Pmax_models: Effect of environmental water potential or temperature on the...

In OnofriAndreaPG/drcSeedGerm: Utilities for data analyses in seed germination/emergence assays

Effect of environmental water potential or temperature on the germination capability of a seed lot

Description

These models are used to describe the germination capability of a seed lot, depending on the environmental water potential or temperature.

Usage

PmaxPsi1(fixed = c(NA, NA, NA), names = c("G", "Psib", "sigma"))
PmaxT1(fixed = c(NA, NA, NA), names = c("G", "Tc", "sigmaTc"))
PmaxPsi1.fun(Psi, G, Psib, sigma)
PmaxT1.fun(Temp, G, Tc, sigmaTc)

Arguments

fixed	numeric vector. Specifies which parameters are fixed and at what value they are fixed. Defaults to NAs for parameter that are not fixed.
names	a vector of character strings giving the names of the parameters (should not contain ":"). The default is reasonable.
Psi	Water potential level
Temp	Temperature level
G	Maximum proportion of germinated seeds
Psib	Base water potential level
sigma	Variability of base water potential within the seed lot
Tc	Ceiling temperature level
sigmaTc	Variability of ceiling temperature level within the population

Details

The R functions 'PmaxPsi1()' and 'PmaxT1()' are meant to be used for model fitting with the 'drm()' function, within the 'drc' package. On the other hand, 'PmaxPsi1.fun()' and 'PmaxT1.fun()' are general purpose functions, to bu used for plotting or other applications.

Value

'PmaxPsi1()' and 'PmaxT1()' return a list containing the nonlinear function, the self starter function and the parameter names, that are internally used for model fitting. 'PmaxPsi1.fun()' and 'PmaxT1.fun()' return the maximum proportion of germinated seeds for any given level of temperature or water potential in the substrate.

Author(s)

Andrea Onofri

References

https://www.statforbiology.com/2021/stat_drcte_12_HTT2step

Examples

library(drcte)
# Pmax vs Psi (shifted exponential)
Psi <- seq(-2.2, 0, by = 0.2)
Pmax <- c(0, 0, 0.076, 0.413, 0.514, 0.643, 0.712,
          0.832, 0.865, 0.849, 0.89, 0.90)
mod <- drm(Pmax ~ Psi, fct = PmaxPsi1())
summary(mod)

# Pmax vs Psi (shifted exponential, with asymptote)
Psi <- seq(-2.2, 0, by = 0.2)
Pmax <- c(0, 0, 0.076, 0.413, 0.514, 0.643, 0.712,
          0.832, 0.865, 0.849, 0.89, 0.90)
mod <- drm(Pmax ~ Psi, fct = PmaxPsi1(fixed = c(1, NA, NA)))
summary(mod)

# Pmax vs temperature
Tval <- c(0, 2.5, 5, 7.5, 10, 12.5, 15, 17.5,
          20, 22.5, 25, 27.5, 30, 32.5, 35)
Pmax2 <- c(0.79, 0.81, 0.807, 0.776, 0.83,
           0.73, 0.744, 0.73, 0.828, 0.818,
           0.805, 0.706, 0.41, 0.002, 0)
mod2 <- drm(Pmax2 ~ Tval, fct = PmaxT1())
summary(mod2)

OnofriAndreaPG/drcSeedGerm documentation built on March 14, 2023, 5:45 p.m.