mcmc_array-class function

Working with 3D MCMC arrays

3D MCMC arrays (Iterations, Chains, Parameters) are produced by as.array()

methods applied to stan_nma or nma_summary objects.

## S3 method for class 'mcmc_array'
summary(object, ..., probs = c(0.025, 0.25, 0.5, 0.75, 0.975))

## S3 method for class 'mcmc_array'
print(x, ...)

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

## S3 method for class 'mcmc_array'
names(x)

## S3 replacement method for class 'mcmc_array'
names(x) <- value

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

Returns

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

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

# 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
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)