CANTRIP: The Canopy Trait Plasticity Database

Contacts:

Trevor Keenan (trevorkeenan@lbl.gov) Climate and Environmental Science Division, Lawrence Berkeley National Lab., Berkeley, CA 94720, USA

Ülo Niinemets (ylo.niinemets@emu.ee) Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia; Estonian Academy of Sciences, Kohtu 6, 10130 Tallinn, Estonia

About

The Canopy Trait Plasticity Database (CANTRIP) contains data on the light-driven plasticity of traits within plant canopies from all over the globe.

These data represent over 200 species from around the world, gathered from previously published scientific studies, along with unpublished data associated with specific publications.

We hope that by publishing this data, along with subsequent updates to the dataset, we can help improve understanding of within canopy changes in plant traits, and the implications for global trait variation.

The data and methodology used to generate the dataset are described further in the publications:

Keenan, T.F., and Ü. Niinemets (2017) Global leaf trait estimates biased due to plasticity in the shade. Nature Plants in press

Niinemets, Ü., T. F. Keenan, and L. Hallik (2015) A worldwide analysis of within-canopy variations in leaf structural, chemical and physiological traits across plant functional types. New Phytologist 205:973–993. 10.1111/nph.13096

Niinemets, Ü. 2016. Leaf age dependent changes in within‑canopy variation in leaf functional traits: a meta ‑ analysis. Journal of Plant Research 129:313–338. 10.1007/s10265-016-0815-2

Niinemets, Ü., and T. F. Keenan (2012). Measures of light in studies on light-driven plant plasticity in artificial environments. Frontiers in Plant Science 3:156. 10.3389/fpls.2012.00156

At time of publication, the CANTRIP database contained 831 within canopy gradients for over 200 different species, for leaf mass per area (LMA), net assimilation (A) and leaf nitrogen (N) on both a mass (m) and area (a) basis.

Using the CANTRIP database

The database is released under the Creative Commons Zero public domain waiver, and can therefore be reused without restriction. To recognise the work that has gone into building the database, we kindly ask that you cite the above articles and acknowledge the database through it's DOI. When using data from only one or a few of the individual studies, please cite the original articles if you prefer. Of course we would love to hear of any interesting science you are doing with the dataset.

Download compiled database

You can download a compiled version of the CANTRIP database from:

Releases we have posted on github.
The traitPlasticity.data package for R (in development).

The database contains the following elements

data: amalgamated dataset (table), with columns as defined in dictionary
dictionary: See config/variableDefinitions.csv for a table of variable definitions
references: as both summary table and bibtex entries containing the primary source for each study
contacts: See config/contacts.csv table with contact information and affiliations
code: A repository of code used with the dataset.
figures: A repository of community contributed figures.
methods: (in dev.) a table with columns as in data, but containing a code for the methods used to collect the data. See config/methodsDefinitions.csv.
docker: (in dev.) use docker to load images containing the source code and required open-source packages to run analyses

These elements are available at both of the above links as a series of CSV and text files.

To download an earlier or more recent version (where version numbers will follow the semantic versioning guidelines. The traitPlasticity.data package caches everything so subsequent calls, even across sessions, are very fast. This should facilitate greater reproducibility by making it easy to depend on the version used for a particular analysis, and allowing different analyses to use different versions of the database.

Further details about the different versions and changes between versions is available on the github releases page and in the CHANGELOG.

Details about the data distribution system

We envisage that there will be periodic updates to the Trait Plasticity database as we add more data. These updates will correspond with changes to the version number of this resource, and each version of the database will be available on github and via the traitPlasticity.data package. If you use this resource for a published analysis, please note the version number in your publication. This will allow anyone in the future to go back and find exactly the same version of the data that you used.

Reproducing older versions of the database and the paper from Nature Plants

You can reproduce any version of the database by checking out the appropriate commit that generated, or using the links provided under the releases tab. For example, to reproduce v1.0.0 of the database, corresponding to the paper in Nature Plants:

git checkout v1.0.0

Then in R run

remake::make("export")
remake::make("manuscript")

Acknowledgements

We are extremely grateful to all the researchers who published these data over the past decades. We thank Kaia Kask for assistance in data digitization and database management, and Anne Aan, Niels Anten, Ismael Aranda, Jan Cerm ak, Robin Chazdon, Theodore DeJong, Tim Fahey, Manfred Forstreuter, Yuko Hanba, Hiromitsu Kisanuki, Patrick Meir, Domingo Morales, Serge Rambal, Maria Soledad Jimenez Parrondo, Ingmar Tulva and Charlie Warren for providing details of the experimental design and/or unpublished data accompanying published datasets. We also thank Takayoshi Koike, Yukihiro Chiba and Ichiro Terashima for help with Japanese papers, and Susanne von Caemmerer for clarifications with regard to Rubisco kinetic characteristics.

Funding sources

T.F. Keenan was funded through a Laboratory Directed Research and Development (LDRD) fund under the auspices of DOE, BER Office of Science at Lawrence Berkeley National Laboratory. Additional funding from a Macquarie University Research Fellowship is also acknowledged.

Ülo Niinemets acknowledges funding support for this study was provided by the Estonian Ministry of Science and Education (institutional grant IUT-8-3) and the European Commission through the European Regional Fund (Center of Excellence in Environmental Adaptation), the European Social Fund (postdoctoral grant MJD122) and the European Research Council (advanced grant 322603, SIP-VOL+).

Cantrip: a word of Gaelic origin to mean a magical spell

syrupglass/traitPlasticity