Get tracerer at rOpenSci

[richelbilderbeek]

• Create an Issue at rOpenSci
• implement feedback

[richelbilderbeek]

Feedback from @bjoelle:

[x] All the packages are missing package documentation (required by rOpenSci guidelines).

Added.

[x] Please also check devtools::spell_check, which shows some typos in documentation in all packages.

Added, fixed typos.

[x] calc_stderr_mean: this function asks for the sample_interval as input but doesn't seem to use it.
Done

[-] To simplify the code I would also suggest using this formula instead of the C code: stderr_mean = stats::sd(trace)/sqrt(length(trace)).

I added this suggestion as a test, validating the results are indeed identical.
Unexpectedly, the current and suggested calculation give different results. I do not know why
Tracer gives this different result, but I do know that tracerer intends to give the same
results as Tracer. Therefore, I choose to keep the old behavior, assuming the Tracer authors
have superior knowledge of the problem (as I only ported their code to C++).

[x] parse_beast_output_files, parse_beast_posterior: these functions need more detailed @return documentation

Added

[x] calc_summary_stats.R: the doc in this entire file refers to calculating ESS but this function calculates other things too: a list of all the stats calculated should be included in the @return doc. The @param traces doc for calc_summary_stats is also confusing ("a numeric vector or data frame or numeric vector")

Added

[x] All function need to have a @return documentation

Added

[richelbilderbeek]

Feedback from @dwinter at the rOpenSci submission

Tracerer

It's a shame traceR was taken as a name on CRAN! (This name is fine, given the shorter one is not available). I only have minor comments about this one.

Minor comments of tracerer

In the package-level documentation consider referring the user to coda, a very widely-used package for MCMC analysis that includes diagnostics and plots that are not implemented here.

• Moved to Refer to coda package #10

In calc_summary_stats the documentation for sample_interval make it clear this is the "sampling interval used in in the MCMC run" or similar (i.e. the sample_interval should match the run that produced the data, and is not used to further thin output in this function).

• Moved to Improve documention of sample_interval parameter in calc_summary_stats  #11

Consider exposing calc_hpd_interval to users. I can imagine users may sometimes one an 80% or 99% HPD for a particular value. At present
calc_summary_stats hard-codes a 95% HPD.

• Moved to Export calc_hpd_interval #12

[richelbilderbeek]

All problems are either closed or moved, thus closing this Issue.