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.

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,
    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.

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 means and variances.

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.