Create a table of estimated group means and variability

Description

Create a table of estimated group means based on a fit by the cg package.

Usage

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grpSummaryTable(fit, mcadjust = FALSE, alpha = 0.05, display = "print",  ...)

Arguments

fit

An fit object created with a fit method from the cg package. The only class of object currently available is cgOneFactorFit, which is prepared by the fit.cgOneFactorData method.

mcadjust

Do a multiple comparisons adjustment, based on the simultaneous inference capabilities of the multcomp package. See Details below. The default value is FALSE. If mcadjust=TRUE is specified, there will be a delay, usually just for a few seconds, due to computing time of the critical point in order to conduct the adjusted comparisons.

alpha

Significance level, by default set to 0.05.

display

One of three valid values:

"print"

The default value; It calls a print method for the created
cgOneFactorGrpSummaryTable object, which is a formatted text output of the table(s).

"none"

Supresses any printing. Useful, for example, when just assignment of the resulting object is desired.

"show"

Calls the default showDefault method, which will just print out the grpSummaryTable object components.

...

Additional arguments, depending on the specific method written for the object. Currently, there is only one such specific method; see grpSummaryTable.cgOneFactorFit for any additional arguments that can be specified.

Details

When mcadjust=TRUE, a status message of "Some time may be needed as the critical point"
"from the multcomp::summary.glht function call is calculated" is displayed at the console. This computed critical point is used for all subsequent p-value and confidence interval calculations.

Value

A method-specific grpSummaryTable object is returned. See the specific methods for discussion of return values.

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

Hothorn, T., Bretz, F., Westfall, P., Heiberger, R.M., and Schuetzenmeister, A. (2010). The multcomp package.

Hothorn, T., Bretz, F., and Westfall, P. (2008). "Simultaneous Inference in General Parametric Models", Biometrical Journal, 50, 3, 346-363.

See Also

grpSummaryTable.cgOneFactorFit

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)

canine.grpsumm <- grpSummaryTable(canine.fit)


data(gmcsfcens)
gmcsfcens.data <- prepareCGOneFactorData(gmcsfcens, format="groupcolumns",
                                         analysisname="cytokine",
                                         endptname="GM-CSF (pg/ml)",
                                         logscale=TRUE)

gmcsfcens.fit <- fit(gmcsfcens.data, type="aft")

gmcsfcens.grpsumm <- grpSummaryTable(gmcsfcens.fit)

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