Assistance for handling ecological trait data and applying the
Ecological Trait-Data Standard terminology (Schneider et al. 2018
Assistance for handling functional trait data and transferring them into the Ecological Trait-Data Standard (Schneider et al. 2018 Towards an Ecological Trait-data Standard, biorxiv.org DOI: 10.1101/328302).
There are two major use cases for the package:
The toolset of the package includes
The package can be installed from Github via the 'devtools' package
The package requires the udunits library for unit conversion to be installed. It should install automatically, but if the package installation throws an error, it might need manual installation (see this thread for help).
pulldata("carabids")thesaurus <- as.thesaurus(body_length = as.trait("body_length",expectedUnit = "mm",identifier = "length"),antenna_length = as.trait("antenna_length",expectedUnit = "mm",identifier = "antenna"),metafemur_length = as.trait("metafemur_length",expectedUnit = "mm",identifier = "metafemur"),eyewidth = as.trait("eyewidth_corr",expectedUnit = "mm",identifier = "eyewidth"))traitdataset1 <- standardize(carabids,thesaurus = thesaurus,taxa = "name_correct",units = "mm")
A documentation is available online at http://ecologicaltraitdata.github.io/traitdataform/ or offline in the package vignette 'traitdataform'.
The traitdataform package links to a couple of datasets, which are used for demo purposes in the vignette and documentation, but can be used for research and production use.
The datasets have been published by their authors under Creative Commons 0 or Creative Commons Attribution license, which means they can be copied, modified, distributed without asking permission. Attribution must be given according to the dataset license.
For additional information and interpretation of the data please refer to the help pages of the data objects (e.g. calling
?carabids in R) and the original data sources given therein.
If you want further datasources published under Creative Commons Licenses or in the public domain being added to this package, feel free to file a pull-request with a script for download and harmonization in the
data/ directory and a documentation appended to
The package invites any contributions e.g. minor fixes and spell-checks, improving interoperability with data and other packages or software for trait-data handling. Please see the Contributing Guidelines for details.
Please note that the 'traitdataform' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
The package is under open source development. You are invited to submit pull-requests with your improvements.
We are aiming to provide the following features in future iterations of the package:
Schneider, F.D. (2018) traitdataform - harmonizing ecological trait data in R, v0.5.0, http://ecologicaltraitdata.github.io/traitdataform
Copyright (c) 2018 F.D. Schneider, [email protected]
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
stable, for submission on CRAN. From this point on, backwards compatibility will be maintained.
minor changes (since v0.4):
standardize.exploratories()to include all columns by default.
standardize.taxonomy(): reset row.names.
carabidsfor handling in
as.metadata()for templating of metadata into an object class, including method
as.traitdata(): enable forwarding of attributes of input object (for metadata etc. )
data(). Also added documentation for all datasets and added more datasets.
rbind.traitdata()for merging standardised datasets into a unified table. includes handling of metadata object in attributes
standardize.exploratories()to extract georeference data for a plotID.
read.service()(provided by Dennis Heimann & Andreas Ostrowski) for access of datasets on BExIS. I added a secure masked prompt using the 'getPass' package.