NEWS

postpack 0.5.2 (2020-09-09)

• Addressed CRAN feedback and resubmitted
• See feedback received and to-do items – none are major or user-facing (#36)

postpack 0.5.1 (2020-09-01)

• Addressed CRAN feedback and resubmitted
• See feedback received and to-do items – none are major or user-facing (#33)

postpack 0.5.0 (2020-08-31)

• First submission to CRAN.

postpack 0.4.4 (2020-08-28)

• Include pkgdown stuff - not much more needs to be said here.
• Site is hosted here

postpack 0.4.3 (2020-08-28)

• Split the large vignette into four (#29).
• This change is in preparation for creating a pkgdown website.

postpack 0.4.2 (2020-08-25)

• Primarily standardization of function argument descriptions (#19, #32)
• Switched to using markdown for writing Roxygen comments – big improvement
• Included more links to other relevant help files

postpack 0.4.1 (2020-08-24)

• Improvements to function examples (#18)
• Some previous examples were entirely hypothetical (non-executable), and some functions didn’t even have them.
• Nearly all examples now rely heavily on the data(cjs) object.

postpack 0.4.0 (2020-08-24)

Renamed Functions

• get_p() became get_params()
• match_p() became match_params()
• base_p() became drop_index()

Renamed Function Arguments

• All functions that previously accepted a p argument now accept a params argument (match_params(), diag_plots() post_subset(), post_summ(), post_remove(), vcov_decomp(), etc.) (#14)
• p_summ has been replaced with probs in post_summ() (#25)
• match_params and get_params now both take a type argument, and both accept only values of "base_only" or "base_index" (#20 - some other function and arguments changed here as well).
• density_plot() and trace_plot() previously accepted a p_one argument – this is now param (distinction between multiple parameters and one parameter); but most users won’t notice this as these are non-exported functions.
• The non-exported functions ins_regex_bracket(), rm_regex_bracket(), ins_regex_lock(), and rm_regex_lock() now take the params argument rather than the string argument, but most users won’t notice this.

Deleted Functions

• matrix2mcmclist() was deleted and now post_convert() does its job (#23).

postpack 0.3.1 (2020-08-23)

• Reset par() after completing diag_plots() (#17)

postpack 0.3.0 (2020-08-23)

• Remove StatonMisc dependencies (#16)
• This change won’t affect users – just what goes on under the hood

postpack 0.2.7 (2020-08-20)

• Updates to post_thin()
  • Remove errors that arise when thin_percent is not a perfect multiple of the number of iterations per chain - this causes the thinning to be “quasi-evenly” spaced. As this function is only ever used in code development and not final products, this should not be an issue (#13).
  • Reversed thin_percent to be keep_percent, and implemented throughout.
  • Added a keep_iters argument – now users can choose to keep either a fixed number of samples (again, may be quasi-equal to keep_iters, due to rounding errors) or a fixed percent of samples.

postpack 0.2.6 (2020-08-20)

• Add a by_chain argument to post_summ() (#10)
  • Sometimes a user may wish to summarize each chain separately rather than the aggregate across chains. They can now do this by setting post_summ(..., by_chain = TRUE). For now, Rhat, ess, and mcse will be ignored if by_chain = TRUE.

postpack 0.2.5 (2020-08-20)

Add a post_convert() function

• postpack requires (for the most part) that MCMC samples be stored in mcmc.list objects. But not all R packages that perform MCMC return samples immediately in this format. This new function may help users get their samples into mcmc.list format, potentially broadening the accessibility of the functions in this package.

postpack 0.2.4 (2020-07-14)

• Fix warnings introduced by R 4.0.0 (#12)
• User-visible behavior is identical to previous versions, but the warnings are no longer returned.

postpack 0.2.3 (2020-04-13)

• Remove density_plot() and trace_plot() from exported list

postpack 0.2.2 (2020-04-13)

Include a post_remove function

• In some circumstances, it might be better to exclude nodes rather than explicitly say which you want to keep. This new function behaves just like post_subset, except that it prompts the user to verify that they wish to exclude the match nodes and returns everything that does not match the p argument.

postpack 0.2.1 (2020-04-10)

• Include ability to return Monte Carlo standard errors in post_summ (#11)

postpack 0.2.0 (2020-04-10)

• Include an auto_escape option (#5)

postpack 0.1.18 (2020-04-09)

• Require that R version 3.5.0 or later is available (#8)

postpack 0.1.17 (2020-04-09)

• Bug fixes when working with one-node mcmc.lists (#7, #9)
  • post_subset() and post_thin() previously used coda::as.mcmc.list() to convert matrices to mcmc.list objects, however, if the matrix contained only one node, this would result in the mcmc.list no longer having a name for that node. Because most of the postpack functions rely on node names, this caused issues (e.g., diag_plots(), post_bind()).
  • These functions now rely on matrix2mcmclist to perform this task, which should fix these issues.

postpack 0.1.16 (2019-12-04)

• Bug fix when displaying NaN Rhat values (#7)

postpack 0.1.15 (2019-11-30)

• Bug fix when calculating Rhat

• When calculating Rhat using post_summ(..., Rhat = T) (which wraps coda::gelman.diag) on an object containing only one node, an error would be thrown:

  Error in data[1:nobs, , drop = FALSE] : incorrect number of dimensions

  Which I tracked down to be a result of the autoburnin argument being true by default. Being able to perform the calculations for only one node was required for the diag_plots(..., show_diags = T) update. So I have forced this argument to be FALSE in its usage within post_summ().

postpack 0.1.14 (2019-11-27)

• Functions that were previously exported but could confuse users include:
  • ins_regex_bracket()
  • rm_regex_bracket()
  • id_mat()
• These functions were removed from the exported NAMESPACE
• Consistency was improved for vcov_decomp(): it now internally uses id_mat()
• post_bind() now allows one of the objects to be a matrix of derived quantities, but still requires that it has the same number of samples as the object it is being binded to.
• The vignette was updated to reflect these and other changes to the package since its initial creation.

postpack 0.1.13 (2019-11-26)

• Include NEWS.md by going through git commit history and documenting changes at each version shift

postpack 0.1.12 (2019-11-26)

• Users now have the option to set a diags_plots(..., show_diags) argument to display Rhat and ESS on the density plot

postpack 0.1.11 (2019-11-24)

• Improved error messages in match_p now uses StatonMisc::list_out to print the unique node names, which makes its printing much cleaner (#2)

postpack 0.1.10 (2019-11-24)

• Removed the warn argument from all functions that call match_p
• Removed the prettify argument to post_summ() was removed

postpack 0.1.9 (2019-11-24)

Improvements to internal consistency

• The updated usage of post_dim(..., kind) was included in other functions including:
  • post_bind
  • post_thin
  • vcov_decomp
• vcov_decomp has improved error messages and relies on StatonMisc::progress_updater to print the progress of the calculation
• error message in post_dim improved to rely on StatonMisc::list_out
• included an id_mat function

Improvements to documentation

• included a vignette and example mcmc.list objects
• readme updated to instruct users to set build_vignettes = T when installing from GitHub and several other simplifications to the readme since there is now a vignette

postpack 0.1.8 (2019-10-03)

• post_dim() now accepts a kind argument, which represents certain element(s) from the returned vector.

postpack 0.1.7 (2019-09-19)

• Added vcov_decomp() function
  • Will decompose the posterior of a variance-covariance node into its correlation matrix and standard deviation vector, and return an mcmc.list object with these nodes

postpack 0.1.6 (2019-09-13)

• Added more layouts to diag_plots (#6)
  • Options for diag_plots(..., layout = "2x1") and diag_plots(..., layout = "4x2") added, and the "auto" option will now consider these when selecting the best option.

postpack 0.1.5 (2019-09-03)

• Added write_model(): I essentially duplicated R2OpenBUGS::write.model because it was the only function I ever used from that package now all my BUGS models are fitted with JAGS.
  • I got sick of having to load it and telling others to install it just for this one function
• Bug fix: post_dim was counting the chain and iters columns as nodes (#1)

postpack 0.1.4 (2019-06-30)

• Renamed codaTools to postpack.
• The name of the package was changed from {codaTools} to {postpack}. This is a better name, because it is not just used for convergence diagnostics.
• Package helpfile created

codaTools 0.1.3 (2019-06-30)

• Improvements to get_nodes and filter_post: better error messages
• Switched format = "matrix" to matrix = T/F argument
• Included match_p function - now all subsetting is handled by this one function
• filter_post became post_subset
• inclusion of ins_regex_lock, rm_regex_lock, and base_p - all intended to improve the behavior of diag_plots
• better usage of StatonMisc functions, they are now imported rather than requiring the whole package at the start of a function that needs them
• summ_post became post_summ
• native_format became array_format
• get_nodes became get_p
• bind_post became post_bind
• thin_post became post_thin
• addition of post_dim
• better titles in diag_plots through the my_title function

codaTools 0.1.2 (2019-04-06)

• Bug fixes: thin_post, native_format
• Creation of readme: basic installation instructions and example functionality

codaTools 0.1.1 (2018-11-16)

• Added new functions
  • bind_post: combines two mcmc.list objects
  • thin_post: thins an mcmc.list object at regularly-spaced intervals from each chain

codaTools 0.1.0 (2018-11-14)

• First substantially usable version of package
• Package now contains functional capabilities to do everything I was doing before (extracting, diagnostic, summarizing particular nodes), now with cleaner functions that do specific tasks, and with the ability to extract particular nodes using regular expressions

codaTools 0.0.9000 (2018-11-05)

Initial Repository Creation

• First attempt at wrapping my commonly used MCMC post-processing functions into an R package, allowing them to be easily accessed during my work