xpose.xtras

xpose.xtras 0.2.2

Documentation

• Fixed derive_shk()’s equation not rendering on the pkgdown site by switching to katex math rendering. (#88)
• Documented as_leveler() as the generic leveler constructor, with an example of defining custom levels directly. (#89)

New features

• Added xtras_data(), a wrapper around xpose::xpose_data() %>% as_xp_xtras() that silences the rlang_warning-batched chatter readr/dplyr can raise while parsing tables with NaN/Inf or otherwise oddly formatted values, without hiding warnings that indicate an actual read failure. xp_from_bbr() now uses it internally. (#77)
• Added recalc_shk(), which recalculates eta shrinkage directly from individual estimates rather than parsing NONMEM’s own reported value, with a .etastype argument to exclude “true zero” (as opposed to merely near-zero) etas from the calculation. Etas are matched to their omega by column name where possible (eg nlmixr2 models), falling back to NONMEM’s ETA<k>/OMEGA(k,k) numbering convention. (#79)
• Added a new shk variable type, plus derive_shk()/backfill_shk() to populate it: a per-individual eta shrinkage contribution diagnostic (log((eta - mean(eta))^2)). (#78)
• Added shk_grid()/shk_vs_cov_grid()/shk_vs_contcov()/ shk_vs_catcov(), mirroring eta_grid()/eta_vs_cov_grid()/ eta_vs_contcov()/eta_vs_catcov() for the new shk diagnostic. (#78)
• Added list = FALSE to eta_vs_contcov()/eta_vs_catcov()/ shk_vs_contcov()/shk_vs_catcov(), combining the per-variable plots onto one shared, faceted plot instead of a list, paginating at 9 panels per page. (#82)
• Added covvar to eta_vs_contcov()/eta_vs_catcov()/ shk_vs_contcov()/shk_vs_catcov() to select specific covariates, mirroring etavar/shkvar; also added as a cols alias on eta_vs_cov_grid()/shk_vs_cov_grid(). (#82)
• Added normalize_etas()/normalise_etas(), which set a top-level xpdb$normalize_etas slot (like $covs, see add_cov_association() – not an xpdb$options entry, and not settable via set_option()) dividing each eta by its omega-implied SD (or, with .use_sd = TRUE, the empirical SD of its individual estimates) in eta_grid()/ eta_vs_cov_grid()/eta_vs_contcov()/eta_vs_catcov() only – the underlying data is never modified. (#81)

Bug fixes

• nlmixr2_as_xtra() now reports the rejected object’s class when xpose.nlmixr2::xpose_data_nlmixr2() doesn’t recognize it as an nlmixr2 fit, instead of only the generic upstream message.
• backfill_iofv() now gives a clear error when called without xpdb instead of a cryptic cli formatting failure. (#84)
• Fixed print.xpose_data()/print.xp_xtras() erroring instead of printing whenever any xpdb$options entry is a multi-element list (eg default_labs/default_watermark with more than one key set). (#81)
• Fixed a critical bug where any xpdb$foo <- value/xpdb[["foo"]] <- value (including inside patch_condn(), run automatically by as_xpdb_x()) could silently strip the xp_xtras/xpose_data classes on ggplot2 versions before 4.0, due to a class-name collision with ggplot2’s internal aes() mapping class. (#74)
• conflicted is now an optional (Suggests) dependency instead of a hard requirement, and is only consulted if the user has loaded it themselves. Package startup no longer prints a “Registered S3 method overwritten” notice for print.xpose_plot, and the reminder to attach xpose now also names any load-order-sensitive bugfix at stake. (#72)
• irep() is no longer deprecated in favor of xpose::irep() for xpose >= 0.5.0: xpose reverted that upstream fix, so this package’s version is needed again regardless of the installed xpose version.
• catdv_vs_ipred() no longer triggers a spurious ggplot2 lifecycle warning (incorrectly blaming xpose) by mapping size to its line layer, where it’s deprecated in favor of linewidth. (#75)
• set_var_types_x() no longer mistypes columns when a tidyselect expression matches 10+ columns for one type (e.g. eta = matches(...)), or when one type name is a prefix of another (e.g. id/idv). (#76)

xpose.xtras 0.2.0

New features

• xp_from_bbr() converts a ‘bbr’ model directly into an xp_xtras object.
• New parameter/covariate association system (add_cov_association(), prm_cov() family) with xplot_forest() / cov_forest() visualization; see the new parameter-associations vignette.
• cormat() visualizes the parameter correlation/covariance matrix, for both NONMEM and nlmixr2 models.
• catdv_vs_occ() and catdv_vs_ipred() add categorical DV diagnostic plots (observed-vs-predicted trend across occasions, and binned calibration).
• left_join_x() backfills missing variables into an xpdb via a coalescing left join.
• Default label overrides, plot watermarking, and a flexible save wrapper (set_default_labs(), add_watermark(), ggsave_xp()), configurable via set_xtras_options() and auto-applied on print/save. See the new plot-output vignette.
• patch_condn() corrects ‘xpose’s condition number calculation for multi-method NONMEM runs, applied automatically byas_xpdb_x()`.
• focus_function() / focus_qapply() now support output-generating functions (plots, tables), not just xpdb-transforming ones.
• New logLik(), AIC(), and BIC() methods for xpose_data and xpose_set objects.
• ind_plots_sample() plots a representative (optionally stratified) sample of individuals instead of the whole dataset.
• plot.xpose_data() runs a configurable batch of diagnostic plots in one call.
• process_preset() family saves and replays a reusable xpdb processing pipeline by name, optionally persisted across sessions.

Bug fixes

• set_dv_probs() no longer crashes when .problem is omitted.
• conflicted preferences are now re-applied regardless of package attach order, fixing spurious “found in 2 packages” errors.
• Fixed inconsistent ‘cli’ message coloring caused by a color-formatting helper being evaluated at install time instead of call time.
• Fixed a title/description typo in %p%.
• Fixed misleading default subtitle/caption labels on model-averaged plots, which previously reported statistics from just one of the averaged models.
• Fixed as_xpdb_x() / check_xpdb_x() erroring on xpose_data objects with no table data.
• Fixed xplot_pairs() silently ignoring a custom catcont_opts$other_fun, and removed an unreachable leftover duplicate-axis-label block in roc_by_mod().

xpose.xtras 0.1.4

• nlmixr2 example datasets replaced with on-demand nlmixr_example() / nlmixr2_example() to avoid loading nlmixr2est when not installed.

xpose.xtras 0.1.3

• Fix for nlmixr2 compatibility checks when nlmixr2est is not installed.

xpose.xtras 0.1.2

• Additional changes relevant to 0.1.1.

xpose.xtras 0.1.1

• Minor compatibility changes for nlmixr2 5.0

xpose.xtras 0.1.0

• Bugs regarding covariate plotting functions were resolved.
• nlmixr2 compatibility implemented
• ROC curve plots added
• Updated documentation and pkgdown site

xpose.xtras 0.0.3

• Patch to support ‘ggplot2’ 4.0.0 release.
• Bugfixes for ‘xpose’ related to ‘ggplot2’ also implemented in a backwards compatible way.
• Contact email changed.

xpose.xtras 0.0.2

• CRAN release planned

xpose.xtras 0.0.1

• Early post-development version
• Completed unit tests and ongoing fixes to bugs and documentation.