smooth_estimates() can now handle
s(x, z, a),te(), t2(), & ti()), e.g. te(x, z, a)s(x, f, bs = "fs")s(f, bs = "re")penalty() provides a tidy representation of the penalty matrices of smooths. The tidy representation is most suitable for plotting with ggplot().
A draw() method is provided, which represents the penalty matrix as a heatmap.
newdata argument to smooth_estimates() has been changed to data as was originally intended.Partial residuals for models can be computed with partial_residuals(). The partial residuals are the weighted residuals of the model added to the contribution of each smooth term (as returned by predict(model, type = "terms").
Wish of #76 (@noamross)
Also, new function add_partial_residuals() can be used to add the partial residuals to data frames.
Users can now control to some extent what colour or fill scales are used when plotting smooths in those draw() methods that use them. This is most useful to change the fill scale when plotting 2D smooths, or to change the discrete colour scale used when plotting random factor smooths (bs = "fs").
The user can pass scales via arguments discrete_colour and continuous_fill.
The effects of certain smooths can be excluded from data simulated from a model using simulate.gam() and predicted_samples() by passing exclude or terms on to predict.gam(). This allows for excluding random effects, for example, from model predicted values that are then used to simulate new data from the conditional distribution. See the example in predicted_samples().
Wish of #74 (@hgoldspiel)
draw.gam() and related functions gain arguments constant and fun to allow for user-defined constants and transformations of smooth estimates and confidence intervals to be applied.
Part of wish of Wish of #79.
confint.gam() now works for 2D smooths also.
smooth_estimates() is an early version of code to replace (or more likely supersede) evaluate_smooth(). smooth_estimates() can currently only handle 1D smooths of the standard types.
The meaning of parm in confint.gam has changed. This argument now requires a smooth label to match a smooth. A vector of labels can be provided, but partial matching against a smooth label only works with a single parm value.
The default behaviour remains unchanged however; if parm is NULL then all smooths are evaluated and returned with confidence intervals.
data_class() is no longer exported; it was only ever intended to be an internal function.
confint.gam() was failing on a tensor product smooth due to matching issues. Reported by @tamas-ferenci #88
This also fixes #80
The vdiffr package is now used conditionally in package tests. Reported by Brian Ripley #93
draw.gam() with scales = "fixed" now applies to all terms that can be plotted, including 2d smooths.
Reported by @StefanoMezzini #73
dplyr::combine() was deprecated. Switch to vctrs::vec_c().
draw.gam() with scales = "fixed" wasn’t using fixed scales where 2d smooths were in the model.
Reported by @StefanoMezzini #73
draw.gam() can now include partial residuals when drawing univariate smooths. Use residuals = TRUE to add partial residuals to each univariate smooth that is drawn. This feature is not available for smooths of more than one variable, by smooths, or factor-smooth interactions (bs = "fs").
The coverage of credible and confidence intervals drawn by draw.gam() can be specified via argument ci_level. The default is arbitrarily 0.95 for no other reason than (rough) compatibility with plot.gam().
This change has had the effect of making the intervals slightly narrower than in previous versions of gratia; intervals were drawn at ± 2 × the standard error. The default intervals are now drawn at ± ~1.96 × the standard error.
New function difference_smooths() for computing differences between factor smooth interactions. Methods available for gam(), bam(), gamm() and gamm4::gamm4(). Also has a draw() method, which can handle differences of 1D and 2D smooths currently (handling 3D and 4D smooths is planned).
New functions add_fitted() and add_residuals() to add fitted values (expectations) and model residuals to an existing data frame. Currently methods available for objects fitted by gam() and bam().
data_sim() is a tidy reimplementation of mgcv::gamSim() with the added ability to use sampling distributions other than the Gaussian for all models implemented. Currently Gaussian, Poisson, and Bernoulli sampling distributions are available.
smooth_samples() can handle continuous by variable smooths such as in varying coefficient models.
link() and inv_link() now work for all families available in mgcv, including the location, scale, shape families, and the more specialised families described in ?mgcv::family.mgcv.
evaluate_smooth(), data_slice(), family(), link(), inv_link() methods for models fitted using gamm4() from the gamm4 package.
data_slice() can generate data for a 1-d slice (a single variable varying).
The colour of the points, reference lines, and simulation band in appraise() can now be specified via arguments
point_col,point_alpha,ci_colci_alphaline_colThese are passed on to qq_plot(), observed_fitted_plot(), residuals_linpred_plot(), and residuals_hist_plot(), which also now take the new arguments were applicable.
Added utility functions is_factor_term() and term_variables() for working with models. is_factor_term() identifies is the named term is a factor using information from the terms() object of the fitted model. term_variables() returns a character vector of variable names that are involved in a model term. These are strictly for working with parametric terms in models.
appraise() now works for models fitted by glm() and lm(), as do the underlying functions it calls, especially qq_plot.
appraise() also works for models fitted with family gaulss(). Further location scale models and models fitted with extended family functions will be supported in upcoming releases.
datagen() is now an internal function and is no longer exported. Use data_slice() instead.
evaluate_parametric_term() is now much stricter and can only evaluate main effect terms, i.e. those whose order, as stored in the terms object of the model is 1.
The draw() method for derivatives() was not getting the x-axis label for factor by smooths correctly, and instead was using NA for the second and subsequent levels of the factor.
The datagen() method for class "gam" couldn’t possibly have worked for anything but the simplest models and would fail even with simple factor by smooths. These issues have been fixed, but the behaviour of datagen() has changed, and the function is now not intended for use by users.
Fixed an issue where in models terms of the form factor1:factor2 were incorrectly identified as being numeric parametric terms. #68
New functions link() and inv_link() to access the link function and its inverse from fitted models and family functions.
Methods for classes: "glm", "gam", "bam", "gamm" currently. #58
Adds explicit family() methods for objects of classes "gam", "bam", and "gamm".
derivatives() now handles non-numeric when creating shifted data for finite differences. Fixes a problem with stringsAsFactors = FALSE default in R-devel. #64
gratia now uses the mvnfast package for random draws from a multivariate normal distribution (mvnfast::rmvn()). Contributed by Henrik Singmann (@singmann) #28
New function basis() for generating tidy representations of basis expansions from an mgcv-like definition of a smooth, e.g. s(), te(), ti(), or t2(). The basic smooth types also have a simple draw() method for plotting the basis. basis() is a simple wrapper around mgcv::smoothCon() with some post processing of the basis model matrix into a tidy format. #42
New function smooth_samples() to draw samples of entire smooth functions from their posterior distribution. Also has a draw() method for plotting the posterior samples.
draw.gam() would produce empty plots between the panels for the parametric terms if there were 2 or more parametric terms in a model. Reported by @sklayn #39.
derivatives() now works with factor by smooths, including ordered factor by smooths. The function also now works correctly for complex models with multiple covariates/smooths. #47
derivatives() also now handles 'fs' smooths. Reported by @tomand-uio #57.
evaluate_parametric_term() and hence draw.gam() would fail on a ziplss() model because i) gratia didn’t handle parametric terms in models with multiple linear predictors correctly, and ii) gratia didn’t convert to the naming convention of mgcv for terms in higher linear predictors. Reported by @pboesu #45.