plot.list.simode: Plot the fit/estimates of a 'list.simode' object

In simode: Statistical Inference for Systems of Ordinary Differential Equations using Separable Integral-Matching

Description

Plot the fit or parameter estimates obtained from a call to simode with obs_sets>1.

Usage

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

Arguments

x	list.simode object.
type	Type of plot - 'fit' to plot the fitted equations 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_mean_sd	Plot the mean and standard deviation for the fit/estimates of the simode objects in x. To be used when x is the result of fitting monte-carlo simulations.
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.

simode documentation built on July 1, 2020, 10:30 p.m.