shinybrms 1.3.0
Major changes
- Use the term “nonpooled effects” instead of “nonvarying effects” and the term “partially pooled effects” instead of “varying effects”.
- Restructured page “Posterior”.
- Up to now, some general MCMC diagnostics (R-hat, bulk-ESS, tail-ESS) were only included implicitly (as part of the warnings introduced in version 1.2.2), besides being accessible from within the shinystan app. Now, these general MCMC diagnostics are accessible from within the shinybrms app and the warnings from version 1.2.2 are handled differently.
- Added a page “Home”.
- Added a page “References” (listed under “More”).
- Removed page “Help” (which was listed under “More”). Its content is now located at other (more appropriate) places in the shinybrms app.
- Added a description how to include an offset. For this, the required version of brms had to be increased to 2.13.3.
Minor changes
- Minor improvements in the UI (e.g. improved and added help texts and notifications, but also added hyperlinks to the online documentation of R functions).
- Added the possibility to download the MCMC diagnostics (including the newly added general MCMC diagnostics).
- Minor improvements in the README file.
- Minor improvements on pages “About” and “Links” (both listed under “More”).
- Added example dataset
roaches
from package rstanarm.
Bug fixes
- Fixed a bug when switching the dataset.
shinybrms 1.2.2 (only GitHub)
Minor changes
- Minor improvements in the UI.
- Show more warnings from the Stan run. Some of these additional warnings overlap with the HMC diagnostics added in v1.2.0, but rather show too many warnings (even if they are partly duplicated) than too few.
Bug fixes
- Fixed a NOTE occurring in some CRAN checks.
shinybrms 1.2.1
Minor changes
- Minor improvements in the UI.
- Updated information about the shinybrms package and app (e.g. added the URL of the shinybrms website).
Bug fixes
- Fixed a bug causing the sampling progress file not to open up if RStudio’s internal
rs_shinyviewer
was used for option "browser"
.
shinybrms 1.2.0 (only GitHub)
Major changes
- Show Hamiltonian Monte Carlo (HMC) diagnostics in the “Output” panel on page “Posterior”.
Minor changes
- Added a package website built with
pkgdown
.
- Added a package logo created with
hexSticker
.
- Require R >= 3.6.0.
Bug fixes
- Fixed a NOTE occurring in some CRAN checks.
shinybrms 1.1.0
Major changes
- Added the possibility to include varying effects.
Minor changes
- All predictor terms (main effects as well as interactions) are now shown in a preview table.
- It is now possible to remove interaction terms one by one.
- Restricted the choices for the outcome and the predictor selections (e.g. remove the outcome from the list of possible predictor variables).
- Removed some example datasets and added new ones.
- Automatically create the R objects needed for the posterior predictive checks in shinystan.
- Added the possibility to download the matrix of posterior draws as a CSV file.
- For the “Advanced options” (for brms and Stan): Use explicit default values and show them to the user. Set
adapt_delta
per default to 0.95 as done in package rstanarm. Set max_treedepth
per default to 15 as done for most models in rstanarm.
- User interface (UI): Numerous minor improvements, especially concerning button labels, input fields, help texts, and notifications.
- Removed argument
launch.browser
from shinybrms::launch_shinybrms()
so that the default from shiny::runApp()
is used.
- Changed the way how RStudio’s default setting for the global option
browser
is avoided. Most importantly, option shinybrms.RStudio_browser
was removed and replaced by the two new options shinybrms.prog_browser
and shinybrms.shinystan_browser
.
- Allowed *.dat files in the file upload.
Bug fixes
“Under the hood”, there have been many changes which should make the shinybrms app more robust. In particular, the following bugs have been fixed:
- Fixed a bug causing the app to crash if the dataset was changed under certain circumstances.
- Fixed a bug making it possible to keep the outcome and the predictor variables selected when clearing the selection of an example dataset.
- Fixed a bug making it possible to clear the selection of an example dataset, the outcome, or the distributional family, but to keep showing the default priors and the custom priors for the former selection.
- Fixed a bug making it possible to add an already existing interaction term with a different order of the involved predictor variables.
- Fixed a bug making it possible to add an interaction term and then remove the main effect of an involved predictor variable while keeping the interaction term involving it.
- Fixed a bug causing the app to crash when selecting a new dataset after having constructed the model formula and chosen the distributional family for an older dataset.
- Fixed a bug preventing the progress file from opening up on Linux (when started interactively from the terminal).
shinybrms 1.0.1
Bug fixes
- Example datasets:
- Added packages required for some example datasets to the “Suggests” list.
- Check for availability of packages required for some example datasets.
- Added links to the online example datasets on page “Links”.
shinybrms 1.0.0 (only GitHub)
First release. Offers support for Bayesian regression models with a Gaussian, Bernoulli, or negative binomial distribution for the (univariate) outcome. For the predictors, only nonvarying (a.k.a. population-level or “fixed”) effects are supported. Varying (a.k.a. group-level or “random”) effects are not supported yet. Neither supported are most of brms’s other features, like monotonic effects for ordinal predictors or non-linear effects. Interactions are supported, though. For the inspection of the output, only a short summary (from brms::summary.brmsfit()
) and the possibility to launch shinystan is offered.