StomatalClosure {pvldcurve}

Point of stomatal closure

Description

Determines the point of stomatal closure in a set of experimentally obtained leaf drying curves. Stomatal closure happens when the curve irreversibly settles to linear water loss.

Usage

StomatalClosure(data, sample = "sample",
  time.since.start = "time.since.start", conductance = "conductance",
  RWD = "RWD.interval", threshold = FALSE, graph = TRUE,
  show.legend = TRUE)

Arguments

data

data frame containing columns of equal length giving the numerical coordinates of the curve: time since start (minutes), conductance (mmol m^-2 s^-1) and RWD (%), ordered by sample by ascending time since start. A column containing the sample IDs is optionally required if several samples were measured.

sample

optional name of the column in data containing the sample ID (if available), default: "sample"

time.since.start

optional name of the column in data containing numeric time since start values (min), default: "time.since.start"

conductance

optional name of the column in data containing numeric leaf conductance values (mmol m^-2 s^-1), default: "conductance"

RWD

optional name of the column in data containing numeric relative water deficit (%) values, default: "RWD.interval" (RWD average of an interval as outputted by RWDInterval)

threshold

sensitivity for the determination of stomatal closure. 60 by default.

graph

set FALSE if no plots are to be returned

show.legend

set FALSE if no legend is to be be shown in the plots

Details

Before using this function, check the raw data for an initial plateau. If the exponential decline does not onset directly, fitting might not succeed.
The conductances by time since start curves are fitted using the Gauss-Newton algorithm of nls() to a combined exponential and linear model. The exponential and linear parts are extracted and time since start at stomatal closure is localized at the point where the slope of the exponential part of the fit is higher than a threshold value. The threshold value is calculated by the use of the parameter b of the exponential part of the fit (a * exp(b * x)): -(b^2 * sens). The sensitivity constant (sens) is 60 by default and can be specified individually by the argument 'threshold'.
Minimum conductance (gmin) at stomatal closure is the conductance value of the overall fit at stomatal closure. RWD at stomatal closure is then calculated by linear regression of RWD and time since start.

Value

List splitted by sample consisting of

stomatal.closure

coordinates of the point of stomatal closure (time.since.start, RWD, conductance)

formula

formula of the exponential and linear part of the combined fits

coef

coefficients of combined model

conf_int

upper (97.5 %) and lower (2.5 %) border of 95 % confidence interval of model parameters

If graph = TRUE, the plotted original data is displayed with the exponential and linear fit of the combined model as well as the x-coordinate (time.since.start) of the point of stomatal closure.

Examples

# get example data
df <- WeatherAllocation(leaf_drying_data, weather_data)   # allocate weather to weight loss data
df <- TimeSinceStart(df) # calculate time since start
df <- df[df$fw.plateau != "yes",] # remove plateauing data
df <- FittedFW(df, graph = FALSE) # correct noises in fresh weight
df <- RWDInterval(df, fresh.weight = "fitted.fw") # calculate RWD based in the intervals
df <- Conductance(df, fresh.weight = "fitted.fw") # calculate conductance

# identify stomatal closure in curve and get graphs
sc <- StomatalClosure(df)