gnlht: Linear/nonlinear functions of model parameters

In OnofriAndreaPG/aomisc: Statistical methods for the agricultural sciences

Linear/nonlinear functions of model parameters

Description

This function calculates linear/nonlinear functions of model parameters and returns their estimates with delta standard errors.

Usage

## S3 method for class 'numeric'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)
## S3 method for class 'lm'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)
## S3 method for class 'nls'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)
## S3 method for class 'lme'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)
## S3 method for class 'nlme'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)
## S3 method for class 'drc'
gnlht(object, func, const, vcov.,
            parameterNames, dfr, ...)

Arguments

object	a named vector of parameter estimates, or a model object for which there are coef and vcov methods. The estimates are asymptotically normally distributed with asymptotic covariance matrix returned by vcov. or passed as an argument
func	a list of functions or quoted strings that are the functions of the parameter estimates to be evaluated
const	If necessary, a dataframe whose columns are the constants to be used in the calculations above. For each row of this dataframe, the functions above are evaluated
vcov.	a variance-covariance matrix, or a function to calculate it from the model object
parameterNames	a character vector with namings for the parameters to be combined
dfr	number of degrees of freedom
...	Additional arguments

Details

Methods are given for several types of model fitting objects (lm, nls, lme, nlme, drc), from where model coefficients and a variance-covariance matrix are automatically retrieved. For other cases, a named vector of model parameters and a variance-covariance matrix can be provided as arguments to the 'gnlht()' function.

Value

Returns a data.frame

Author(s)

Andrea Onofri

Examples

data(metamitron)

#Fit nls grouped model
modNlin <- nls(Conc ~ A[Herbicide] * exp(-k[Herbicide] * Time), 
               start=list(A=rep(100, 4), k=rep(0.06, 4)), 
               data=metamitron)
summary(modNlin)


# Compare parameters #######
funList <- list(~k1 - k2, ~k1 - k3, ~k1 - k4)
gnlht(modNlin, funList)

# Combine parameters
funList <- list(~ -log(0.5)/k1, ~ -log(0.5)/k2,
                ~ -log(0.5)/k3, ~ -log(0.5)/k4)
gnlht(modNlin, funList)

# Combine more flexibly
funList <- list(~ -log(prop)/k1, ~ -log(prop)/k2,
                ~ -log(prop)/k3, ~ -log(prop)/k4)
gnlht(modNlin, funList, const = data.frame(prop = 0.5))

funList <- list(~ -log(prop)/k1, ~ -log(prop)/k2,
                ~ -log(prop)/k3, ~ -log(prop)/k4)
gnlht(modNlin, funList, const = data.frame(prop = c(0.7, 0.5, 0.3)))

# Other possibilities
funList <- list(~ (k2 - k1)/(k1 * k2) * log(prop),
                ~ (k3 - k1)/(k1 * k3) * log(prop), 
                ~ (k4 - k1)/(k1 * k4) * log(prop))
gnlht(modNlin, funList, const = data.frame(prop = c(0.7, 0.5, 0.3)))

# Predictions
funList <- list(~ A1 * exp (- k1 * Time), ~ A2 * exp (- k2 * Time), 
                ~ A3 * exp (- k3 * Time), ~ A4 * exp (- k4 * Time))
propdF <- data.frame(Time = seq(0, 67, 1))
func <- funList
const <- propdF
pred <- gnlht(modNlin, funList, const = propdF)
head(pred)
tail(pred)

# Back transformation of means
library(emmeans)
data(mixture)
head(mixture)
mod <- lm(sqrt(Weight) ~ Treat, data = mixture)
med <- emmeans(mod, ~Treat)
coefs <- as.data.frame(med)[,2]
#parameterNames <- paste("b", 1:4, sep = "")
parameterNames <- as.data.frame(med)$Treat
pn <- parameterNames
# func <- as.list(paste("(1 -", pn, ")/", pn, sep = ""))
# func <- as.list(paste("exp(", pn, ") - 1", sep = ""))
# func <- as.list(paste("(1 -", pn, ")/", pn, sep = ""))
func <- as.list(paste(pn, "^2", sep = ""))
vcov. <- diag(as.data.frame(med)[,3]^2)
sigma <- vcov.
const <- NULL

medieBack <- gnlht(coefs, func,  vcov. = sigma,
                           parameterNames = pn, dfr = 12)
medieBack
emmeans(mod, ~Treat, regrid = "response")

OnofriAndreaPG/aomisc documentation built on Feb. 26, 2024, 8:21 p.m.