bifrost 0.1.3
- Addressed CRAN reviewer feedback following review of 0.1.2:
- Added explicit return-value documentation (
@return /
\value{}) for the exported
print.bifrost_search() method, clarifying that the function
returns the input object invisibly and is called for its printing side
effects.
- Plotting:
plot_ic_acceptance_matrix() gains an optional
baseline_ic argument to plot and compute
diff(IC) relative to the true no-shift baseline (useful
when matrix_data begins at the first evaluated shift model
rather than the true baseline).
- Documentation / vignettes:
- Updated the jaw-shape vignette with additional static figures
(evolutionary correlation heatmap, IC-trajectory plot, and branch-rate
visualization) and improved plotting annotations.
bifrost 0.1.2
- Addressed CRAN reviewer feedback following review of 0.1.1:
plot_ic_acceptance_matrix() now saves and restores the
user’s graphical parameters via an immediate on.exit()
(prevents leaking par() settings across calls).
- Plotting:
- Added
rate_limits argument to
plot_ic_acceptance_matrix() (default
c(-400, 150)) to control the secondary y-axis limits for
the rate-of-improvement overlay (validated numeric length-2,
finite).
- Search results output:
- Added a
bifrost_search S3 class and
print.bifrost_search() method for
searchOptimalConfiguration() results (compact console
summary; optional ASCII IC-history plot via txtplot when
store_model_fit_history = TRUE; prints IC weights when
present).
- Print output includes a citation hint
(
citation("bifrost")); package citation metadata updated in
inst/CITATION.
- IC weights / no-shift behavior:
- Standardized
ic_weights output across serial and
parallel uncertainty-weight modes; always returns a
data.frame with consistent columns, and returns an empty
data.frame with the same schema when no shifts are
detected.
- When no shifts are detected,
model_no_uncertainty now
returns the baseline mvgls model (instead of
NULL).
- Documentation / vignettes / tests:
- Updated jaw-shape vignette chunk printing of
ic_weights
to avoid RStudio paged/Unicode rendering issues.
- Expanded and stabilized unit tests and CI configuration (including
Config/testthat/parallel: false).
bifrost 0.1.1
- Addressed CRAN reviewer feedback following review of 0.1.0:
- Replaced all uses of shorthand
T/F with
TRUE/FALSE.
- Ensured all informational output is suppressible via
message()/warning() and controlled by a
verbose flag.
- Redirected all on-disk output generated during model fitting to
tempdir() to comply with CRAN file system policies and
avoid writing to the user’s working directory.
- Ensured graphical parameters and global options are restored using
immediate
on.exit() calls.
- Refined parallelization behavior to be CRAN-safe and cross-platform:
- Parallel candidate evaluation uses
future with
multicore on Unix outside RStudio and
multisession otherwise.
- BLAS/OpenMP threads are capped to one per worker during parallel
execution to avoid CPU oversubscription.
- Sequential execution remains the default when
num_cores = 1.
- Improved documentation clarity around parallel execution, verbosity,
and model fit history storage.
bifrost 0.1.0