fitacis2: Fit A-Ci curves with custom kinetics

In plantecowrap: Enhancing Capabilities of 'plantecophys'

Description

Fit A-Ci curves with custom kinetics

Usage

fitacis2(
  data,
  group1,
  group2 = NA,
  group3 = NA,
  gm25 = 0.08701,
  Egm = 47.65,
  K25 = 718.4,
  Ek = 65.50828,
  Gstar25 = 42.75,
  Egamma = 37.83,
  fitmethod = "default",
  fitTPU = TRUE,
  Tcorrect = FALSE,
  useRd = FALSE,
  citransition = NULL,
  alphag = 0,
  PPFD = NULL,
  Tleaf = NULL,
  alpha = 0.24,
  theta = 0.85,
  varnames = list(ALEAF = "Photo", Tleaf = "Tleaf", Ci = "Ci", PPFD = "PARi", Rd = "Rd",
    Press = "Press"),
  ...
)

Arguments

data	data frame with A/Ci curves. Requires net CO2 assimilation (Anet/Photo/ALEAF in umol m-2 s-1), leaf temperature (Tleaf in Celsius), intercellular CO2 concentration (Ci, in umol mol-1), incident irradiance on the leaf (PPFD/PARi in umol m-2 s-1), atmospheric pressure (Patm/Press in kPa), and (optional, set useRd = TRUE for this option) respiration (Rd, in umol m-2 s-1).
group1	grouping variable 1, could be species, temperature, ID
group2	grouping variable 2
group3	grouping variable 3
gm25	mesophyll conductance at 25 Celsius in mol m-2 s-1 bar-1
Egm	activation energy of mesophyll conductance in kJ mol-1
K25	Km in 21 in umol mol-1 (equivalent to ubar bar-1)
Ek	activation energy of Kcair in kJ mol-1
Gstar25	photorespiratory CO2 compensation point at 25 Celsius in umol mol-1 (equivalent to ubar bar-1)
Egamma	activation energy of GammaStar in kJ mol-1
fitmethod	Set to either "bilinear" or "default". Default option in this package is "default". See ?fitaci in plantecophys for more details.
fitTPU	Should TPU limitations be fit? Set to TRUE/FALSE. See ?fitaci in plantecophys for more details.
Tcorrect	Should outputs be temperature corrected? Default here is FALSE. See ?fitaci in plantecophys for more details.
useRd	Should respiration be used? Default is FALSE. See ?fitaci in plantecophys for more details.
citransition	Pre-specify Ci transition point? Units in umol mol-1 (ubar bar-1) Default is FALSE. See ?fitaci in plantecophys for more details.
alphag	Fraction of photorespiratory 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. See ?fitaci in plantecophys for more details.
PPFD	Light intensity? Can be retrieved from dataframe. Default is NULL. Units are umol m-2 s-1. See ?fitaci in plantecophys for more details.
Tleaf	Leaf temperature? Can be retrieved from dataframe. Default is NULL. Units are Celsius. See ?fitaci in plantecophys for more details.
alpha	Quantum yield of CO2 assimilation. Default is 0.24. Units are umol CO2 fixed / umol incident photons. See ?fitaci in plantecophys for more details.
theta	Curvature of the photosynthetic light response. Default is 0.85. If light response has sharper transition, increase up to 1. If light response has shallower curves, decrease towards 0. See ?fitaci in plantecophys for more details.
varnames	Variable names in your dataframe. ALEAF is net CO2 assimilation in umol m-2 s-1, Tleaf is leaf temperature in Celsius, Ci is intercellular CO2 concentration in umol mol-1, PPFD is light intensity in umol m-2 s-1, Rd is respiration rate in umol m-2 s-1, and Press is atmospheric pressure in kPa. See ?fitaci in plantecophys for more details.
...	Further arguments for plantecophys::fitaci(). See ?fitaci for details.

Value

fitacis2 allows gmeso, GammaStar, and Km to vary with Tleaf. Output matches the fitacis function from plantecophys. Note that the temperature response function of Km is derived from the temperature responses of Ko and Kc in Bernacchi et al.2001, as is the GammaStar temperature response defaults. The gm defaults are from Bernacchi et al. 2002 fitted between 1and 35 Celsius. Also note that this ALWAYS uses gm. To fit data on a "Ci-basis", set gm25 really high (e.g. 10000 mol m-2 s-1 bar-1) and Egm to 0 kJ mol-1.

In some instances (e.g. very low stomatal conductance), fitacis2 will fail. In these cases, the output for that curve will be "Failed", rather than an A-Ci curve fit object.

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

Examples

#Read in data
data <- read.csv(system.file("extdata", "example_2.csv",
package = "plantecowrap"), stringsAsFactors = FALSE)
#Run ACi curve fitting
fits <- fitacis2(data, group1 = "Grouping",
varnames = list(ALEAF = "A",
                Tleaf = "Tleaf",
                Ci = "Ci",
                PPFD = "PPFD",
                Rd = "Rd",
                Press = "Press"),
fitmethod = "bilinear", fitTPU = TRUE, Tcorrect = FALSE)

plantecowrap documentation built on April 14, 2020, 7:45 p.m.