View source: R/convergence.plot.R
convergence.plot | R Documentation |
The function produces a .pdf file containing some convergence plots for the Monte Carlo draws.
convergence.plot( model, file = "convergence-output.pdf", plotfun = "all", pars = NULL, point_est = "median", prob = 0.5, prob_outer = 0.9, lags = 10, warmup = F, width = 7, height = 7 )
model |
an object of class |
file |
a character string giving the name of the file (with extension .pdf). |
plotfun |
an optional character vector of diagnostics plots. The default is to compute |
pars |
an optional character vector of parameter names. If |
point_est |
an optional character to specify the point estimate to be shown between |
prob |
the probability mass to be included in the inner interval ( |
prob_outer |
the probability mass to be included in the outer interval of the |
lags |
the number of lags to be shown in the |
warmup |
a logical scalar indicating whether to include the warmup draws or not (default). |
width, height |
the width and height of the graphics region of each plot in inches. The default values are 7. |
The plots can be further customized using the ggplot2
package.
density
returns a density plot for each parameter in pars
computed from the posterior draws. See bayesplot::mcmc_areas
for further details.
trace
returns a trace plot for each parameter in pars
computed from the posterior draws. See bayesplot::mcmc_trace
for further details.
intervals
returns a plot of uncertainty interval for each parameter in pars
computed from the posterior draws. See bayesplot::mcmc_intervals
for further details.
rate
returns a plot for each parameter in pars
with the number of iterations on the x-axis and the Monte Carlo mean until iteration i-th on the y-axis.
rhat
returns a plot with the Rhat values for each parameter in pars
. See bayesplot::mcmc_rhat
for further details.
acf
returns the autocorrelation plots (one for each parameter in pars
). See bayesplot::mcmc_acf
for further details.
A .pdf file with one plot per page.
Brooks, SP., Gelman, A. (1998). General methods for monitoring convergence of iterative simulations. Journal of Computational and Graphical Statistics, 7, 434-455.
Stan Development Team (2020). RStan: the R interface to Stan. R package version 2.19.3. https://mc-stan.org
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