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
Install from CRAN via
The development version of 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, v0.5.5, DOI: 10.5281/zenodo.1489527 http://ecologicaltraitdata.github.io/traitdataform
Copyright (c) 2018 F.D. Schneider, email@example.com
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