plot.nma_summary function

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()).

## 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

Returns

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

# Run smoking RE NMA example if not already available
if (!exists("smk_fit_RE")) example("example_smk_re", run.donttest = TRUE)

# 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)