Nicer output for tp_run()

[foersterst]

tp_run() used to return a list built directly from the output JSON via jsonlite. That list was long and hard to read, and it always needed a tp_parse…() call afterward to become usable. This PR changes that. Now, tp_run() returns a tidy data frame produced by tp_parse_smc() or tp_parse_mcmc(), called internally for any model those two functions support (models that return trees still need dedicated parsers, which we haven't built yet).

tp_run() picks the right parser automatically, based on the inference method and model passed to tp_compile(). It reads that information from the sampler and decides which parser to call. For models without a parser yet, it returns the path to the output JSON along with a message instead.

The PR also updates the documentation for all functions involved.

NB: I accidentally created the branch tidy-output from my branch vignettes rather than main, so it inherited the commits under consideration in #30.

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TreePPL Release Notes

Added

• treepplr 0.4: At the end of a run, tp_run() prints a summary with some runtime information and output directories/files. We can add more to this summary later if needed.
• treepplr 0.4: A test for tp_run() when using MCMC.
• treepplr 0.4: Argument wide to tp_parse_smc() and tp_parse_mcmc() to let users decide whether the resulting data frame is in wide (standard in other software) or long (good for plotting) format. Default = TRUE.
• treepplr 0.4: importFrom("methods", "new") to NAMESPACE to suppress one of the warnings during R CMD check.

Changed

• treepplr 0.4: Changed the output of tp_run() from a list object to a (humanly readable) tidy data frame.
• treepplr 0.4: Changed the expected input of tp_parse_smc() and tp_parse_mcmc() from a list object to a character vector containing the path to the JSON output file(s). Before, the parsers only worked on the list previously returned by tp_run(), creating a strict dependency between tp_run() and the parser functions and vice-versa. Now the parser functions can also be used by anyone who ran a TreePPL analysis from the terminal and wants to do the post-processing in R with treepplr.
• treepplr 0.4: Because the output of tp_run() changed, I redesigned its tests, keeping the same logic as the old ones.
• treepplr 0.4: tp_run() now returns data frames in wide format by default.
• treepplr 0.4: tp_mcmc_convergence() and tp_smc_convergence() accept data frames in either long or wide format.

Deprecated

Removed

Fixed

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