NEWS.md

In javifar/ggeffects: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs

ggeffects 1.1.2

General

• Speed improvement for some models when calculating uncertainty intervals of predictions.

ggeffects 1.1.1

Changes to functions

• Add more informative error message for brmsfit models using mo() with numeric predictors, which only allow to predict for values that are actually present in the data.

Bug fixes

• Fixed issue with adding raw data points for plots from logistic regression models, when the response variable was no factor with numeric levels.

• Fixed issues with CRAN checks.

ggeffects 1.1.0

New supported models

• orm (package rms)

Breaking Changes

• Prediction intervals (where possible, or when type = "random"), are now always based on sigma^2 (i.e. insight::get_sigma(model)^2). This is in line with interval = "prediction" for lm, or for predictions based on simulations (when type = "simulate").

• print() now uses the name of the focal variable as column name (instead) of "x").

New function

• collapse_by_group(), to generate a data frame where the response value of the raw data is averaged over the levels of a (random effect) grouping factor.

General

• A new vignette was added related to the definition and meaning of "marginal effects" and "adjusted predictions". To be more strict and to avoid confusion with the term "marginal effect", which meaning may vary across fields, either "marginal effects" was replaced by "adjusted predictions", or "adjusted predictions" was added as term throughout the package's documentation and vignettes.

• Allow confidence intervals when predictions are conditioned on random effect groups (i.e. when type = "random" and terms includes a random effect group factor).

• Predicted response values based on simulate() (i.e. when type = "simulate") is now possible for more model classes (see ?ggpredict).

• ggpredict() now computes confidence intervals for some edge cases where it previously failed (e.g. some models that do not compute standard errors for predictions, and where a factor was included in the model and not the focal term).

• plot() gains a collapse.group argument, which - in conjunction with add.data - averages ("collapses") the raw data by the levels of the group factors (random effects).

• data_grid() was added as more common alias for new_data().

Bug fixes

• ggpredict() and plot() for survival-models now always start with time = 1.

• Fixed issue in print() for survival-models.

• Fixed issue with type = "simulate" for glmmTMB models.

• Fixed issue with gamlss models that had random() function in the model formula.

• Fixed issue with incorrect back-transformation of predictions for geeglm models.

ggeffects 1.0.2

Breaking changes

• residuals.type argument in plot() is deprecated. Always using "working" residuals.

General

• pretty_range() and values_at() can now also be used as function factories.

• plot() gains a limit.range argument, to limit the range of the prediction bands to the range of the data.

Bug fixes

• Fixed issue with unnecessary back-transformation of log-transformed offset-terms from glmmTMB models.

• Fixed issues with plotting raw data when predictor on x-axis was a character vector.

• Fixed issues from CRAN checks.

ggeffects 1.0.1

General

• Fixed CRAN check issues.
• Added argument interval to ggemmeans(), to either compute confidence or prediction intervals.

ggeffects 1.0.0

New supported models

• averaging (package MuMIn)

New functions

• pool_predictions(), to pool multiple ggeffects objects. This can be used when predicted values or estimated marginal means are calculated for models fit to multiple imputed datasets.

General

• The function residualize_over_grid() is now exported.
• The back-transformation of the response-variable (if these were log- or square root-transformed in the model) now also works with square root-transformations and correctly handles log1p() and log(mu + x).
• Since standard errors were on the link-scale and not back-transformed for non-Gaussian models, these are now no longer printed (to avoid confusion between standard errors on the link-scale and predictions and confidence intervals on the response-scale).

Bug fixes

• Fixed issue for mixed models when predictions should be conditioned on random effects variances (e.g. type = "random" or "zi_random"), but random effects variances could not be calculated or were almost zero.
• Fixed issue with confidence intervals for multinom models in ggemmeans().
• Fixed issue in ggemmeans() for models from nlme.
• Fixed issue with plot() for some models in ggeffect().
• Fixed issue with computation of confidence intervals for zero-inflated models with offset-term.

ggeffects 0.16.0

Breaking changes

• Package insight since version 0.9.5 now returns the "raw" (untransformed, i.e. original) data that was used to fit the model also for log-transformed variables. Thus, exponentiation like using terms = "predictor [exp]" is no longer necessary.

New supported models

• mlogit (package mlogit)

General

• plot() now can also create partial residuals plots. There, arguments residuals, residuals.type and residuals.line were added to add partial residuals, the type of residuals and a possible loess-fit regression line for the residual data.

Bug fixes

• The message for models with a back-transformation to the response scale (all non-Gaussian models), that standard errors are still on the link-scale, did not show up for models of class glm since some time. Should be fixed now.
• Fixed issue with ggpredict() and rlmerMods models when using factors as adjusted terms.
• Fixed issue with brms-multi-response models.

ggeffects 0.15.1

New supported models

• mclogit (package mclogit)

Bug fixes

• Fixed issues due to latest rstanarm update.
• Fixed some issues around categorical/cumulative brms models when the outcome is numeric.
• Fixed bug with factor level ordering when plotting raw data from ggeffect().

ggeffects 0.15.0

Changes to functions

• ggpredict() gets a new type-option, "zi.prob", to predict the zero-inflation probability (for models from pscl, glmmTMB and GLMMadaptive).
• When model has log-transformed response variable and add.data = TRUE in plot(), the raw data points are also transformed accordingly.
• plot() with add.data = TRUE first adds the layer with raw data, then the points / lines for the marginal effects, so raw data points to not overlay the predicted values.
• The terms-argument now also accepts the name of a variable to define specific values. See vignette Marginal Effects at Specific Values.

Bug fixes

• Fix issues in cluster-robust variance-covariance estimation when vcov.type was not specified.

ggeffects 0.14.3

General

• Fixed issues to due changes in other CRAN packages.

ggeffects 0.14.2

General

• ggeffects now requires glmmTMB version 1.0.0 or higher.
• Added human-readable alias-options to the type-argument.

Bug fixes

• Fixed issue when log-transformed predictors where held constant and their typical value was negative.
• Fixed issue when plotting raw data to a plot with categorical predictor in the x-axis, which had numeric factor levels that did not start at 1.
• Fixed issues for model objects that used (log) transformed offset() terms.

ggeffects 0.14.1

General

• Reduce package dependencies.
• New package-vignette (Cluster) Robust Standard Errors.

New supported models

• mixor (package mixor), cgam, cgamm (package cgam)

Bug fixes

• Fix CRAN check issues due to latest emmeans update.

ggeffects 0.14.0

Breaking Changes

• The argument x.as.factor is considered as less useful and was removed.

New supported models

• fixest (package fixest), glmx (package glmx).

General

• Reduce package dependencies.
• plot(rawdata = TRUE) now also works for objects from ggemmeans().
• ggpredict() now computes confidence intervals for predictions from geeglm models.
• For brmsfit models with trials() as response variable, ggpredict() used to choose the median value of trials were the response was hold constant. Now, you can use the condition-argument to hold the number of trials constant at different values.
• Improve print().

Bug fixes

• Fixed issue with clmm-models, when group factor in random effects was numeric.
• Raw data is no longer omitted in plots when grouping variable is continuous and added raw data doesn't numerically match the grouping levels (e.g., mean +/- one standard deviation).
• Fix CRAN check issues due to latest geepack update.

ggeffects 0.13.0

Breaking Changes

• The use of emm() is discouraged, and so it was removed.

New supported models

• bracl, brmultinom (package brglm2) and models from packages bamlss and R2BayesX.

General

• Updated package dependencies.
• plot() now uses dodge-position for raw data for categorical x-axis, to align raw data points with points and error bars geoms from predictions.
• Updated and re-arranged internal color palette, especially to have a better behaviour when selecting colors from continuous palettes (see show_pals()).

New functions

• Added a vcov() function to calculate variance-covariance matrix for marginal effects.

Changes to Functions

• ggemmeans() now also accepts type = "re" and type = "re.zi", to add random effects variances to prediction intervals for mixed models.
• The ellipses-argument ... is now passed down to the predict()-method for gamlss-objects, so predictions can be computed for sigma, nu and tau as well.

Bug fixes

• Fixed issue with wrong order of plot x-axis for ggeffect(), when one term was a character vector.

ggeffects 0.12.0

Breaking Changes

• The use of ggaverage() is discouraged, and so it was removed.
• The name rprs_values() is now deprecated, the function is named values_at(), and its alias is representative_values().
• The x.as.factor-argument defaults to TRUE.

General

• ggpredict() now supports cumulative link and ordinal vglm models from package VGAM.
• More informative error message for clmm-models when terms included random effects.
• add.data is an alias for the rawdata-argument in plot().
• ggpredict() and ggemmeans() now also support predictions for gam models from ziplss family.

Changes to Functions

• Improved print()-method for ordinal or cumulative link models.
• The plot()-method no longer changes the order of factor levels for groups and facets.
• pretty_data() gets a length() argument to define the length of intervals to be returned.

Bug fixes

• Added "population level" to output from print-method for lme objects.
• Fixed issue with correct identification of gamm/gamm4 models.
• Fixed issue with weighted regression models from brms.
• Fixed broken tests due to changes of forthcoming effects update.

ggeffects 0.11.0

General

• Revised docs and vignettes - the use of the term average marginal effects was replaced by a less misleading wording, since the functions of ggeffects calculate marginal effects at the mean or at representative values, but not average marginal effects.
• Replace references to internal vignettes in docstrings to website-vignettes, so links on website are no longer broken.
• values_at() is an alias for rprs_values().

New supported models

• betabin, negbin (package aod), wbm (package panelr)

Changes to functions

• ggpredict() now supports prediction intervals for models from MCMCglmm.
• ggpredict() gets a back.transform-argument, to tranform predicted values from log-transformed responses back to their original scale (the default behaviour), or to allow predictions to remain on log-scale (new).
• ggpredict() and ggemmeans() now can calculate marginal effects for specific values from up to three terms (i.e. terms can be of lenght four now).
• The ci.style-argument from plot() now also applies to error bars for categorical variables on the x-axis.

Bug fixes

• Fixed issue with glmmTMB models that included model weights.

ggeffects 0.10.0

General

• Better support, including confidence intervals, for some of the already supported model types.
• New package-vignette Logistic Mixed Effects Model with Interaction Term.

New supported models

• gamlss, geeglm (package geepack), lmrob and glmrob (package robustbase), ols (package rms), rlmer (package robustlmm), rq and rqss (package quantreg), tobit (package AER), survreg (package survival)

Changes to functions

• The steps for specifying a range of values (e.g. terms = "predictor [1:10]") can now be changed with by, e.g. terms = "predictor [1:10 by=.5]" (see also vignette Marginal Effects at Specific Values).
• Robust standard errors for predictions (see argument vcov.fun in ggpredict()) now also works for following model-objects: coxph, plm, polr (and probably also lme and gls, not tested yet).
• ggpredict() gets an interval-argument, to compute prediction intervals instead of confidence intervals.
• plot.ggeffects() now allows different horizontal and vertical jittering for rawdata when jitter is a numeric vector of length two.

Bug fixes

• Models with AsIs-conversion from division of two variables as dependent variable, e.g. I(amount/frequency), now should work.
• ggpredict() failed for MixMod-objects when ci.lvl=NA.

javifar/ggeffects documentation built on Jan. 21, 2022, 12:04 a.m.