f.fitting: Fitting function for photosynthesis data (light curve or Aci...

In TESTgroup-BNL/LeafGasExchange: A package containing functions for fitting photosynthetic response curves, simulat leaf and canopy photosynthesis

Fitting function for photosynthesis data (light curve or Aci curve)

Description

Function to fit model to data. The parameters to fit have to be described in the list Start. All the other parameters of the f.Aci functions have to be in param. If the parameters from Start are repeated in param, the later ones will be ignored. This function uses two methods to fit the data. First by minimizing the residual sum-of-squares of the residuals and then by maximizing the likelihood function. The first method is more robust but the second one allows to calculate the confident interval of the parameters.

Usage

f.fitting(
  measures,
  id.name = NULL,
  Start = list(JmaxRef = 90, VcmaxRef = 70, RdRef = 1),
  param = f.make.param(),
  modify.init = TRUE,
  do.plot = TRUE,
  type = "Aci"
)

Arguments

measures	Data frame of measures obtained from gas exchange analyser with at least the columns A, Ci, Qin (the light at the leaf surface in micro mol m-2 s-1) and Tleaf (in K). If RHs, Tair, Patm, VPDleaf are also present, their mean will be added in the output, but those columns are not needed to estimate the parameters.
id.name	Name of the column in the data frame measures with the name for the curve.
Start	List of parameters to fit with their initial values.
param	See f.make.param() for details.
modify.init	TRUE or FALSE, allows to modify the Start values before fitting the data
do.plot	TRUE or FALSE, plot data and fitted curves ?

Value

Return a list with 3 components, 1 the result of the optim function which is used to estimate the parameters, 2 the output of the function bbmle, 3 the mean variable of the environment during the measurement

Examples

##Simulation of a CO2 curve
data=data.frame(Tleaf=rep(300,20),
Ci=seq(40,1500,75),Qin=rep(2000,20),Tair=300,RHs=70,VPDleaf=2,Patm=101,A=f.Aci(PFD=2000,Tleaf=300,ci=seq(40,1500,75),
param=f.make.param())$A+rnorm(n = 20,mean = 0,sd = 0.5))

f.fitting(measures=data,id.name=NULL,Start=list(JmaxRef=90,VcmaxRef=70,RdRef=1),param=f.make.param())

TESTgroup-BNL/LeafGasExchange documentation built on May 17, 2024, 8:11 p.m.