stat_fit_augment {ggpmisc}

Augment data with fitted values and statistics

Description

stat_fit_augment fits a model and returns a "tidy" version of the model's data with prediction added, using 'augmnent() methods from packages 'broom', 'broom.mixed', or other sources. The prediction can be added to the plot as a curve.

Usage

stat_fit_augment(
  mapping = NULL,
  data = NULL,
  geom = "smooth",
  method = "lm",
  method.args = list(formula = y ~ x),
  n.min = 2L,
  augment.args = list(),
  level = 0.95,
  y.out = ".fitted",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping

The aesthetic mapping, usually constructed with aes. Only needs to be set at the layer level if you are overriding the plot defaults.

data

A layer specific dataset - only needed if you want to override the plot defaults.

geom

The geometric object to use display the data

method

character or function.

method.args, augment.args

list of arguments to pass to method and to to broom::augment.

n.min

integer Minimum number of distinct values in the explanatory variable (on the rhs of formula) for fitting to the attempted.

level

numeric Level of confidence interval to use (0.95 by default)

y.out

character (or numeric) index to column to return as y.

position

The position adjustment to use for overlapping points on this layer

na.rm

logical indicating whether NA values should be stripped before the computation proceeds.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders.

...

other arguments passed on to layer. This can include aesthetics whose values you want to set, not map. See layer for more details.

Details

stat_fit_augment together with stat_fit_glance and stat_fit_tidy, based on package 'broom' can be used with a broad range of model fitting functions as supported at any given time by 'broom'. In contrast to stat_poly_eq which can generate text or expression labels automatically, for these functions the mapping of aesthetic label needs to be explicitly supplied in the call, and labels built on the fly.

A ggplot statistic receives as data a data frame that is not the one passed as argument by the user, but instead a data frame with the variables mapped to aesthetics. In other words, it respects the grammar of graphics and consequently within arguments passed through method.args names of aesthetics like $x$ and $y$ should be used instead of the original variable names, while data is automatically passed the data frame. This helps ensure that the model is fitted to the same data as plotted in other layers.

Warning!

Not all ‘glance()' methods are defined in package ’broom'. 'glance()' specializations for mixed models fits of classes 'lme', 'nlme', ‘lme4', and many others are defined in package ’broom.mixed'.

Handling of grouping

stat_fit_augment applies the function given by method separately to each group of observations; in ggplot2 factors mapped to aesthetics generate a separate group for each level. Because of this, stat_fit_augment is not useful for annotating plots with results from t.test() or ANOVA or ANCOVA. In such cases use instead stat_fit_tb() which applies the model fitting per panel.

Computed variables

The output of augment() is returned as is, except for y which is set based on y.out and y.observed which preserves the y returned by the generics::augment methods. This renaming is needed so that the geom works as expected.

To explore the values returned by this statistic, which vary depending on the model fitting function and model formula we suggest the use of geom_debug. An example is shown below.

Note

The statistic stat_fit_augment can be used only with methods that accept formulas under any formal parameter name and a data argument. Use ggplot2::stat_smooth() instead of stat_fit_augment in production code if the additional features are not needed.

Although arguments passed to parameter augment.args will be passed to [generics::augment()] whether they are silently ignored or obeyed depends on each specialization of [augment()], so do carefully read the documentation for the version of [augment()] corresponding to the 'method' used to fit the model.

See Also

broom and broom.mixed for details on how the tidying of the result of model fits is done.

Other ggplot statistics for model fits: stat_fit_deviations(), stat_fit_glance(), stat_fit_residuals(), stat_fit_tb(), stat_fit_tidy()

Examples

# Package 'broom' needs to be installed to run these examples.
# We check availability before running them to avoid errors.

if (requireNamespace("broom", quietly = TRUE)) {
  broom.installed <- TRUE
  library(broom)
  library(quantreg)

# Inspecting the returned data using geom_debug()
  if (requireNamespace("gginnards", quietly = TRUE)) {
    library(gginnards)

# Regression by panel, inspecting data
    ggplot(mtcars, aes(x = disp, y = mpg)) +
      geom_point(aes(colour = factor(cyl))) +
      stat_fit_augment(method = "lm",
                       method.args = list(formula = y ~ x),
                       geom = "debug",
                       summary.fun = colnames)
  }
}

# Regression by panel example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg)) +
    geom_point(aes(colour = factor(cyl))) +
    stat_fit_augment(method = "lm",
                     method.args = list(formula = y ~ x))

# Residuals from regression by panel example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg)) +
    geom_hline(yintercept = 0, linetype = "dotted") +
    stat_fit_augment(geom = "point",
                     method = "lm",
                     method.args = list(formula = y ~ x),
                     y.out = ".resid")

# Regression by group example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg, colour = factor(cyl))) +
    geom_point() +
    stat_fit_augment(method = "lm",
                     method.args = list(formula = y ~ x))

# Residuals from regression by group example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg, colour = factor(cyl))) +
    geom_hline(yintercept = 0, linetype = "dotted") +
    stat_fit_augment(geom = "point",
                     method.args = list(formula = y ~ x),
                     y.out = ".resid")

# Weighted regression example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg, weight = cyl)) +
    geom_point(aes(colour = factor(cyl))) +
    stat_fit_augment(method = "lm",
                     method.args = list(formula = y ~ x,
                                        weights = quote(weight)))

# Residuals from weighted regression example
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg, weight = cyl)) +
    geom_hline(yintercept = 0, linetype = "dotted") +
    stat_fit_augment(geom = "point",
                     method.args = list(formula = y ~ x,
                                        weights = quote(weight)),
                     y.out = ".resid")

# Quantile regression
if (broom.installed)
  ggplot(mtcars, aes(x = disp, y = mpg)) +
    geom_point() +
    stat_fit_augment(method = "rq")