Updated the list of allowed function names when specifying a prior
via a Stan function name (for security reasons, it is not possible to
enter arbitrary code in the prior distribution text field). Now, all
distributions implemented in Stan v2.37.0 are supported (although not
all of them are useful in the context of
shinybrms).
shinybrms 1.8.0
Major changes
The threshold for worrying E-BFMI values was increased from 0.2 to
0.3 (to comply with Betancourt, 2018, arXiv:1701.02434v2).
The term “pooled” (effects) is replaced by “population-level”
(effects). Correspondingly, the term “partially pooled” (effects) is
replaced by “group-level” (effects). In v1.6.0, the term “pooled” was
introduced as an improvement for continuous predictors (which cannot
have partially pooled or group-level effects), but this now turned out
to be incorrect for those categorical predictors which do not have
partially pooled effects. The “population-level”/“group-level”
terminology is used in brms, so it makes sense already
in terms of consistency to use it in shinybrms,
too.
Minor changes
In the table showing the default priors, column “Prior” should not
have any empty fields anymore. The reason for this change is that empty
fields arising from a flat prior could have been confounded too easily
with empty fields arising from the vectorization (“inheritance”) of the
prior within a given parameter class. This was especially problematic
because the former help text underneath the table was worded
mistakably.
A recompilation of the C++ code is now avoided more often. More
specifically, affected cases are those where
brms:::update.brmsfit() is used with a formula that was
extended on its right-hand side. In those cases,
shinybrms now avoids a recompilation by specifying
argument newdata of
brms:::update.brmsfit().
The brms::gen_extreme_value() family has been removed
from the drop-down list of advanced distributional families, due to
brms’s issue paul-buerkner/brms#1345.
(Note that before, the brms::gen_extreme_value() family was
misclassified under “Continuous outcome on the positive real line”: In
fact, the support of this family depends on its shape parameter.)
Bug fixes
Avoid a warning about a deprecated icon called "home"
when launching the app. This required increasing the required
shiny version to 1.7.0.
shinybrms 1.7.0
Major changes
Support for more distributional families for the outcome.
Minor changes
Use a darker gray color for help texts (which constitute the
majority of the in-app text). This should make them easier to read and
reduce the contrast with regard to the dark red hyperlinks.
Adapt to changes in brms’s CRAN version
2.17.0.
Perform some basic sanity checks with respect to bounds of custom
priors.
Enhance and generalize the help text for the link functions.
Bug fixes
Previously, advanced option “Range of random initial values […]”
could have had an effect even if “Zero” was chosen under “Initial
values” (namely, for the cmdstanr backend in
brms versions <= 2.16.3). Now, advanced option
“Range of random initial values […]” only has an effect if “Random” is
chosen under “Initial values”.
Show errors thrown by brms::brm() to the user.
shinybrms 1.6.0
Major changes
Allow for offset() terms without the need to resort to
the previous workaround based on a constant() prior (see
brms’s GitHub issue #923 solved
in brms v2.16.0). This increases the required
brms version to at least 2.16.0.
Allow the upload of a previously created brmsfit object
(page “Posterior”, tab “Run Stan”, panel “Run Stan”). This required
increasing the default size limit for file uploads (global option
shiny.maxRequestSize; now at 50 MB if not set by the
user).
If a previous brmsfit exists (i.e., it is currently
presented on page “Posterior”), then—if possible—a click on the “Run
Stan” button causes this previous brmsfit to get updated
using brms:::update.brmsfit(), saving the compilation time.
Note that shinybrms automatically takes care of the
fact that brms:::update.brmsfit() does not recompute the
default priors if the dataset has changed. However, for uploaded
brmsfits which were not fitted through
shinybrms, this is not possible (and for uploaded
brmsfits which were fitted through
shinybrms, this is still complicated), so an uploaded
brmsfit may not be updated. The updating of a previous
brmsfit may be turned off using the global option
shinybrms.allow_upd (see ?launch_shinybrms for
details).
Allow the cmdstanr backend for
brms. The global option brms.backend can
be used to control the default backend selected in the “Advanced
options” in the shinybrms app (see
?launch_shinybrms for details).
Replace the term “nonpooled” (effects) by “pooled” (effects). This
confusion was introduced by the replacement of “nonvarying” (effects) by
“nonpooled” (effects) in v1.3.0 (which was obviously incorrect since
“pooled” is the opposite of “varying”).
Minor changes
UI: Minor formatting and wording improvements in help texts and
other UI elements.
UI: In case of a failed file upload, a modal dialog is shown now
(instead of a notification in the lower right corner).
Theme: Some colors have been slightly changed to match the overall
theme better.
Improved documentation of global options used by
shinybrms.
Page “Posterior” (tab “Run Stan”, panel “Run Stan”) now also shows
important software versions used for the Stan run.
The download of the MCMC diagnostics was moved from tab “Run Stan”
to tab “MCMC diagnostics” (both on page “Posterior”).
The “Default summary” from page “Posterior” may now be downloaded
(as a text file).
UI: The width of some UI elements in panel “Run Stan” has been
adjusted.
Bug fixes
Clear the input field for the name of a custom summary expression as
soon as new Stan results are obtained.
Fix a typo in the “Get started” vignette shown on the
pkgdown website. (The scale parameter for the
Student-t prior is 4.)
Fix an error for Stan runs with advanced option “Open progress” set
to FALSE.
shinybrms 1.5.2
Minor changes
Append trailing zeros in the rounding of the E-BFMI values.
Set a minimum width for the output on tab “Default summary”.
UI: Minor wording improvements.
Bug fixes
Fixed a NOTE occurring in some CRAN checks.
Avoid the deprecation warning for
brms::parnames().
UI: Fixed some typos and incorrect spacing in the text.
shinybrms 1.5.1
Minor changes
Renamed tab “Summary” (page “Posterior”) to “Default summary”.
Improved help texts in the UI.
Now using parallel::detectCores(logical = FALSE)
instead of parallel::detectCores() when determining the
default number of cores for the Stan run.
Updated some references.
shinybrms 1.5.0
Major changes
Added the possibility to perform custom posterior summary analyses,
e.g., for a transformation of parameters or for a sum of
parameters.
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.
Minor changes
Minor improvements in the documentation for
launch_shinybrms().
Added CITATION file.
Changed package description.
Included some changes necessary for brms version
2.14.0 (and above).
Minor cosmetic improvement in the CSS theme.
UI: Minor improvements (e.g., in label and notification texts).
Example dataset kidiq: Converted column
mom_hs to factor.
For partially pooled main effects, numeric (including integer)
variables are not allowed anymore.
Tab “Summary”: Replaced posterior mean and posterior standard
deviation by posterior median and posterior median absolute deviation,
respectively.
Tab “Summary”: Increased the number of printed decimal digits from 2
to 4.
Bug fixes
Fixed a possible security issue for the text input field “Prior
distribution”.
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.
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
UI: Added internal links.
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.
UI: Minor improvements (e.g., improved button labels and help
texts).
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).
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 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).
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).
shinybrms 1.3.0
Major changes
Added a description how to include an offset. For this, the required
version of brms had to be increased to 2.13.3.
Removed page “Help” (which was listed under “More”). Its content is
now located at other (more appropriate) places in the
shinybrms app.
Added a page “References” (listed under “More”).
Added a page “Home”.
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.
Restructured page “Posterior”.
Use the term “nonpooled effects” instead of “nonvarying effects” and
the term “partially pooled effects” instead of “varying effects”.
Minor changes
Added example dataset roaches from package
rstanarm.
Minor improvements on pages “About” and “Links” (both listed under
“More”).
Minor improvements in the README file.
Added the possibility to download the MCMC diagnostics (including
the newly added general MCMC diagnostics).
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).
Bug fixes
Fixed a bug when switching the dataset.
shinybrms 1.2.2
(only GitHub)
Minor changes
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.
Minor improvements in the UI.
Bug fixes
Fixed a NOTE occurring in some CRAN checks.
shinybrms 1.2.1
Minor changes
Updated information about the shinybrms package and
app (e.g., added the URL of the shinybrmswebsite).
Minor improvements in the UI.
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
Require R >= 3.6.0.
Added a package logo created with hexSticker.
Added a package website built with pkgdown.
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
Allowed *.dat files in the file upload.
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.
Removed argument launch.browser from
shinybrms::launch_shinybrms() so that the default from
shiny::runApp() is used.
User interface (UI): Numerous minor improvements, especially
concerning button labels, input fields, help texts, and
notifications.
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.
Added the possibility to download the matrix of posterior draws as a
CSV file.
Automatically create the R objects needed for the posterior
predictive checks in shinystan.
Removed some example datasets and added new ones.
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).
It is now possible to remove interaction terms one by one.
All predictor terms (main effects as well as interactions) are now
shown in a preview table.
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 preventing the progress file from opening up on Linux
(when started interactively from the terminal).
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 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 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 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 keep the outcome and the predictor
variables selected when clearing the selection of an example
dataset.
Fixed a bug causing the app to crash if the dataset was changed
under certain circumstances.
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.
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