1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
\name{plot.mkinfit}
\alias{plot.mkinfit}
\alias{plot_sep}
\title{
Plot the observed data and the fitted model of an mkinfit object
}
\description{
Solves the differential equations with the optimised and fixed parameters
from a previous successful call to \code{\link{mkinfit}} and plots
the observed data together with the solution of the fitted model.
If the current plot device is a \code{\link[tikzDevice]{tikz}} device,
then latex is being used for the formatting of the chi2 error level,
if \code{show_errmin = TRUE}.
}
\usage{
\method{plot}{mkinfit}(x, fit = x,
obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time),
ylim = "default",
col_obs = 1:length(obs_vars), pch_obs = col_obs,
lty_obs = rep(1, length(obs_vars)),
add = FALSE, legend = !add,
show_residuals = FALSE, maxabs = "auto",
sep_obs = FALSE, rel.height.middle = 0.9,
lpos = "topright", inset = c(0.05, 0.05),
show_errmin = FALSE, errmin_digits = 3, \dots)
plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots)
}
\arguments{
\item{x}{
Alias for fit introduced for compatibility with the generic S3 method.
}
\item{fit}{
An object of class \code{\link{mkinfit}}.
}
\item{obs_vars}{
A character vector of names of the observed variables for which the
data and the model should be plotted. Defauls to all observed variables
in the model.
}
\item{xlab}{
Label for the x axis.
}
\item{ylab}{
Label for the y axis.
}
\item{xlim}{
Plot range in x direction.
}
\item{ylim}{
Plot range in y direction.
}
\item{col_obs}{
Colors used for plotting the observed data and the corresponding model prediction lines.
}
\item{pch_obs}{
Symbols to be used for plotting the data.
}
\item{lty_obs}{
Line types to be used for the model predictions.
}
\item{add}{
Should the plot be added to an existing plot?
}
\item{legend}{
Should a legend be added to the plot?
}
\item{show_residuals}{
Should residuals be shown? If only one plot of the fits is shown, the
residual plot is in the lower third of the plot? Otherwise, i.e. if
"sep_obs" is given, the residual plots will be located to the right of
the plots of the fitted curves.
}
\item{maxabs}{
Maximum absolute value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".
}
\item{sep_obs}{
Should the observed variables be shown in separate subplots? If yes, residual plots
requested by "show_residuals" will be shown next to, not below the plot of the fits.
}
\item{rel.height.middle}{
The relative height of the middle plot, if more than two rows of plots are shown.
}
\item{lpos}{
Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument.
If not length one, this should be of the same length as the obs_var argument.
}
\item{inset}{
Passed to \code{\link{legend}} if applicable.
}
\item{show_errmin}{
Should the FOCUS chi2 error value be shown in the upper margin of the plot?
}
\item{errmin_digits}{
The number of significant digits for rounding the FOCUS chi2 error percentage.
}
\item{\dots}{
Further arguments passed to \code{\link{plot}}.
}
}
\value{
The function is called for its side effect.
}
\examples{
# One parent compound, one metabolite, both single first order, path from
# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
m1 = mkinsub("SFO", full = "Metabolite M1" ))
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
plot(fit)
plot(fit, show_residuals = TRUE)
# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
show_errmin = TRUE)
# The same can be obtained with less typing, using the convenience function plot_sep
plot_sep(fit, lpos = c("topright", "bottomright"))
}
\author{
Johannes Ranke
}
|
