The object of a report created by this package:

• algorithm: Algorithm that created the samples (currently assumes it is a PT struct). Optional, nothing if unspecfied.

• chains: Samples, stored in a Chains struct.

• original_dim: The original dimensionality of chains (the one stored might be truncated via options.max_dim)

Information passed to the processors:

• inference: The Inference on which the report will be based on.

• output_directory: The resolved location of the output report.

• generated_markdown: Vector of Strings used internally to create the markdown page.

• generated_dict: Generated dictionary used internally to create a JSON object for indexing purposes.

• options: The ReportOptions.

Options to control report:

• max_moving_plot_iters: Maximum number of iterations in moving_pair_plot. Set to zero to avoid creating such movie.

  Creating movies are a bit slow, so in interactive mode the default is zero, and 100 in headless mode.

• target_name: Name of the target. If nothing, will attempt to auto-detect a name via multiple dispatch of the functions target_name or pigeons_target_name.

• target_description: Description of the target, specified using a TargetDescription. If nothing, will attempt to auto-detect it via target_description and pigeons_target_description.

• render: If true, the report webpage's md files are rendered into html files.

• view: If true, the report webpage will be opened automatically.

• postprocessors: The postprocessors to use. Default is default_postprocessors.

• exec_folder: The directory where the report will be created. A unique folder in results/all will be created by default and symlinked in results/latest.

• reproducibility_command: A command to instruct users how to reproduce.

  At the moment implicitly assumes Pigeons will be used, and running these commands should return the Inputs.

• writer: A Documenter.Writer instance used to render the document. Default is an HTML page, but other options including Documenter.LaTeX() are also possible.

• show_error_traces: Useful for debugging, false by default.

• max_dim: Upper bound on the number of dimensions to process. If the number of dimensions exceed this bound, only the prefix of dimensions will be processed.

• interval_probability: Nominal coverage of intervals.

Description of a target.

• keywords: Keywords for the target.

• bibliography: Contents of TeX bib file used to provide bibliographical references in the text, or nothing if no bibliography should be generated.

• text: Description of the target.

add_markdown(context; title, contents)

add_plot(context; file, title, url_help, description, movie)

add_table(
    context;
    table,
    title,
    url_help,
    description,
    kw_pretty_table_args...
)

as_doc_page(context)

Pass to the pages argument of makedocs to properly include the generated page in the Documenter.jl navigation bar.

default_postprocessors()

gcb_progress(context)

Progression of the global communication barrier estimate as a function of the round.

get_pt(context)

headless(lambda)

Enclose calls to report_to_docs and report with different defaults for the view and render options, setting them to false by default.

intervals(chain, probability)

intervals(context)

Table of credible intervals.

lcb(context)

The local communication barrier estimated in the last round.

logz_progress(context)

Progression of the log-normalization constant estimate as a function of the round.

moments(context)

Table of posterior means, variances, MCSE, ESS, R-hat.

moving_pair_plot(context)

A PairPlot movie showing the sample in the reference chain moving in the state space.

mpi_standard_out(context)

MPI standard output.

pair_plot(context)

Create a pair plot using PairPlot.jl.

pigeons_inputs(context)

Table of inputs used in Pigeons.

pigeons_summary(context)

The summary table produced by Pigeons during its execution.

pigeons_target_description(target)

By default, dispatch to pigeons_target_description(target, Val(Symbol(pigeons_target_name(target)))), to handle "vague types" such as TuringLogPotential and StanLogPotential.

pigeons_target_name(target)

render(context)

report(algo_or_chains, options)

report(algo_or_chains; args...)

algo_or_chains can be either a PT struct (returned by pigeons(..)) or a Chains.

args are used to create a ReportOptions.

report_to_docs(algo_or_chains; doc_root, args...)

Similar to report but with different defaults to facilitate including the result as part of a larger documentation site.

Use in combination with as_doc_page.

reproducibility_info(context)

Generated reproducibility script.

round_trip_progress(context)

Progression of the number of round trips as a function of the round.

swaps_plot(context)

A plot showing progression of mean swap acceptance per chain as a function of round.

target_description(context)

target_name(context)

trace_plot(context)

Trace plots.

trace_plot_cumulative(context)

Cumulative averages as a function of iteration.

view_webpage(exec_folder)

Returns a pair, where the first argument is the provided expression verbatim, and the second, the expression as a string to be used as the reproducibility_command argument in report and report_to_docs.