From e05656d57668688b971c28e32b4cfd4d3eac4662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:03:50 +0200 Subject: Correct and rebuild docs - Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown --- docs/reference/plot.mkinfit.html | 82 +++++++++++++++++++++++----------------- 1 file changed, 48 insertions(+), 34 deletions(-) (limited to 'docs/reference/plot.mkinfit.html') diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 7c6f2aac..795262f8 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -52,6 +54,7 @@ If the current plot device is a tikz device, + @@ -121,6 +124,7 @@ If the current plot device is a tikz device, +
@@ -136,28 +140,28 @@ 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, +

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.

- 
# 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,
-  lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, …)
-plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …)
+ 
# 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,
+  lpos = "topright", inset = c(0.05, 0.05),
+  show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ...)
+plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, ...)

Arguments

@@ -242,12 +246,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … - - + @@ -258,8 +262,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … - - + + + + + +
lpos

Position(s) of the legend(s). Passed to legend as the first 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

Passed to legend if applicable.

Passed to legend if applicable.
show_errmin

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

Further arguments passed to plot.

frame

Should a frame be drawn around the plots?

...

Further arguments passed to plot.
@@ -269,21 +277,23 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …

Examples

- 
# One parent compound, one metabolite, both single first order, path from
-# parent to sink included
-
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(fit, show_residuals = TRUE)
plot(fit, show_errplot = TRUE)

+    
# 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(fit, show_residuals = TRUE)
plot(fit, show_errplot = TRUE)

 # Show the observed variables separately
-plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

+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"),
+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"))
+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)

+plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
+     show_errmin = TRUE)
# }
+
+ + + -- cgit v1.2.1