plot.simode {simode}

Plot the fit/estimates of a simode object

Description

Plot the fit or parameter estimates obtained from a call to simode.

Usage

## S3 method for class 'simode'
plot(
  x,
  type = c("fit", "est"),
  show = c("nls", "im", "both"),
  which = NULL,
  pars_true = NULL,
  time = NULL,
  plot_im_smooth = F,
  legend = F,
  mfrow = par("mfrow"),
  cols = list(nls_fit = "blue", im_fit = "green", true = "black", obs = "red", im_smooth
    = "magenta"),
  ...
)

Arguments

x

simode object returned by a call to simode.

type

Type of plot - 'fit' to plot the fitted variables and 'est' to plot the parameter estimates.

show

Whether to plot the fit/estimates obtained using nonlinear least squares ('nls'), integral-matching ('im') or both ('both').

which

Which variables to plot in case type='fit', or which parameters to plot in case type='est'. If empty, the plot will include all of the variables/parameters in x.

pars_true

The true parameter values (if are known). Should be named using the parameter names. If given, the true values for the variables/parameters will be added to the plot.

time

The time points to use for the fitted curves (relevant only for type='fit'). If not given then the time points of the observations in x will be used.

plot_im_smooth

Whether or not to plot the smoothed curves created and used by the integral-matching procedure (relevant only for type='fit').

legend

Whether or not to add a figure legend.

mfrow

A vector of the form c(nr,nc) setting the layout of subplots in one plot (see also par).

cols

List of colors for each element of the plot.

...

Additional argument(s) for methods.