3D MCMC arrays (Iterations, Chains, Parameters) are produced by as.array()
methods applied to stan_nma
or nma_summary
objects.
Arguments
- ...
Further arguments passed to other methods
- probs
Numeric vector of quantiles of interest
- x, object
A 3D MCMC array of class
mcmc_array
- value
Character vector of replacement parameter names
Value
The summary()
method returns a nma_summary object, the print()
method returns x
invisibly. The names()
method returns a character
vector of parameter names, and names()<-
returns the object with updated
parameter names. The plot()
method is a shortcut for
plot(summary(x), ...)
, passing all arguments on to plot.nma_summary()
.
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{
# Working with arrays of posterior draws (as mcmc_array objects) is
# convenient when transforming parameters
# Transforming log odds ratios to odds ratios
LOR_array <- as.array(relative_effects(smk_fit_RE))
OR_array <- exp(LOR_array)
# mcmc_array objects can be summarised to produce a nma_summary object
smk_OR_RE <- summary(OR_array)
# This can then be printed or plotted
smk_OR_RE
#> mean sd 2.5% 25% 50% 75% 97.5% Bulk_ESS Tail_ESS
#> d[Group counselling] 3.32 1.54 1.32 2.28 2.97 3.99 7.10 2243 2523
#> d[Individual counselling] 2.41 0.60 1.47 2.00 2.33 2.73 3.83 1190 2147
#> d[Self-help] 1.78 0.74 0.74 1.28 1.64 2.13 3.59 1897 2560
#> Rhat
#> d[Group counselling] 1
#> d[Individual counselling] 1
#> d[Self-help] 1
plot(smk_OR_RE, ref_line = 1)
# Transforming heterogeneity SD to variance
tau_array <- as.array(smk_fit_RE, pars = "tau")
tausq_array <- tau_array^2
# Correct parameter names
names(tausq_array) <- "tausq"
# Summarise
summary(tausq_array)
#> mean sd 2.5% 25% 50% 75% 97.5% Bulk_ESS Tail_ESS Rhat
#> tausq 0.72 0.33 0.29 0.49 0.65 0.87 1.52 1286 1830 1
# }