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bmstate

R package for Bayesian multistate modeling.

Installation

  • Install cmdstanr following the instructions here.
  • Install bmstate using
remotes::install_github("generable/bmstate", ref = "main", build_vignettes = TRUE)

Building the vignettes can take some time, so consider using build_vignettes = FALSE. Use ref = "develop" if you want the current development version.

Getting started

More info is in the documentation, which you can view with

library(bmstate)
?bmstate

See also the vignettes.

Development

Versioning

The package mostly conforms to semantic versioning. The version number has the format MAJOR.MINOR.PATCH, where

  • MAJOR is incremented if incompatible API changes are made
  • MINOR version is incremented if significant new functionality is added
  • PATCH version is incremented when making small bug fixes, very minor new functionality, improved documentation or new or improved vignettes

The version update can be done with usethis::use_version().

Development branches

When starting a new feature or a bug fix, create a branch off the develop branch. The version in the develop branch should be something like MAJOR.MINOR.PATCH.9000 where MAJOR.MINOR.PATCH is the version that exists in the main branch. This increment can be done with usethis::use_dev_version(). When finishing the edits, create a PR to develop. Before the develop branch is merged to main, the patch version should be incremented. Also, make sure to run

  • styler::style_dir() in the package root directory.
  • devtools::document()
  • R CMD check

Known NOTEs in R CMD check

  • The exported Stan functions seem to have no bindings in R code
   Undefined global functions or variables:
     compute_log_hazard_multiplier compute_theta_pk
     pop_2cpt_partly_ss_stage1 pop_2cpt_partly_ss_stage2
  • Other
❯ checking package dependencies ... NOTE
  Imports includes 22 non-default packages.
  Importing from so many packages makes the package vulnerable to any of
  them becoming unavailable.  Move as many as possible to Suggests and
  use conditionally.

❯ checking for future file timestamps ... NOTE
  unable to verify current time

❯ checking dependencies in R code ... NOTE
  Namespaces in Imports field not imported from:
    ‘Matrix’ ‘msm’ ‘mstate’
    All declared Imports should be used.

There should not be errors or warnings.