Version 0.9.2 of gratia now on CRAN

[gavinsimpson]

Version 0.9.2 released to CRAN, June 25, 2024

This patch release is largely motivated to fix a few bugs that came to light recently as I was teaching my GAM course for Physalia and preparing a paper for submission to the Journal of Open Source Software. Version 0.9.1 was never released (submission was rejected by CRAN as the package vignettes took the package over the 5Mb limit and CRAN finally said "Nope").

The entries below summarise the changes in this version of gratia. Nothing major here, but I have started building in support for location, scale, shape families in fitted_samples(), although currently only the location parameter of those models is supported.

Breaking changes

• parametric_effects() slightly escaped the great renaming that happened for
  0.9.0. Columns type and term did not gain a prefix .. This is now
  rectified and these two columns are now .type and .term.

User visible changes

• Plots of random effects are now labelled with their smooth label. Previously,
  the title was taken fro the variable involved in the smooth, but this doesn't
  work for terms like s(subject, continuous_var, bs = "re") for random slopes,
  which previsouly would have the title "subject". Now such terms will have
  title "s(subject,continuous_var)". Simple random intercept terms,
  s(subject, bs = "re"), are now titled "s(subject)". Plot titles for s(fac, continuous, bs = "re") only use the first variable involved in the smooth #287

• The vignettes

  1. custom-plotting.Rmd, and
  2. posterior-simulation.Rmd
     were moved to vignettes/articles and thus are no longer available as package
     vignettes. Instead, they are accessible as Articles through the package
     website: https://gavinsimpson.github.io/gratia/

New features

• fitted_samples() now works for gam() models with multiple linear
  predictors, but currently only the location parameter is supported. The
  parameter is indicated through a new variable .parameter in the returned
  object.

Bug fixes

• partial_residuals() was computing partial residuals from the deviance
  residuals. For compatibility with mgcv::plot.gam(), partial residuals are
  now computed from the working residuals. Reported by @wStockhausen compute_partial_residuals is wrong if deviance residuals are not equivalent to pearson residuals? #273

• appraise() was not passing the ci_col argument on qq_plot() and
  worm_plot(). Reported by Sate Ahmed.

• Couldn't pass mvn_method on to posterior sampling functions from user facing
  functions fitted_samples(), posterior_samples(), smooth_samples(),
  derivative_samples(), and repsonse_derivatives(). Reported by @stefgehrig
  Select mvn_method when running fitted_samples() #279

• fitted_values() works again for quantile GAMs fitted by qgam().

• confint.gam() was not applying shift to the estimate and upper and lower
  interval. shift=TRUE not working for confint.gam() #280 reported by @TIMAVID & @rbentham

• parametric_effects() and draw.parametric_effects() would forget about the
  levels of factors (intentionally), but this would lead to problems with
  ordered factors where the ordering of levels was not preserved. Now,
  parametric_effects() returns a named list of factor levels as attribute
  "factor_levels" containing the required information and the order of levels
  is preserved when plotting. draw forgets order of ordered factor #284 Reported by @mhpob

• parametric_effects() would fail if there were parametric terms in the model
  but they were all interaction terms (which we don't currently handle). draw() fails with parametric = TRUE if there aren't any parametric effects to actually plot #282

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This discussion was created from the release Version 0.9.2 of gratia now on CRAN.