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Changelog

Source: NEWS.md

sure 0.3.0

Added

  • Added direct exact Gumbel and multivariate normal samplers for multinomial residuals.
  • Added S3 methods resids.multinom and resids.matrix for multinomial and general ML classifiers.
  • Added latent surrogate residual method for general, non-binary vanilla GLMs.
  • Added case weights support (prior.weights) for Gaussian and Gamma GLMs.
  • Added a new public function sim_data() to dynamically simulate datasets representing different model misspecifications.
  • Added a Quick start section to the README, codecov.yml, and a curated _pkgdown.yml reference index.

Changed

  • Migrated residual diagnostic plots from ggplot2/gridExtra to tinyplot via standard S3 plot() methods.
  • Simplified plot.resid() arguments to leverage standard base R graphical parameters (col, pch, cex, etc.).
  • Refactored internal utilities from a single utils.R file into separate generic-specific files.
  • Abstracted duplicate bootstrap replication loops into a single shared helper run_bootstrap_reps().
  • Upgraded minimum R dependency version from 3.1 to 4.0.0 in DESCRIPTION.
  • Adopted the devel/main branch model; devel is now the default development branch.
  • Consolidated generate_surrogate()/generate_residuals() (previously ~90% duplicated) into a single code path.
  • Deduplicated get_bounds.orm/ncat.orm/get_mean_response.orm (now aliased to their lrm equivalents) and collapsed get_distribution_function()/get_quantile_function() from 12 S3 methods into two functions over shared lookup tables.
  • Converted remaining legacy Rd markup to markdown roxygen and modernized the package-doc file to the "_PACKAGE" sentinel.
  • Rewrote the stale DESCRIPTION paragraph describing the removed ggplot2-based autoplot().

Deprecated

  • Deprecated the ggplot2-based autoplot() methods in favor of standard plot() S3 methods.

Removed

  • Removed ggplot2 and gridExtra package dependencies from Imports.
  • Removed testthat testing framework and rebuilt the entire test suite using tinytest.
  • Removed the redundant slowtests/ directory as its test cases are fully covered by the package vignette and the unit test suite.
  • Removed the static datasets df1 through df5 and their documentation, replacing them completely with sim_data().
  • Removed the unused mgcv Suggests entry, the stale LazyData field, the pr-commands.yaml workflow, and a stray tracked vignettes/sure.R build artifact.

Fixed

  • Fixed a bug in gof() validation checking due to operator precedence.
  • Fixed a bug in the jittering methods where category interval mapping caused binary successes to collapse.
  • Fixed nsim > 1 bootstrap crashes on model classes that do not support nobs().
  • Fixed link function name matching for vglm models containing "link" suffixes.
  • Fixed dimension mismatch crashes in clm and polr models with collinear (aliased) predictors.
  • Fixed tinytest::at_home() gating: test_package()’s own default silently skipped roughly 63% of the test suite (104 of 164 expectations) in every environment, including CI, regardless of any environment variable.
  • Fixed a stale Rd cross-reference to the undeclared truncdist package.
  • Fixed missing stats @importFrom entries (pgamma, pnbinom, ppois) flagged by R CMD check.
  • Fixed a leftover vignette placeholder title.

sure 0.2.2

  • Incorporated pkgdown website.

  • Added paper URLs and ORCIDs to DESCRIPTION file (#30).

  • Added sure vignette

  • incorporated autoplot methods for glm, lrm, orm, polr, vglm

  • autoplot() can now return multiple plots (#16).

  • Specifying method = "latent" now works for binomial GLMs (27).

  • Specifying method = "jittering" now issues a warning (at least until it has been fully tested).

sure 0.2.0

CRAN release: 2017-09-19

  • New function surrogate for returning the surrogate response values used in calculating the surrogate-based residuals. The surrogate response values can be useful for checking the proportionality assumption of fitted cumulative link models, among other things.

  • Jittering (on both the probability scale and the response scale) is now available for fitted cumulative link models based on packages MASS, ordinal, rms, and VGAM (#18).

  • Added support for vector generalized additive models from the VGAM package (i.e., objects of class "vgam").

  • New data sets df4 and df5 for illustrating various uses of the surrogate residual for diagnostics an ordinal regression models.

sure 0.1.2

CRAN release: 2017-08-20

  • Initial release.