Skip to contents

Changelog

Source: NEWS.md

ggBoostedTrees 0.9.3

  • The README’s Installation section now leads with hvtiR::install(), which installs the whole HVTI R family in one call, and then gives pak::pak("ehrlinger/ggBoostedTrees") for this package alone.

  • Remotes: installs boostmtree 2.0.4 from the CCF fork (v2.0.4-ccf), and the README’s backend install line names that tag. 2.0.4 adds boostmtree.control(cv.cores = ), which runs the cross-validated fit’s out-of-bag update on several cores, and is about 30% faster on one core; the fit is identical to 2.0.3’s. The Imports: floor stays at 2.0.1, because nothing in this package uses the new argument.

  • The README and the getting-started vignette say what cv.flag = TRUE costs: cross-validation’s time grows with the square of the number of subjects, with measured timings, and boostmtree 2.0.4’s boostmtree.control(cv.cores = ) runs it on several cores without changing the fit.

ggBoostedTrees 0.9.2

  • DESCRIPTION now declares the Quarto command line tool in SystemRequirements, which the new vignette needs to build.

  • New overview vignette, vignette("ggBoostedTrees"), walks one small simulated boostmtree fit through every figure the package draws, in the order you would look at them. On the pkgdown site, the article puts the table of contents on the left, as in the other HVTI packages.

ggBoostedTrees 0.9.1

  • Remotes: now pins the boostmtree fork at v2.0.3-ccf (was v2.0.2-ccf). That release only drops an unused parallel import; the cv.flag fix came in 2.0.2, so the boostmtree (>= 2.0.1) floor is unchanged. Downstream packages that pin their own boostmtree ref can now move to v2.0.3-ccf without handing pak two refs for one package.

ggBoostedTrees 0.9.0

  • gg_boost_vimp() accepts a BoostMLR predict object made with predictBoostMLR(..., importance = TRUE). BoostMLR splits the covariate-time interaction over its time intervals; these are summed to one interaction value per covariate, and the per-interval matrices are kept in the interaction.by.interval attribute (#9).
  • New boostmlr_partial() computes BoostMLR partial effects for one or more covariates, naming the covariates and responses that BoostMLR::partial.BoostMLR() leaves unnamed. gg_boost_effect() accepts the result and extracts the lowess-smoothed curves, one block per response. All six figures now accept a BoostMLR fit. BoostMLR support remains partial: marginal effects and joint importance are not supported (#9).
  • gg_boost_effect() now accepts the partial.plot() and marginal.plot() output of a multi-response (ordinal or nominal) boostmtree fit, which it previously refused. Every result gains a response factor, labelled from the object’s response.labels; a single-response fit is labelled "response" and otherwise unchanged. autoplot() facets by response, as a grid of response by variable when there are several of each (#19).

ggBoostedTrees 0.0.7

  • The README function reference now lists gg_boost_calibration() and its autoplot() method alongside the other shipped figure-data objects.
  • New gg_boost_calibration() compares observed and fitted values over follow-up. Observations are binned by time into equal-count bins, and each bin reports the observed mean with a 95% interval, the fitted mean at the same observations, and how many observations and distinct subjects stand behind it. It accepts boostmtree and BoostMLR fits.
  • Supplying a boostmtree predict object as pred adds the cohort mean curve. A predict object made with tm and id is refused, because each subject is then predicted at its own times and a mean across subjects would change composition along the curve.
  • The renderer draws each bin’s time span, so a thin tail shows as a long late bin.

ggBoostedTrees 0.0.6

  • BoostMLR fits are now accepted by gg_boost_trajectory(), gg_boost_error() and gg_boost_path(). Adding the backend required extractor methods only; no renderer changed, which is what the tidy intermediate exists to guarantee.
  • BoostMLR selects no optimal boosting iteration, so gg_boost_error() flags none for that backend rather than deriving one.
  • BoostMLR’s Lambda_List holds per-iteration basis coefficients rather than a scalar smoothing parameter, so gg_boost_path() offers rho and phi for that backend and says so if lambda is requested.
  • gg_boost_vimp() and gg_boost_effect() remain boostmtree only.
  • gg_boost_error() refuses use.rmse = FALSE on a BoostMLR fit, by name or by position: that backend records no y.sd, so its Error_Rate cannot be unstandardized. The generic declares use.rmse as its second formal, so the positional form is valid syntax, and it previously fell through and returned standardized values to a caller who had asked for the other scale. use.rmse = TRUE is accepted, being the default and the scale BoostMLR already returns, so a caller that always passes the argument runs against either backend unchanged.
  • autoplot.gg_boost_trajectory() accepts a repeated subject identifier in subset rather than failing with an internal factor level [2] is duplicated. The caller’s ordering still determines the factor levels.
  • gg_boost_path()’s boostmtree method validates parameters the same way its BoostMLR sibling and gg_boost_vimp()’s components argument do: an empty vector is rejected and duplicates are de-duplicated rather than reaching an opaque factor() error.

ggBoostedTrees 0.0.5

  • gg_boost_effect() now handles factor covariates. It previously coerced their labels with as.numeric(), producing an all-NA covariate column and a blank figure. The contract gains an x_label column, and the renderer draws discrete covariates as points on a labelled axis.
  • An object mixing continuous and discrete covariates is refused with guidance, since one figure permits only one scale type per aesthetic.
  • gg_boost_vimp() validates components: an empty vector is rejected and duplicates are de-duplicated rather than reaching an opaque factor() error.
  • Corrected the description of marginal.plot()’s $data, which holds unsmoothed fitted predictions rather than raw observations.

ggBoostedTrees 0.0.4

  • gg_boost_vimp() and plot()/autoplot() for variable importance, covering both the main effect of each covariate and its interaction with time. The axis is labelled with the metric recorded on the source object rather than a hard-coded string.
  • gg_boost_effect() and plot()/autoplot() for partial and marginal covariate effects over time, as one class distinguished by kind.
  • Neither partial.plot() nor marginal.plot() computes a confidence interval, so gg_boost_effect() reports none.

ggBoostedTrees 0.0.3

  • gg_boost_trajectory() and plot()/autoplot() for observed and fitted subject trajectories over time. Rows are sorted within subject, because boostmtree stores observations in input order and a line drawn from that order zigzags.
  • The trajectory renderer thins large cohorts with subset and n_max, and scales transparency to the number of subjects drawn so that an overplotted cohort reads as a density.

ggBoostedTrees 0.0.2

ggBoostedTrees 0.0.1

  • Package skeleton, shared utilities, and the testthat scaffold.