Skip to contents

Post-process Stan output

Source: R/utils_output.R
tar_stan_output.Rd

Not a user-side function. Do not invoke directly.

Usage

tar_stan_output(
  fit,
  output_type,
  summaries,
  summary_args,
  transform,
  variables,
  inc_warmup,
  data,
  data_copy,
  seed
)

Arguments

fit

A Stan fit object.

output_type

Type of output to create, either "summaries", "draws", or "diagnostics".

summaries

Optional list of summary functions passed to ... in posterior::summarize_draws() through $summary() on the CmdStanFit object.

summary_args

Optional list of summary function arguments passed to .args in posterior::summarize_draws() through $summary() on the CmdStanFit object.

transform

Symbol or NULL, name of a function that accepts arguments data and draws and returns a data frame. Here, data is the JAGS data list supplied to the model, and draws is a data frame with one column per model parameter and one row per posterior sample. Any arguments other than data and draws must have valid default values because stantargets will not populate them. See the simulation-based calibration (SBC) section of the simulation vignette for an example.

variables

(character vector) The variables to include.

inc_warmup

Logical, whether to include the warmup draws.

data

List, Stan dataset.

data_copy

Character vector of names of scalars in data. These values will be inserted as columns in the output data frame for each rep. To join more than just scalars, include a .join_data element of your Stan data list with names and dimensions corresponding to those of the model. For details, read https://docs.ropensci.org/stantargets/articles/simulation.html.

seed

Integer vector, random number generator seed used to run Stan.

Value

A data frame of user-friendly Stan output.