_traits

signature(object = "Tr8"): method to extract the object@results dataframe from a Tr8 object

lookup

signature(.Object = "Tr8"): a method to show brief reference for the downloaded data

issues

signature(.Object = "Tr8"): method to print species names for which data retrieval was problematic (e.g. double entries in remote databases).

Note

Additional datasets may be added in future.

Author(s)

Gionata Bocci boccigionata@gmail.com

See Also

tr8

Examples

## 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)

A dataframe containing the traits available for download.

Description

The available_tr8 dataframe can be used as a reference in order to know which traits can be downloaded with the TR8 package.

Usage

data("available_tr8")

Format

A data frame with the following variables:

short_code

contains the codes that should be used when using the tr8() function

description

contains a short description of the traits

db

indicates from which databases the traits will be downloaded

Details

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.

Author(s)

Gionata Bocci <boccigionata@gmail.com>

Examples

data(available_tr8)
## Not run: 
tr8(species_list=c("Salix alba","Populus nigra"),download_list=c("life_form_P"))

## End(Not run)

available_traits shows which traits are available for download

Description

The function is meant to help users in showing which traits (and from which databases) can be downloaded

Usage

available_traits()

Details

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.

Value

a data frame

Author(s)

Gionata Bocci <boccigionata@gmail.com>

See Also

tr8

Examples

## 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)

biolflor_lookup

Description

This dataframe is used to retrieve species URLs from the BiolFlor website (‘⁠http://www.ufz.de/biolflor/index.jsp⁠’).

Usage

biolflor_lookup

Format

A data frame with 3688 observations on the following 8 variables.

submittedname

a character vector containing the original species' names as used in BiolFlor

acceptedname

a character vector containing the acceptedanme according to the tnrs function

sourceid

a character vector; all the names are checked against the iPlant\_TNRS database

score

a character vector expressing the score for matching submitted and accepted names

matchedname

name matched by the tnrs function

authority

a character vector

V1

a character vector

V2

url of the BiolFlor web page for the species of interest

References

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)

Examples

head(biolflor_lookup)

column_list

Description

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.

Format

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

height_max

:c( "h_max","Maximum height","Ecoflora")

height_min

:c( "h_min","Minimum height","Ecoflora")

leaf_area

:c( "le_area","Leaf area","Ecoflora")

leaf_longevity

:c( "le_long","Leaf longevity","Ecoflora")

Photosynthetic_pathway

:c( "phot_path","Photosynthetic pathway","Ecoflora")

life_form

:c( "li_form","Life form","Ecoflora")

Vegetative_reprod_method

:c("reprod_meth","Vegetative reprod method","Ecoflora")

Flowering_earliest_month

:c("flw_early","Flowering earliest month","Ecoflora")

Flowering_latest_month

:c( "flw_late","Flowering latest month","Ecoflora")

Pollen_vector

:c( "poll_vect","Pollen vector","Ecoflora")

Seed_weight_mean

:c( "seed_wght","Seed weight mean","Ecoflora")

Method_of_propagation

:c( "propag","Method of propagation","Ecoflora")

Ellenberg_light_Eco

:c( "ell_light_uk","Ellenberg light","Ecoflora")

Ellenberg_moisture_Eco

:c( "ell_moist_uk","Ellenberg moisture","Ecoflora")

Ellenberg_pH_Eco

:c( "ell_pH_uk","Ellenberg pH","Ecoflora")

Ellenberg_nitrogen_Eco

:c( "ell_N","Ellenberg nitrogen","Ecoflora")

Ellenberg_salt_Eco

:c( "ell_S","Ellenberg salt","Ecoflora")

age_of_first_flowering

:c( "age_first_flowering","Age of first flowering","LEDA")

branching

:c( "branching","Branching","LEDA")

bud_bank_seasonality_soil

c( "bud_bank_seasonality_soil","Bud bank seasonality at soil level","LEDA")

buoyancy

:c( "buoyancy","Buoyancy","LEDA")

canopy_height

:c( "canopy_height","Mean canopy height","LEDA")

dispersal

:c( "dispersal","Dispersal type","LEDA")

leaf_distribution

:c( "leaf_distribution","Leaf distribution along the stem","LEDA")

leaf_dmc

:c( "leaf_dmc","Leaf dry matter content ","LEDA")

leaf_mass

:c( "leaf_mass","Leaf mass","LEDA")

leaf_size

:c( "leaf_size","Leaf size","LEDA")

dispersal_morphology

:c( "dispersal_morphology","Dispersal morphology","LEDA")

growth_form

:c( "growth_form","Growth form","LEDA")

life_span

:c( "life_span","Life span","LEDA")

releasing_height

:c( "releasing_height","Releasing height","LEDA")

sbank

:c( "sbank","Seed bank","LEDA")

seed_mass

:c( "seed_mass","Seed mass","LEDA")

shoot_growth_form

:c( "shoot_growth_form","Shoot growth form","LEDA")

seed_number_per_shoot

:c( "seed_number_per_shoot","Seed number per shoot","LEDA")

woodiness

:c( "woodiness","Woodiness","LEDA")

terminal_velocity

:c( "terminal_velocity","Terminal velocity","LEDA")

Life form

:c( "li_form_B","Life form","BiolFlor")

Life span

:c( "li_span","Life span","BiolFlor")

Rosettes

:c( "ros","Rosettes","BiolFlor")

Type of reproduction

:c( "reprod_B","Type of reproduction","BiolFlor")

Strategy type

:c( "strategy","Strategy type","BiolFlor")

Pollen vector

:c( "poll_vect_B","Pollen vector","BiolFlor")

L

:c( "ell_L_it","Ellenberg value for light in Italy","Pignatti")

T

:c( "ell_T_it","Ellenberg value for temperature in Italy","Pignatti")

C

:c( "ell_C_it","Ellenberg value for continentality in Italy","Pignatti")

U

:c( "ell_U_it","Ellenberg value for humidity in Italy","Pignatti")

R

:c( "ell_R_it","Ellenberg value for soil reaction in Italy","Pignatti")

N

:c( "ell_N_it","Ellenberg value for nitrogen in Italy","Pignatti")

S

:c( "ell_S_it","Ellenberg value for salinity in Italy","Pignatti")

life_form_P

:c( "life_form_P","Life form for Italian Flora","Pignatti")

corotipo

:c( "distribution_p","Distributions of species for the Italian Flora","Pignatti")

IT_beg_flow

:c( "IT_beg_flow","Beginning of flowering in Italy","Pignatti")

IT_end_flow

:c( "IT_end_flow","End of flowering in Italy","Pignatti")

Myco_infection

:c( "Myco_infection","Infection of AMF according to Akhmetzhanova et al.","AMF")

MycoFlor

:c( "MycoFlor","Infection of AMF according to MycoFlor","AMF")

inflorescence_fr

:c( "inflorescence_fr","Type of inflorescence","Catminat")

sex_reprod_fr

:c( "sex_reprod_fr","Type of sexual reproduction","Catminat")

poll_vect_fr

:c( "poll_vect_fr","Pollen vector","Catminat")

fruit_type_fr

:c( "fruit_type_fr","Type of fruit","Catminat")

dissemination_fr

:c( "dissemination_fr","Type of dissemination","Catminat")

flower_colour_fr

:c( "flower_colour_fr","Flower colour","Catminat")

ell_L_fr

:c( "ell_L_fr","Ellenberg values for Light","Catminat")

ell_T_fr

:c( "ell_T_fr","Ellenberg values for temperature","Catminat")

ell_C_fr

:c( "ell_C_fr","Ellenberg values for continentality","Catminat")

ell_U_atm_fr

:c( "ell_U_atm_fr","Ellenberg values for atmospheric moisture","Catminat")

ell_U_fr

:c( "ell_U_fr","Ellenberg values for moisture","Catminat")

ell_R_fr

:c( "ell_R_fr","Ellenberg values for soil reaction","Catminat")

ell_N_fr

:c( "ell_N_fr","Ellenberg values for nitrogen","Catminat")

ell_S_fr

:c( "ell_S_fr","Ellenberg values for salt","Catminat")

Soil_texture_fr

:c( "Soil_texture_fr","Type of soil texture","Catminat")

organic_matter_fr

:c( "organic_matter_fr","Organic matter in the soil","Catminat")

beg_flow_fr

:c( "beg_flow_fr","Beginning of flowering (month)","Catminat")

end_flow_fr

:c( "end_flow_fr","End of flowering (month)","Catminat")

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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

Examples

## inspect the structure of the list
str(column_list)

Set of plant species names to be corrected.

Description

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.

Format

The format is: a list of pairs of plant species names, each pair contains the original name and the corrected name.

References

‘⁠http://users.telenet.be/imkerbondzoersel/bijenplanten.html⁠’

Examples

## observe the sructure of the dataset
str(imkerbond_check)

A utility to download a local copy of the LEDA data files.

Description

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.

Usage

leda_download_to_local_directory(directory)

Arguments

directory

is the directory where the downloaded data will be stored (in order to be used in future R sessions); default is NULL.

Details

The function uses a GUI created via the gWidgets package, to let the user select a folder where the datasets has to be stored.

Value

The function save a local copy of LEDA data in a file called leda_database.Rda

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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’

leda_fc

Description

Downloads the mean floating capacity values from LEDA traitbase.

Usage

leda_fc(species_list)

Arguments

species_list

a vector of plant species names

Value

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.

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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’

See Also

tr8()

List with reference variables needed to download traits from LEDA Traitbase

Description

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.

Usage

data(leda_lookup)

Format

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.

age_of_first_flowering
branching
bud_bank_seasonality_soil
buoyancy
canopy_height
dispersal
leaf_distribution
leaf_dmc
leaf_mass
leaf_size
dispersal_morphology
growth_form
life_span
releasing_height
sbank
seed_mass
shoot_growth_form
seed_number_per_shoot
woodiness
terminal_velocity

Source

‘⁠http://www.leda-traitbase.org/LEDAportal/citation.jsp⁠’

References

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.

Examples

head(leda_lookup)

list_of_traits_Biolflor

Description

a vector containing traits that can be downloaded from Biolflor

Format

A vector of plant traits

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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)

Examples

## have a look at the first rows of the dataset
##head(list_of_traits_Biolflor)

A utility to storage a local copy of traits data

Description

local_storage can download traits data from LEDA and Akhmetzhanova databases and store them in a local folder.

Usage

local_storage(db,directory)

Arguments

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

Details

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.

Value

nothing

Author(s)

Gionata Bocci <boccigionata@gmail.com>>

pignatti

Description

pignatti is a dataframe containing traits data for italian species

Format

Contains the following traits data about Italian Flora species

Specie.Pignatti

: species name in the original dataset

numero

: numeric code

codice

: numeric code

nome.scientifico

: scientific name with authors

forma_biologica

: life form

corotipo

: distribution of species

L

: Ellenberg value for light

T

: Ellenberg value for temperature

C

: Ellenberg value for continentality

U

: Ellenberg value for soil humidity

R

: Ellenberg value for soil pH

N

: Ellenberg value for Nutrients in the soil

S

: Ellenberg value for soil salinity

Name.tnrs

: species name according to tnrs

References

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.

Examples

## inspect the first rows of the dataset
head(pignatti)

ref_PLANTS

Description

Contains species names without outhors which correspond to the ones in PLANTS traitbase.

Usage

data("ref_PLANTS")

Format

Scientific.Name

: this is the name used in the original dataset

acceptedname

the 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

Details

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

Source

‘⁠http://www.bricol.net/⁠’

References

‘⁠http://www.bricol.net/⁠’

Examples


data(ref_PLANTS)

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)

tr8_config a GUI to configure TR8 package.

Description

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.

Usage

tr8_config()

Value

Returns a list containing the selected traits for each source of information

Author(s)

Gionata Bocci <boccigionata@gmail.com>

See Also

tr8()

A function to download the most recent url-tables for some traitbases.

Description

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).

Usage

tr8_setup()

Details

At the moment BiolFlor and Ecoflora lookup tables are re-generated by this function.

Value

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.

Warning

The function takes a lot to run; I suggest to run it just at your first installation of the TR8 package.

Author(s)

Gionata Bocci <boccigionata@gmail.com>

Examples

## Not run: 
tr8_setup()

## End(Not run)

Set of functional traits to be retrieved by Ecoflora.

Description

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’).

Format

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":

height_max

: num 3.05

height_min

: num 3.06

leaf_area

: num 3.17

leaf_longevity

: num 3.22

Photosynthetic_pathway

: num 4.02

life_form

: num 5.01

Vegetative_reprod_method

: num 5.05

Flowering_earliest_month

: num 5.07

Flowering_latest_month

: num 5.08

Pollen_vector

: num 5.15

Seed_weight_mean

: num 5.34

Method_of_propagation

: num 5.52

Ellenberg_light_Eco

: num 7.14

Ellenberg_moisture_Eco

: num 7.15

Ellenberg_pH_Eco

: num 7.16

Ellenberg_nitrogen_Eco

: num 7.17

Ellenberg_salt_Eco

: num 7.18

References

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

Examples

## Not run: 
data(traits_eco)

## End(Not run)

traits_pollen_Biolflor

Description

a vector containing traits that can be downloaded from Biolflor

Format

A vector of plant traits

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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)

Examples

## Not run: 
#data(traits_pollen_Biolflor)

## End(Not run)

traits_special_Biolflor

Description

a vector containing traits that can be downloaded from Biolflor

Format

A vector of plant traits

Author(s)

Gionata Bocci <boccigionata@gmail.com>

References

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)

Examples

## Not run: 
#data(traits_special_Biolflor)

## End(Not run)

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