I am looking for a fully functional R package for modeling Amax (maximum photosynthesis rate), VCmax (maximum rate of Rubisco carboxylation), Jmax (maximum rate of electron transport for RuBP regeneration) triose phosphate utilization (TPU) limitations and other parameters from gas exchange measurements. This can be an alternative for Photosyn Assistant (http://www.ddsci.com/photosyn.htm). Any supporting comment/answer is highly appreciated. Thank You.
The page of Licor offers some link, but an Excel spreadsheet would suffice as in Sharkey et al. 2007 http://www.licor.com/env/newsline/2015/09/software-for-fitting-photosynthetic-co2-or-light-response-curves/ Staistics can be implemented using Pop tools add-on in excel
ecophys can do this, but also, LeafWeb has an optimization-based process and will return the parameters to you in exchange for submission of data.
http://leafweb.ornl.gov/Pages/LeafWeb.aspx
Hi, Anthony, It's great to hear directly from someone involved with LeafWeb. Is it possible to reanalyze data with and without the extra parameter estimations (mesophyll conductance etc.)?
Great, I'll be submitting some files soon. Is there any way for me to follow LeafWeb to get updates when there are changes?
Would add that several parameters like rubisco activase, leaf heterogeneity, humidity response and mesophyll resistance are variables on temperature and that there is no easy way to adapt concepts in vivo.
it looks like the 'plantecophys' in R can model several gas exchange processes: ACi curves, stomatal conductance, leaf energy balance etc.
To make this thread more complete, see Moualeu-Ngangue et al 2016 who report a brand new method to fit A-Ci curves. There is a supplementary excel tool and SAS code to estimate parameters. See details here.
Moualeu-Ngangue, D. P.; Chen, T.-W. W.; Stützel, H. A New Method to Estimate Photosynthetic Parameters through Net Assimilation Rate-Intercellular Space CO2 Concentration (A-Ci ) Curve and Chlorophyll Fluorescence Measurements. New phytologist 2017, 213, 1543–1554.
http://onlinelibrary.wiley.com/doi/10.1111/nph.14260/abstract
Take a look at recent publication
https://www.frontiersin.org/articles/10.3389/fpls.2018.00448/full
and associated code using R package rjags
https://github.com/jrpleban/Bayes_Farquhar_Models_2_level_Hierarchy
Pretty simple set of implementations in a hierarchal Bayesian scheme for fitting multiple curves at once.
Modifying these codes based on updates such as Moualeu-Ngangue et al 2016 would be reasonable.
Li-COR's answer: http://www.licor.com/env/newsline/2017/09/software-for-fitting-photosynthetic-co2-or-light-response-curves/
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