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Get posterior samples from a fitted model

Source: R/get.R
get_samples.Rd

Extracts posterior samples from a fitted model. By default, combines all parameters into a single <data.table> with dates and metadata added.

Usage

get_samples(object, ...)

# S3 method for class 'estimate_infections'
get_samples(object, format = c("data.table", "list"), ...)

# S3 method for class 'epinow'
get_samples(object, format = c("data.table", "list"), ...)

# S3 method for class 'forecast_infections'
get_samples(object, ...)

# S3 method for class 'estimate_secondary'
get_samples(object, format = c("data.table", "list"), ...)

# S3 method for class 'forecast_secondary'
get_samples(object, ...)

# S3 method for class 'estimate_truncation'
get_samples(object, format = c("data.table", "list"), ...)

Arguments

object

A fitted model object (e.g., from estimate_infections())

...

Additional arguments (currently unused)

format

Character string specifying the output format. For model classes backed by a Stan fit (estimate_infections, epinow, estimate_secondary, estimate_truncation):

  • "data.table" (default): a long-format <data.table> with dates and other metadata added.

  • "list": the raw named list of arrays as returned by rstan::extract(), with no dates or metadata added.

Value

If format = "data.table", a data.table with columns: date, variable, strat, sample, time, value, type. Contains all posterior samples for all parameters. If format = "list", a named list of arrays, one per parameter.

Examples

if (FALSE) { # \dontrun{
# After fitting a model
samples <- get_samples(fit)
# Filter to specific parameters
R_samples <- samples[variable == "R"]

# Get the raw list of arrays instead
raw_samples <- get_samples(fit, format = "list")
} # }