photosynthesis (version 2.1.5)

fit_aci_response: Fitting ACi curves

Description

Fitting ACi curves

Usage

fit_aci_response(
  data,
  varnames = list(A_net = "A_net", T_leaf = "T_leaf", C_i = "C_i", PPFD = "PPFD", g_mc =
    "g_mc"),
  P = 100,
  fitTPU = TRUE,
  alpha_g = 0,
  R_d_meas = NULL,
  useR_d = FALSE,
  useg_mc = FALSE,
  useg_mct = FALSE,
  usegamma_star = FALSE,
  useK_M = FALSE,
  useK_C_K_O = FALSE,
  alpha = 0.24,
  theta_J = 0.85,
  gamma_star25 = 42.75,
  Ea_gamma_star = 37830,
  K_M25 = 718.4,
  Ea_K_M = 65508.28,
  g_mc25 = 0.08701,
  Ea_g_mc = 0,
  K_C25 = NULL,
  Ea_K_C = NULL,
  K_O25 = NULL,
  Ea_K_O = NULL,
  Oconc = 21,
  gamma_star_set = NULL,
  K_M_set = NULL,
  ...
)

Value

fit_aci_response fits ACi curves using an approach similar to Gu et al. 2010. Iterates all possible C_i transition points and checks for inadmissible curve fits. If no curves are admissible (either due to poor data or poor assumed parameters), the output will include a dataframe of NA values. Default parameters are all from Bernacchi et al. 2001, 2002.

Arguments

data

Dataframe for A-Ci curve fitting

varnames

List of variable names. varnames = list(A_net = "A_net", T_leaf = "T_leaf", C_i = "C_i", PPFD = "PPFD", g_mc = "g_mc"), where A_net is net CO2 assimilation, T_leaf is leaf temperature in Kelvin, C_i is intercellular CO2 concentration in umol/mol, PPFD is incident irradiance in umol m-2 s-1 (note that it is ASSUMED to be absorbed irradiance, so be sure to adjust according to light absorbance and PSI/PSII partitioning accordingly OR interpret the resultant values of J and J_max with caution), g_mc is mesophyll conductance to CO2 in mol m-2 s-1 Pa-1.

P

Atmospheric pressure in kPa

fitTPU

Should triose phosphate utilization (V_TPU) be fit?

alpha_g

Fraction of respiratory glycolate carbon that is not returned to the chloroplast (von Caemmerer, 2000). If ACi curves show high-CO2 decline, then this value should be > 0.

R_d_meas

Measured value of respiratory CO2 efflux in umol m-2 s-1. Input value should be positive to work as expected with the equations.

useR_d

Use a measured value of R_d? Set to TRUE if using R_d_meas.

useg_mc

Use mesophyll conductance? Set to TRUE if specifying g_mc in varnames above.

useg_mct

Use mesophyll conductance temperature response? Set to TRUE if using a temperature response of mesophyll conductance.

usegamma_star

Specify gamma_star value? If FALSE, uses a temperature response function with Nicotiana tabacum defaults from Bernacchi et al. 2001.

useK_M

Specify K_M? If FALSE, uses an Arrhenius temperature response function with Nicotiana tabacum defaults from Bernacchi et al. 2001.

useK_C_K_O

Use individual carboxylation/oxygenation constants for rubisco? If TRUE, need to specify values at 25C and activation energy for the Arrhenius temperature response function.

alpha

Quantum yield of CO2 assimilation

theta_J

Curvature of the photosynthetic light response curve

gamma_star25

gamma_star at 25C in umol mol-1

Ea_gamma_star

Activation energy of gamma_star in J mol-1

K_M25

Michaelis-Menten constant for rubisco at 25C

Ea_K_M

Activation energy for K_M in J mol-1

g_mc25

Mesophyll conductance at 25C in mol m-2 s-1

Ea_g_mc

Activation energy of g_mc in J mol-1

K_C25

Michaelis-Menten constant for rubisco carboxylation at 25C

Ea_K_C

Activation energy for K_C in J mol-1

K_O25

Michaelis-Menten constant for rubisco oxygenation at 25C

Ea_K_O

Activation energy for K_O in J mol-2

Oconc

O2 concentration in %. Used with P to calculate intracellular O2 when using K_C_K_O

gamma_star_set

Value of gamma_star to use (in ppm) if usegamma_star = TRUE

K_M_set

Value of K_M to use if useK_M = TRUE

...

Other arguments to pass on

References

Bernacchi CJ, Singsaas EL, Pimentel C, Portis AR, Long SP. 2001. Improved temperature response functions for models of rubisco-limited photosynthesis. Plant Cell Environment 24:253-259.

Bernacchi CJ, Portis AR, Nakano H, von Caemmerer S, Long SP. 2002. Temperature response of mesophyll conductance. Implications for the determination of rubisco enzyme kinetics and for limitations to photosynthesis in vivo. Plant Physiology 130:1992-1998.

Gu L, Pallardy SG, Tu K, Law BE, Wullschleger SD. 2010. Reliable estimation of biochemical parameters from C3 leaf photosynthesis-intercellular carbon dioxide response curves. Plant Cell Environment 33:1852-1874.

von Caemmerer S. 2000. Biochemical models of leaf photosynthesis. CSIRO Publishing, Collingwood.

Examples

# \donttest{
# Read in your data
# Note that this data is coming from data supplied by the package
# hence the complicated argument in read.csv()
# This dataset is a CO2 by light response curve for a single sunflower
data <- read.csv(system.file("extdata", "A_Ci_Q_data_1.csv",
  package = "photosynthesis"
))

# Define a grouping factor based on light intensity to split the ACi
# curves
data$Q_2 <- as.factor((round(data$Qin, digits = 0)))

# Convert leaf temperature to K
data$T_leaf <- data$Tleaf + 273.15

# Fit ACi curve. Note that we are subsetting the dataframe
# here to fit for a single value of Q_2
fit <- fit_aci_response(data[data$Q_2 == 1500, ],
  varnames = list(
    A_net = "A",
    T_leaf = "T_leaf",
    C_i = "Ci",
    PPFD = "Qin"
  )
)

# View fitted parameters
fit[[1]]

# View graph
fit[[2]]

# View data with modelled parameters attached
fit[[3]]

# Fit many curves
fits <- fit_many(
  data = data,
  varnames = list(
    A_net = "A",
    T_leaf = "T_leaf",
    C_i = "Ci",
    PPFD = "Qin"
  ),
  funct = fit_aci_response,
  group = "Q_2"
)

# Print the parameters
# First set of double parentheses selects an individual group value
# Second set selects an element of the sublist
fits[[3]][[1]]

# Print the graph
fits[[3]][[2]]

# Compile graphs into a list for plotting
fits_graphs <- compile_data(fits,
  list_element = 2
)

# Compile parameters into dataframe for analysis
fits_pars <- compile_data(fits,
  output_type = "dataframe",
  list_element = 1
)
# }