ggpmisc (version 0.3.9)

stat_fit_augment: 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),
  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 or 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.

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.

Warning!

Not all `glance()` methods are defined in package 'broom'. `glance()` especializations 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.

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 wich 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 intead 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.

See Also

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

Other Statistics calling generic tidier methods.: stat_fit_glance(), stat_fit_tb(), stat_fit_tidy()

Examples

# NOT RUN {
library(broom)
library(gginnards)
library(quantreg)

# Regression by panel, using geom_debug() to explore computed variables
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
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
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
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
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
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
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
ggplot(mtcars, aes(x = disp, y = mpg)) +
  geom_point() +
  stat_fit_augment(method = "rq",
                  label.y = "bottom")

# }