IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0143346.html
   My bibliography  Save this article

Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data

Author

Listed:
  • Remko A Duursma

Abstract

Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO2 in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO2 response curves ('A-Ci curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.

Suggested Citation

  • Remko A Duursma, 2015. "Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-13, November.
    • Handle: RePEc:plo:pone00:0143346
    DOI: 10.1371/journal.pone.0143346
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143346
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0143346&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0143346?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Mirindi Eric Dusenge & Jeffrey M. Warren & Peter B. Reich & Eric J. Ward & Bridget K. Murphy & Artur Stefanski & Raimundo Bermudez & Marisol Cruz & David A. McLennan & Anthony W. King & Rebecca A. Mon, 2023. "Boreal conifers maintain carbon uptake with warming despite failure to track optimal temperatures," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. David S. Ellsworth & Kristine Y. Crous & Martin G. Kauwe & Lore T. Verryckt & Daniel Goll & Sönke Zaehle & Keith J. Bloomfield & Philippe Ciais & Lucas A. Cernusak & Tomas F. Domingues & Mirindi Eric , 2022. "Convergence in phosphorus constraints to photosynthesis in forests around the world," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Marc C. Heuermann & Dominic Knoch & Astrid Junker & Thomas Altmann, 2023. "Natural plant growth and development achieved in the IPK PhenoSphere by dynamic environment simulation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Aaron M Shew & Alvaro Durand-Morat & Lawton L Nalley & Xin-Gen Zhou & Clemencia Rojas & Greg Thoma, 2019. "Warming increases Bacterial Panicle Blight (Burkholderia glumae) occurrences and impacts on USA rice production," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-18, July.
    5. Yang, Zhenfeng & Tian, Juncang & Wang, Zhi & Feng, Kepeng & Ouyang, Zan & Zhang, Lixin & Yan, Xinfang, 2023. "Coupled soil water stress and environmental effects on changing photosynthetic traits in wheat and maize," Agricultural Water Management, Elsevier, vol. 282(C).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0143346. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.