From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Feb 2021 16:41:31 +0100 Subject: Prepare for v1.0.0 - Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest --- docs/reference/plot.mixed.mmkin.html | 313 +++++++++++++++++++++++++++++++++++ 1 file changed, 313 insertions(+) create mode 100644 docs/reference/plot.mixed.mmkin.html (limited to 'docs/reference/plot.mixed.mmkin.html') diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html new file mode 100644 index 00000000..232d26e7 --- /dev/null +++ b/docs/reference/plot.mixed.mmkin.html @@ -0,0 +1,313 @@ + + + + + + + + +Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ +
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+ + +
+

Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object

+
+ +
# S3 method for mixed.mmkin
+plot(
+  x,
+  i = 1:ncol(x$mmkin),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  xlim = range(x$data$time),
+  resplot = c("predicted", "time"),
+  pred_over = NULL,
+  ymax = "auto",
+  maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.02 + 0.07 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
+  ...
+)
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
x

An object of class mixed.mmkin, nlme.mmkin

i

A numeric index to select datasets for which to plot the individual predictions, +in case plots get too large

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.

standardized

Should the residuals be standardized? Only takes effect if +resplot = "time".

xlab

Label for the x axis.

xlim

Plot range in x direction.

resplot

Should the residuals plotted against time or against +predicted values?

pred_over

Named list of alternative predictions as obtained +from mkinpredict with a compatible mkinmod.

ymax

Vector of maximum y axis values

maxabs

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

ncol.legend

Number of columns to use in the legend

nrow.legend

Number of rows to use in the legend

rel.height.legend

The relative height of the legend shown on top

rel.height.bottom

The relative height of the bottom plot row

pch_ds

Symbols to be used for plotting the data.

col_ds

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

lty_ds

Line types to be used for the model predictions.

frame

Should a frame be drawn around the plots?

...

Further arguments passed to plot.

+ +

Value

+ +

The function is called for its side effect.

+

Author

+ +

Johannes Ranke

+ +

Examples

+
ds <- lapply(experimental_data_for_UBA_2019[6:10], + function(x) x$data[c("name", "time", "value")]) +names(ds) <- paste0("ds ", 6:10) +dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO"), quiet = TRUE) +# \dontrun{ +f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) +plot(f[, 3:4], standardized = TRUE) +
+# For this fit we need to increase pnlsMaxiter, and we increase the +# tolerance in order to speed up the fit for this example evaluation +f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) +plot(f_nlme) +
+# } +
+
+ +
+ + + +
+ + + + + + + + -- cgit v1.2.1