AFIT-R/ordr
Surrogate Residuals for Ordinal and General Regression Models

Package index
Search the AFIT-R/ordr package
Vignettes
Functions
90
Source code
25
Man pages
11
Home
/
GitHub
/
AFIT-R/ordr
/
autoplot.resid: Residual plots

autoplot.resid: Residual plots
In AFIT-R/ordr: Surrogate Residuals for Ordinal and General Regression Models

Description Usage Arguments Value Examples

View source: R/autoplot.R

Description

Residual-based diagnostic plots for cumulative link and general regression models using ggplot2 graphics.

Usage

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
autoplot.resid(
  object,
  what = 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,
  ...
)

autoplot.clm(
  object,
  what = 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,
  ...
)

autoplot.glm(
  object,
  what = 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,
  ...
)

autoplot.lrm(
  object,
  what = 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,
  ...
)

autoplot.orm(
  object,
  what = 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,
  ...
)

autoplot.polr(
  object,
  what = 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,
  ...
)

autoplot.vglm(
  object,
  what = 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,
  ...
)

Arguments

object

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

what

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

x

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

fit

The fitted model from which the residuals were extracted. (Only required if what = "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.

...

Additional optional arguments to be passed onto resids.

Value

A "ggplot" object.

Examples

1
2
# See ?resids for an example
?resids

AFIT-R/ordr documentation built on Feb. 6, 2020, 1:17 a.m.

Related to autoplot.resid in AFIT-R/ordr...

AFIT-R/ordr index
README.md

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close