Package 'ggfortify'

Title: Data Visualization Tools for Statistical Analysis Results
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'.
Authors: 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]
Maintainer: Yuan Tang <[email protected]>
License: MIT + file LICENSE
Version: 0.4.17
Built: 2024-08-23 02:47:29 UTC
Source: https://github.com/sinhrks/ggfortify

Help Index

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 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 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 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 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 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 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 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 = TRUE,
  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 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

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 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 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 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 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 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 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)

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

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'))

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)

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')

ggfortify

Description

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

Author(s)

Maintainer: Yuan Tang [email protected] (ORCID)

Authors:

Other contributors:

  • Austin Dickey [contributor]

  • Matthias Grenié [contributor]

  • Ryan Thompson [contributor]

  • Luciano Selzer [contributor]

  • Dario Strbenac [contributor]

  • Kirill Voronin [contributor]

  • Damir Pulatov [contributor]

See Also

Useful links:

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 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')

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)

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))