C4EstimateWithCAT: Estimate photosynthesis parameters for C4 species using...

In zhouhaoran06/C4-Parameter-Estimation: Estimate C4 photosynthesis parameters using ACi curve

Description

Using the gas exchange measurement (A_Ci curve), C4 photosynthesis model with carbonic anhydrase reaction and Sharkey et al. (2007) fitting processure to do nonlinear curve fitting (using nlminb package) for estimating photosynthesis parameters (Vcmax,J,Rd,gm and Vpmax) for C4 species. The difference between this method with C4EstimateWithCA is that temperature response parameters need to be provided by the users. Thus, this method provides the option to alter temperature response parameters. If only planing to alter several parameters, not all of them, one can use the other parameters provided by Table S1 in Zhou et al. (2019) ("Deriving C4 photosynthesis parameters by fitting intensive A/Ci curves"). Make sure to load the "stats" package before intstalling and using the "C4Estimation" package.

Usage

C4EstimateWithCAT(ACi, Tleaf, Patm, alpha1, x, CaBreakL, CaBreakH, startp,
  TresponseKc, TresponseKo, Tresponsegammastar, TresponseKp, Tresponsegbs,
  TresponseVcmax, TresponseJ, TresponseRd, Tresponsegm, TresponseVpmax,
  TresponseKp2, Tresponsekr, Tresponsekf, TresponseKH, TresponsekCA)

Arguments

ACi	Gas exchange measurement from Li6400 or other equipment. It is a dataframe iput. Ci with the unit of ppm. You can prepare the data in Excel file like the given example and save it as "tab delimited text". Then import data by ACi <- read.table(file = "/Users/haoranzhou/Desktop/Learn R/ACi curve.txt", header = TRUE)
Tleaf	Leaf temperature when A_Ci curve is measured.
Patm	Atmosphere pressure when A_Ci curve is measured.
alpha1	The fraction of O2 evolution occurring in the bundle sheath. Unless you have enough information, input it as the 0.15.
x	the fraction of total electron transport that are confined to be used for the PEP regeneration out of J, which is the total electron transport.
CaBreakL	Higher bound of Ci below which A is thought to be controled by Rubisco Carboxylation (Ac). Start with 10.
CaBreakH	Lower bound of Ci above which A is thought to be controled by RuBP regeneration (Aj). Start with 50. If the estimation results showed "inadmissible fits", change the CaBreakL and CaBreakH until "inadmissible fits" disappear.
startp	A vector that gives the start points for the estimation (c(Vcmax,J,Rd,gm,Vpmax,KCA))
TresponseKc	A vector that gives the temperature response parameters for the Kc (c(Kc25,deltaHaKc))
TresponseKo	A vector that gives the temperature response parameters for the Ko (c(Ko25,deltaHaKo))
Tresponsegammastar	A vector that gives the temperature response parameters for the gammastar (c(gammastar25,deltaHagammastar))
TresponseKp	A vector that gives the temperature response parameters for the Kp for CO2 (c(Kp25,deltaHaKp))
Tresponsegbs	A vector that gives the temperature response parameters for the gbs (c(gbs25,deltaHagbs,deltaHdgbs,deltaSgbs))
TresponseVcmax	A vector that gives the temperature response parameters for the Vcmax (c(deltaHaVcmax))
TresponseJ	A vector that gives the temperature response parameters for the J (c(deltaHaJ,deltaHdJ,deltaSJ))
TresponseRd	A vector that gives the temperature response parameters for the Rd (c(deltaHaRd))
Tresponsegm	A vector that gives the temperature response parameters for the gm (c(deltaHagm,deltaHdgm,deltaSgm))
TresponseVpmax	A vector that gives the temperature response parameters for the Vpmax (c(deltaHaVpmax,deltaHdVpmax,deltaSVpmax))
TresponseKp2	A vector that gives the temperature response parameters for the Kp for HCO3- (c(Kp225,deltaHaKp2))
Tresponsekr	A vector that gives the temperature response parameters for the kr (c(kr25,deltaHakr))
Tresponsekf	A vector that gives the temperature response parameters for the kf (c(kf25,deltaHakf))
TresponseKH	A vector that gives the temperature response parameters for the KH (c(KH25))
TresponsekCA	A vector that gives the temperature response parameters for the kCA (c(deltaHakCA,deltaHdkCA,deltaSkCA))

Value

This package will return a dataframe that contains the following values (c(Vcmax,J,Rd,gm,Vpmax and KCA)). You can try with c(30, 150, 3, 10, 50, 80).

Parameter at leaf temperature: A vector (c(Vcmax,J,Rd,gm,Vpmax and KCA)) returns the estimation parameters at leaf temperature.

Parameter at 25°C: A vector (c(Vcmax,J,Rd,gm,Vpmax and KCA)) returns the estimation parameters at leaf temperature.

Objective: The final objective value based on the estimation results.

Convergence: An integer code. 0 indicates successful convergence.

Message: A character string giving any additional information returned by the optimizer, or NULL. For details, see PORT documentation.

Iterations: Number of iterations performed.

Evaluations: Number of objective function and gradient function evaluations.

zhouhaoran06/C4-Parameter-Estimation documentation built on Dec. 23, 2021, 9:20 p.m.