Quantile-Quantile (QQ) Graphs of a cgOneFactorFit object

Description

Create a Q-Q Gaussian graph of the residuals of a cgOneFactorFit object

Usage

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## S4 method for signature 'cgOneFactorFit'
qqGraph(fit, line=NULL, cgtheme = TRUE, device = "single", ...)  

Arguments

fit

A fit object of class cgOneFactorFit.

line

Add a line through the estimated 25th and 75th percentiles. When set to the default NULL, the addition of a line depends on the following: When there is no censored data, the line will be added with the qqline algorithm. If any censored data residuals are present, no line is added unless line=TRUE is explicitly specified below.

cgtheme

When set to the default TRUE, ensures a trellis device is active with limited color scheme. Namely, background, strip.shingle, and strip.background are each set to "white".

device

Can be one of three values:

"single"

The default, which will put all graphs on the same device page. For example, when resistant & robust and classical least squares are present and model="both" (the default), a 2 x 1 paneled graph will be created.

"multiple"

Relevant only when resistant & robust and classical least squares are present and model="both" (the default) or model="extended". In those cases, a new graphics device is generated to hold the resistant & robust version, as a single-paneled graph, and the classical least squares version is on the previous device. If model="extended", then a second new graphics device is generated to hold the unweighted resistant & robust residuals, as another single-paneled graph.

"ask"

Relevant only when resistant & robust and classical least squares are present and model="both" (the default) or model="extended". In that case, each are portrayed as a single-paneled graph, with the ask=TRUE argument specified in par so that the user input confirmation is needed before the graphs are drawn.

...

Additional arguments. One is currently valid:

model

For cgOneFactorFit fit objects that have classical least squares lm() or resistant & robust rlm() fits, the following argument values are possible:

"both"

Q-Q graphs of the residuals from both the ordinary classical least squares and resistant & robust fits are plotted. This is the default when both fits are present in the cgOneFactorFit object specified in the fit argument. If the resistant & robust fit is not available, this value is not relevant.

"olsonly"

Only a Q-Q graph of the residuals from the ordinary classical least squares olsfit fit is performed.

"rronly" or "rrwtdonly"

Only a Q-Q graph of the weighted residuals from the resistant and robust rrfit fit is plotted.

"rrunwtdonly"

Only a Q-Q graph of the unweighted residuals from the resistant and robust rrfit fit is plotted.

For other possible cgOneFactorFit fit slots such as accelerated failure time or unequal variance models, the model argument is not relevant, and the appropriate Q-Q graph will be plotted for these model types.

Details

For censored data residuals, left-censored values are shown as a shallow "V", which is actually just a rotated downward "<" sign. Similarly, right-censored values are shown as a deeper "^", which is a rotated upwared ">" sign.

For the line argument, an added line when censored data residuals are present needs to be interpreted very cautiously. If "too many" censored data values are present, the line will appear nonsensical if indeed it can even be estimated with 25th and 75th percentiles in the presence of the the censored data residuals. These percentiles are estimated via the Kaplan-Meier method as proposed by Gentleman and Crowley (1991), with the survival::survfit function.

The heading for the graph is taken from the cgOneFactorData object, which prepareCGOneFactorData sets from its analysisname argument.

The label for the Y-axis of residuals is derived from the cgOneFactorData object, which prepareCGOneFactorData sets from its endptname argument.

The number of decimal places printed in the ticks on the Y-axis is taken from the cgOneFactorData object, which prepareCGOneFactorData sets from its digits argument.

The minimum and maximum values from the range of the residuals are respectively labeled in the bottom and top left corners of the graph region.

Value

qqGraph.cgOneFactorFit returns an invisible NULL. The main purpose is the side effect of graphing to the current device.

Note

Contact cg@billpikounis.net for bug reports, questions, concerns, and comments.

Author(s)

Bill Pikounis [aut, cre, cph], John Oleynick [aut], Eva Ye [ctb]

References

Gentleman, R.C. and Crowley, J. (1991). "Graphical Methods for Censored Data", Journal of the American Statistical Association, Volume 86, 678-683.

See Also

qqline

Examples

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data(canine)
canine.data <- prepareCGOneFactorData(canine, format="groupcolumns",
                                      analysisname="Canine",
                                      endptname="Prostate Volume",
                                      endptunits=expression(plain(cm)^3),
                                      digits=1, logscale=TRUE, refgrp="CC")
canine.fit <- fit(canine.data)

qqGraph(canine.fit)

qqGraph(canine.fit, model="olsonly")

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