MCMCtraces.Rd
Trace plot (or traceplot) of MCMC draws. See the Plot Descriptions section, below, for details.
mcmc_trace(x, pars = character(), regex_pars = character(), transformations = list(), facet_args = list(), ..., n_warmup = 0, window = NULL, size = NULL, np = NULL, np_style = trace_style_np(), divergences = NULL) mcmc_trace_highlight(x, pars = character(), regex_pars = character(), transformations = list(), facet_args = list(), ..., n_warmup = 0, window = NULL, size = NULL, alpha = 0.2, highlight = 1) trace_style_np(div_color = "red", div_size = 0.25, div_alpha = 1)
x  A 3D array, matrix, list of matrices, or data frame of MCMC draws. The MCMCoverview page provides details on how to specify each these allowed inputs. 

pars  An optional character vector of parameter names. If neither

regex_pars  An optional regular expression to use for
parameter selection. Can be specified instead of 
transformations  Optionally, transformations to apply to parameters
before plotting. If Note: due to partial argument matching 
facet_args  A named list of arguments (other than 
...  Currently ignored. 
n_warmup  An integer; the number of warmup iterations included in

window  An integer vector of length two specifying the limits of a range of iterations to display. 
size  An optional value to override the default line size
( 
np  For models fit using 
np_style  A call to the 
divergences  Deprecated. Use the 
alpha  For 
highlight  For 
div_color, div_size, div_alpha  Optional arguments to the

A ggplot object that can be further customized using the ggplot2 package.
mcmc_trace
Standard trace plots of MCMC draws. For models fit using NUTS
,
the np
argument can be used to also show divergences on the trace plot.
mcmc_trace_highlight
Traces are plotted using points rather than lines and the opacity of all
chains but one (specified by the highlight
argument) is reduced.
Other MCMC: MCMCcombos
,
MCMCdiagnostics
,
MCMCdistributions
,
MCMCintervals
, MCMCnuts
,
MCMCoverview
, MCMCparcoord
,
MCMCrecover
,
MCMCscatterplots
# some parameter draws to use for demonstration x < example_mcmc_draws(chains = 4, params = 6) dim(x)#> [1] 250 4 6dimnames(x)#> $Iteration #> NULL #> #> $Chain #> [1] "chain:1" "chain:2" "chain:3" "chain:4" #> #> $Parameter #> [1] "alpha" "sigma" "beta[1]" "beta[2]" "beta[3]" "beta[4]" #># use traditional ggplot discrete color scale mcmc_trace(x, pars = c("alpha", "sigma")) + ggplot2::scale_color_discrete()#>#># zoom in on a window of iterations, increase line size, # add tick marks, move legend to the top, add gray background color_scheme_set("viridisA") mcmc_trace(x[,, 1:4], window = c(100, 130), size = 1) + panel_bg(fill = "gray90", color = NA) + legend_move("top")# NOT RUN { # parse facet label text color_scheme_set("purple") p < mcmc_trace( x, regex_pars = "beta\\[[1,3]\\]", facet_args = list(labeller = ggplot2::label_parsed) ) p + facet_text(size = 15) # mark first 100 draws as warmup mcmc_trace(x, n_warmup = 100) # plot as points, highlighting chain 2 color_scheme_set("brightblue") mcmc_trace_highlight(x, pars = "sigma", highlight = 2, size = 2) # for models fit using HMC/NUTS divergences can be displayed in the trace plot library("rstanarm") fit < stan_glm(mpg ~ ., data = mtcars, # next line to keep example fast and also ensure we get some divergences prior = hs(), iter = 400, adapt_delta = 0.8) # extract draws using as.array (instead of as.matrix) to keep # chains separate for trace plot posterior < as.array(fit) # for stanfit and stanreg objects use nuts_params() to get the divergences mcmc_trace(posterior, pars = "sigma", np = nuts_params(fit)) color_scheme_set("viridis") mcmc_trace( posterior, pars = c("wt", "sigma"), size = 0.5, facet_args = list(nrow = 2), np = nuts_params(fit), np_style = trace_style_np(div_color = "black", div_size = 0.5) ) color_scheme_set("viridis") mcmc_trace( posterior, pars = c("wt", "sigma"), size = 0.8, facet_args = list(nrow = 2), divergences = nuts_params(fit), div_color = "black" ) # }