From aa5aeeb5d55017774eff1066a495df59b97ca233 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Nov 2019 23:55:09 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/news/index.html | 1 + docs/reference/mkinresplot.html | 20 +++++++++++++------- docs/reference/plot.mkinfit-2.png | Bin 57593 -> 62528 bytes docs/reference/plot.mkinfit-3.png | Bin 61280 -> 62528 bytes docs/reference/plot.mkinfit-4.png | Bin 59080 -> 61280 bytes docs/reference/plot.mkinfit-5.png | Bin 65273 -> 59080 bytes docs/reference/plot.mkinfit-6.png | Bin 0 -> 64639 bytes docs/reference/plot.mkinfit-7.png | Bin 0 -> 65273 bytes docs/reference/plot.mkinfit.html | 27 ++++++++++++++++++--------- 9 files changed, 32 insertions(+), 16 deletions(-) create mode 100644 docs/reference/plot.mkinfit-6.png create mode 100644 docs/reference/plot.mkinfit-7.png (limited to 'docs') diff --git a/docs/news/index.html b/docs/news/index.html index 5aef06f9..48ba25e5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,6 +134,7 @@ mkin 0.9.49.8 (unreleased) Unreleased diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 1ac2cdbe..4429798b 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -72,7 +72,7 @@ argument show_residuals = TRUE." /> mkin - 0.9.49.6 + 0.9.49.8 @@ -143,7 +143,8 @@ argument show_residuals = TRUE.

mkinresplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
-  1.1 * max(object$data$time)), xlab = "Time", ylab = "Residual",
+  1.1 * max(object$data$time)), standardized = FALSE, xlab = "Time",
+  ylab = ifelse(standardized, "Standardized residual", "Residual"),
   maxabs = "auto", legend = TRUE, lpos = "topright",
   col_obs = "auto", pch_obs = "auto", frame = TRUE, ...)
@@ -164,14 +165,18 @@ the model

xlim

plot range in x direction.

+ + standardized +

Should the residuals be standardized by dividing by the +standard deviation given by the error model of the fit?

+ xlab -

Label for the x axis. Defaults to "Time [days]".

+

Label for the x axis.

ylab -

Label for the y axis. Defaults to "Residual [% of applied -radioactivity]".

+

Label for the y axis.

maxabs @@ -180,7 +185,7 @@ scaling of the y axis and defaults to "auto".

legend -

Should a legend be plotted? Defaults to "TRUE".

+

Should a legend be plotted?

lpos @@ -212,7 +217,8 @@ be passed on to legendSee also

mkinplot, for a way to plot the data and the fitted - lines of the mkinfit object.

+ lines of the mkinfit object, and plot_res for a function + combining the plot of the fit and the residual plot.

Examples


diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png
index 6910ae47..72bc331e 100644
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diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png
index 8d399598..72bc331e 100644
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diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 20f30221..8d399598 100644
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diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png
index ad2ffa8c..20f30221 100644
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diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png
new file mode 100644
index 00000000..0b3769ce
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diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png
new file mode 100644
index 00000000..ad2ffa8c
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diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 04ef75e4..a3b912bb 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -71,7 +71,7 @@ observed data together with the solution of the fitted model." />
       
       
         mkin
-        0.9.49.6
+        0.9.49.8
       
     

 
@@ -150,9 +150,13 @@ observed data together with the solution of the fitted model.

   lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
   errmin_digits = 3, frame = TRUE, ...)
 
-plot_sep(fit, show_errmin = TRUE, ...)
+plot_sep(fit, show_errmin = TRUE,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
+  "standardized"), ...)
 
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
+plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
+  "standardized"), ...)
 
 plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
@@ -216,7 +220,9 @@ corresponding model prediction lines.

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.

+to the right of the plots of the fitted curves. If this is set to +'standardized', a plot of the residuals divided by the standard deviation + given by the fitted error model will be shown.

show_errplot @@ -274,6 +280,10 @@ chi2 error percentage.

...

Further arguments passed to plot.

+ + standardized +

For

+

Value

@@ -291,16 +301,15 @@ latex is being used for the formatting of the chi2 error level, if # 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)
+ 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_res(fit, standardized = FALSE)
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
#> Warning: "standardized" ist kein Grafikparameter
plot_err(fit)
# 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")) - +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)
# }
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