autoplot: Residual-based diagnostic plots

Description

Residual-based diagnostic plots for cumulative link and general regression models using ggplot graphics.

Usage

# S3 method for resid
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for glm
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for clm
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for lrm
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for orm
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for polr
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)
# S3 method for vglm
autoplot(
  object,
  output = c("qq", "fitted", "covariate"),
  x = NULL,
  fit = NULL,
  distribution = qnorm,
  ncol = NULL,
  alpha = 1,
  xlab = NULL,
  color = "#444444",
  shape = 19,
  size = 2,
  qqpoint.color = "#444444",
  qqpoint.shape = 19,
  qqpoint.size = 2,
  qqline.color = "#888888",
  qqline.linetype = "dashed",
  qqline.size = 1,
  smooth = TRUE,
  smooth.color = "red",
  smooth.linetype = 1,
  smooth.size = 1,
  fill = NULL,
  resp_name = NULL,
  ...
)

Arguments

object

An object of class resids, clm, glm, lrm, orm, polr, or vglm.

output

Character string specifying what to plot. Default is "qq" which produces a quantile-quantile plots of the residuals.

A vector giving the covariate values to use for residual-by- covariate plots (i.e., when output = "covariate").

fit

The fitted model from which the residuals were extracted. (Only required if output = "fitted" and object inherits from class "resid".)

distribution

Function that computes the quantiles for the reference distribution to use in the quantile-quantile plot. Default is qnorm which is only appropriate for models using a probit link function. When jitter.scale = "probability", the reference distribution is always U(-0.5, 0.5). (Only required if object inherits from class "resid".)

ncol

Integer specifying the number of columns to use for the plot layout (if requesting multiple plots). Default is NULL.

alpha

A single values in the interval [0, 1] controlling the opacity alpha of the plotted points. Only used when nsim > 1.

xlab

Character string giving the text to use for the x-axis label in residual-by-covariate plots. Default is NULL.

color

Character string or integer specifying what color to use for the points in the residual vs fitted value/covariate plot. Default is "black".

shape

Integer or single character specifying a symbol to be used for plotting the points in the residual vs fitted value/covariate plot.

size

Numeric value specifying the size to use for the points in the residual vs fitted value/covariate plot.

qqpoint.color

Character string or integer specifying what color to use for the points in the quantile-quantile plot.

qqpoint.shape

Integer or single character specifying a symbol to be used for plotting the points in the quantile-quantile plot.

qqpoint.size

Numeric value specifying the size to use for the points in the quantile-quantile plot.

qqline.color

Character string or integer specifying what color to use for the points in the quantile-quantile plot.

qqline.linetype

Integer or character string (e.g., "dashed") specifying the type of line to use in the quantile-quantile plot.

qqline.size

Numeric value specifying the thickness of the line in the quantile-quantile plot.

smooth

Logical indicating whether or not too add a nonparametric smooth to certain plots. Default is TRUE.

smooth.color

Character string or integer specifying what color to use for the nonparametric smooth.

smooth.linetype

Integer or character string (e.g., "dashed") specifying the type of line to use for the nonparametric smooth.

smooth.size

Numeric value specifying the thickness of the line for the nonparametric smooth.

fill

Character string or integer specifying the color to use to fill the boxplots for residual-by-covariate plots when x is of class "factor". Default is NULL which colors the boxplots according to the factor levels.

resp_name

Character string to specify the response name that will be displayed in the figure.

...

Additional optional arguments to be passed onto ggplot.

Value

A "ggplot" object.

Examples

Run this code

# NOT RUN {
# Load data
data(df1)
# Fit cumulative link model
fit <- glm(y ~ x + I(x ^ 2), data = df1, family = binomial)
# Construct residual plots
p1 <- ggplot2::autoplot(fit, jitter.scale = "probability", output = "qq")
p2 <- ggplot2::autoplot(fit, output = "covariate", x = df1$x)
p3 <- ggplot2::autoplot(fit, output = "fitted")
p4 <- ggplot2::autoplot(fit, output = "fitted", nsim = 10)

# }

Run the code above in your browser using DataLab