Help for package ggfortify

Type:

Package

Title:

Data Visualization Tools for Statistical Analysis Results

Version:

0.4.18

Date:

2025-07-02

Maintainer:

Yuan Tang <terrytangyuan@gmail.com>

URL:

https://github.com/sinhrks/ggfortify

BugReports:

https://github.com/sinhrks/ggfortify/issues

Encoding:

UTF-8

Description:

Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.

License:

MIT + file LICENSE

Depends:

methods, ggplot2 (≥ 2.0.0)

Imports:

dplyr (≥ 0.3), tidyr, gridExtra, grid, scales, stringr, tibble

Suggests:

testthat, cluster, changepoint, fGarch, forecast, ggrepel, glmnet, grDevices, KFAS, knitr, lintr, mapdata, markdown, MASS, MSwM, nlme, raster, ROCR, sp, stats, strucchange, survival, timeSeries, tseries, utils, vars, xts, zoo, lfda

RoxygenNote:

7.3.2

NeedsCompilation:

Packaged:

2025-07-03 01:58:10 UTC; terrytangyuan

Author:

Masaaki Horikoshi [aut], Yuan Tang

[aut, cre], Austin Dickey [ctb], Matthias Grenié [ctb], Ryan Thompson [ctb], Luciano Selzer [ctb], Dario Strbenac [ctb], Kirill Voronin [ctb], Damir Pulatov [ctb]

Repository:

CRAN

Date/Publication:

2025-07-03 06:40:02 UTC

ggfortify

Description

Define Fortify and Autoplot to Allow 'ggplot2' to Draw Some Popular Packages

Author(s)

Maintainer: Yuan Tang terrytangyuan@gmail.com (ORCID)

Authors:

Masaaki Horikoshi sinhrks@gmail.com

Other contributors:

Austin Dickey [contributor]
Matthias Grenié [contributor]
Ryan Thompson [contributor]
Luciano Selzer [contributor]
Dario Strbenac [contributor]
Kirill Voronin [contributor]
Damir Pulatov [contributor]

Generic add operator for `ggmultiplot`

Description

Generic add operator for ggmultiplot

Usage

## S4 method for signature 'ggmultiplot,ANY'
e1 + e2

Arguments

e1

first argument

e2

second argument

Value

ggmultiplot

Apply facets to to `ggplot2::ggplot`

Description

Apply facets to to ggplot2::ggplot

Usage

apply_facets(
  p,
  formula,
  facets = TRUE,
  nrow = NULL,
  ncol = 1,
  scales = "free_y",
  ...
)

Arguments

p

ggplot2::ggplot instance

formula

stats::formula instance

facets

Logical value to specify use facets

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

scales

Scale value passed to ggplot2

...

other arguments passed to methods

Value

ggplot

Apply grid to to `ggplot2::ggplot`

Description

Apply grid to to ggplot2::ggplot

Usage

apply_grid(p, formula, scales = "free_y", ...)

Arguments

p

ggplot2::ggplot instance

formula

stats::formula instance

scales

Scale value passed to ggplot2

...

other arguments passed to methods

Convert a spline basis to a tibble

Description

Convert a spline basis to a tibble

Usage

## S3 method for class 'basis'
as_tibble(x, ...)

Arguments

x

object of class "basis"

...

Ignored.

Details

This function is needed because the default method for converting a matrix object with an additional class attribute to a tibble causes issues because each column of the resulting tibble has the attributes, including the matrix class, copied from the source. Having matrices as columns in a tibble causes dplyr to throw errors, so a special method is needed to avoid copying the class attribute.

Value

A tibble constructed from the underlying matrix of the basis object. Each column will possess all the attributes from the source object, except that the "class" attribute will be renamed to "basis.class" to avoid interfering with dplyr operations.

Examples

## Not run: 
library(splines)
library(tibble)
x <- seq(0, 1, by=0.001)
spl <- bs(x, df=6)
as_tibble(spl)

## End(Not run)

Autoplot `MSwM::MSM.lm`

Description

Autoplot MSwM::MSM.lm

Usage

## S3 method for class 'MSM.lm'
autoplot(object, prob.colour = "#FF0000", prob.linetype = "dashed", ...)

Arguments

object

MSwM::MSM.lm instance

prob.colour

Line colour for probabilities

prob.linetype

Line type for probabilities

...

other arguments passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
library(MSwM)
d <- data.frame(Data = c(rnorm(50, mean = -10), rnorm(50, mean = 10)),
                exog = cos(seq(-pi/2, pi/2, length.out = 100)))
d.mswm <- MSwM::msmFit(lm(Data ~.-1, data = d), k=2, sw=rep(TRUE, 2),
                       control = list(parallelization = FALSE))
autoplot(d.mswm)

## End(Not run)

Autoplot `raster::raster`

Description

Only plot the first layer of the given raster

Usage

## S3 method for class 'RasterCommon'
autoplot(
  object,
  raster.layer = NULL,
  p = NULL,
  alpha = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = "",
  ylab = "",
  asp = NULL,
  ...
)

Arguments

object

raster::raster instance

raster.layer

name of the layer to plot

p

ggplot2::ggplot instance

alpha

alpha

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Autoplot `maps::map`

Description

Autoplot maps::map

Usage

## S3 method for class 'SpatialCommon'
autoplot(
  object,
  p = NULL,
  group = NULL,
  colour = "black",
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  fill = NULL,
  shape = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = "",
  ylab = "",
  asp = NULL,
  ...
)

Arguments

object

maps::map instance

p

ggplot2::ggplot instance

group

key for grouping geoms

colour

line colour

size

point size

linetype

line type

alpha

alpha

fill

fill colour

shape

point shape

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Autoplot `survival::aareg`

Description

Autoplot survival::aareg

Usage

## S3 method for class 'aareg'
autoplot(
  object,
  maxtime = NULL,
  surv.connect = TRUE,
  facets = TRUE,
  ncol = NULL,
  xlab = "",
  ylab = "",
  ...
)

Arguments

object

survival::aareg instance

maxtime

truncate the input to the model at time "maxtime"

surv.connect

logical frag indicates whether connects survival curve to the origin

facets

Logical value to specify use facets

ncol

Number of facet/subplot columns

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

...

other arguments passed to autoplot.survfit

Value

ggplot

Examples

## Not run: 
if (requireNamespace("survival", quietly = TRUE)) {
  autoplot(aareg(Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1))
}

## End(Not run)

Autoplot `stats::acf`. Note to pass 'plot = FALSE' to original function to suppress standard plot output

Description

Autoplot stats::acf. Note to pass 'plot = FALSE' to original function to suppress standard plot output

Usage

## S3 method for class 'acf'
autoplot(
  object,
  colour = "#000000",
  linetype = "solid",
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "dashed",
  conf.int.fill = NULL,
  conf.int.alpha = 0.3,
  conf.int.value = 0.95,
  conf.int.type = "white",
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = "ACF",
  asp = NULL,
  ...
)

Arguments

object

stats::acf instance

colour

Line colour

linetype

Line type

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

conf.int.value

Coverage probability for confidence interval

conf.int.type

Type of confidence interval, 'white' for white noise or 'ma' MA(k-1) model

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
autoplot(stats::acf(AirPassengers, plot = FALSE))
autoplot(stats::pacf(AirPassengers, plot = FALSE))
autoplot(stats::ccf(AirPassengers, AirPassengers, plot = FALSE))

## End(Not run)

Autoplot spline basis instances

Description

Autoplot spline basis instances

Usage

## S3 method for class 'basis'
autoplot(object, data, n = 256, ...)

Arguments

object

spline basis object

data

x-values at which to evaluate the splines. Optional. By default, an evenly spaced sequence of 256 values covering the range of the splines will be used.

n

If data is not provided, instead use an evenly-spaced sequence of x-values of this length (plus one, since both endpoints are included). If data is provided, this argument is ignored.

...

Ignored.

Value

ggplot

Examples

## Not run: 
library(splines)
x <- seq(0, 1, by=0.001)
spl <- bs(x, df=6)
autoplot(spl)
autoplot(spl, n=5)

## End(Not run)

Autoplot `strucchange::breakpoints`

Description

Autoplot strucchange::breakpoints

Usage

## S3 method for class 'breakpoints'
autoplot(
  object,
  data = NULL,
  cpt.colour = "#FF0000",
  cpt.linetype = "dashed",
  ...
)

Arguments

object

strucchange::breakpoints or strucchange::breakpointsfull instance.

data

Original time series. Mandatory for plotting strucchange::breakpoints instance.

cpt.colour

Line colour for changepoints

cpt.linetype

Line type for changepoints

...

other arguments passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
library(strucchange)
bp.nile <- breakpoints(Nile ~ 1)
autoplot(bp.nile)
autoplot(bp.nile, is.date = TRUE)
autoplot(breakpoints(bp.nile, breaks = 2), data = Nile)

## End(Not run)

Autoplot `changepoint::cpt`

Description

Autoplot changepoint::cpt

Usage

## S3 method for class 'cpt'
autoplot(
  object,
  is.date = NULL,
  cpt.colour = "#FF0000",
  cpt.linetype = "dashed",
  ...
)

Arguments

object

changepoint::cpt instance

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

cpt.colour

Line colour for changepoints

cpt.linetype

Line type for changepoints

...

other arguments passed autoplot.ts

Value

ggplot

Examples

## Not run: 
library(changepoint)
autoplot(cpt.mean(AirPassengers))
autoplot(cpt.meanvar(AirPassengers))

## End(Not run)

Autoplot `glmnet::cv.glmnet`

Description

Autoplot glmnet::cv.glmnet

Usage

## S3 method for class 'cv.glmnet'
autoplot(
  object,
  sign.lambda = 1,
  label.n = 12,
  label = TRUE,
  label.label = "nz",
  label.colour = NULL,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

glmnet::cv.glmnet instance

sign.lambda

Either plot against log(lambda) (default) or its negative if sign.lambda=-1.

label.n

Number of Df labels

label

Logical value whether to display labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

label.repel

Logical flag indicating whether to use ggrepel, enabling this may take some time for plotting

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  autoplot(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3])))
}

Autoplot `stats::density`

Description

Autoplot stats::density

Usage

## S3 method for class 'density'
autoplot(
  object,
  p = NULL,
  colour = "#000000",
  linetype = NULL,
  fill = NULL,
  alpha = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

stats::density instance

p

ggplot2::ggplot instance to plot

colour

Line colour

linetype

Line type

fill

Fill colour

alpha

Alpha

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to PDC/CDF func

Value

ggplot

Examples

autoplot(stats::density(stats::rnorm(1:50)))
autoplot(stats::density(stats::rnorm(1:50)), fill = 'blue')

Autoplot `forecast::forecast`

Description

Autoplot forecast::forecast

Usage

## S3 method for class 'forecast'
autoplot(
  object,
  is.date = NULL,
  ts.connect = TRUE,
  predict.geom = "line",
  predict.colour = "#0000FF",
  predict.size = NULL,
  predict.linetype = NULL,
  predict.alpha = NULL,
  predict.fill = NULL,
  predict.shape = NULL,
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "none",
  conf.int.fill = "#000000",
  conf.int.alpha = 0.3,
  ...
)

Arguments

object

forecast::forecast instance

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12

ts.connect

Logical frag indicates whether connects original time-series and predicted values

predict.geom

geometric string for predicted time-series

predict.colour

line colour for predicted time-series

predict.size

point size for predicted time-series

predict.linetype

line type for predicted time-series

predict.alpha

alpha for predicted time-series

predict.fill

fill colour for predicted time-series

predict.shape

point shape for predicted time-series

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

...

other arguments passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
d.arima <- forecast::auto.arima(AirPassengers)
autoplot(forecast::forecast(d.arima, h = 10))
autoplot(forecast::forecast(d.arima, level = c(85), h = 10))
autoplot(forecast::forecast(d.arima, h = 5), conf.int = FALSE, is.date = FALSE)
autoplot(forecast::forecast(stats::HoltWinters(UKgas), h = 10))
autoplot(forecast::forecast(forecast::ets(UKgas), h = 5))

## End(Not run)

Autoplot `ggmultiplot` instances. It returns the passed instance as it is.

Description

Autoplot ggmultiplot instances. It returns the passed instance as it is.

Usage

## S3 method for class 'ggmultiplot'
autoplot(object, ...)

Arguments

object

ggmultiplot instance

...

Not used.

Value

ggmultiplot

Autoplot `ggplot` instances. It returns the passed instance as it is.

Description

Autoplot ggplot instances. It returns the passed instance as it is.

Usage

## S3 method for class 'ggplot'
autoplot(object, ...)

Arguments

object

ggplot instance

...

Not used.

Value

ggplot

Autoplot `glmnet::glmnet`

Description

Autoplot glmnet::glmnet

Usage

## S3 method for class 'glmnet'
autoplot(
  object,
  xvar = c("norm", "lambda", "dev"),
  label.n = 7,
  label = TRUE,
  label.label = "Df",
  label.colour = NULL,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = "Coefficients",
  asp = NULL,
  ...
)

Arguments

object

glmnet::glmnet instance

xvar

values to be dranw on the X axis. Either "norm" (L1-norm), "lambda" (log-lambda sequence) or "dev" (percent deviance)

label.n

Number of Df labels

label

Logical value whether to display labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
autoplot(glmnet::glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3])))

## End(Not run)

Autoplot cluster instances

Description

Autoplot cluster instances

Usage

## S3 method for class 'kmeans'
autoplot(object, data = NULL, colour = "cluster", ...)

Arguments

object

Clustered instance

data

Original data used for clustering. Mandatory for stats::kmeans.

colour

line colour for points

...

other arguments passed to autoplot::prcomp

Value

ggplot

Examples

## Not run: 
autoplot(stats::kmeans(iris[-5], 3), data = iris)
autoplot(cluster::clara(iris[-5], 3), label = TRUE)
autoplot(cluster::fanny(iris[-5], 3))
autoplot(cluster::fanny(iris[-5], 3), frame = TRUE)
autoplot(cluster::pam(iris[-5], 3), data = iris, colour = 'Species')
autoplot(cluster::pam(iris[-5], 3), data = iris, frame = TRUE, frame.type = 't')

## End(Not run)

Autoplot list

Description

Autoplot list

Usage

## S3 method for class 'list'
autoplot(object, data = NULL, nrow = NULL, ncol = NULL, scales = "free_y", ...)

Arguments

object

list instance

data

original dataset, if needed

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

scales

Scale value passed to ggplot2

...

other arguments passed to methods

Value

ggplot

Autoplot `stats::lm` and `stats::glm`

Description

Autoplot stats::lm and stats::glm

Usage

## S3 method for class 'lm'
autoplot(
  object,
  which = c(1:3, 5),
  data = NULL,
  colour = "#444444",
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  fill = NULL,
  shape = NULL,
  label = TRUE,
  label.label = ".label",
  label.colour = "#000000",
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  label.n = 3,
  smooth.colour = "#0000FF",
  smooth.linetype = "solid",
  ad.colour = "#888888",
  ad.linetype = "dashed",
  ad.size = 0.2,
  nrow = NULL,
  ncol = NULL,
  ...
)

Arguments

object

stats::lm instance

which

If a subset of the plots is required, specify a subset of the numbers 1:6.

data

original dataset, if needed

colour

line colour

size

point size

linetype

line type

alpha

alpha

fill

fill colour

shape

point shape

label

Logical value whether to display labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

label.repel

Logical flag indicating whether to use ggrepel, enabling this may take some time for plotting

label.n

Number of points to be laeled in each plot, starting with the most extreme

smooth.colour

Line colour for smoother lines

smooth.linetype

Line type for smoother lines

ad.colour

Line colour for additional lines

ad.linetype

Line type for additional lines

ad.size

Fill colour for additional lines

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
autoplot(lm(Petal.Width ~ Petal.Length, data = iris))
autoplot(glm(Petal.Width ~ Petal.Length, data = iris), which = 1:6)
autoplot(lm(Petal.Width~Petal.Length, data = iris), data = iris, colour = 'Species')

## End(Not run)

Autoplot `maps::map`

Description

Autoplot maps::map

Usage

## S3 method for class 'map'
autoplot(
  object,
  p = NULL,
  geom = "path",
  group = "group",
  colour = "black",
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  fill = NULL,
  shape = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = "",
  ylab = "",
  asp = NULL,
  ...
)

Arguments

object

maps::map instance

p

ggplot2::ggplot instance

geom

geometric string for map. 'path', 'point' or 'polygon'

group

key for grouping geoms

colour

line colour

size

point size

linetype

line type

alpha

alpha

fill

fill colour

shape

point shape

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Plot `base::matrix`

Description

Plot base::matrix

Usage

## S3 method for class 'matrix'
autoplot(
  object,
  original = NULL,
  geom = "tile",
  colour = NULL,
  size = NULL,
  alpha = NULL,
  fill = "#0000FF",
  shape = NULL,
  label = FALSE,
  label.label = "rownames",
  label.colour = colour,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  scale = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

base::matrix instance

original

Combined to data by column if provided. Intended to be used for stat functions which returns not containing original data.

geom

Geometric string for plotting. 'tile' or 'point'.

colour

colour for points ('point' only)

size

point size

alpha

alpha

fill

fill colour. Ignored if scale keyword is passed. ('tile' Only)

shape

point shape

label

Logical value whether to display labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

label.repel

Logical flag indicating whether to use ggrepel, enabling this may take some time for plotting

scale

(Deprecated) ggplot2::scale instance to plot. ('tile' Only)

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

autoplot(matrix(rnorm(20), nc = 5))
autoplot(matrix(rnorm(20), nc = 5), fill = 'red')
autoplot(matrix(rnorm(20), nc = 2), geom = 'point')

Autoplot PCA-likes

Description

Autoplot PCA-likes

Usage

## S3 method for class 'pca_common'
autoplot(
  object,
  data = NULL,
  scale = 1,
  x = 1,
  y = 2,
  variance_percentage = TRUE,
  ...
)

Arguments

object

PCA-like instance

data

Joined to fitting result if provided.

scale

scaling parameter, disabled by 0

x

principal component number used in x axis

y

principal component number used in y axis

variance_percentage

show the variance explained by the principal component?

...

other arguments passed to [ggbiplot()]

Examples

autoplot(stats::prcomp(iris[-5]))
autoplot(stats::prcomp(iris[-5]), data = iris)
autoplot(stats::prcomp(iris[-5]), data = iris, colour = 'Species')
autoplot(stats::prcomp(iris[-5]), label = TRUE, loadings = TRUE, loadings.label = TRUE)
autoplot(stats::prcomp(iris[-5]), frame = TRUE)
autoplot(stats::prcomp(iris[-5]), data = iris, frame = TRUE,
         frame.colour = 'Species')
autoplot(stats::prcomp(iris[-5]), data = iris, frame = TRUE,
         frame.type = 't', frame.colour = 'Species')

autoplot(stats::princomp(iris[-5]))
autoplot(stats::princomp(iris[-5]), data = iris)
autoplot(stats::princomp(iris[-5]), data = iris, colour = 'Species')
autoplot(stats::princomp(iris[-5]), label = TRUE, loadings = TRUE, loadings.label = TRUE)

#Plot PC 2 and 3
autoplot(stats::princomp(iris[-5]), x = 2, y = 3)

#Don't show the variance explained
autoplot(stats::princomp(iris[-5]), variance_percentage = FALSE)

d.factanal <- stats::factanal(state.x77, factors = 3, scores = 'regression')
autoplot(d.factanal)
autoplot(d.factanal, data = state.x77, colour = 'Income')
autoplot(d.factanal, label = TRUE, loadings = TRUE, loadings.label = TRUE)

Autoplot `ROCR::performance`

Description

Autoplot ROCR::performance

Usage

## S3 method for class 'performance'
autoplot(object, p = NULL, bins = 5, ...)

Arguments

object

ROCR::performance instance

p

ggplot2::ggplot instances

bins

If object represents a measure whose value is just a scalar (e.g. performance(predObj, 'auc')), a histogram will be plotted of this scalar's values for different runs. bins is the number of bins for this histogram.

...

other arguments passed to methods

Value

ggplot

Autoplot silhouette instances

Description

Autoplot silhouette instances

Usage

## S3 method for class 'silhouette'
autoplot(
  object,
  colour = "red",
  linetype = "dashed",
  size = 0.5,
  bar.width = 1,
  ...
)

Arguments

object

Silhouette instance

colour

reference line color

linetype

reference line type

size

reference line size

bar.width

bar width

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
model = cluster::pam(iris[-5], 3L)
sil = cluster::silhouette(model)
autoplot(sil)

autoplot(cluster::silhouette(cluster::clara(iris[-5], 3)))
autoplot(cluster::silhouette(cluster::fanny(iris[-5], 3)))

model = stats::kmeans(iris[-5], 3)
sil = cluster::silhouette(model$cluster, stats::dist(iris[-5]))
autoplot(sil)

## End(Not run)

Autoplot `stats::spec`

Description

Autoplot stats::spec

Usage

## S3 method for class 'spec'
autoplot(
  object,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "y",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

stats::spec instance

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
autoplot(stats::spec.ar(AirPassengers))
autoplot(stats::spec.pgram(AirPassengers))

## End(Not run)

Plot `stats::stepfun`

Description

Plot stats::stepfun

Usage

## S3 method for class 'stepfun'
autoplot(
  object,
  colour = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  shape = 1,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

stats::stepfun instance

colour

colour

size

point size

linetype

line type

alpha

alpha

shape

point shape

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

autoplot(stepfun(c(1, 2, 3), c(4, 5, 6, 7)))
autoplot(stepfun(c(1), c(4, 5)), shape = NULL)
autoplot(stepfun(c(1, 3, 4, 8), c(4, 5, 2, 3, 5)), linetype = 'dashed')
autoplot(stepfun(c(1, 2, 3, 4, 5, 6, 7, 8, 10), c(4, 5, 6, 7, 8, 9, 10, 11, 12, 9)), colour = 'red')

Autoplot `survival::survfit`

Description

Autoplot survival::survfit

Usage

## S3 method for class 'survfit'
autoplot(
  object,
  fun = NULL,
  surv.geom = "step",
  surv.colour = NULL,
  surv.size = NULL,
  surv.linetype = NULL,
  surv.alpha = NULL,
  surv.fill = NULL,
  surv.shape = NULL,
  surv.connect = FALSE,
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "none",
  conf.int.fill = "#000000",
  conf.int.alpha = 0.3,
  censor = TRUE,
  censor.colour = NULL,
  censor.size = 3,
  censor.alpha = NULL,
  censor.shape = "+",
  facets = FALSE,
  nrow = NULL,
  ncol = 1,
  grid = FALSE,
  strip_swap = FALSE,
  scales = "free_y",
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

object

survival::survfit instance

fun

an arbitrary function defining a transformation of the survival curve

surv.geom

geometric string for survival curve. 'step', 'line' or 'point'

surv.colour

line colour for survival curve

surv.size

point size for survival curve

surv.linetype

line type for survival curve

surv.alpha

alpha for survival curve

surv.fill

fill colour survival curve

surv.shape

point shape survival curve

surv.connect

logical frag indicates whether connects survival curve to the origin

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

censor

Logical flag indicating whether to plot censors

censor.colour

colour for censors

censor.size

size for censors

censor.alpha

alpha for censors

censor.shape

shape for censors

facets

Logical value to specify use facets

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

grid

Logical flag indicating whether to draw grid

strip_swap

swap facet or grid strips

scales

Scale value passed to ggplot2

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
if (requireNamespace("survival", quietly = TRUE)) {
  autoplot(survfit(Surv(time, status) ~ sex, data = lung))
  autoplot(survfit(Surv(time, status) ~ sex, data = lung), facets = TRUE)
  autoplot(survfit(Surv(time, status) ~ 1, data = lung))
  autoplot(survfit(Surv(time, status) ~ sex, data=lung), conf.int = FALSE, censor = FALSE)
  autoplot(survfit(coxph(Surv(time, status) ~ sex, data = lung)))
}

## End(Not run)

Autoplot time-series-like

Description

Autoplot time-series-like

Usage

## S3 method for class 'ts'
autoplot(
  object,
  columns = NULL,
  group = NULL,
  is.date = NULL,
  index.name = "Index",
  p = NULL,
  ts.scale = FALSE,
  stacked = FALSE,
  facets = TRUE,
  nrow = NULL,
  ncol = 1,
  scales = "free_y",
  ts.geom = "line",
  ts.colour = NULL,
  ts.size = NULL,
  ts.linetype = NULL,
  ts.alpha = NULL,
  ts.fill = NULL,
  ts.shape = NULL,
  geom = ts.geom,
  colour = ts.colour,
  size = ts.size,
  linetype = ts.linetype,
  alpha = ts.alpha,
  fill = ts.fill,
  shape = ts.shape,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = "",
  ylab = "",
  asp = NULL,
  ...
)

Arguments

object

time-series-like instance

columns

Character vector specifies target column name(s)

group

Character vector specifies grouping

is.date

Logical frag indicates whether the stats::ts is date or not If not provided, regard the input as date when the frequency is 4 or 12

index.name

Specify column name for time series index when passing data.frame via data.

p

ggplot2::ggplot instance

ts.scale

Logical flag indicating whether to perform scaling each timeseries

stacked

Logical flag indicating whether to stack multivariate timeseries

facets

Logical value to specify use facets

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

scales

Scale value passed to ggplot2

ts.geom

geometric string for time-series. 'line', 'bar', 'ribbon', or 'point'

ts.colour

line colour for time-series

ts.size

point size for time-series

ts.linetype

line type for time-series

ts.alpha

alpha for time-series

ts.fill

fill colour for time-series

ts.shape

point shape for time-series

geom

same as ts.geom

colour

same as ts.colour

size

same as ts.size

linetype

same as ts.linetype

alpha

same as ts.alpha

fill

same as ts.fill

shape

same as ts.shape

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Examples

## Not run: 
data(Canada, package = 'vars')
autoplot(AirPassengers)
autoplot(UKgas, ts.geom = 'bar')
autoplot(Canada)
autoplot(Canada, facets = FALSE)

library(zoo)
autoplot(xts::as.xts(AirPassengers))
autoplot(timeSeries::as.timeSeries(AirPassengers))
its <- tseries::irts(cumsum(rexp(10, rate = 0.1)), matrix(rnorm(20), ncol=2))
autoplot(its)

autoplot(stats::stl(UKgas, s.window = 'periodic'))
autoplot(stats::decompose(UKgas))

## End(Not run)

Autoplot time series models (like AR, ARIMA)

Description

Autoplot time series models (like AR, ARIMA)

Usage

## S3 method for class 'tsmodel'
autoplot(
  object,
  data = NULL,
  predict = NULL,
  is.date = NULL,
  ts.connect = TRUE,
  fitted.geom = "line",
  fitted.colour = "#FF0000",
  fitted.size = NULL,
  fitted.linetype = NULL,
  fitted.alpha = NULL,
  fitted.fill = NULL,
  fitted.shape = NULL,
  predict.geom = "line",
  predict.colour = "#0000FF",
  predict.size = NULL,
  predict.linetype = NULL,
  predict.alpha = NULL,
  predict.fill = NULL,
  predict.shape = NULL,
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "none",
  conf.int.fill = "#000000",
  conf.int.alpha = 0.3,
  ...
)

Arguments

object

Time series model instance

data

original dataset, needed for stats::ar, stats::Arima

predict

Predicted stats::ts If not provided, try to retrieve from current environment using variable name.

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12

ts.connect

Logical frag indicates whether connects original time-series and predicted values

fitted.geom

geometric string for fitted time-series

fitted.colour

line colour for fitted time-series

fitted.size

point size for fitted time-series

fitted.linetype

line type for fitted time-series

fitted.alpha

alpha for fitted time-series

fitted.fill

fill colour for fitted time-series

fitted.shape

point shape for fitted time-series

predict.geom

geometric string for predicted time-series

predict.colour

line colour for predicted time-series

predict.size

point size for predicted time-series

predict.linetype

line type for predicted time-series

predict.alpha

alpha for predicted time-series

predict.fill

fill colour for predicted time-series

predict.shape

point shape for predicted time-series

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

...

Keywords passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
d.ar <- stats::ar(AirPassengers)
autoplot(d.ar)
autoplot(d.ar, predict = predict(d.ar, n.ahead = 5))
autoplot(stats::arima(UKgas), data = UKgas)
autoplot(forecast::arfima(AirPassengers))
autoplot(forecast::nnetar(UKgas), is.date = FALSE)

d.holt <- stats::HoltWinters(USAccDeaths)
autoplot(d.holt)
autoplot(d.holt, predict = predict(d.holt, n.ahead = 5))
autoplot(d.holt, predict = predict(d.holt, n.ahead = 5, prediction.interval = TRUE))

## End(Not run)

Autoplot `vars::varprd`

Description

Autoplot vars::varprd

Usage

## S3 method for class 'varprd'
autoplot(
  object,
  is.date = NULL,
  ts.connect = TRUE,
  scales = "free_y",
  predict.geom = "line",
  predict.colour = "#0000FF",
  predict.size = NULL,
  predict.linetype = NULL,
  predict.alpha = NULL,
  predict.fill = NULL,
  predict.shape = NULL,
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "none",
  conf.int.fill = "#000000",
  conf.int.alpha = 0.3,
  ...
)

Arguments

object

vars::varpred instance

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

ts.connect

Logical frag indicates whether connects original time-series and predicted values

scales

Scale value passed to ggplot2

predict.geom

geometric string for predicted time-series

predict.colour

line colour for predicted time-series

predict.size

point size for predicted time-series

predict.linetype

line type for predicted time-series

predict.alpha

alpha for predicted time-series

predict.fill

fill colour for predicted time-series

predict.shape

point shape for predicted time-series

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

...

other arguments passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
data(Canada, package = 'vars')
d.var <- vars::VAR(Canada, p = 3, type = 'const')
autoplot(stats::predict(d.var, n.ahead = 50), is.date = TRUE)
autoplot(stats::predict(d.var, n.ahead = 50), conf.int = FALSE)

## End(Not run)

Wrapper for cbind

Description

Wrapper for cbind

Usage

cbind_wraps(df1, df2)

Arguments

df1

1st data

df2

2nd data

Value

list

Examples

ggfortify:::cbind_wraps(iris[1:2], iris[3:5])

Check data names are equal with expected

Description

Check data names are equal with expected

Usage

check_names(data, expected)

Arguments

data

list instance to be checked

expected

expected character vector

Value

logical

Calculate confidence interval for `stats::acf`

Description

Calculate confidence interval for stats::acf

Usage

## S3 method for class 'acf'
confint(x, ci = 0.95, ci.type = "white")

Arguments

x

stats::acf instance

ci

Float value for confidence interval

ci.type

"white" or "ma"

Value

vector

Examples

## Not run: 
air.acf <- acf(AirPassengers, plot = FALSE)
ggfortify:::confint.acf(air.acf)
ggfortify:::confint.acf(air.acf, ci.type = 'ma')

## End(Not run)

Show deprecate warning

Description

Show deprecate warning

Usage

deprecate.warning(old.kw, new.kw)

Arguments

old.kw

Keyword being deprecated

new.kw

Keyword being replaced

Examples

ggfortify:::deprecate.warning('old', 'new')

Calculate fitted values for `stats::ar`

Description

Calculate fitted values for stats::ar

Usage

## S3 method for class 'ar'
fitted(object, ...)

Arguments

object

stats::ar instance

...

other keywords

Value

ts An time series of the one-step forecasts

Examples

## Not run: 
fitted(ar(WWWusage))

## End(Not run)

Flatten dataframe contains matrix

Description

tains list or matrix as column

Usage

flatten(df)

Arguments

df

data.frame to be flatten

Convert `MSwM::MSM.lm` to `data.frame`

Description

Convert MSwM::MSM.lm to data.frame

Usage

## S3 method for class 'MSM.lm'
fortify(model, data = NULL, melt = FALSE, ...)

Arguments

model

MSwM::MSM.lm instance

data

original dataset, if needed

melt

Logical flag indicating whether to melt each models

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
library(MSwM)
d <- data.frame(Data = c(rnorm(50, mean = -10), rnorm(50, mean = 10)),
                exog = cos(seq(-pi/2, pi/2, length.out = 100)))
d.mswm <- MSwM::msmFit(lm(Data ~.-1, data = d), k=2, sw=rep(TRUE, 2),
                       control = list(parallelization = FALSE))
fortify(d.mswm)

## End(Not run)

Convert `raster` to `data.frame`

Description

Convert raster to data.frame

Usage

## S3 method for class 'RasterCommon'
fortify(model, data = NULL, maxpixels = 1e+05, rename = TRUE, ...)

Arguments

model

raster instances

data

original dataset, if needed

maxpixels

number of pixels for resampling

rename

logical flag indicating whether to rename coordinates to long and lat

...

other arguments passed to methods

Value

data.frame

Convert `sp` instances to `data.frame`.

Description

Convert sp instances to data.frame.

Usage

## S3 method for class 'SpatialCommon'
fortify(model, data = NULL, rename = TRUE, ...)

Arguments

model

sp instances

data

original dataset, if needed

rename

logical flag indicating whether to rename coordinates to long and lat

...

other arguments passed to methods

Value

data.frame

Convert `survival::aareg` to `data.frame`

Description

Convert survival::aareg to data.frame

Usage

## S3 method for class 'aareg'
fortify(
  model,
  data = NULL,
  maxtime = NULL,
  surv.connect = TRUE,
  melt = FALSE,
  ...
)

Arguments

model

survival::aareg instance

data

original dataset, if needed

maxtime

truncate the input to the model at time "maxtime"

surv.connect

logical frag indicates whether connects survival curve to the origin

melt

Logical flag indicating whether to melt each timeseries as variable

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
if (requireNamespace("survival", quietly = TRUE)) {
  fortify(aareg(Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1))
  fortify(aareg(Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1), melt = TRUE)  
}

## End(Not run)

Convert `stats::acf` to `data.frame`

Description

Convert stats::acf to data.frame

Usage

## S3 method for class 'acf'
fortify(
  model,
  data = NULL,
  conf.int = TRUE,
  conf.int.value = 0.95,
  conf.int.type = "white",
  ...
)

Arguments

model

stats::acf instance

data

original dataset, if needed

conf.int

Logical flag indicating whether to attach confidence intervals

conf.int.value

Coverage probability for confidence interval

conf.int.type

Type of confidence interval, 'white' for white noise or 'ma' MA(k-1) model

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(stats::acf(AirPassengers))
fortify(stats::pacf(AirPassengers))
fortify(stats::ccf(AirPassengers, AirPassengers))

fortify(stats::acf(AirPassengers), conf.int = TRUE)

## End(Not run)

Convert spline basis instances to `data.frame`

Description

Convert spline basis instances to data.frame

Usage

## S3 method for class 'basis'
fortify(model, data, n = 256, ...)

Arguments

model

spline basis object

data

x-values at which to evaluate the splines. Optional. By default, an evenly spaced sequence of 256 values covering the range of the splines will be used.

n

If data is not provided, instead use an evenly-spaced sequence of x-values of this length (plus one, since both endpoints are included). If data is provided, this argument is ignored.

...

other arguments passed to methods

Value

data.frame with 3 columns: Spline (character), x (numeric), and y (numeric); giving the interpolated x and y values for each of the splines in the basis.

Examples

## Not run: 
library(splines)
x <- seq(0, 1, by=0.001)
spl <- bs(x, df=6)
fortify(spl)

## End(Not run)

Convert `changepoint::cpt` and `strucchange::breakpoints` to `data.frame`

Description

Convert changepoint::cpt and strucchange::breakpoints to data.frame

Usage

## S3 method for class 'cpt'
fortify(model, data = NULL, is.date = NULL, ...)

Arguments

model

chantepoint::cpt or strucchange::breakpoints instance

data

original dataset, if needed

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
library(changepoint)
fortify(cpt.mean(AirPassengers))
fortify(cpt.var(AirPassengers))
fortify(cpt.meanvar(AirPassengers))

library(strucchange)
bp.nile <- breakpoints(Nile ~ 1)
fortify(bp.nile)
fortify(breakpoints(bp.nile, breaks = 2))
fortify(breakpoints(bp.nile, breaks = 2), data = Nile)

## End(Not run)

Convert `glmnet::cv.glmnet` to `data.frame`

Description

Convert glmnet::cv.glmnet to data.frame

Usage

## S3 method for class 'cv.glmnet'
fortify(model, data = NULL, ...)

Arguments

model

glmnet::cv.glmnet instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  fortify(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3])))
}

Convert `stats::density` to `data.frame`

Description

Convert stats::density to data.frame

Usage

## S3 method for class 'density'
fortify(model, data = NULL, ...)

Arguments

model

stats::density instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

fortify(stats::density(stats::rnorm(1:50)))

Convert `stats::dist` to `data.frame`

Description

Convert stats::dist to data.frame

Usage

## S3 method for class 'dist'
fortify(model, data = NULL, ...)

Arguments

model

stats::dist instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

fortify(eurodist)

Convert `forecast::bats` and `forecast::ets` to `data.frame`

Description

Convert forecast::bats and forecast::ets to data.frame

Usage

## S3 method for class 'ets'
fortify(model, data = NULL, ...)

Arguments

model

forecast::bats or forecast::ets instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(forecast::bats(UKgas))
fortify(forecast::ets(UKgas))

## End(Not run)

Convert `stats::factanal` to `data.frame`

Description

Convert stats::factanal to data.frame

Usage

## S3 method for class 'factanal'
fortify(model, data = NULL, ...)

Arguments

model

stats::factanal instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
d.factanal <- stats::factanal(state.x77, factors = 3, scores = 'regression')
fortify(d.factanal)
fortify(d.factanal, data = state.x77)

## End(Not run)

Convert `forecast::forecast` to `data.frame`

Description

Convert forecast::forecast to data.frame

Usage

## S3 method for class 'forecast'
fortify(model, data = NULL, is.date = NULL, ts.connect = FALSE, ...)

Arguments

model

forecast::forecast instance

data

original dataset, if needed

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

ts.connect

Logical frag indicates whether connects original time-series and predicted values

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
d.arima <- forecast::auto.arima(AirPassengers)
d.forecast <- forecast::forecast(d.arima, level = c(95), h = 50)
fortify(d.forecast)
fortify(d.forecast, ts.connect = TRUE)

## End(Not run)

Convert `glmnet::glmnet` to `data.frame`

Description

Convert glmnet::glmnet to data.frame

Usage

## S3 method for class 'glmnet'
fortify(model, data = NULL, ...)

Arguments

model

glmnet::glmnet instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(glmnet::glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3])))

## End(Not run)

Convert cluster instances to `data.frame`

Description

Convert cluster instances to data.frame

Usage

## S3 method for class 'kmeans'
fortify(model, data = NULL, ...)

Arguments

model

Clustered instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(stats::kmeans(iris[-5], 3))
fortify(stats::kmeans(iris[-5], 3), data = iris)
fortify(cluster::clara(iris[-5], 3))
fortify(cluster::fanny(iris[-5], 3))
fortify(cluster::pam(iris[-5], 3), data = iris)

## End(Not run)

Convert `lfda::lfda` or `lfda::klfda` or `lfda::self` to `data.frame`

Description

Convert lfda::lfda or lfda::klfda or lfda::self to data.frame

Usage

## S3 method for class 'lfda'
fortify(model, data = NULL, ...)

Arguments

model

lfda::lfda or lfda::klfda or lfda::self instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
model <- lfda::lfda(iris[, -5], iris[, 5], 3, metric = "plain")
fortify(model)

## End(Not run)

Convert list to data.frame

Description

Convert list to data.frame

Usage

## S3 method for class 'list'
fortify(model, data = NULL, ...)

Arguments

model

list instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Convert `base::matrix` to `data.frame`

Description

Different from as.data.frame

Usage

## S3 method for class 'matrix'
fortify(model, data = NULL, compat = FALSE, ...)

Arguments

model

base::matrix instance

data

original dataset, if needed

compat

Logical frag to specify the behaviour when converting matrix which has no column name. If FALSE, result has character columns like c('1', '2', ...). If TRUE, result has character columns like c('V1', 'V2', ...).

...

other arguments passed to methods

Value

data.frame

Examples

fortify(matrix(1:6, nrow=2, ncol=3))

Convert `ROCR::performance` objects to `data.frame`

Description

Convert ROCR::performance objects to data.frame

Usage

## S3 method for class 'performance'
fortify(model, data = NULL, ...)

Arguments

model

performance instances

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Convert `stats::prcomp`, `stats::princomp` to `data.frame`

Description

Convert stats::prcomp, stats::princomp to data.frame

Usage

## S3 method for class 'prcomp'
fortify(model, data = NULL, ...)

Arguments

model

stats::prcomp or stats::princomp instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(stats::prcomp(iris[-5]))
fortify(stats::prcomp(iris[-5]), data = iris)

fortify(stats::princomp(iris[-5]))
fortify(stats::princomp(iris[-5]), data = iris)

## End(Not run)

Convert `cluster::silhouette` to `data.frame`

Description

Convert cluster::silhouette to data.frame

Usage

## S3 method for class 'silhouette'
fortify(model, data = NULL, ...)

Arguments

model

Silhouette instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(cluster::silhouette(cluster::pam(iris[-5], 3)))
fortify(cluster::silhouette(cluster::clara(iris[-5], 3)))
fortify(cluster::silhouette(cluster::fanny(iris[-5], 3)))

mod = stats::kmeans(iris[-5], 3)
fortify(cluster::silhouette(mod$cluster, stats::dist(iris[-5])))

## End(Not run)

Convert `stats::spec` to `data.frame`

Description

Convert stats::spec to data.frame

Usage

## S3 method for class 'spec'
fortify(model, data = NULL, ...)

Arguments

model

stats::spec instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(spectrum(AirPassengers))
fortify(stats::spec.ar(AirPassengers))
fortify(stats::spec.pgram(AirPassengers))

## End(Not run)

Convert `stats::stepfun` to `data.frame`

Description

Convert stats::stepfun to data.frame

Usage

## S3 method for class 'stepfun'
fortify(model, data, ...)

Arguments

model

stats::stepfun instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

fortify(stepfun(c(1, 2, 3), c(4, 5, 6, 7)))
fortify(stepfun(c(1), c(4, 5)))
fortify(stepfun(c(1, 3, 4, 8), c(4, 5, 2, 3, 5)))
fortify(stepfun(c(1, 2, 3, 4, 5, 6, 7, 8, 10), c(4, 5, 6, 7, 8, 9, 10, 11, 12, 9)))

Convert `survival::survfit` to `data.frame`

Description

Convert survival::survfit to data.frame

Usage

## S3 method for class 'survfit'
fortify(model, data = NULL, surv.connect = FALSE, fun = NULL, ...)

Arguments

model

survival::survfit instance

data

original dataset, if needed

surv.connect

logical frag indicates whether connects survival curve to the origin

fun

an arbitrary function defining a transformation of the survival curve

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
if (requireNamespace("survival", quietly = TRUE)) {
  fortify(survfit(Surv(time, status) ~ sex, data = lung))
  fortify(survfit(Surv(time, status) ~ 1, data = lung))
  fortify(survfit(coxph(Surv(time, status) ~ sex, data = lung)))
  fortify(survfit(coxph(Surv(time, status) ~ 1, data = lung)))
}

## End(Not run)

Convert `base::table` to `data.frame`

Description

Convert base::table to data.frame

Usage

## S3 method for class 'table'
fortify(model, data, ...)

Arguments

model

base::table instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Examples

fortify(Titanic)

Convert time-series-like to data.frame

Description

Convert time-series-like to data.frame

Usage

## S3 method for class 'ts'
fortify(
  model,
  data = NULL,
  columns = NULL,
  is.date = NULL,
  index.name = "Index",
  data.name = "Data",
  scale = FALSE,
  melt = FALSE,
  ...
)

Arguments

model

time-series-like instance

data

original dataset, if needed

columns

character vector specifies target column name(s)

is.date

logical frag indicates whether the stats::ts is date or not If not provided, regard the input as date when the frequency is 4 or 12

index.name

specify column name for time series index

data.name

specify column name for univariate time series data. Ignored in multivariate time series.

scale

logical flag indicating whether to perform scaling each timeseries

melt

logical flag indicating whether to melt each timeseries as variable

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(AirPassengers)
fortify(timeSeries::as.timeSeries(AirPassengers))
fortify(tseries::irts(cumsum(rexp(10, rate = 0.1)), matrix(rnorm(20), ncol=2)))
fortify(stats::stl(UKgas, s.window = 'periodic'))
fortify(stats::decompose(UKgas))

## End(Not run)

Convert time series models (like AR, ARIMA) to `data.frame`

Description

Convert time series models (like AR, ARIMA) to data.frame

Usage

## S3 method for class 'tsmodel'
fortify(
  model,
  data = NULL,
  predict = NULL,
  is.date = NULL,
  ts.connect = TRUE,
  ...
)

Arguments

model

Time series model instance

data

original dataset, needed for stats::ar, stats::Arima

predict

Predicted stats::ts If not provided, try to retrieve from current environment using variable name.

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

ts.connect

Logical frag indicates whether connects original time-series and predicted values

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
fortify(stats::ar(AirPassengers))
fortify(stats::arima(UKgas))
fortify(stats::arima(UKgas), data = UKgas, is.date = TRUE)
fortify(forecast::auto.arima(austres))
fortify(forecast::arfima(AirPassengers))
fortify(forecast::nnetar(UKgas))
fortify(stats::HoltWinters(USAccDeaths))

data(LPP2005REC, package = 'timeSeries')
x = timeSeries::as.timeSeries(LPP2005REC)
d.Garch = fGarch::garchFit(LPP40 ~ garch(1, 1), data = 100 * x, trace = FALSE)
fortify(d.Garch)

## End(Not run)

Convert `vars::varprd` to `data.frame`

Description

Convert vars::varprd to data.frame

Usage

## S3 method for class 'varprd'
fortify(
  model,
  data = NULL,
  is.date = NULL,
  ts.connect = FALSE,
  melt = FALSE,
  ...
)

Arguments

model

vars::varprd instance

data

original dataset, if needed

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

ts.connect

Logical frag indicates whether connects original time-series and predicted values

melt

Logical flag indicating whether to melt each timeseries as variable

...

other arguments passed to methods

Value

data.frame

Examples

## Not run: 
data(Canada, package = 'vars')
d.var <- vars::VAR(Canada, p = 3, type = 'const')
fortify(stats::predict(d.var, n.ahead = 50))

## End(Not run)

Convert `base::table` to `data.frame`

Description

Convert base::table to data.frame

Usage

fortify_base(model, data, ...)

Arguments

model

base::table instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Convert `maps::map` to `data.frame`.

Description

Convert maps::map to data.frame.

Usage

fortify_map(model, data = NULL, ...)

Arguments

model

maps::map instance

data

original dataset, if needed

...

other arguments passed to methods

Value

data.frame

Connect observations by stairs.

Description

Connect observations by stairs.

Usage

geom_confint(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  ...
)

Arguments

mapping

the aesthetic mapping

data

a layer specific dataset

stat

the statistical transformation to use on the data for this layer

position

the position adjustment to use for overlapping points on this layer

na.rm

logical frag whether silently remove missing values

...

other arguments passed to methods

Factory function to control `ggplot2::geom_xxx` functions

Description

Factory function to control ggplot2::geom_xxx functions

Usage

geom_factory(geomfunc, data = NULL, position = NULL, ...)

Arguments

geomfunc

ggplot2::geom_xxx function

data

plotting data

position

A position function or character

...

other arguments passed to methods

Value

proto

Convert `ts` index to `Date` `vector`

Description

Convert ts index to Date vector

Usage

get.dtindex(data, is.tsp = FALSE, is.date = NULL)

Arguments

data

ts instance

is.tsp

Logical frag whether data is tsp itself or not

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

Value

vector

Examples

## Not run: 
ggfortify:::get.dtindex(AirPassengers)
ggfortify:::get.dtindex(UKgas)
ggfortify:::get.dtindex(Nile, is.date = FALSE)
ggfortify:::get.dtindex(Nile, is.date = TRUE)

## End(Not run)

Get `Date` `vector` continue to `ts` index

Description

Get Date vector continue to ts index

Usage

get.dtindex.continuous(data, length, is.tsp = FALSE, is.date = NULL)

Arguments

data

ts instance

length

A number to continue

is.tsp

Logical frag whether data is tsp itself or not

is.date

Logical frag indicates whether the stats::ts is date or not. If not provided, regard the input as date when the frequency is 4 or 12.

Value

vector

Examples

## Not run: 
ggfortify:::get.dtindex.continuous(AirPassengers, length = 10)
ggfortify:::get.dtindex.continuous(UKgas, length = 10)

## End(Not run)

Calcurate layout matrix for `ggmultiplot`

Description

Calcurate layout matrix for ggmultiplot

Usage

get.layout(nplots, ncol, nrow)

Arguments

nplots

Number of plots

ncol

Number of grid columns

nrow

Number of grid rows

Value

matrix

Examples

ggfortify:::get.layout(3, 2, 2)

Factory function to control `ggplot2::geom_xxx` functions

Description

Factory function to control ggplot2::geom_xxx functions

Usage

get_geom_function(geom, allowed = c("line", "bar", "point"))

Arguments

geom

string representation of ggplot2::geom_xxx function

allowed

character vector contains allowed values

Value

function

Examples

ggfortify:::get_geom_function('point')
ggfortify:::get_geom_function('line', allowed = c('line'))

Draw `biplot` using `ggplot2`.

Description

Draw biplot using ggplot2.

Usage

ggbiplot(
  plot.data,
  loadings.data = NULL,
  colour = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  fill = NULL,
  shape = NULL,
  label = FALSE,
  label.label = "rownames",
  label.colour = colour,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  label.position = "identity",
  loadings = FALSE,
  loadings.arrow = grid::arrow(length = grid::unit(8, "points")),
  loadings.colour = "#FF0000",
  loadings.linewidth = 0.5,
  loadings.label = FALSE,
  loadings.label.label = "rownames",
  loadings.label.colour = "#FF0000",
  loadings.label.alpha = NULL,
  loadings.label.size = NULL,
  loadings.label.angle = NULL,
  loadings.label.family = NULL,
  loadings.label.fontface = NULL,
  loadings.label.lineheight = NULL,
  loadings.label.hjust = NULL,
  loadings.label.vjust = NULL,
  loadings.label.repel = FALSE,
  label.show.legend = NA,
  frame = FALSE,
  frame.type = NULL,
  frame.colour = colour,
  frame.level = 0.95,
  frame.alpha = 0.2,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

plot.data

data.frame

loadings.data

data.frame

colour

colour

size

size

linetype

line type

alpha

alpha

fill

fill

shape

shape

label

Logical value whether to display data labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

label.repel

Logical flag indicating whether to use ggrepel, enabling this may take some time for plotting

label.position

Character or a position function

loadings

Logical value whether to display loadings arrows

loadings.arrow

An arrow definition

loadings.colour

Point colour for data

loadings.linewidth

Segment linewidth for loadings

loadings.label

Logical value whether to display loadings labels

loadings.label.label

Column name used for loadings text labels

loadings.label.colour

Colour for loadings text labels

loadings.label.alpha

Alpha for loadings text labels

loadings.label.size

Size for loadings text labels

loadings.label.angle

Angle for loadings text labels

loadings.label.family

Font family for loadings text labels

loadings.label.fontface

Fontface for loadings text labels

loadings.label.lineheight

Lineheight for loadings text labels

loadings.label.hjust

Horizontal adjustment for loadings text labels

loadings.label.vjust

Vertical adjustment for loadings text labels

loadings.label.repel

Logical flag indicating whether to use ggrepel automatically

label.show.legend

Logical value indicating whether to show the legend of text labels

frame

Logical value whether to draw outliner convex / ellipse

frame.type

Character specifying frame type. 'convex' or types supporeted by ggplot2::stat_ellipse can be used.

frame.colour

Colour for frame

frame.level

Passed for ggplot2::stat_ellipse 's level. Ignored in 'convex'.

frame.alpha

Alpha for frame

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

...

other arguments passed to methods

Value

ggplot

Plots a cumulative periodogram

Description

Plots a cumulative periodogram

Usage

ggcpgram(
  ts,
  taper = 0.1,
  colour = "#000000",
  linetype = "solid",
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "dashed",
  conf.int.fill = NULL,
  conf.int.alpha = 0.3
)

Arguments

ts

stats::ts instance

taper

Proportion tapered in forming the periodogram

colour

Line colour

linetype

Line type

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

Value

ggplot

Examples

## Not run: 
ggcpgram(AirPassengers)

## End(Not run)

Plot distribution

Description

Plot distribution

Usage

ggdistribution(
  func,
  x,
  p = NULL,
  colour = "#000000",
  linetype = NULL,
  fill = NULL,
  alpha = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

func

PDF or CDF function

x

Numeric vector to be passed to func

p

ggplot2::ggplot instance to plot

colour

Line colour

linetype

Line type

fill

Fill colour

alpha

Alpha

xlim

X axis limit

ylim

Y axis limit

log

log

main

main

xlab

xlab

ylab

ylab

asp

asp

...

Keywords passed to PDC/CDF func

Value

ggplot

Examples

ggdistribution(dnorm, seq(-3, 3, 0.1), mean = 0, sd = 1)
ggdistribution(ppois, seq(0, 30), lambda = 20)

p <- ggdistribution(pchisq, 0:20, df = 7, fill = 'blue')
ggdistribution(pchisq, 0:20, p = p, df = 9, fill = 'red')

Plot seasonal subseries of time series, generalization of `stats::monthplot`

Description

Plot seasonal subseries of time series, generalization of stats::monthplot

Usage

ggfreqplot(
  data,
  freq = NULL,
  nrow = NULL,
  ncol = NULL,
  conf.int = FALSE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "dashed",
  conf.int.fill = NULL,
  conf.int.alpha = 0.3,
  conf.int.value = 0.95,
  facet.labeller = NULL,
  ...
)

Arguments

data

stats::ts instance

freq

Length of frequency. If not provided, use time-series frequency

nrow

Number of plot rows

ncol

Number of plot columns

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

conf.int.value

Coverage probability for confidence interval

facet.labeller

A vector used as facet labels

...

Keywords passed to autoplot.ts

Value

ggplot

Examples

## Not run: 
ggfreqplot(AirPassengers)
ggfreqplot(AirPassengers, freq = 4)
ggfreqplot(AirPassengers, conf.int = TRUE)

## End(Not run)

An S4 class to hold multiple `ggplot2::ggplot` instances

Description

An S4 class to hold multiple ggplot2::ggplot instances

Usage

## S4 method for signature 'ggmultiplot'
length(x)

## S4 method for signature 'ggmultiplot,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'ggmultiplot'
x[[i, j, ..., drop]]

## S4 replacement method for signature 'ggmultiplot,ANY,ANY,ANY'
x[i, j, ...] <- value

## S4 replacement method for signature 'ggmultiplot'
x[[i, j, ...]] <- value

Arguments

x

ggmultiplot

i

elements to extract or replace

j

not used

...

not used

drop

not used

value

value to be set

Slots

plots: List of ggplot2::ggplot instances
ncol: Number of grid columns
nrow: Number of grid rows

Plots time-series diagnostics

Description

Plots time-series diagnostics

Usage

ggtsdiag(
  object,
  gof.lag = 10,
  conf.int = TRUE,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "dashed",
  conf.int.fill = NULL,
  conf.int.alpha = 0.3,
  ad.colour = "#888888",
  ad.linetype = "dashed",
  ad.size = 0.2,
  nrow = NULL,
  ncol = 1,
  ...
)

Arguments

object

A fitted time-series model

gof.lag

The maximum number of lags for a Portmanteau goodness-of-fit test

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

ad.colour

Line colour for additional lines

ad.linetype

Line type for additional lines

ad.size

Fill colour for additional lines

nrow

Number of facet/subplot rows

ncol

Number of facet/subplot columns

...

other keywords

Value

ggplot

Examples

## Not run: 
ggtsdiag(arima(AirPassengers))

## End(Not run)

The implemented grid.draw method for ggmultiplot, in order to work with ggsave() properly

Description

The implemented grid.draw method for ggmultiplot, in order to work with ggsave() properly

Usage

## S3 method for class 'ggmultiplot'
grid.draw(x, recording = TRUE)

Arguments

x

ggmultiplot

recording

ggmultiplot

Infer class name

Description

Infer class name

Usage

infer(data)

Arguments

data

list instance

Value

character

Check if Validates number of `ts` variates

Description

Check if Validates number of ts variates

Usage

is.univariate(data, raise = TRUE)

Arguments

data

ts instance

raise

Logical flag whether raise an error

Value

logical

Examples

## Not run: 
ggfortify:::is.univariate(AirPassengers)

## End(Not run)

Check object is target class, or object is `data.frame` fortified from target.

Description

Check object is target class, or object is data.frame fortified from target.

Usage

is_derived_from(object, target)

Arguments

object

instance to be checked. For data.frame, check whether it is fortified from target class

target

class name

Value

logical

Examples

ggfortify:::is_derived_from(prcomp(iris[-5]), 'prcomp')

Attach confidence interval to `ggplot2::ggplot`

Description

Attach confidence interval to ggplot2::ggplot

Usage

plot_confint(
  p,
  data = NULL,
  lower = "lower",
  upper = "upper",
  conf.int = TRUE,
  conf.int.geom = "line",
  conf.int.group = NULL,
  conf.int.colour = "#0000FF",
  conf.int.linetype = "none",
  conf.int.fill = "#000000",
  conf.int.alpha = 0.3
)

Arguments

p

ggplot2::ggplot instance

data

data contains lower and upper confidence intervals

lower

column name for lower confidence interval

upper

column name for upper confidence interval

conf.int

Logical flag indicating whether to plot confidence intervals

conf.int.geom

geometric string for confidence interval. 'line' or 'step'

conf.int.group

name of grouping variable for confidence intervals

conf.int.colour

line colour for confidence intervals

conf.int.linetype

line type for confidence intervals

conf.int.fill

fill colour for confidence intervals

conf.int.alpha

alpha for confidence intervals

Value

ggplot

Examples

d <- fortify(stats::acf(AirPassengers, plot = FALSE))
p <- ggplot(data = d, mapping = aes(x = Lag))
ggfortify:::plot_confint(p, data = d)

Attach label to `ggplot2::ggplot`

Description

Attach label to ggplot2::ggplot

Usage

plot_label(
  p,
  data,
  x = NULL,
  y = NULL,
  label = TRUE,
  label.label = "rownames",
  label.colour = NULL,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  label.show.legend = NA,
  label.position = "identity"
)

Arguments

p

ggplot2::ggplot instance

data

Data contains text label

x

x coordinates for label

y

y coordinates for label

label

Logical value whether to display labels

label.label

Column name used for label text

label.colour

Colour for text labels

label.alpha

Alpha for text labels

label.size

Size for text labels

label.angle

Angle for text labels

label.family

Font family for text labels

label.fontface

Fontface for text labels

label.lineheight

Lineheight for text labels

label.hjust

Horizontal adjustment for text labels

label.vjust

Vertical adjustment for text labels

label.repel

Logical flag indicating whether to use ggrepel, enabling this may take some time for plotting

label.show.legend

Logical value indicating whether to show the legend of the text labels

label.position

Character or a position function

Value

ggplot

Post process for fortify. Based on `ggplot2::qplot`

Description

Post process for fortify. Based on ggplot2::qplot

Usage

post_autoplot(
  p,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL
)

Arguments

p

ggplot2::ggplot instances

xlim

limits for x axis

ylim

limits for y axis

log

which variables to log transform ("x", "y", or "xy")

main

character vector or expression for plot title

xlab

character vector or expression for x axis label

ylab

character vector or expression for y axis label

asp

the y/x aspect ratio

Value

data.frame

Examples

p <- qplot(Petal.Length, Petal.Width, data = iris)
ggfortify:::post_autoplot(p, xlim = c(1, 5), ylim = c(1, 5), log = 'xy', main = 'title',
                          xlab = 'x', ylab = 'y', asp = 1.5)

Post process for fortify.

Description

Post process for fortify.

Usage

post_fortify(data, klass = NULL)

Arguments

data

data.frame

klass

instance to be added as base_class attr, should be original model before fortified

Value

data.frame

Generic print function for `ggmultiplot`

Description

Generic print function for ggmultiplot

Usage

## S4 method for signature 'ggmultiplot'
print(x)

Arguments

x

ggmultiplot

Rbind original and predicted time-series-like instances as fortified `data.frame`

Description

Rbind original and predicted time-series-like instances as fortified data.frame

Usage

rbind_ts(
  data,
  original,
  ts.connect = TRUE,
  index.name = "Index",
  data.name = "Data"
)

Arguments

data

Predicted/forecasted ts instance

original

Original ts instance

ts.connect

Logical frag indicates whether connects original time-series and predicted values

index.name

Specify column name for time series index

data.name

Specify column name for univariate time series data. Ignored in multivariate time series.

Value

data.frame

Examples

## Not run: 
predicted <- predict(stats::HoltWinters(UKgas), n.ahead = 5, prediction.interval = TRUE)
rbind_ts(predicted, UKgas, ts.connect = TRUE)

## End(Not run)

Calculate residuals for `stats::ar`

Description

Calculate residuals for stats::ar

Usage

## S3 method for class 'ar'
residuals(object, ...)

Arguments

object

stats::ar instance

...

other keywords

Value

ts Residuals extracted from the object object.

Examples

## Not run: 
residuals(ar(WWWusage))

## End(Not run)

Generic show function for `ggmultiplot`

Description

Generic show function for ggmultiplot

Usage

## S4 method for signature 'ggmultiplot'
show(object)

Arguments

object

ggmultiplot

Check if passed object is supported by `ggplot2::autoplot`

Description

Check if passed object is supported by ggplot2::autoplot

Usage

support_autoplot(obj)

Arguments

obj

object

Value

logical

Backtransform `scale`-ed object

Description

Backtransform scale-ed object

Usage

unscale(data, center = NULL, scale = NULL)

Arguments

data

Scaled data

center

Centered vector

scale

Scale vector

Value

data.frame

Examples

df <- iris[-5]
ggfortify::unscale(base::scale(df))

ggfortify

Description

Author(s)

See Also

Generic add operator for ggmultiplot

Description

Usage

Arguments

Value

Apply facets to to ggplot2::ggplot

Description

Usage

Arguments

Value

Apply grid to to ggplot2::ggplot

Description

Usage

Arguments

Convert a spline basis to a tibble

Description

Usage

Arguments

Details

Value

Examples

Autoplot MSwM::MSM.lm

Description

Usage

Arguments

Value

Examples

Autoplot raster::raster

Description

Usage

Arguments

Value

Autoplot maps::map

Description

Usage

Arguments

Value

Autoplot survival::aareg

Description

Usage

Arguments

Value

Examples

Autoplot stats::acf. Note to pass 'plot = FALSE' to original function to suppress standard plot output

Description

Usage

Arguments

Value

Examples

Autoplot spline basis instances

Description

Usage

Arguments

Value

Examples

Autoplot strucchange::breakpoints

Description

Usage

Arguments

Value

Examples

Autoplot changepoint::cpt

Description

Usage

Arguments

Value

Examples

Autoplot glmnet::cv.glmnet

Description

Usage

Arguments

Value

Examples

Autoplot stats::density

Description

Usage

Generic add operator for `ggmultiplot`

Apply facets to to `ggplot2::ggplot`

Apply grid to to `ggplot2::ggplot`

Autoplot `MSwM::MSM.lm`

Autoplot `raster::raster`

Autoplot `maps::map`

Autoplot `survival::aareg`

Autoplot `stats::acf`. Note to pass 'plot = FALSE' to original function to suppress standard plot output

Autoplot `strucchange::breakpoints`

Autoplot `changepoint::cpt`

Autoplot `glmnet::cv.glmnet`

Autoplot `stats::density`

Autoplot `forecast::forecast`

Autoplot `ggmultiplot` instances. It returns the passed instance as it is.

Autoplot `ggplot` instances. It returns the passed instance as it is.

Autoplot `glmnet::glmnet`

Autoplot `stats::lm` and `stats::glm`

Autoplot `maps::map`

Plot `base::matrix`

Autoplot `ROCR::performance`