Plots of summary results

The plot method for nma_summary objects is used to produce plots of parameter estimates (when called on a stan_nma object or its summary), relative effects (when called on the output of relative_effects()), absolute predictions (when called on the output of predict.stan_nma()), posterior ranks and rank probabilities (when called on the output of posterior_ranks() or posterior_rank_probs()).

Usage

# S3 method for class 'nma_summary'
plot(
  x,
  ...,
  stat = "pointinterval",
  orientation = c("horizontal", "vertical", "y", "x"),
  ref_line = NA_real_
)

# S3 method for class 'nma_parameter_summary'
plot(
  x,
  ...,
  stat = "pointinterval",
  orientation = c("horizontal", "vertical", "y", "x"),
  ref_line = NA_real_
)

# S3 method for class 'nma_rank_probs'
plot(x, ...)

# S3 method for class 'surv_nma_summary'
plot(x, ..., stat = "lineribbon")

Arguments

x

A nma_summary object

...

Additional arguments passed on to the underlying ggdist plot stat, see Details

stat

Character string specifying the ggdist plot stat to use, default "pointinterval", except when plotting estimated survival/hazard/cumulative hazard curves from survival models where the default is "lineribbon"

orientation

Whether the ggdist geom is drawn horizontally ("horizontal") or vertically ("vertical"), default "horizontal"

ref_line

Numeric vector of positions for reference lines, by default no reference lines are drawn

Value

A ggplot object.

Details

Plotting is handled by ggplot2 and the stats and geoms provided in the ggdist package. As a result, the output is very flexible. Any plotting stats provided by ggdist may be used, via the argument stat.

The default uses ggdist::stat_pointinterval(), to produce medians and 95% Credible Intervals with 66% inner bands. Additional arguments in ... are passed to the ggdist stat, to customise the output. For example, to produce means and Credible Intervals, specify point_interval = "mean_qi". To produce an 80% Credible Interval with no inner band, specify .width = c(0, 0.8).

Alternative stats can be specified to produce different summaries. For example, specify stat = "[half]eye" to produce (half) eye plots, or stat = "histinterval" to produce histograms with intervals.

A full list of options and examples is found in the ggdist vignette vignette("slabinterval", package = "ggdist").

For survival/hazard/cumulative hazard curves estimated from survival models, the default uses ggdist::stat_lineribbon() which produces curves of posterior medians with 50%, 80%, and 95% Credible Interval bands. Again, additional arguments in ... are passed to the ggdist stat. For example, to produce posterior means and 95% Credible bands, specify point_interval = "mean_qi" and .width = 0.95.

A ggplot object is returned which can be further modified through the usual ggplot2 functions to add further aesthetics, geoms, themes, etc.

Examples

## Smoking cessation
# \donttest{
# Run smoking RE NMA example if not already available
if (!exists("smk_fit_RE")) example("example_smk_re", run.donttest = TRUE)
# }
# \donttest{
# Produce relative effects
smk_releff_RE <- relative_effects(smk_fit_RE)
plot(smk_releff_RE, ref_line = 0)


# Customise plot options
plot(smk_releff_RE, ref_line = 0, stat = "halfeye")


# Further customisation is possible with ggplot commands
plot(smk_releff_RE, ref_line = 0, stat = "halfeye", slab_alpha = 0.6) +
  ggplot2::aes(slab_fill = ggplot2::after_stat(ifelse(x < 0, "darkred", "grey60")))


# Produce posterior ranks
smk_rank_RE <- posterior_ranks(smk_fit_RE, lower_better = FALSE)
plot(smk_rank_RE)


# Produce rank probabilities
smk_rankprob_RE <- posterior_rank_probs(smk_fit_RE, lower_better = FALSE)
plot(smk_rankprob_RE)


# Produce cumulative rank probabilities
smk_cumrankprob_RE <- posterior_rank_probs(smk_fit_RE, lower_better = FALSE,
                                           cumulative = TRUE)
plot(smk_cumrankprob_RE)


# Further customisation is possible with ggplot commands
plot(smk_cumrankprob_RE) +
  ggplot2::facet_null() +
  ggplot2::aes(colour = Treatment)

# }