# MCMC-traces

##### Trace plots of MCMC draws

Trace plot (or traceplot) of MCMC draws. See the **Plot Descriptions**
section, below, for details.

##### Usage

```
mcmc_trace(x, pars = character(), regex_pars = character(),
transformations = list(), ..., facet_args = list(), n_warmup = 0,
iter1 = 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)

mcmc_rank_overlay(x, pars = character(), regex_pars = character(),
transformations = list(), ..., n_bins = 20, ref_line = FALSE)

mcmc_rank_hist(x, pars = character(), regex_pars = character(),
transformations = list(), ..., facet_args = list(), n_bins = 20,
ref_line = FALSE)

mcmc_trace_data(x, pars = character(), regex_pars = character(),
transformations = list(), ..., highlight = NULL, n_warmup = 0,
iter1 = 0)

##### Arguments

- x
A 3-D array, matrix, list of matrices, or data frame of MCMC draws. The MCMC-overview page provides details on how to specify each these allowed inputs. It is also possible to use an object with an

`as.array()`

method that returns the same kind of 3-D array described on the MCMC-overview page.- pars
An optional character vector of parameter names. If neither

`pars`

nor`regex_pars`

is specified then the default is to use*all*parameters. As of version`1.7.0`

,**bayesplot**also supports 'tidy' parameter selection by specifying`pars = vars(...)`

, where`...`

is specified the same way as in dplyr::select(...) and similar functions. Examples of using`pars`

in this way can be found on the Tidy parameter selection page.- regex_pars
An optional regular expression to use for parameter selection. Can be specified instead of

`pars`

or in addition to`pars`

. When using`pars`

for tidy parameter selection, the`regex_pars`

argument is ignored since select helpers perform a similar function.- transformations
Optionally, transformations to apply to parameters before plotting. If

`transformations`

is a function or a single string naming a function then that function will be used to transform all parameters. To apply transformations to particular parameters, the`transformations`

argument can be a named list with length equal to the number of parameters to be transformed. Currently only univariate transformations of scalar parameters can be specified (multivariate transformations will be implemented in a future release). If`transformations`

is a list, the name of each list element should be a parameter name and the content of each list element should be a function (or any item to match as a function via`match.fun()`

, e.g. a string naming a function). If a function is specified by its name as a string (e.g.`"log"`

), then it can be used to construct a new parameter label for the appropriate parameter (e.g.`"log(sigma)"`

). If a function itself is specified (e.g.`log`

or`function(x) log(x)`

) then`"t"`

is used in the new parameter label to indicate that the parameter is transformed (e.g.`"t(sigma)"`

).Note: due to partial argument matching

`transformations`

can be abbreviated for convenience in interactive use (e.g.,`transform`

).- ...
Currently ignored.

- facet_args
A named list of arguments (other than

`facets`

) passed to`ggplot2::facet_wrap()`

or`ggplot2::facet_grid()`

to control faceting.- n_warmup
An integer; the number of warmup iterations included in

`x`

. The default is`n_warmup = 0`

, i.e. to assume no warmup iterations are included. If`n_warmup > 0`

then the background for iterations`1:n_warmup`

is shaded gray.- iter1
An integer; the iteration number of the first included draw (default is

`0`

). This can be used to make it more obvious that the warmup iterations have been discarded from the traceplot. It cannot be specified if`n_warmup`

is also set to a positive value.- 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 for

`mcmc_trace()`

or the default point size for`mcmc_trace_highlight()`

.- np
For models fit using NUTS (more generally, any symplectic integrator), an optional data frame providing NUTS diagnostic information. The data frame should be the object returned by

`nuts_params()`

or one with the same structure. If`np`

is specified then tick marks are added to the bottom of the trace plot indicating within which iterations there was a divergence (if there were any). See the end of the**Examples**section, below.- np_style
A call to the

`trace_style_np()`

helper function to specify arguments controlling the appearance of tick marks representing divergences (if the`np`

argument is specified).- divergences
Deprecated. Use the

`np`

argument instead.- alpha
For

`mcmc_trace_highlight()`

, passed to`ggplot2::geom_point()`

to control the transparency of the points for the chains not highlighted.- highlight
For

`mcmc_trace_highlight()`

, an integer specifying one of the chains that will be more visible than the others in the plot.- div_color, div_size, div_alpha
Optional arguments to the

`trace_style_np()`

helper function that are eventually passed to`ggplot2::geom_rug()`

if the`np`

argument is also specified. They control the color, size, and transparency specifications for showing divergences in the plot. The default values are displayed in the**Usage**section above.- n_bins
For the rank plots, the number of bins to use for the histogram of rank-normalized MCMC samples. Defaults to

`20`

.- ref_line
For the rank plots, whether to draw a horizontal line at the average number of ranks per bin. Defaults to

`FALSE`

.

##### Value

The plotting functions return a ggplot object that can be further
customized using the **ggplot2** package. The functions with suffix
`_data()`

return the data that would have been drawn by the plotting
function.

`mcmc_trace_data()`

returns the data for the trace *and* rank plots
in the same data frame.

##### Plot Descriptions

`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.`mcmc_rank_hist()`

Whereas traditional trace plots visualize how the chains mix over the course of sampling, rank histograms visualize how the values from the chains mix together in terms of ranking. An ideal plot would show the rankings mixing or overlapping in a uniform distribution. See Vehtari et al. (2019) for details.

`mcmc_rank_overlay()`

Ranks from

`mcmc_rank_hist()`

are plotted using overlaid lines in a single panel.

##### References

Vehtari, A., Gelman, A., Simpson, D., Carpenter, B., B<U+00FC>rkner, P.
(2019). Rank-normalization, folding, and localization: An improved *R*-hat
for assessing convergence of MCMC. arXiv preprint.

##### See Also

Other MCMC: `MCMC-combos`

,
`MCMC-diagnostics`

,
`MCMC-distributions`

,
`MCMC-intervals`

, `MCMC-nuts`

,
`MCMC-overview`

, `MCMC-parcoord`

,
`MCMC-recover`

,
`MCMC-scatterplots`

##### Examples

```
# NOT RUN {
# some parameter draws to use for demonstration
x <- example_mcmc_draws(chains = 4, params = 6)
dim(x)
dimnames(x)
# trace plots of the betas
color_scheme_set("viridis")
mcmc_trace(x, regex_pars = "beta")
# }
# NOT RUN {
color_scheme_set("viridisA")
mcmc_trace(x, regex_pars = "beta")
color_scheme_set("viridisC")
mcmc_trace(x, regex_pars = "beta")
# }
# NOT RUN {
# mix color schemes
color_scheme_set("mix-blue-red")
mcmc_trace(x, regex_pars = "beta")
# 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")
# Rank-normalized histogram plots. Instead of showing how chains mix over
# time, look at how the ranking of MCMC samples mixed between chains.
color_scheme_set("viridisE")
mcmc_rank_hist(x, "alpha")
mcmc_rank_hist(x, pars = c("alpha", "sigma"), ref_line = TRUE)
mcmc_rank_overlay(x, "alpha")
# }
# 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, refresh = 0,
# 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)
)
mcmc_trace(
posterior,
pars = c("wt", "sigma"),
size = 0.8,
facet_args = list(nrow = 2),
divergences = nuts_params(fit),
div_color = "black"
)
# }
# NOT RUN {
# }
```

*Documentation reproduced from package bayesplot, version 1.7.0, License: GPL (>= 3)*