AQ_curves

by Nick Tomeo / @Tomeopaste / tomeonj [at] gmail

Fitting [multiple] photosynthetic light response curves in R [simultaneously].

In this repo you will find:

A script (file="AQ_curve_function.R") containing a function for fitting photosynthetic light response curves: fit_AQ_curve().
A script containing the function diagnostic_AQ_plot(). This takes the output from the fit_AQ_curve() along with the original curve data and produces a plot for each A-Q curve. Each plot has the fit curve plotted on top of the original A-Q points for visualizing how well the fit model matches the data. This has not yet (2017-11-11) had thorough testing, though does work for the curves I've thrown at it.
An R-markdown doc (Introduction_to_AQ_curve_fitting.Rmd) that introduces the fit_AQ_curve() and diagnostic_AQ_plot() functions with an example analysis provided as an instructional guide for using the above functions.
A directory (AQ_curves/ExampleDataFiles) with example light curves used in testing out the above functions.
A directory (AQ_curves/OriginalPieces) with earlier pieces of the above functions before they were sufficiently functional.

Documentation

fit_AQ_curve {AQ_curves} R Documentation

Description

Fits a non-rectangular hyperbola model to photosynthetic light response gas exchange data and solves for the commonly used parameters: light-saturated photosynthetic rate (A_sat), quantum efficiency (Phi), mitochondrial respiration in the light (R_d), curvature/convexivity of light saturation (Theta), light compensation point (LCP), and the irradiance required to saturate photosynthesis.

Usage

fit_AQ_curve(df, group_id, Photo, PARi, fit_type = "onls")

Arguments

Argument	Description
`df`	A data frame with your gas exchange data that contains a column with unique identifiers for each curve (e.g., "curve_1", "curve_2", etc), a column of net photosynthetic values, and a column of irradiance/Q/PAR/PPFD values.
`group_id`	The name of the column containing curve identification values.
`Photo`	The name of the column containing net photosynthetic values.
`PARi`	The name of the column containing irradiance values.
`fit_type`	The type of regression model to use for fitting. Defaults to orthogonal difference with `onls::onls()`. Can optionally switch to `base::nls()` by explicityly setting to "nls".

Details

The model fit is the standard non-rectangular hyperbola (e.g., see Lobo et al., 2013, Photosynthetica, v51, doi.org/10.1007/s11099-013-0045-y) of the form:
A_N = ((Phi x Q + A_sat - sqrt[(Phi x Q + A_sat)^2 - 4 x Theta x Phi x Q x A_sat])/(2 x Theta)] - R_d
where, A_N (µmol CO_2 m^-2 s^-1) is the net photosynthetic rate, Phi (mol CO_2 mol^-1 photons) is quantum efficiency, Q (µmol photons m^-2 s^-1) is irradiance in the range of photosynthetically active radiation, A_sat (µmol CO_2 m^-2 s^-1) is the light-saturated photosynthetic rate, Theta (unitless, range 0-1) is a convexivity parameter relating the curvature of the response, and R_d (µmol CO_2 m^-2 s^-1) is the respiration rate in the day/light. NB: GitHub needs support for LaTeX equation rendering in markdown files.

Value

Returns an object of class data.frame that contains nine columns:

The group_id's
Light saturated net photosynthesis (Asat)
Quantum yield (Phi)
Mitochondrial respiration in the light (Rd)
The curvature/convexivity factor of the curve (theta)
The residual sum-of-squares (resid_SSs) from the model fit
The light compensation point (LCP)
PARi at 75% saturation of photosynthesis (Q_sat_75) - reliable
PARi at 85% saturation (Q_sat_85) - much less reliable

Examples

Default fitting with orthogonal distance regression, i.e., onls::onls():
fit_AQ_curve(df = soy_AQ_curves, group_id = "curve_ids", Photo = "Photo", PARi = "PARi")

Fitting with standard least-squares non-linear regression, i.e., base::nls()
fit_AQ_curve(df = soy_AQ_curves, group_id = "curve_ids", Photo = "Photo", PARi = "PARi", fit_type = "nls")

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Tomeopaste/AQ_curves