resid_panel: Panel of Diagnostic Residual Plots.

In ggResidpanel: Panels and Interactive Versions of Diagnostic Plots using 'ggplot2'

Description

Creates a panel of residual diagnostic plots given a model. Currently accepts models of type "lm", "glm", "lmerMod", "lmerModLmerTest", "lme", and "glmerMod".

Usage

resid_panel(model, plots = "default", type = NA, bins = 30,
  smoother = FALSE, qqline = TRUE, qqbands = FALSE, scale = 1,
  theme = "bw", axis.text.size = 10, title.text.size = 12,
  title.opt = TRUE, nrow = NULL)

Arguments

model	Model fit using either lm, glm, lmer, lmerTest, lme, or glmer.
plots	Plots chosen to include in the panel of plots. The default panel includes a residual plot, a normal quantile plot, an index plot, and a histogram of the residuals. (See details for the options available.)
type	Type of residuals to use in the plot. If not specified, the default residual type for each model type is used. (See details for the options available.)
bins	Number of bins to use when creating a histogram of the residuals. Default is set to 30.
smoother	Indicates whether or not to include a smoother on the index, residual-leverage, location-scale, and residual plots. Specify TRUE or FALSE. Default is set to FALSE.
qqline	Indicates whether to include a 1-1 line on the qq-plot. Specify TRUE or FALSE. Default is set to TRUE.
qqbands	Indicates whether to include confidence bands on the qq-plot. Specify TRUE or FALSE. Default is set to FALSE.
scale	Scales the size of the graphs in the panel. Takes values in (0,1].
theme	ggplot2 theme to be used. Current options are "bw", "classic", and "grey" (or "gray"). Default is "bw".
axis.text.size	Specifies the size of the text for the axis labels of all plots in the panel.
title.text.size	Specifies the size of the text for the titles of all plots in the panel.
title.opt	Indicates whether or not to include a title on the plots in the panel. Specify TRUE or FALSE. Default is set to TRUE.
nrow	Sets the number of rows in the panel.

Details

The first two sections below contain information on the available input options for the plots and type arguments in resid_panel. The third section contains details relating to the creation of the plots.

Options for Plots

The following options can be chosen for the plots argument.

• "all": This creates a panel of all plot types included in the package that are available for the model type input into resid_panel. (See note below.)

• "default": This creates a panel with a residual plot, a normal quantile plot of the residuals, an index plot of the residuals, and a histogram of the residuals.

• "R": This creates a panel with a residual plot, a normal quantile plot of the residuals, a location-scale plot, and a residuals versus leverage plot. This was modeled after the plots shown in R if the plot() base function is applied to an lm model. This option can only be used with an lm or glm model.

• "SAS": This creates a panel with a residual plot, a normal quantile plot of the residuals, a histogram of the residuals, and a boxplot of the residuals. This was modeled after the residualpanel option in proc mixed from SAS version 9.4.

• A vector of individual plots can also be specified. For example, one can specify plots = c("boxplot", "hist") or plots = "qq". The individual plot options are as follows.

  • "boxplot": A boxplot of residuals

  • "cookd": A plot of Cook's D values versus observation numbers

  • "hist": A histogram of residuals

  • "index": A plot of residuals versus observation numbers

  • "ls": A location scale plot of the residuals

  • "qq": A normal quantile plot of residuals

  • "lev": A plot of standardized residuals versus leverage values

  • "resid": A plot of residuals versus predicted values

  • "yvp":: A plot of observed response values versus predicted values

Note: "cookd", "ls", and "lev" are only available for "lm" and "glm" models.

Options for Type

Several residual types are available to be requested based on the model type that is input into resid_panel. These currently are as follows.

• lm residual options

  • "pearson":The Pearson residuals

  • "response": The raw residuals (Default for "lm")

  • "standardized": The standardized raw residuals

• glm residual options

  • "pearson": The Pearson residuals

  • "deviance": The deviance residuals (Default for "glm")

  • "response": The raw residuals

  • "stand.deviance": The standardized deviance residuals

  • "stand.pearson": The standardized Pearson residuals

• lmer, lmerTest, and lme residual options

  • "pearson": The Pearson residuals (Default for "lmer", "lmerTest", and "lme")

  • "response": The raw residuals

• glmer residual options

  • "pearson": The Pearson residuals

  • "deviance": The deviance residuals (Default for "glmer")

  • "response": The raw residuals

Note: The plots of "ls" and "lev" only accept standardized residuals.

Details on the Creation of Plots

Boxplot (boxplot)

Boxplot of the residuals.

Cook's D (cookd)

The horizontal line represents a cut-off to identify highly influential points. The horizontal line is placed at 4/n where n is the number of data points used in the model.

Histogram (hist)

Plots a histogram of the residuals. The density curve overlaid has mean equal to zero and standard deviation equal to the standard deviation of the residuals.

Index Plot (index)

Plots the residuals on the y-axis and the observation number associated with the residual on the x-axis.

Residual-Leverage Plot (lev)

Plots the standardized residuals on the y-axis and the leverage values on the x-axis with a loess curve is overlaid. Cook's D contour lines (which are a function of leverage and standardized residuals) are plotted as the red dashed lines for Cook's D values of 0.5 and 1.

Location-Scale Plot (ls)

Plots the square root of the absolute value of the standardized residuals on the y-axis and the predicted values on the x-axis. The predicted values are plotted on the original scale for glm and glmer models. A loess curve is overlaid.

QQ Plot (qq)

Makes use of the R package qqplotr for creating a normal quantile plot of the residuals.

Residual Plot (resid)

Plots the residuals on the y-axis and the predicted values on the x-axis. The predicted values are plotted on the original scale for glm and glmer models.

Response vs. Predicted (yvp)

Plots the response variable from the model on the y-axis and the predicted values on the x-axis. Both response variable and predicted values are plotted on the original scale for glm and glmer models.

Value

A panel of residual diagnostic plots containing plots specified.

Examples

# Fit a model to the penguin data
penguin_model <- lme4::lmer(heartrate ~ depth + duration + (1|bird), data = penguins)

# Create the default panel
resid_panel(penguin_model)

# Select all plots to include in the panel and set the smoother option to TRUE
resid_panel(penguin_model, plots = "all", smoother = TRUE)

# Select only the residual plot and qq-plot to be included in the panel,
# request confidence bands on the qq plot, and set the number of rows to 2
resid_panel(penguin_model, plots = c("resid", "qq"), qqbands = TRUE, nrow = 2)

# Choose the SAS panel of plots, change the theme to classic, and remove the
# titles of the plots
resid_panel(penguin_model, plots = "SAS", theme = "classic", title.opt = FALSE)

ggResidpanel documentation built on June 1, 2019, 1:04 a.m.