eda_qqmat: QQ plot matrix

In mgimond/tukeyedar: Tukey Inspired Exploratory Data Analysis Functions

QQ plot matrix

Description

eda_qqmat Generates a matrix of empirical QQ plots

Usage

eda_qqmat(
  dat,
  x,
  fac,
  p = 1L,
  tukey = FALSE,
  q.type = 5,
  upper = FALSE,
  xylim = NULL,
  resid = FALSE,
  stat = mean,
  plot = TRUE,
  grey = 0.6,
  pch = 21,
  p.col = "grey40",
  p.fill = "grey60",
  size = 1,
  text.size = 1,
  tail.pch = 21,
  tail.p.col = "grey70",
  tail.p.fill = NULL,
  tic.size = 0.7,
  alpha = 0.8,
  q = FALSE,
  tails = FALSE,
  med = FALSE,
  inner = 0.75,
  ...
)

Arguments

dat	Data frame.
x	Continuous variable.
fac	Categorical variable.
p	Power transformation to apply to the continuous variable.
tukey	Boolean determining if a Tukey transformation should be adopted (FALSE adopts a Box-Cox transformation).
q.type	An integer between 1 and 9 selecting one of the nine quantile algorithms. (See quantiletile function).
upper	Boolean determining if both upper and lower triangular matrix should be plotted. If set to FALSE, only the lower triangular matrix is plotted.
xylim	X and Y axes limits.
resid	Boolean determining if residuals should be plotted. Residuals are computed using the stat parameter.
stat	Statistic to use if residuals are to be computed. Currently mean (default) or median.
plot	Boolean determining if plot should be generated.
grey	Grey level to apply to plot elements (0 to 1 with 1 = black).
pch	Point symbol type.
p.col	Color for point symbol.
p.fill	Point fill color passed to bg (Only used for pch ranging from 21-25).
size	Point symbol size (0-1).
text.size	Size for category text in diagonal box.
tail.pch	Tail-end point symbol type (See tails).
tail.p.col	Tail-end color for point symbol (See tails).
tail.p.fill	Tail-end point fill color passed to bg (Only used for tail.pch ranging from 21-25).
tic.size	Size of tic labels (defaults to 0.8).
alpha	Point transparency (0 = transparent, 1 = opaque). Only applicable if rgb() is not used to define point colors.
q	Boolean determining if grey box highlighting the inner region should be displayed.
tails	Boolean determining if points outside of the inner region should be symbolized differently. Tail-end points are symbolized via the tail.pch, tail.p.col and tail.p.fill arguments.
med	Boolean determining if median lines should be drawn.
inner	Fraction of mid-values to highlight in q or tails. Defaults to the inner 75 percent of values.
...	Not used

Details

The function will generate an empirical QQ plot matrix. Most of the arguments available in eda_qq are echoed in this function. The one notable difference is the default settings. By default, eda_qqmat will generate a plain vanilla set of plots.

The QQ plot matrix is most effective in comparing residuals after the data are fitted by the mean or median. To plot the residuals, set resid=TRUE. By default, the mean is used. You can change the statistic to the median by setting stat=median.

The function also allows for batch transformation of values via the p argument. The transformation is applied to the data prior to computing the residuals.

Value

Returns a list with the following components:

• data: List with input x and y values for each group. May be interpolated to smallest quantile batch if batch sizes don't match. Values will reflect power transformation defined in p.

• p: Transformation applied to original values.

References

• John M. Chambers, William S. Cleveland, Beat Kleiner, Paul A. Tukey. Graphical Methods for Data Analysis (1983)

• Quantile-Quantile plot article

Examples

# Default output
singer <- lattice::singer
eda_qqmat(singer, height, voice.part)

# Symbolize points outside of the "inner" region using an open point symbol
eda_qqmat(singer, height, voice.part, tails = TRUE)

# Set the inner region to cover 80% and change the outer point symbol to "+"
eda_qqmat(singer, height, voice.part, inner = 0.8, tails = TRUE, tail.pch = 3)

# Add the upper triangle to the matrix
eda_qqmat(singer, height, voice.part, upper = TRUE)

# Plot residuals after fitting mean to each batch
eda_qqmat(singer, height, voice.part, resid = TRUE)

# Log transform the data, then plot the residuals after fitting the mean model
eda_qqmat(iris, Petal.Length, Species, resid = TRUE, p = 0)

# Fit the median model instead of the mean
eda_qqmat(iris, Petal.Length, Species, resid = TRUE, p = 0, stat = median)

# Shade the "inner" regions (defaults to the mid 70% of values)
eda_qqmat(iris, Petal.Length, Species, resid = TRUE, q = TRUE, p = 0)

# Change inner region point symbols to dark orange and change inner region
# range to cover 90% of mid values
eda_qqmat(iris, Petal.Length, Species, resid = TRUE, p = 0, inner = 0.9,
          tail.pch = 3, p.fill = "orange2")

mgimond/tukeyedar documentation built on Feb. 1, 2025, 4:02 a.m.