plantecophys (version 0.6-3)

fitaci: Fit the Farquhar-Berry-von Caemmerer model of leaf photosynthesis

Description

Fits the Farquhar-Berry-von Caemmerer model of photosynthesis to measurements of photosynthesis and intercellular $CO_2$ concentration (Ci). Estimates Jmax, Vcmax, Rd and their standard errors. A simple plotting method is also included, as well as the function fitacis which quickly fits multiple A-Ci curves. Temperature dependencies are taken into account, see Photosyn.

Usage

fitaci(data, varnames = list(ALEAF = "Photo", Tleaf = "Tleaf", Ci = "Ci", PPFD
  = "PARi", Rd = "Rd"), Tcorrect = TRUE, citransition = NULL,
  quiet = FALSE, startValgrid = TRUE, algorithm = "default",
  useRd = FALSE, ...)

## S3 method for class 'acifit':
print(x, ...)

## S3 method for class 'acifit':
summary(object, ...)

## S3 method for class 'acifit':
coef(object, ...)

## S3 method for class 'acifit':
fitted(object, ...)

## S3 method for class 'acifit':
plot(x, what = c("data", "model"), xlim = NULL,
  ylim = NULL, whichA = c("Ac", "Aj", "Amin"), add = FALSE, pch = 19,
  addzeroline = TRUE, addlegend = !add, transitionpoint = TRUE,
  lwd = c(1, 2), ...)

fitacis(data, group, progressbar = TRUE, quiet = FALSE, ...)

## S3 method for class 'acifits':
plot(x, how = c("manyplots", "oneplot"), ...)

## S3 method for class 'acifits':
coef(object, ...)

Arguments

data

Dataframe with Ci, Photo, Tleaf, PPFD (the last two are optional). For fitacis, also requires a grouping variable.

varnames

List of names of variables in the dataset (see Details).

Tcorrect

If TRUE, Vcmax and Jmax are corrected to 25C. Otherwise, Vcmax and Jmax are estimated at measurement temperature.

citransition

If provided, fits the Vcmax and Jmax limited regions separately (see Details).

quiet

If TRUE, no messages are written to the screen.

startValgrid

If TRUE (the default), uses a fine grid of starting values to increase the chance of finding a solution.

algorithm

Passed to nls, sets the algorithm for finding parameter values.

useRd

If Rd provided in data, and useRd=TRUE (default is FALSE), uses measured Rd in fit. Otherwise it is estimatied from the fit to the A-Ci curve.

x

For plot.acifit, an object returned by fitaci

object

For coef.acifit, and print.acifit, the object returned by fitaci

what

The default is to plot both the data and the model fit, or specify 'data' or 'model' to plot one of them.

xlim

Limits for the X axis, if left blank estimated from data

ylim

Limits for the Y axis, if left blank estimated from data

whichA

By default all three photosynthetic rates are plotted (Aj=Jmax-limited (blue), Ac=Vcmax-limited (red), Hyperbolic minimum (black)). Or, specify one or two of them.

add

If TRUE, adds to the current plot

pch

The plotting symbol for the data

addzeroline

If TRUE, the default, adds a dashed line at y=0

addlegend

If TRUE, adds a legend (by default does not add a legend if add=TRUE)

transitionpoint

For plot.acifit, whether to plot a symbol at the transition point.

lwd

Line widths, can be a vector of length 2 (first element for both rates, second one for the limiting rate).

group

For batch analysis using fitacis, the name of the grouping variable in the dataframe.

progressbar

For fitacis, whether to display a progress bar (default is TRUE).

how

If 'manyplots', produces a single plot for each A-Ci curve. If 'oneplot' overlays all of them.

...

Further arguments passed to Photosyn

Value

• A list of class 'acifit', with five components: [object Object],[object Object],[object Object],[object Object],[object Object]

Details

Uses non-linear regression to fit an A-Ci curve. No assumptions are made on which part of the curve is Vcmax or Jmax limited. Three parameters are estimated, Jmax, Vcmax and Rd. When Tcorrect=TRUE (the defualt), Jmax and Vcmax are re-scaled to 25C, using the temperature response parameters provided (but Rd is always at measurement temperature). When Tcorrect=FALSE, estimates of all parameters are at measurement temperature. When citransition is set, it splits the data into a Vcmax-limited (where Ci < citransition), and Jmax-limited region (Ci > citransition). Both parameters are then estimated separately for each region (Rd is estimated only for the Vcmax-limited region). Note that the actual transition point as shown in the standard plot of the fitted A-Ci curve may be quite different from that provided, since the fitting method simply decides which part of the dataset to use for which limitation, it does not constrain the actual estimated transition point directly. See the example below. When plotting the fit, the A-Ci curve is simulated using the Aci function, with leaf temperature (Tleaf) and PPFD set to the mean value for the dataset. If PPFD is not provided in the dataset, it is assumed to equal 1800 mu mol m-2 s-1.

Examples

# Fit an A-Ci curve on a dataframe that contains Ci, Photo and optionally Tleaf and PPFD.
# Here, we use the built-in example dataset 'acidata1'.
f <- fitaci(acidata1)

# Note that the default behaviour is to correct Vcmax and Jmax for temperature,
# so the estimated values are at 25C. To turn this off:
f2 <- fitaci(acidata1, Tcorrect=FALSE)

# To use different T response parameters (see ?Photosyn),
f3 <- fitaci(acidata1, Tcorrect=TRUE, EaV=25000)

# Make a standard plot
plot(f)

# Look at a summary of the fit
summary(f)

# Extract coefficients only
coef(f)

# The object 'f' also contains the original data with predictions.
# Here, Amodel are the modelled (fitted) values, Ameas are the measured values.
with(f$df, plot(Amodel, Ameas))
abline(0,1)

# The fitted values can also be extracted with the fitted() function:
fitted(f)

# The non-linear regression (nls) fit is stored as well,
summary(f$nlsfit)

# The curve generator is stored as f$Photosyn:
# Calculate photosynthesis at some value for Ci, using estimated parameters and mean Tleaf,
# PPFD for the dataset.
f$Photosyn(Ci=820)

# Photosynthetic rate at the transition point:
f$Photosyn(Ci=f$Ci_transition)$ALEAF

# Set the transition point; this will fit Vcmax and Jmax separately. Note that the *actual*
# transition is quite different from that provided, this is perfectly fine :
# in this case Jmax is estimated from the latter 3 points only (Ci>800), but the actual
# transition point is at ca. 400ppm.
g <- fitaci(acidata1, citransition=800)
plot(g)
g$Ci_transition

# Use measured Rd instead of estimating it from the A-Ci curve.
# The Rd measurement must be added to the dataset used in fitting,
# and you must set useRd=TRUE.
acidata1$Rd <- 2
f2 <- fitaci(acidata1, useRd=TRUE)
f2