2021-10-15 shinybrms 1.5.2

Minor changes

• UI: Minor wording improvements.
• Set a minimum width for the output on tab “Default summary”.
• Append trailing zeros in the rounding of the E-BFMI values.

Bug fixes

• UI: Fixed some typos and incorrect spacing in the text.
• Avoid the deprecation warning for brms::parnames().
• Fixed a NOTE occurring in some CRAN checks.

2021-03-06 shinybrms 1.5.1

Minor changes

• Updated some references.
• Now using parallel::detectCores(logical = FALSE) instead of parallel::detectCores() when determining the default number of cores for the Stan run.
• Improved help texts in the UI.
• Renamed tab “Summary” (page “Posterior”) to “Default summary”.

2020-11-21 shinybrms 1.5.0

Major changes

• Use the automatic rstan::rstan_options("javascript" = FALSE) fix on all platforms (not only Windows) if rstan version 2.21.1 or above is used.
• Added support for conditional-effects plots (see brms::conditional_effects()).
• Added the possibility to perform custom posterior summary analyses, e.g., for a transformation of parameters or for a sum of parameters.

Minor changes

• Tab “Summary”: Increased the number of printed decimal digits from 2 to 4.
• Tab “Summary”: Replaced posterior mean and posterior standard deviation by posterior median and posterior median absolute deviation, respectively.
• For partially pooled main effects, numeric (including integer) variables are not allowed anymore.
• Example dataset kidiq: Converted column mom_hs to factor.
• UI: Minor improvements (e.g., in label and notification texts).
• Minor cosmetic improvement in the CSS theme.
• Included some changes necessary for brms version 2.14.0 (and above).
• Changed package description.
• Minor improvements in the documentation for launch_shinybrms().

Bug fixes

• Fixed a possible security issue for the text input field “Prior distribution”.

2020-09-29 shinybrms 1.4.1

Bug fixes

• Corrected a mistake in the DESCRIPTION file: The contributors and copyright holders for external components have to be listed among the authors.

2020-09-13 shinybrms 1.4.0

Major changes

• A new theme is used for the shinybrms app. This theme is basically the “United” theme from Bootswatch v3.3.7 with just a few minor modifications. For the font, the “Open Sans” font from Google Fonts is used. See the new file “LICENSE” for details concerning the licenses of these new components.

Minor changes

• When deselecting a variable from the list for the nonpooled main effects or deselecting a variable from the list for the partially pooled main effects, the interactions involving this variable are now reduced to the corresponding lower-order interactions (instead of being simply removed).
• When updating the selections for the class or the coefficient of a custom prior, the former value is now selected if it exists among the new choices.
• When specifying a custom prior and switching the class or the coefficient, the input field for the group is now only cleared (automatically) if necessary. Before, it was cleared at every change of class or coefficient (provided that the clearing was allowed, meaning that such a combination was present in the table of the default priors).
• UI: Minor improvements (e.g., improved button labels and help texts).
• On Windows with rstan version >= 2.21.1: Automatically run rstan::rstan_options("javascript" = FALSE) at the launch of the shinybrms app to prevent occasional crashes of the R session when starting the Stan run.

Bug fixes

• Fixed the bug that when setting the input field “Group” (of a custom prior) to a nonempty value and later switching back to an empty value, the “Group” was empty in the UI, but internally, the former value was kept. This bug was solved by initializing the input field “Group” with a choose prompt (which made it necessary to catch impossible combinations of “Class”, “Coefficient”, and “Group” with a user notification).

2020-08-06 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 “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).
• 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.

Unreleased 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.

2020-06-25 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".

Unreleased 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.

2020-06-09 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., the outcome variable is now automatically removed 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.
• 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 stable. 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 or the outcome, 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).

2020-03-26 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.
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.