plot_model: Plot regression models

Description Usage Arguments Details Value References Examples

View source: R/plot_model.R

Description

plot_model() creates plots from regression models, either estimates (as so-called forest or dot whisker plots) or marginal effects.

Usage

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plot_model(model, type = c("est", "re", "eff", "pred", "int", "std",
  "std2", "slope", "resid", "diag"), transform, terms = NULL,
  sort.est = NULL, rm.terms = NULL, group.terms = NULL,
  order.terms = NULL, pred.type = c("fe", "re"),
  mdrt.values = c("minmax", "meansd", "zeromax", "quart", "all"),
  ri.nr = NULL, title = NULL, axis.title = NULL,
  axis.labels = NULL, legend.title = NULL, wrap.title = 50,
  wrap.labels = 25, axis.lim = NULL, grid.breaks = NULL,
  ci.lvl = NULL, se = NULL, colors = "Set1",
  show.intercept = FALSE, show.values = FALSE, show.p = TRUE,
  show.data = FALSE, show.legend = TRUE, show.zeroinf = TRUE,
  value.offset = NULL, value.size, jitter = NULL, digits = 2,
  dot.size = NULL, line.size = NULL, vline.color = NULL,
  p.threshold = c(0.05, 0.01, 0.001), grid, case, auto.label = TRUE,
  prefix.labels = c("none", "varname", "label"), bpe = "median",
  bpe.style = "line", bpe.color = "white", ...)

get_model_data(model, type = c("est", "re", "eff", "pred", "int", "std",
  "std2", "slope", "resid", "diag"), transform, terms = NULL,
  sort.est = NULL, rm.terms = NULL, group.terms = NULL,
  order.terms = NULL, pred.type = c("fe", "re"), ri.nr = NULL,
  ci.lvl = NULL, colors = "Set1", grid, case = "parsed",
  digits = 2, ...)

Arguments

model

A regression model object. Depending on the type, many kinds of models are supported, e.g. from packages like stats, lme4, nlme, rstanarm, survey, glmmTMB, MASS, brms etc.

type

Type of plot. There are three groups of plot-types:

Coefficients (related vignette)

type = "est"

Forest-plot of estimates. If the fitted model only contains one predictor, slope-line is plotted.

type = "re"

For mixed effects models, plots the random effects.

type = "std"

Forest-plot of standardized beta values.

type = "std2"

Forest-plot of standardized beta values, however, standardization is done by dividing by two sd (see 'Details').

Marginal Effects (related vignette)

type = "pred"

Predicted values (marginal effects) for specific model terms. See ggpredict for details.

type = "eff"

Similar to type = "pred", however, discrete predictors are held constant at their proportions (not reference level). See ggeffect for details.

type = "int"

Marginal effects of interaction terms in model.

Model diagnostics

type = "slope"

Slope of coefficients for each single predictor, against the response (linear relationship between each model term and response).

type = "resid"

Slope of coefficients for each single predictor, against the residuals (linear relationship between each model term and residuals).

type = "diag"

Check model assumptions.

Note: For mixed models, the diagnostic plots like linear relationship or check for Homoscedasticity, do not take the uncertainty of random effects into account, but is only based on the fixed effects part of the model.

transform

A character vector, naming a function that will be applied on estimates and confidence intervals. By default, transform will automatically use "exp" as transformation for applicable classes of model (e.g. logistic or poisson regression). Estimates of linear models remain untransformed. Use NULL if you want the raw, non-transformed estimates.

terms

Character vector with the names of those terms from model that should be plotted. This argument depends on the plot-type:

Coefficients

Select terms that should be plotted. All other term are removed from the output. Note that the term names must match the names of the model's coefficients. For factors, this means that the variable name is suffixed with the related factor level, and each category counts as one term. E.g. rm.terms = "t_name [2,3]" would remove the terms "t_name2" and "t_name3" (assuming that the variable t_name is categorical and has at least the factor levels 2 and 3). Another example for the iris-dataset: terms = "Species" would not work, instead you would write terms = "Species [versicolor,virginica]" to remove these two levels, or terms = "Speciesversicolor" if you just want to remove the level versicolor from the plot.

Marginal Effects

Here terms indicates for which terms marginal effects should be displayed. At least one term is required to calculate effects, maximum length is three terms, where the second and third term indicate the groups, i.e. predictions of first term are grouped by the levels of the second (and third) term. terms may also indicate higher order terms (e.g. interaction terms). Indicating levels in square brackets allows for selecting only specific groups. Term name and levels in brackets must be separated by a whitespace character, e.g. terms = c("age", "education [1,3]"). It is also possible to specify a range of numeric values for the predictions with a colon, for instance terms = c("education [1,3]", "age [30:50]"). Furthermore, it is possible to specify a function name. Values for predictions will then be transformed, e.g. terms = "income [exp]". This is useful when model predictors were transformed for fitting the model and should be back-transformed to the original scale for predictions. Finally, using pretty for numeric variables (e.g. terms = "age [pretty]") calculates a pretty range of values for the term, roughly of proportional length to the term's value range. For more details, see ggpredict.

sort.est

Determines in which way estimates are sorted in the plot:

  • If NULL (default), no sorting is done and estimates are sorted in the same order as they appear in the model formula.

  • If TRUE, estimates are sorted in descending order, with highest estimate at the top.

  • If sort.est = "sort.all", estimates are re-sorted for each coefficient (only applies if type = "re" and grid = FALSE), i.e. the estimates of the random effects for each predictor are sorted and plotted to an own plot.

  • If type = "re", specify a predictor's / coefficient's name to sort estimates according to this random effect.

rm.terms

Character vector with names that indicate which terms should be removed from the plot. Counterpart to terms. rm.terms = "t_name" would remove the term t_name. Default is NULL, i.e. all terms are used. For factors, levels that should be removed from the plot need to be explicitely indicated in square brackets, and match the model's coefficient names, e.g. rm.terms = "t_name [2,3]" would remove the terms "t_name2" and "t_name3" (assuming that the variable t_name was categorical and has at least the factor levels 2 and 3). Another example for the iris dataset would be rm.terms = "Species [versicolor,virginica]". Note that the rm.terms-argument does not apply to Marginal Effects plots.

group.terms

Numeric vector with group indices, to group coefficients. Each group of coefficients gets its own color (see 'Examples').

order.terms

Numeric vector, indicating in which order the coefficients should be plotted. See examples in this package-vignette.

pred.type

Character, only applies for Marginal Effects plots with mixed effects models. Indicates whether predicted values should be conditioned on random effects (pred.type = "re") or fixed effects only (pred.type = "fe", the default). For details, see documentation of the type-argument in ggpredict.

mdrt.values

Indicates which values of the moderator variable should be used when plotting interaction terms (i.e. type = "int").

"minmax"

(default) minimum and maximum values (lower and upper bounds) of the moderator are used to plot the interaction between independent variable and moderator(s).

"meansd"

uses the mean value of the moderator as well as one standard deviation below and above mean value to plot the effect of the moderator on the independent variable (following the convention suggested by Cohen and Cohen and popularized by Aiken and West (1991), i.e. using the mean, the value one standard deviation above, and the value one standard deviation below the mean as values of the moderator, see Grace-Martin K: 3 Tips to Make Interpreting Moderation Effects Easier).

"zeromax"

is similar to the "minmax" option, however, 0 is always used as minimum value for the moderator. This may be useful for predictors that don't have an empirical zero-value, but absence of moderation should be simulated by using 0 as minimum.

"quart"

calculates and uses the quartiles (lower, median and upper) of the moderator value.

"all"

uses all values of the moderator variable.

ri.nr

Numeric vector. If type = "re" and fitted model has more than one random intercept, ri.nr indicates which random effects of which random intercept (or: which list elements of ranef) will be plotted. Default is NULL, so all random effects will be plotted.

title

Character vector, used as plot title. By default, get_dv_labels is called to retrieve the label of the dependent variable, which will be used as title. Use title = "" to remove title.

axis.title

Character vector of length one or two (depending on the plot function and type), used as title(s) for the x and y axis. If not specified, a default labelling is chosen. Note: Some plot types may not support this argument sufficiently. In such cases, use the returned ggplot-object and add axis titles manually with labs. Use axis.title = "" to remove axis titles.

axis.labels

Character vector with labels for the model terms, used as axis labels. By default, get_term_labels is called to retrieve the labels of the coefficients, which will be used as axis labels. Use axis.labels = "" or auto.label = FALSE to use the variable names as labels instead. If axis.labels is a named vector, axis labels (by default, the names of the model's coefficients) will be matched with the names of axis.label. This ensures that labels always match the related axis value, no matter in which way axis labels are sorted.

legend.title

Character vector, used as legend title for plots that have a legend.

wrap.title

Numeric, determines how many chars of the plot title are displayed in one line and when a line break is inserted.

wrap.labels

Numeric, determines how many chars of the value, variable or axis labels are displayed in one line and when a line break is inserted.

axis.lim

Numeric vector of length 2, defining the range of the plot axis. Depending on plot-type, may effect either x- or y-axis. For Marginal Effects plots, axis.lim may also be a list of two vectors of length 2, defining axis limits for both the x and y axis.

grid.breaks

Numeric value or vector; if grid.breaks is a single value, sets the distance between breaks for the axis at every grid.breaks'th position, where a major grid line is plotted. If grid.breaks is a vector, values will be used to define the axis positions of the major grid lines.

ci.lvl

Numeric, the level of the confidence intervals (error bars). Use ci.lvl = NA to remove error bars. For stanreg-models, ci.lvl defines the (outer) probability for the hdi (High Density Interval) that is plotted. By default, stanreg-models are printed with two intervals: the "inner" interval, which defaults to the 50%-HDI; and the "outer" interval, which defaults to the 89%-HDI. ci.lvl affects only the outer interval in such cases. See prob.inner and prob.outer under the ...-argument for more details.

se

Either a logical, and if TRUE, error bars indicate standard errors, not confidence intervals. Or a character vector with a specification of the covariance matrix to compute robust standard errors (see argument vcov of robust for valid values; robust standard errors are only supported for models that work with coeftest). se overrides ci.lvl: if not NULL, arguments ci.lvl and transform will be ignored. Currently, se only applies to Coefficients plots.

colors

May be a character vector of color values in hex-format, valid color value names (see demo("colors")) or a name of a pre-defined color palette. Following options are valid for the colors argument:

  • If not specified, a default color brewer palette will be used, which is suitable for the plot style.

  • If "gs", a greyscale will be used.

  • If "bw", and plot-type is a line-plot, the plot is black/white and uses different line types to distinguish groups (see this package-vignette).

  • If colors is any valid color brewer palette name, the related palette will be used. Use display.brewer.all to view all available palette names.

  • There are some pre-defined color palettes in this package, see sjPlot-themes for details.

  • Else specify own color values or names as vector (e.g. colors = "#00ff00" or colors = c("firebrick", "blue")).

show.intercept

Logical, if TRUE, the intercept of the fitted model is also plotted. Default is FALSE. If transform = "exp", please note that due to exponential transformation of estimates, the intercept in some cases is non-finite and the plot can not be created.

show.values

Logical, whether values should be plotted or not.

show.p

Logical, adds asterisks that indicate the significance level of estimates to the value labels.

show.data

Logical, for Marginal Effects plots, also plots the raw data points.

show.legend

For Marginal Effects plots, shows or hides the legend.

show.zeroinf

Logical, if TRUE, shows the zero-inflation part of hurdle- or zero-inflated models.

value.offset

Numeric, offset for text labels to adjust their position relative to the dots or lines.

value.size

Numeric, indicates the size of value labels. Can be used for all plot types where the argument show.values is applicable, e.g. value.size = 4.

jitter

Numeric, between 0 and 1. If show.data = TRUE, you can add a small amount of random variation to the location of each data point. jitter then indicates the width, i.e. how much of a bin's width will be occupied by the jittered values.

digits

Numeric, amount of digits after decimal point when rounding estimates or values.

dot.size

Numeric, size of the dots that indicate the point estimates.

line.size

Numeric, size of the lines that indicate the error bars.

vline.color

Color of the vertical "zero effect" line. Default color is inherited from the current theme.

p.threshold

Numeric vector of length 3, indicating the treshold for annotating p-values with asterisks. Only applies if p.style = "asterisk".

grid

Logical, if TRUE, multiple plots are plotted as grid layout.

case

Desired target case. Labels will automatically converted into the specified character case. See to_any_case for more details on this argument. By default, if case is not specified, it will be set to "parsed", unless prefix.labels is not "none". If prefix.labels is either "label" (or "l") or "varname" (or "v") and case is not specified, it will be set to NULL - this is a more convenient default when prefixing labels.

auto.label

Logical, if TRUE (the default), plot-labels are based on value and variable labels, if the data is labelled. See get_label and get_term_labels for details. If FALSE, original variable names and value labels (factor levels) are used.

prefix.labels

Indicates whether the value labels of categorical variables should be prefixed, e.g. with the variable name or variable label. See argument prefix in get_term_labels for details.

bpe

For Stan-models (fitted with the rstanarm- or brms-package), the Bayesian point estimate is, by default, the median of the posterior distribution. Use bpe to define other functions to calculate the Bayesian point estimate. bpe needs to be a character naming the specific function, which is passed to the fun-argument in typical_value. So, bpe = "mean" would calculate the mean value of the posterior distribution.

bpe.style

For Stan-models (fitted with the rstanarm- or brms-package), the Bayesian point estimate is indicated as a small, vertical line by default. Use bpe.style = "dot" to plot a dot instead of a line for the point estimate.

bpe.color

Character vector, indicating the color of the Bayesian point estimate. Setting bpe.color = NULL will inherit the color from the mapped aesthetic to match it with the geom's color.

...

Other arguments, passed down to various functions. Here is a list of supported arguments and their description in detail.

prob.inner and prob.outer

For Stan-models (fitted with the rstanarm- or brms-package) and coefficients plot-types, you can specify numeric values between 0 and 1 for prob.inner and prob.outer, which will then be used as inner and outer probabilities for the uncertainty intervals (HDI). By default, the inner probability is 0.5 and the outer probability is 0.89 (unless ci.lvl is specified - in this case, ci.lvl is used as outer probability).

size.inner

For Stan-models and Coefficients plot-types, you can specify the width of the bar for the inner probabilities. Default is 0.1. Setting size.inner = 0 removes the inner probability regions.

width, alpha, and scale

Passed down to geom_errorbar() or geom_density_ridges(), for forest or diagnostic plots.

width, alpha, dot.alpha, dodge and log.y

Passed down to plot.ggeffects for Marginal Effects plots.

show.loess

Logical, for diagnostic plot-types "slope" and "resid", adds (or hides) a loess-smoothed line to the plot.

Marginal Effects plot-types

When plotting marginal effects, arguments are also passed down to ggpredict, ggeffect or plot.ggeffects.

Case conversion of labels

For case conversion of labels (see argument case), arguments sep_in and sep_out will be passed down to to_any_case. This only applies to automatically retrieved term labels, not if term labels are provided by the axis.labels-argument.

Details

get_model_data() simply calls plot_model() and returns the data from the ggplot-object. Hence, it is rather inefficient and should be used as alternative to brooms tidy()-function only in specific situations.

Some notes on the different plot-types:

type = "std2"

Plots standardized beta values, however, standardization follows Gelman's (2008) suggestion, rescaling the estimates by dividing them by two standard deviations instead of just one. Resulting coefficients are then directly comparable for untransformed binary predictors.

type = "pred"

Plots marginal effects. Simply wraps ggpredict.

type = "eff"

Plots marginal effects. Simply wraps ggeffect.

type = "int"

A shortcut for marginal effects plots, where interaction terms are automatically detected and used as terms-argument. Furthermore, if the moderator variable (the second - and third - term in an interaction) is continuous, type = "int" automatically chooses useful values based on the mdrt.values-argument, which are passed to terms. Then, ggpredict is called. type = "int" plots the interaction term that appears first in the formula along the x-axis, while the second (and possibly third) variable in an interaction is used as grouping factor(s) (moderating variable). Use type = "pred" or type = "eff" and specify a certain order in the terms-argument to indicate which variable(s) should be used as moderator.

Value

Depending on the plot-type, plot_model() returns a ggplot-object or a list of such objects. get_model_data returns the associated data with the plot-object as tidy data frame, or (depending on the plot-type) a list of such data frames.

References

Gelman A (2008) "Scaling regression inputs by dividing by two standard deviations." Statistics in Medicine 27: 2865–2873. http://www.stat.columbia.edu/~gelman/research/published/standardizing7.pdf

Aiken and West (1991). Multiple Regression: Testing and Interpreting Interactions.

Examples

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# prepare data
library(sjmisc)
data(efc)
efc <- to_factor(efc, c161sex, e42dep, c172code)
m <- lm(neg_c_7 ~ pos_v_4 + c12hour + e42dep + c172code, data = efc)

# simple forest plot
plot_model(m)

# grouped coefficients
plot_model(m, group.terms = c(1, 2, 3, 3, 3, 4, 4))

# keep only selected terms in the model: pos_v_4, the
# levels 3 and 4 of factor e42dep and levels 2 and 3 for c172code
plot_model(m, terms = c("pos_v_4", "e42dep [3,4]", "c172code [2,3]"))

# multiple plots, as returned from "diagnostic"-plot type,
# can be arranged with 'plot_grid()'
## Not run: 
p <- plot_model(m, type = "diag")
plot_grid(p)
## End(Not run)

# plot random effects
library(lme4)
m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
plot_model(m, type = "re")

# plot marginal effects
plot_model(m, type = "pred", terms = "Days")

# plot interactions
## Not run: 
m <- glm(
  tot_sc_e ~ c161sex + c172code * neg_c_7,
  data = efc,
  family = poisson()
)
# type = "int" automatically selects groups for continuous moderator
# variables - see argument 'mdrt.values'. The following function call is
# identical to:
# plot_model(m, type = "pred", terms = c("c172code", "neg_c_7 [7,28]"))
plot_model(m, type = "int")

# switch moderator
plot_model(m, type = "pred", terms = c("neg_c_7", "c172code"))
# same as
# ggeffects::ggpredict(m, terms = c("neg_c_7", "c172code"))
## End(Not run)

# plot Stan-model
## Not run: 
if (require("rstanarm")) {
  data(mtcars)
  m <- stan_glm(mpg ~ wt + am + cyl + gear, data = mtcars, chains = 1)
  plot_model(m, bpe.style = "dot")
}
## End(Not run)

sjPlot documentation built on Oct. 15, 2018, 1:03 a.m.