From af2e1540cdad2fd00bb6216a38a754ff748629ad Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Oct 2019 02:10:08 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/plot.mkinfit.html | 126 +++++++++++++++++++-------------------- 1 file changed, 63 insertions(+), 63 deletions(-) (limited to 'docs/reference/plot.mkinfit.html') diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index df01a00b..04ef75e4 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -8,11 +8,13 @@ Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin + + @@ -32,18 +34,16 @@ - + +from a previous successful call to mkinfit and plots the +observed data together with the solution of the fitted model." /> + @@ -114,7 +114,6 @@ If the current plot device is a tikz device, News - @@ -136,42 +135,34 @@ If the current plot device is a tikz device,
-

Solves the differential equations with the optimised and fixed parameters - from a previous successful call to mkinfit and plots - the observed data together with the solution of the fitted model.

-

If the current plot device is a tikz device, - then latex is being used for the formatting of the chi2 error level, - if show_errmin = TRUE.

- +from a previous successful call to mkinfit and plots the +observed data together with the solution of the fitted model.

# S3 method for mkinfit
-plot(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,
-  show_errplot = FALSE,
-  maxabs = "auto",
-  sep_obs = FALSE, rel.height.middle = 0.9,
-  row_layout = FALSE,
-  lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ...)
+plot(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, show_errplot = FALSE, maxabs = "auto",
+  sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE,
+  lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
+  errmin_digits = 3, frame = TRUE, ...)
+
 plot_sep(fit, show_errmin = TRUE, ...)
+
 plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
+
 plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
- +

Arguments

- + @@ -179,9 +170,9 @@ If the current plot device is a tikz device, - + @@ -201,7 +192,8 @@ If the current plot device is a tikz device, - + @@ -221,41 +213,44 @@ If the current plot device is a tikz device, - + - + - + - + - + - + - + @@ -263,11 +258,13 @@ If the current plot device is a tikz device, - + - + @@ -278,38 +275,41 @@ If the current plot device is a tikz device,
x

Alias for fit introduced for compatibility with the generic S3 method.

Alias for fit introduced for compatibility with the generic S3 +method.
fit
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.

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.
xlab
col_obs

Colors used for plotting the observed data and the corresponding model prediction lines.

Colors used for plotting the observed data and the +corresponding model prediction lines.
pch_obs
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.

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.
show_errplot

Should squared residuals and the error model be shown? If only one plot of - the fits is shown, this 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.

Should squared residuals and the error model be shown? +If only one plot of the fits is shown, this 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.
maxabs

Maximum absolute value of the residuals. This is used for the scaling of - the y axis and defaults to "auto".

Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".
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.

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.
rel.height.middle

The relative height of the middle plot, if more than two rows of plots are shown.

The relative height of the middle plot, if more +than two rows of plots are shown.
row_layout

Should we use a row layout where the residual plot or the error model plot is shown - to the right?

Should we use a row layout where the residual plot or the +error model plot is shown to the right?
lpos

Position(s) of the legend(s). Passed to legend as the first argument. - If not length one, this should be of the same length as the obs_var argument.

Position(s) of the legend(s). Passed to legend as +the first argument. If not length one, this should be of the same length +as the obs_var argument.
inset
show_errmin

Should the FOCUS chi2 error value be shown in the upper margin of the plot?

Should the FOCUS chi2 error value be shown in the upper +margin of the plot?
errmin_digits

The number of significant digits for rounding the FOCUS chi2 error percentage.

The number of significant digits for rounding the FOCUS +chi2 error percentage.
frame

Further arguments passed to plot.
- +

Value

The function is called for its side effect.

- +

Details

+ +

If the current plot device is a tikz device, then +latex is being used for the formatting of the chi2 error level, if +show_errmin = TRUE.

Examples

- 
# One parent compound, one metabolite, both single first order, path from
+    

+# One parent compound, one metabolite, both single first order, path from
 # parent to sink included
 # \dontrun{
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
                    m1 = mkinsub("SFO", full = "Metabolite M1" ))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot_res(fit)
plot_err(fit)

-# 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)

+     show_errmin = TRUE)

 # The same can be obtained with less typing, using the convenience function plot_sep
 plot_sep(fit, lpos = c("topright", "bottomright"))
 
 # Show the observed variables separately, with the error model
 plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
-     show_errmin = TRUE)
# }
+     show_errmin = TRUE)
# }
+