Merge branch 'master' into compile_odes

Conflicts
(resolved manually, deleting code that I had
integrated into the RUnit tests for testing the
compiled version):
	.gitignore
	DESCRIPTION
	inst/unitTests/runit.mkinerrmin.R
	inst/unitTests/runit.mkinfit.R
	tests/testthat/test_mkinpredict_SFO_SFO.R
	vignettes/FOCUS_L.html

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+\name{synthetic_data_for_UBA_2014}

+\alias{synthetic_data_for_UBA_2014}

+\docType{data}

+\title{

+  Synthetic datasets for one parent compound with two metabolites

+}

+\description{

+ The 12 datasets were generated using four different models and three different

+ variance components. The four models are either the SFO or the DFOP model with either

+ two sequential or two parallel metabolites.

+

+ Variance component 'a' is based on a normal distribution with standard deviation of 3,

+ Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.

+ Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the 

+ minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07

+ for the increase of the standard deviation with y.

+

+ Initial concentrations for metabolites and all values where adding the variance component resulted

+ in a value below the assumed limit of detection of 0.1 were set to \code{NA}.

+

+ As an example, the first dataset has the title \code{SFO_lin_a} and is based on the SFO model

+ with two sequential metabolites (linear pathway), with added variance component 'a'.

+

+ Compare also the code in the example section to see the degradation models.

+}

+\usage{synthetic_data_for_UBA_2014}

+\format{

+  A list containing datasets in the form internally used by the 'gmkin' package.

+  The list has twelfe components. Each of the components is one dataset that has,

+  among others, the following components

+  \describe{

+    \item{\code{title}}{The name of the dataset, e.g. \code{SFO_lin_a}}

+    \item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}}

+  }

+}

+\source{

+  Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative

+  zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452

+ 

+  Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for

+  measurement error in analytical chemistry. Technometrics 37(2), 176-184.

+}

+\examples{

+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),

+                           M1 = list(type = "SFO", to = "M2"),

+                           M2 = list(type = "SFO"), use_of_ff = "max")

+

+

+m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),

+                                         sink = FALSE),

+                           M1 = list(type = "SFO"),

+                           M2 = list(type = "SFO"), use_of_ff = "max")

+

+m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),

+                            M1 = list(type = "SFO", to = "M2"),

+                            M2 = list(type = "SFO"), use_of_ff = "max")

+

+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),

+                                          sink = FALSE),

+                            M1 = list(type = "SFO"),

+                            M2 = list(type = "SFO"), use_of_ff = "max")

+

+mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)

+}

+\keyword{datasets}