From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/reference/plot.mkinfit.html | 205 +++++++++++++++++++++++++-------------- 1 file changed, 131 insertions(+), 74 deletions(-) (limited to 'docs/reference/plot.mkinfit.html') diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 23cf27b5..cf96990e 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model.">< mkin - 1.1.0 + 1.2.0 @@ -46,11 +46,14 @@ observed data together with the solution of the fitted model.">< Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
  • - Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Calculation of time weighted average concentrations with mkin
    • @@ -58,7 +61,10 @@ observed data together with the solution of the fitted model.">< Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -91,50 +97,50 @@ 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 = "Residue",
-  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,
-  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"),
-  ...
-)
-
-plot_res(
-  fit,
-  sep_obs = FALSE,
-  show_errmin = sep_obs,
-  standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE),
-  ...
-)
-
-plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
    + 
    # S3 method for mkinfit
+plot(
+  x,
+  fit = x,
+  obs_vars = names(fit$mkinmod$map),
+  xlab = "Time",
+  ylab = "Residue",
+  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,
+  show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"),
+  ...
+)
+
+plot_res(
+  fit,
+  sep_obs = FALSE,
+  show_errmin = sep_obs,
+  standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE),
+  ...
+)
+
+plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
    @@ -142,32 +148,56 @@ observed data together with the solution of the fitted model.

    x

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

    + +
    fit

    An object of class mkinfit.

    + +
    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.

    + +
    xlab

    Label for the x axis.

    + +
    ylab

    Label for the y axis.

    + +
    xlim

    Plot range in x direction.

    + +
    ylim

    Plot range in y direction. If given as a list, plot ranges for the different plot rows can be given for row layout.

    + +
    col_obs

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

    + +
    pch_obs

    Symbols to be used for plotting the data.

    + +
    lty_obs

    Line types to be used for the model predictions.

    + +
    add

    Should the plot be added to an existing plot?

    + +
    legend

    Should a legend be added to the plot?

    + +
    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. @@ -175,47 +205,74 @@ Otherwise, i.e. if "sep_obs" is given, the residual plots will be located 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

    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".

    + +
    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.

    + +
    rel.height.middle

    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?

    + +
    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.

    + +
    inset

    Passed to legend if applicable.

    + +
    show_errmin

    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.

    + +
    frame

    Should a frame be drawn around the plots?

    + +
    ...

    Further arguments passed to plot.

    + +
    standardized

    When calling 'plot_res', should the residuals be standardized in the residual plot?

    +

    Value

    -

    The function is called for its side effect.

    + + +

    The function is called for its side effect.

    Details

    @@ -230,41 +287,41 @@ latex is being used for the formatting of the chi2 error level, if

    Examples

    - 
    
-# 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" ))
+    
    
+# 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" ))
 #> Temporary DLL for differentials generated and loaded
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 #> Warning: Observations with value of zero were removed from the data
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
+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)
 
-plot_res(fit)
+plot_res(fit)
 
-plot_res(fit, standardized = FALSE)
+plot_res(fit, standardized = FALSE)
 
-plot_err(fit)
+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 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"))
+
+# 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 the observed variables separately, with the error model
+plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
+     show_errmin = TRUE)
 
-# }
-
+# }
+
    @@ -279,7 +336,7 @@ latex is being used for the formatting of the chi2 error level, if
    -

    Site built with pkgdown 2.0.3.

    +

    Site built with pkgdown 2.0.6.

    -- cgit v1.2.1