Please cite this database as:
Flores-Moreno, Habacuc, Treseder, Kathleen, K., , Cornwell, William, K., Maynard, Daniel S., Milo, Amy, M., Abarenkov, Kessy, Afkhami, Michelle, E., Aguilar-Trigueros, Carlos, A., Bates, Scott, Bhatnagar, Jennifer, M., Busby, Posy, E., Christian, Natalie, Crowther, Thomas W., Floudas, Dimitri, Gazis, Romina, Hibbett, David, Kennedy, Peter, F., Lindner, Daniel, L., Nilsson, R. Henrik, Powell, Jeff, Schildhauer, Mark, Schilling, Jonathan, Zanne, Amy, E. 2019. fungaltraits aka funfun: a dynamic functional trait database for the world's fungi. Dataset: https://github.com/traitecoevo/fungaltraits.
install.packages("devtools")
devtools::install_github("ropenscilabs/datastorr")
# devtools::install_github("traitecoevo/fungaltraits")
install.packages("fungaltraits", repos = c('https://traitecoevo.r-universe.dev', 'https://cloud.r-project.org'))
library(fungaltraits)
fungal_traits()
This will download the data, and load it into R, and you're ready to do analyses. The meta-data associated with the data is in the zip file that can be downloaded here.
If you use this package in a published paper, please note the version number. This will allow others to reproduce your work later. There is a Zenodo DOI associated with each release, insuring that it will be stable in the future.
The current doi is
That's it, really. Below is information about the data sources, how to contribute data and the versioned data distribution system (which we think is really cool), feel free to check it out, but you don't need to read the rest of this to use the package.
funfun leverages the ecological guilds present in the FUNGuild dataset. Currently funfun collates the most common fungal guild at the genus level and matches it to each observation. As the end user wants different resolution a separate query to FUNGuild can be run.
Thank you for contributing to Funfun (a fungal functional trait database). Below you will find a simple set of instructions to contribute to this DB. For assistance or enquiries please contact funtothefun@gmail.com. Before submitting keep in mind that this a living, open access DB, which we think is pretty cool (i.e. it will update as taxonomy changes, more data get added, and errors are corrected, all this while preserving previous versions; free on all restrictions on access).
It is essential that in your submission at least include the information below (if you prefer to fill-in some templates follow this link):
Submission: Once that you have fill in the essential information detailed below submit your data to funtothefun@gmail.com
Data file: It must include a column with a scientific name (genus, genus and species epithet) for each entry (row), and a column for each other variable included. See an example here.
Units for each variable included in your data file: International system units are preferred. (i.e. g, kg, bp, etc) OR you can fill in the dataMatchColumns.csv file, see here .
Essential metadata: Provide here a descriptor of your study, to whatever detail you are willing, that will help end users when examining your data in the future. This often includes such information as “experiment_type” whether the data was collected in the lab, field, data compilation; “tissue_type” (did you measure sporocarps, mycelium, fruiting bodies?). Don’t really know what to include? See this file for some inspiration.
Reference for your study OR .bib file: Not published yet? Not a problem! Grab this template and fill in as much information as you can! We will update this information as studies get published. Just let us know.
Contact information: Please give us a name, email address and physical address for the main contact person in your study.
Note that comma-separated files (.csv) are the preferred format for these files.
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Endophytes:
Genes and Chemistry:
Guilds:
Mycorrhizae:
Pathogens:
Saprobes:
Taxonomy:
Database:
This is for database maintainers
DESCRIPTION file to increase the version number. Once we are past version 1.0.0, we will use semantic versioning so be aware of when to change what number.funtothefun.csv and funtothefun.zip making whatever improvements/fixes are necessaryDESCRIPTION and push to GitHubfungaltraits:::fungal_traits_release("<description>")
where "<description>" is a brief description of new features of the release.