HaloTL: Halotime model with logistic distribution of base salt...

In OnofriAndreaPG/drcSeedGerm: Utilities for Data Analyses in Seed Germination/Emergence Assays

Halotime model with logistic distribution of base salt concentration (derived from Bakhshandeh et al., 2020)

Description

This model relates the time-course of the proportion of germinated seeds to salt concentration (C) in the substrate. It is based on a logistic distribution of base salt concentration within the seed lot. The equation is:

P(t) = 1 - \Phi \left\{ \frac{C + (\theta_{halo} / t) - C_b }{\sigma_{C_b}} \right\}

where \Phi is a logistic cumulative distribution function. This models describes the distribution of base salt concentration within the population, while the distribution of germination times is indirectly modelled, but it is not, in itself, logistic (you see that 't' is at the denominator). The 'HaloTL.fun()' is a generic function, which can be used for plotting or other applications, while the 'HaloTL()' function is meant to be used for model fitting with the 'drmte()' function in the 'drcte()' package.

Usage

HaloTL()
HaloTL.fun(time, SConc, ThetaHalo, SConcb50, sigma)

Arguments

The 'HaloTL()' function has no arguments. The 'HaloTL.fun()' function has the following arguments:

time	time
SConc	salt concentration in the substrate
ThetaHalo	halotime constant
SConcb50	median base salt concentration
sigma	shape parameter for the base salt concentration within the seed lot

Details

This model is derived from the halo-thermal time model described in Bakhshandeh et al. (2020).

Value

The 'HaloTL.fun()' function returns the proportion of germinated seeds, for any given values of time and salt concentration in the substrate. The 'HaloTL()' function returns a list containing the nonlinear function, the self-starter function, the parameter names and other items which are internally used by the 'drmte()' function.

Note

This function is for use with the R function 'drmte()'

Author(s)

Andrea Onofri

References

Bakhshandeh, E., Bradford, K.J., Pirdashti, H., Vahabinia, F., Abdellaoui, R., 2020. A new halothermal time model describes seed germination responses to salinity across both sub- and supra-optimal temperatures. Acta Physiologia Plantarum 42, 137.

Examples

# Read data
datasetOr <- read.csv("https://www.casaonofri.it/_datasets/Halotime4genotypes.csv",
                      check.names = FALSE)
datasetOr[,4:9] <- lapply(datasetOr[,4:9], as.numeric)
dataset <- melt_te(datasetOr, count_cols = 4:9, treat_cols = 1:3,
            monitimes = c(3,4,5,7,10,14), n.subjects = 50)
dataset <- dataset[dataset$CV == "Saturnin",]

# Model fitting
modg <- drmte(count ~ timeBef + timeAf + SConc, fct=HaloTL(),
              data=dataset)
summary(modg)

OnofriAndreaPG/drcSeedGerm documentation built on Jan. 13, 2025, 5:53 a.m.