plot_trace: Plot optimization trace of a call to 'simode'

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

Description

Plot a trace of the loss values and parameter estimates during the integral-matching/nonlinear least squares optimization within a call to simode. For the traces to exist, the arguments save_im_trace and/or save_nls_trace in simode.control should be set to true, when calling simode.

Usage

plot_trace(
  x,
  show = c("nls", "im", "both"),
  which = NULL,
  mfrow = par("mfrow"),
  cols = list(nls_fit = "blue", im_fit = "green"),
  ...
)

Arguments

x	simode object returned by a call to simode.
show	Whether to plot the estimates obtained using nonlinear least squares ('nls'), integral-matching ('im') or both ('both').
which	Which parameters' traces to plot. If NULL, the trace for all the parameters in x will be plotted.
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.