Prepare Stan data from a list of dataset summaries

Converts a list of dataset descriptors (each providing summary statistics and a sample size) into the named list expected by the hierarchical_data_synthesis_summary_stats Stan model.

Usage

prepare_stan_data_from_datasets(
  datasets,
  dist_type = 1,
  use_custom_priors = 0,
  custom_priors = list()
)

Arguments

datasets

A named list of lists. Each element must contain one of the following combinations of summary statistics:

median, min, max

Median and range (summary type 1). n (sample size) is required.

median, Q1, Q3

Median and inter-quartile range (summary type 2). n is required.

mean, sd

Mean and standard deviation (summary type 3). n is required.

freq_value, freq_count

Frequency table of (value, count) pairs (summary type 4). n is optional and defaults to sum(freq_count).

freq_lower, freq_upper, freq_count

Interval-censored frequency table (summary type 5). Each entry gives the lower and upper bound of the censoring interval and the count of individuals in that interval. When freq_lower[i] == freq_upper[i] the observation is treated as exact. n is optional and defaults to sum(freq_count).

Each element may also contain an optional source field — a free-text character string recording the bibliographic reference for that dataset (e.g. "Surname (year), doi: doi.org/xyz"). This field is ignored during Stan data preparation and is never passed to the model.

dist_type

Integer distribution code: 1 = log-normal, 2 = gamma, 3 = Weibull. Defaults to 1.

use_custom_priors

Integer flag (0 or 1) for custom prior use. Currently unused; reserved for future extension. Defaults to 0.

custom_priors

Named list of prior overrides. Any values not supplied fall back to distribution-appropriate defaults (see Details). Recognised names: mu0_sd, log_tau_mean, log_tau_sd, log_phi_mean, log_phi_sd.

Value

A named list suitable for passing to rstan::sampling() as the data argument. The list always includes freq_lower and freq_upper fields (populated with zeros for non-type-5 datasets), as these are required by the Stan model regardless of which summary types are present.

Details

Distribution-specific defaults for log_phi:

Because phi has a different meaning in each distribution, the default prior for log_phi_mean is chosen per dist_type:

dist_type	Distribution	phi	Default log_phi_mean	Prior median phi
1	Lognormal	log-SD (σ)	-0.7	0.50
2	Gamma	shape	2.5	12.2
3	Weibull	shape	1.0	2.7

Users can override any individual prior by passing only the relevant element(s) in custom_priors, e.g. custom_priors = list(log_phi_mean = 3.0) — all other priors will use the distribution-appropriate defaults above.

Note

Backward compatibility: The Stan model requires freq_lower and freq_upper to be present in the data list for all runs, including those that contain only type 1–4 datasets. This is handled automatically when using this function. If you construct the Stan data list manually (rather than via this function), you must include these fields explicitly, e.g.:

stan_data$freq_lower <- rep(0, stan_data$n_freq_total)
stan_data$freq_upper <- rep(0, stan_data$n_freq_total)