Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.

Results of regression models are typically presented as tables that are easy to understand. For more complex models that include interaction or quadratic / spline terms, tables with numbers are less helpful and difficult to interpret. In such cases, *marginal effects* are far easier to understand. In particular, the visualization of marginal effects allows to intuitively get the idea of how predictors and outcome are associated, even for complex models.

**ggeffects** computes marginal effects at the mean or average marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the **ggplot2**-package.

Please visit https://strengejacke.github.io/ggeffects/ for documentation and vignettes. In case you want to file an issue or contribute in another way to the package, please follow this guide. For questions about the functionality, you may either contact me via email or also file an issue.

Marginal effects can be calculated for many different models. Currently supported model-objects are: `betareg`

, `bglmer`

, `blmer`

, `brglm`

, `brmsfit`

, `clm`

, `clm2`

, `clmm`

, `coxph`

, `gam`

(package **mgcv**), `Gam`

(package **gam**), `gamlss`

, `gamm`

, `gamm4`

, `gee`

, `geeglm`

, `glm`

, `glm.nb`

, `glmer`

, `glmer.nb`

, `glmmTMB`

, `glmmPQL`

, `glmrob`

, `glmRob`

, `gls`

, `hurdle`

, `ivreg`

, `lm`

, `lm_robust`

, `lme`

, `lmer`

, `lmrob`

, `lmRob`

, `logistf`

, `lrm`

, `MixMod`

, `MCMCglmm`

, `multinom`

, `nlmer`

, `ols`

, `plm`

, `polr`

, `rlm`

, `rlmer`

, `rq`

, `rqss`

, `stanreg`

, `survreg`

, `svyglm`

, `svyglm.nb`

, `tobit`

, `truncreg`

, `vgam`

, `zeroinfl`

and `zerotrunc`

. Other models not listed here are passed to a generic predict-function and might work as well, or maybe with `ggeffect()`

or `ggemmeans()`

, which effectively do the same as `ggpredict()`

.

Interaction terms, splines and polynomial terms are also supported. The main functions are `ggpredict()`

, `ggemmeans()`

and `ggeffect()`

. There is a generic `plot()`

-method to plot the results using **ggplot2**.

The returned data frames always have the same, consistent structure and column names, so it's easy to create ggplot-plots without the need to re-write the function call. `x`

and `predicted`

are the values for the x- and y-axis. `conf.low`

and `conf.high`

could be used as `ymin`

and `ymax`

aesthetics for ribbons to add confidence bands to the plot. `group`

can be used as grouping-aesthetics, or for faceting.

`ggpredict()`

requires at least one, but not more than three terms specified in the `terms`

-argument. Predicted values of the response, along the values of the first term are calucalted, optionally grouped by the other terms specified in `terms`

.

```
data(efc)
fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
ggpredict(fit, terms = "c12hour")
#>
#> # Predicted values of Total score BARTHEL INDEX
#> # x = average number of hours of care per week
#>
#> x predicted std.error conf.low conf.high
#> 0 75.444 1.116 73.257 77.630
#> 15 71.644 0.965 69.753 73.535
#> 35 66.578 0.851 64.911 68.245
#> 50 62.779 0.852 61.108 64.449
#> 70 57.713 0.970 55.811 59.614
#> 85 53.913 1.122 51.713 56.113
#> 100 50.113 1.309 47.547 52.680
#> 120 45.047 1.591 41.929 48.166
#> 135 41.248 1.817 37.686 44.810
#> 170 32.382 2.373 27.732 37.033
#>
#> Adjusted for:
#> * neg_c_7 = 11.84
#> * c161sex = 1.76
#> * c172code = 1.97
```

A possible call to ggplot could look like this:

```
library(ggplot2)
mydf <- ggpredict(fit, terms = "c12hour")
ggplot(mydf, aes(x, predicted)) +
geom_line() +
geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .1)
```

However, there is also a `plot()`

-method. This method uses convenient defaults, to easily create the most suitable plot for the marginal effects.

```
mydf <- ggpredict(fit, terms = "c12hour")
plot(mydf)
```

**ggeffects** has a `plot()`

-method with some convenient defaults, which allows quickly creating ggplot-objects.

With three variables, predictions can be grouped and faceted.

```
ggpredict(fit, terms = c("c12hour", "c172code", "c161sex"))
#>
#> # Predicted values of Total score BARTHEL INDEX
#> # x = average number of hours of care per week
#>
#> # low level of education
#> # [1] Male
#> x predicted std.error conf.low conf.high
#> 0 73.954 2.347 69.354 78.554
#> 45 62.556 2.208 58.228 66.883
#> 85 52.424 2.310 47.896 56.951
#> 170 30.893 3.085 24.847 36.939
#>
#> # low level of education
#> # [2] Female
#> x predicted std.error conf.low conf.high
#> 0 74.996 1.831 71.406 78.585
#> 45 63.597 1.603 60.456 66.738
#> 85 53.465 1.702 50.130 56.800
#> 170 31.934 2.606 26.827 37.042
#>
#> # intermediate level of education
#> # [1] Male
#> x predicted std.error conf.low conf.high
#> 0 74.673 1.845 71.055 78.290
#> 45 63.274 1.730 59.883 66.665
#> 85 53.142 1.911 49.397 56.887
#> 170 31.611 2.872 25.982 37.241
#>
#> # intermediate level of education
#> # [2] Female
#> x predicted std.error conf.low conf.high
#> 0 75.714 1.225 73.313 78.115
#> 45 64.315 0.968 62.418 66.213
#> 85 54.183 1.209 51.815 56.552
#> 170 32.653 2.403 27.943 37.362
#>
#> # high level of education
#> # [1] Male
#> x predicted std.error conf.low conf.high
#> 0 75.391 2.220 71.040 79.741
#> 45 63.992 2.176 59.727 68.258
#> 85 53.860 2.364 49.226 58.494
#> 170 32.330 3.257 25.946 38.713
#>
#> # high level of education
#> # [2] Female
#> x predicted std.error conf.low conf.high
#> 0 76.432 1.809 72.887 79.977
#> 45 65.034 1.712 61.679 68.388
#> 85 54.902 1.910 51.158 58.646
#> 170 33.371 2.895 27.697 39.045
#>
#> Adjusted for:
#> * neg_c_7 = 11.84
mydf <- ggpredict(fit, terms = c("c12hour", "c172code", "c161sex"))
ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
stat_smooth(method = "lm", se = FALSE) +
facet_wrap(~facet)
```

`plot()`

works for this case, as well:

```
plot(mydf)
```

There are some more features, which are explained in more detail in the package-vignette.

Please follow this guide if you like to contribute to this package.

To install the latest development snapshot (see latest changes below), type following commands into the R console:

`library(devtools)devtools::install_github("strengejacke/ggeffects")`

Please note the package dependencies when installing from GitHub. The GitHub version of this package may depend on latest GitHub versions of my other packages, so you may need to install those first, if you encounter any problems. Here's the order for installing packages from GitHub:

sjlabelled → sjmisc → sjstats → ggeffects → sjPlot

To install the latest stable release from CRAN, type following command into the R console:

`install.packages("ggeffects")`

In case you want / have to cite my package, please use `citation('ggeffects')`

for citation information.

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

`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**)

- 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.

- 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`

.

- Minor revisions to docs and vignettes.
- Reduce package dependencies.
- Better support, including confidence intervals, for some of the already supported model types.
- New package-vignette
*Customize Plot Appearance*.

`ggemmeans()`

now supports`type = "fe.zi"`

for**glmmTMB**-models, i.e. predicted values are conditioned on the fixed effects and the zero-inflation components of glmmTMB-models.`ggpredict()`

now supports**MCMCglmm**,**ivreg**and**MixMod**(package**GLMMadaptive**) models.`ggemmeans()`

now supports**MCMCglmm**and**MixMod**(package**GLMMadaptive**) models.`ggpredict()`

now computes confidence intervals for**gam**models (package**gam**).

`new_data()`

, to create a data frame from all combinations of predictor values. This data frame typically can be used for the`newdata`

-argument in`predict()`

, in case it is necessary to quickly create an own data frame for this argument.

`ggpredict()`

no longer stops when predicted values with confidence intervals for**glmmTMB**- and other zero-inflated models can't be computed with`type = "fe.zi"`

, and only returns the predicted values without confidence intervals.- When
`ggpredict()`

fails to compute confidence intervals, a more informative error message is given. `plot()`

gets a`connect.lines`

-argument, to connect dots from plots with discrete x-axis.

`ggpredict()`

did not work with**glmmTMB**- and other zero-inflated models, when`type = "fe.zi"`

and model- or zero-inflation formula had a polynomial term that was held constant (i.e. not part of the`terms`

-argument).- Confidence intervals for zero-inflated models and
`type = "fe.zi"`

could not be computed when the model contained polynomial terms and a*very*long formula (issue with`deparse()`

, cutting off very long formulas). - The
`plot()`

-method put different spacing between groups when a numeric factor was used along the x-axis, where the factor levels where non equal-spaced. - Minor fixes regarding calculation of predictions from some already supported models
- Fixed issues with multiple response models of class
`lm`

in`ggeffects()`

. - Fixed issues with encoding in help-files.

- Minor changes to meet forthcoming changes in purrr.
- For consistency reasons, both
`type = "fe"`

and`type = "re"`

return population-level predictions for mixed effects models (**lme4**,**glmmTMB**). The difference is that`type = "re"`

also takes the random effect variances for prediction intervals into account. Predicted values at specific levels of random effect terms is described in the package-vignettes*Marginal Effects for Random Effects Models*and*Marginal Effects at Specific Values*. - Revised docs and vignettes.
- Give more informative warning for misspelled variable names in
`terms`

-argument. - Added custom (pre-defined) color-palettes, that can be used with
`plot()`

. Use`show_pals()`

to show all available palettes. - Use more appropriate calculation for confidence intervals of predictions for model with zero-inflation component.

`ggpredict()`

and`ggeffect()`

now support**brms**-models with additional response information (like`trial()`

).`ggpredict()`

now supports**Gam**,**glmmPQL**,**clmm**, and**zerotrunc**-models.- All models supported by the
**emmeans**should also work with the new`ggemmeans()`

-function. Since this function is quite new, there still might be some bugs, though.

`ggemmeans()`

to compute marginal effects by calling`emmeans::emmeans()`

.`theme_ggeffects()`

, which can be used with`ggplot2::theme_set()`

to set the**ggeffects**-theme as default plotting theme. This makes it easier to add further theme-modifications like`sjPlot::legend_style()`

or`sjPlot::font_size()`

.

- Added prediction-type based on simulations (
`type = "sim"`

) to`ggpredict()`

, currently for models of class**glmmTMB**and**merMod**. `x.cat`

is a new alias for the argument`x.as.factor`

.- The
`plot()`

-method gets a`ci.style`

-argument, to define different styles for the confidence bands for numeric x-axis-terms. - The
`print()`

-method gets a`x.lab`

-argument to print value labels instead of numeric values if`x`

is categorical. `emm()`

now also supports all prediction-types, like`ggpredict()`

.

- Fixed issue where confidence intervals could not be computed for variables with very small values, that differ only after the second decimal part.
- Fixed issue with
`ggeffect()`

, which did not work if data had variables with more that 8 digits (fractional part longer than 8 numbers). - Fixed issue with multivariate response models fitted with
**brms**or**rstanarm**when argument`ppd = TRUE`

. - Fixed issue with glmmTMB-models for
`type = "fe.zi"`

, which could mess up the correct order of predicted values for`x`

. - Fixed minor issue with glmmTMB-models for
`type = "fe.zi"`

or`type = "re.zi"`

, when first terms had the`[all]`

-tag. - Fixed minor issue in the
`print()`

-method for mixed effects models, when predictions were conditioned on all model terms and adjustment was only done for random effects (output-line "adjusted for"). - Fixed issue for mixed models, where confidence intervals were not completely calculated, if
`terms`

included a factor and`contrasts`

were set to other values than`contr.treatment`

. - Fixed issue with messed up order of confidence intervals for
`glm`

-object and heteroskedasticity-consistent covariance matrix estimation. - Fixed issue for
**glmmTMB**-models, when variables in dispersion or zero-inflation formula did not appear in the fixed effects formula. - The
`condition`

-argument was not always considered for some model types when calculating confidence intervals for predicted values.

- 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. - Revised
`print()`

-method, that - for larger data frames - only prints representative data rows. Use the`n`

-argument inside the`print()`

-method to force a specific number of rows to be printed.

- 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`

).

- 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.

- 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).

- 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.

- 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.

- New vignette
*Different Output between Stata and ggeffects*.

`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.

- 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.