From a5874ab7fce4616e80be69366ff0685332f47bf1 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 27 Oct 2020 15:34:14 +0100
Subject: Add summary method for nlme.mmkin objects

Improve and update docs
---
 man/summary.nlme.mmkin.Rd | 99 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 man/summary.nlme.mmkin.Rd

(limited to 'man/summary.nlme.mmkin.Rd')

diff --git a/man/summary.nlme.mmkin.Rd b/man/summary.nlme.mmkin.Rd
new file mode 100644
index 00000000..ea625dd7
--- /dev/null
+++ b/man/summary.nlme.mmkin.Rd
@@ -0,0 +1,99 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/summary.nlme.mmkin.R
+\name{summary.nlme.mmkin}
+\alias{summary.nlme.mmkin}
+\alias{print.summary.nlme.mmkin}
+\title{Summary method for class "nlme.mmkin"}
+\usage{
+\method{summary}{nlme.mmkin}(
+  object,
+  data = FALSE,
+  verbose = FALSE,
+  distimes = TRUE,
+  alpha = 0.05,
+  ...
+)
+
+\method{print}{summary.nlme.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
+}
+\arguments{
+\item{object}{an object of class \link{nlme.mmkin}}
+
+\item{data}{logical, indicating whether the full data should be included in
+the summary.}
+
+\item{verbose}{Should the summary be verbose?}
+
+\item{distimes}{logical, indicating whether DT50 and DT90 values should be
+included.}
+
+\item{alpha}{error level for confidence interval estimation from the t
+distribution}
+
+\item{\dots}{optional arguments passed to methods like \code{print}.}
+
+\item{x}{an object of class \link{summary.nlme.mmkin}}
+
+\item{digits}{Number of digits to use for printing}
+}
+\value{
+The summary function returns a list based on the \link{nlme} object
+obtained in the fit, with at least the following additional components
+\item{nlmeversion, mkinversion, Rversion}{The nlme, mkin and R versions used}
+\item{date.fit, date.summary}{The dates where the fit and the summary were
+produced}
+\item{diffs}{The differential equations used in the degradation model}
+\item{use_of_ff}{Was maximum or minimum use made of formation fractions}
+\item{data}{The data}
+\item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}
+\item{confint_back}{Backtransformed parameters, with confidence intervals if available}
+\item{ff}{The estimated formation fractions derived from the fitted
+model.}
+\item{distimes}{The DT50 and DT90 values for each observed variable.}
+\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}
+The print method is called for its side effect, i.e. printing the summary.
+}
+\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.
+}
+\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)
+
+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]]
+})
+
+# 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)
+
+}
+\author{
+Johannes Ranke for the mkin specific parts
+José Pinheiro and Douglas Bates for the components inherited from nlme
+}
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