NEWS.md

ggeffects 0.7.0

General

• Support for monotonic predictors in brms models (mo()).
• For generalized additive models, values for splines are no longer automatically prettified (which ensures smooth plots, without the need to use the [all] tag, i.e. terms="... [all]").
• If splines or plolynomial terms are used, a message is printed to indicate that using the [all] tag, i.e. terms="... [all]", will produce smoother plots.
• The package-vignette Marginal Effects at Specific Values now has examples on how to get marginal effects for each group level of random effects in mixed models.

Changes to functions

• Added an n-tag for the terms-argument in ggpredict() and ggeffect(), to give more flexibility according to how many values are used for "prettifying" large value ranges.
• Added a sample-tag for the terms-argument in ggpredict() and ggeffect(), to pick a random sample of values for plotting.
• ggpredict() and ggeffect() now also return the standard error of predictions, if available.
• The jitter-argument in plot() now also changes the amount of noise for plots of models with binary outcome (when rawdata = TRUE).

Bug fixes

• Fix issue with proper calculation of random effect variances for glmmTMB models for type="re" and type="re.zi" in general, and also for models with ar1 random effects structure.

ggeffects 0.6.0

General

• Reduce package dependencies.
• Moved package effects from dependencies to suggested packages, due to the restrictive requirements (R >= 3.5).
• New print()-method, with a nicer print of the returned data frame. This method replaces the summary()-method, which was removed.
• ggeffect() now supports clm2-models from the ordinal-package.
• ggpredict() has improved support for coxph-models from the survival-package (survival probabilities, cumulative hazards).

Changes to functions

• The type-argument in ggpredict() now has additional options, type = "fe.zi" and type = "re.zi", to explicitely condition zero-inflated (mixed) models on their zero-inflation component.
• The type-argument in ggpredict() now has additional options, type = "surv" and type = "cumhaz", to plot probabilities of survival or cumulative hazards from coxph-models.
• ggpredict() gets arguments vcov.fun, vcov.type and vcov.args to calculate robust standard errors for confidence intervals of predicted values. These are based on the various sandwich::vcov*()-functions, hence robust standard errors can be calculated for all models that are supported by sandwich::vcov*().
• The plot()-method gets two arguments line.size and dot.size, to determine the size of the geoms.
• The ci-argument for the plot()-method now also accepts the character values "dash" and "dot" to plot dashed or dotted lines as confidence bands.
• The terms-argument in ggpredict() and ggeffect() may also be a formula, which is more convenient for typing, but less flexible than specifying the terms as character vector with specific options.

Bug fixes

• Fixed improper calculation of confidence intervals for hurdle- and zero-inflated models (from package pscl), which could exceed the range of plausible values (e.g. below zero for incidence rates).
• Fixed issues with calculation of confidence intervals for mixed models with polynomial terms.

ggeffects 0.5.0

General

• New vignette Different Output between Stata and ggeffects.

Changes to functions

• ggpredict() now automatically back-transforms predictions to the response scale for model with log-transformed response.
• ggeffect() and ggpredict() now automatically set numeric vectors with 10 or more unique values to representative values (see rprs_values()), if these are used as second or third value in the terms-argument (to represent a grouping structure).
• Fix memory allocation issue in ggeffect().
• rprs_values() is now exported.
• The pretty-argument is deprecated, because prettifying values almost always makes sense - so this is done automatically.
• ggpredict() now supports brmsfit-objects with categorical-family.
• ggalleffect() has been removed. ggeffect() now plots effects for all model terms if terms = NULL.
• gginteraction() and ggpoly() have been removed, as ggpredict() and ggeffect() are more efficient and generic for plotting interaction or polynomial terms.

Bug fixes

• Fix issues with categorical or ordinal outcome models (polr, clm, multinom) for ggeffect().
• Fix issues with confidence intervals for mixed models with log-transformed response value.
• Fix issues with confidence intervals for generalized mixed models when response value was a rate or proportion created with cbind() in model formula.

ggeffects 0.4.0

General

• Removed alias names mem(), eff() and ame().
• For mixed models (packages lme4, nlme, glmmTMB), the uncertainty of the random effect variances is now taken into account when type = "re".
• Computing confidence intervals for mixed models should be much more memory efficient now, resulting less often in warnings about memory allocation problems.
• Updated reference in CITATION to the publication in the Journal of Open Source Software.
• A test-suite was added to the package.

New functions

• pretty_range(), to create a pretty sequence of integers of a vector.

Changes to functions

• ggpredict() gets a condition-argument to specify values at which covariates should be held constant, instead of their typical value.
• The pretty-option for ggpredict() now calculates more values, leading to smoother plots.
• The terms-argument in ggpredict() can now also select a range of feasible values for numeric values, e.g. terms = "age [pretty]". In contrast to the pretty-argument, which prettyfies all terms, you can selectively prettify specific terms with this option.
• The terms-argument in ggpredict() now also supports all shortcuts that are possible for the mdrt.values-argument in gginteraction(), so for instance term = "age [meansd]" would return three values: mean(age) - sd(age), mean(age) and mean(age) + sd(age).
• plot() gets some new arguments to control which plot-title to show or hide: show.title, show.x.title and show.y.title.
• plot() gets a log.y argument to transform the y-axis to logarithmic scale, which might be useful for binomial models with predicted probabilities, or other models with log-alike link-functions.
• The plot()-method for plotting all effects with ggpredict() (when term = NULL) now allows to arrange the plot in facets (using facets = TRUE).
• Values in dot-argument for plot() are now passed down to ggplot::scale_y*(), to control the appearance of the y-axis (like breaks).

Bug fixes

• Fixed issue with binomial models that used cbind(...) as response variable.
• Fixed issue with suboptimal precision of confidence resp. prediction intervals for mixed models (packages lme4, nlme), which are now more accurate.

ggeffects 0.3.4

General

• Prediction for glmmTMB-objects now compute proper confidence intervals, due to fix in package glmmTMB 0.2.1
• If terms in ggpredict() is missing or NULL, marginal effects for each model term are calculated. ggpredict() then returns a list of data frames, which can also be plotted with plot().

Changes to functions

• The jitter-argument from plot() now accepts a numeric value between 0 and 1, to control the width of the random variation in data points.
• ggpredict() and ggeffect() can now predict transformed values, which is useful, for instance, to exponentiate predictions for log(term) on the original scale of the variable. See package vignette, section Marginal effects at specific values or levels for examples.

Bug fixes

• Multivariate response models in brms with variable names with underscores and dots were not correctly plotted.

ggeffects 0.3.3

General

• Better support for multivariate-response-models from brms.
• Support for cumulative-link-models from brms.
• ggpredict() now supports linear multivariate response models, i.e. lm() with multiple outcomes.

Changes to functions

• ggpredict() gets a pretty-argument to reduce and "prettify" the value range from variables in terms for predictions. This applies to all variables in terms with more than 25 unique values.

Bug fixes

• Recognize negative binomial family from brmsfit-models.

ggeffects 0.3.2

General

• ggpredict(), ggeffect() and gginteraction() get a x.as.factor-argument to preserve factor-class for the x-column in the returned data frame.
• The terms-argument now also allows the specification of a range of numeric values in square brackets, e.g. terms = "age [30:50]".

Bug fixes

• Give proper warning that clm-models don't support full.data-argument.
• emm() did not work properly for some random effects models.

ggeffects 0.3.1

General

• Use convert_case() from sjlabelled, in preparation for the latest snakecase-package update.

Bug fixes

• Model weights are now correctly taken into account.