summary.nlme.mmkin: Summary method for class "nlme.mmkin"

In jranke/mkin: Kinetic Evaluation of Chemical Degradation Data

Summary method for class "nlme.mmkin"

Description

Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.

Usage

## S3 method for class 'nlme.mmkin'
summary(
  object,
  data = FALSE,
  verbose = FALSE,
  distimes = TRUE,
  alpha = 0.05,
  ...
)

## S3 method for class 'summary.nlme.mmkin'
print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

Arguments

object	an object of class nlme.mmkin
data	logical, indicating whether the full data should be included in the summary.
verbose	Should the summary be verbose?
distimes	logical, indicating whether DT50 and DT90 values should be included.
alpha	error level for confidence interval estimation from the t distribution
...	optional arguments passed to methods like print.
x	an object of class summary.nlme.mmkin
digits	Number of digits to use for printing

Value

The summary function returns a list based on the nlme object obtained in the fit, with at least the following additional components

nlmeversion, mkinversion, Rversion	The nlme, mkin and R versions used
date.fit, date.summary	The dates where the fit and the summary were produced
diffs	The differential equations used in the degradation model
use_of_ff	Was maximum or minimum use made of formation fractions
data	The data
confint_trans	Transformed parameters as used in the optimisation, with confidence intervals
confint_back	Backtransformed parameters, with confidence intervals if available
ff	The estimated formation fractions derived from the fitted model.
distimes	The DT50 and DT90 values for each observed variable.
SFORB	If applicable, eigenvalues of SFORB components of the model.

The print method is called for its side effect, i.e. printing the summary.

Author(s)

Johannes Ranke for the mkin specific parts José Pinheiro and Douglas Bates for the components inherited from nlme

Examples

# Generate five datasets following SFO kinetics
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
dt50_sfo_in_pop <- 50
k_in_pop <- log(2) / dt50_sfo_in_pop
set.seed(1234)
k_in <- rlnorm(5, log(k_in_pop), 0.5)
SFO <- mkinmod(parent = mkinsub("SFO"))

pred_sfo <- function(k) {
  mkinpredict(SFO,
    c(k_parent = k),
    c(parent = 100),
    sampling_times)
}

ds_sfo_mean <- lapply(k_in, pred_sfo)
names(ds_sfo_mean) <- paste("ds", 1:5)

set.seed(12345)
ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
  add_err(ds,
    sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
    n = 1)[[1]]
})

## Not run: 
# Evaluate using mmkin and nlme
library(nlme)
f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
f_nlme <- nlme(f_mmkin)
summary(f_nlme, data = TRUE)

## End(Not run)

jranke/mkin documentation built on April 29, 2024, 7:33 a.m.