check_conv: Graphical diagnoses to check if the simulation converges

In simlandr: Simulation-Based Landscape Construction for Dynamical Systems

Graphical diagnoses to check if the simulation converges

Description

Compare the distribution of different stages of simulation (for plot_type == "bin" or plot_type = "density"), or show how the percentails of the distribution evolve over time (for plot_type == cumuplot, see coda::cumuplot() for details). More convergence checking methods for MCMC data are available at the coda package. Be cautious: each convergence checking method has its shortcomings, so do not blindly use any results as the definitive conclusion that a simulation converges or not.

Usage

check_conv(output, vars, sample_perc = 0.2, plot_type = "bin")

## S3 method for class 'check_conv'
print(x, ask = TRUE, ...)

Arguments

output	A matrix of simulation output.
vars	The names of variables to check.
sample_perc	The percentage of data sample for the initial, middle, and final stage of the simulation. Not required if plot_type == "cumuplot".
plot_type	Which type of plots should be generated? ("bin", "density", or "cumuplot" which uses coda::cumuplot())
x	The object.
ask	Ask to press enter to see the next plot?
...	Not in use.

Value

A check_conv object that contains the convergence checking result(for plot_type == "bin" or plot_type = "density"), or draw the cumuplot without a return value (for plot_type == cumuplot).

Methods (by generic)

• print(check_conv): Print a check_conv object.

simlandr documentation built on Nov. 16, 2022, 1:12 a.m.