ggeffects - Estimated Marginal Means and Marginal Effects from Regression Models
Lüdecke D (2018). ggeffects: Tidy Data Frames of Marginal Effects from Regression Models. Journal of Open Source Software, 3(26), 772. doi: 10.21105/joss.00772
Why marginal effects?
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.
Aim of this package
ggeffects is a light-weight package that aims at easily calculating marginal effects (or: estimated marginal means) at the mean or at representative values (see definitions here) from statistical models, i.e. predictions generated by a model when one holds the non-focal variables constant and varies the focal variable(s). This is achieved by three core ideas that describe the philosophy of the function design:
Functions are type-safe and always return a data frame with the same, consistent structure;
there is a simple, unique approach to calculate marginal effects and estimated marginal means for many different models;
the package supports “labelled data” (Lüdecke 2018), which allows human readable annotations for graphical outputs.
This means, users do not need to care about any expensive steps after
modeling to visualize the results. The returned as data frame is ready
to use with the ggplot2-package, however, there is also a
plot()
-method to easily create publication-ready figures.
Documentation and Support
Please visit https://strengejacke.github.io/ggeffects/ for documentation and vignettes. For questions about the functionality, you may either contact me via email or also file an issue.
ggeffects supports many different models and is easy to use
Marginal effects can be calculated for many different models. Currently
supported model-objects are: bamlss
, bayesx
, betabin
, betareg
,
bglmer
, blmer
, bracl
, brglm
, brmsfit
, brmultinom
, cgam
,
cgamm
, clm
, clm2
, clmm
, coxph
, fixest
, gam
(package
mgcv), Gam
(package gam), gamlss
, gamm
, gamm4
, gee
,
geeglm
, glm
, glm.nb
, glmer
, glmer.nb
, glmmTMB
, glmmPQL
,
glmrob
, glmRob
, glmx
, gls
, hurdle
, ivreg
, lm
, lm_robust
,
lme
, lmer
, lmrob
, lmRob
, logistf
, lrm
, mclogit
, mlogit
,
MixMod
, MCMCglmm
, mixor
, multinom
, negbin
, nlmer
, ols
,
plm
, polr
, rlm
, rlmer
, rq
, rqss
, stanreg
, survreg
,
svyglm
, svyglm.nb
, tobit
, truncreg
, vgam
, wbm
, zeroinfl
and zerotrunc
.
Support for models varies by function, i.e. although ggpredict()
,
ggemmeans()
and ggeffect()
support most models, some models are only
supported exclusively by one of the three functions. Other models not
listed here might work as well, but are currently not tested.
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.
Examples
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 four terms
specified in the terms
-argument. Predicted values of the response,
along the values of the first term are calculated, optionally grouped by
the other terms specified in terms
.
library(ggeffects)
library(splines)
data(efc)
fit <- lm(barthtot ~ c12hour + bs(neg_c_7) * c161sex + e42dep, data = efc)
ggpredict(fit, terms = "c12hour")
#>
#> # Predicted values of Total score BARTHEL INDEX
#> # x = average number of hours of care per week
#>
#> x | Predicted | SE | 95% CI
#> ---------------------------------------
#> 4 | 67.89 | 1.06 | [65.81, 69.96]
#> 12 | 67.07 | 1.01 | [65.10, 69.05]
#> 22 | 66.06 | 0.96 | [64.19, 67.94]
#> 36 | 64.64 | 0.92 | [62.84, 66.45]
#> 49 | 63.32 | 0.93 | [61.51, 65.14]
#> 70 | 61.20 | 1.01 | [59.22, 63.17]
#> 100 | 58.15 | 1.25 | [55.71, 60.60]
#> 168 | 51.26 | 2.04 | [47.27, 55.25]
#>
#> Adjusted for:
#> * neg_c_7 = 11.83
#> * c161sex = 1.76
#> * e42dep = 2.93
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)
With three variables, predictions can be grouped and faceted.
ggpredict(fit, terms = c("neg_c_7", "c161sex", "e42dep"))
#>
#> # Predicted values of Total score BARTHEL INDEX
#> # x = Negative impact with 7 items
#>
#> # c161sex = Male
#> # e42dep = [1] independent
#>
#> x | Predicted | SE | 95% CI
#> ----------------------------------------
#> 7 | 102.74 | 3.45 | [95.97, 109.51]
#> 12 | 102.27 | 2.64 | [97.10, 107.44]
#> 17 | 93.79 | 3.49 | [86.96, 100.63]
#> 28 | 164.57 | 35.00 | [95.98, 233.17]
#>
#> # c161sex = Female
#> # e42dep = [1] independent
#>
#> x | Predicted | SE | 95% CI
#> ----------------------------------------
#> 7 | 109.54 | 2.21 | [105.20, 113.87]
#> 12 | 99.81 | 1.97 | [ 95.94, 103.68]
#> 17 | 94.90 | 2.39 | [ 90.21, 99.60]
#> 28 | 90.26 | 9.42 | [ 71.79, 108.74]
#>
#> # c161sex = Male
#> # e42dep = [2] slightly dependent
#>
#> x | Predicted | SE | 95% CI
#> ----------------------------------------
#> 7 | 83.73 | 3.27 | [77.32, 90.14]
#> 12 | 83.26 | 2.20 | [78.95, 87.58]
#> 17 | 74.79 | 3.11 | [68.68, 80.89]
#> 28 | 145.57 | 34.98 | [77.00, 214.14]
#>
#> # c161sex = Female
#> # e42dep = [2] slightly dependent
#>
#> x | Predicted | SE | 95% CI
#> --------------------------------------
#> 7 | 90.53 | 1.95 | [86.71, 94.35]
#> 12 | 80.80 | 1.34 | [78.17, 83.44]
#> 17 | 75.90 | 1.84 | [72.29, 79.51]
#> 28 | 71.26 | 9.28 | [53.07, 89.45]
#>
#> # c161sex = Male
#> # e42dep = [3] moderately dependent
#>
#> x | Predicted | SE | 95% CI
#> ----------------------------------------
#> 7 | 64.72 | 3.29 | [58.28, 71.16]
#> 12 | 64.26 | 2.02 | [60.30, 68.21]
#> 17 | 55.78 | 2.93 | [50.04, 61.52]
#> 28 | 126.56 | 34.99 | [57.98, 195.14]
#>
#> # c161sex = Female
#> # e42dep = [3] moderately dependent
#>
#> x | Predicted | SE | 95% CI
#> --------------------------------------
#> 7 | 71.52 | 2.01 | [67.59, 75.45]
#> 12 | 61.79 | 1.02 | [59.79, 63.80]
#> 17 | 56.89 | 1.54 | [53.86, 59.91]
#> 28 | 52.25 | 9.21 | [34.21, 70.29]
#>
#> # c161sex = Male
#> # e42dep = [4] severely dependent
#>
#> x | Predicted | SE | 95% CI
#> ----------------------------------------
#> 7 | 45.72 | 3.50 | [38.86, 52.57]
#> 12 | 45.25 | 2.15 | [41.03, 49.47]
#> 17 | 36.77 | 2.96 | [30.97, 42.58]
#> 28 | 107.55 | 35.01 | [38.93, 176.18]
#>
#> # c161sex = Female
#> # e42dep = [4] severely dependent
#>
#> x | Predicted | SE | 95% CI
#> --------------------------------------
#> 7 | 52.51 | 2.36 | [47.88, 57.15]
#> 12 | 42.79 | 1.27 | [40.29, 45.28]
#> 17 | 37.88 | 1.64 | [34.66, 41.10]
#> 28 | 33.24 | 9.20 | [15.21, 51.28]
#>
#> Adjusted for:
#> * c12hour = 42.10
mydf <- ggpredict(fit, terms = c("neg_c_7", "c161sex", "e42dep"))
ggplot(mydf, aes(x = x, y = predicted, colour = group)) +
geom_line() +
facet_wrap(~facet)
plot()
works for this case, as well:
plot(mydf)
More features are explained in detail in the package-vignettes.
Installation
Latest development build
To install the latest development snapshot (see latest changes below), type following commands into the R console:
library(devtools)
devtools::install_github("strengejacke/ggeffects")
Officiale, stable release
To install the latest stable release from CRAN, type following command into the R console:
install.packages("ggeffects")
Citation
In case you want / have to cite my package, please use
citation('ggeffects')
for citation information:
Lüdecke D (2018). ggeffects: Tidy Data Frames of Marginal Effects from Regression Models. Journal of Open Source Software, 3(26), 772. doi: 10.21105/joss.00772
References
Lüdecke, Daniel. 2018. “Sjlabelled: Labelled Data Utility Functions,” May. https://doi.org/10.5281/zenodo.1249215.