gMCP (version 0.7-8)

gMCP: A graphical approach to sequentially rejective multiple test procedures

Description

Performs a sequentially rejective multiple test procedure on a graph given unadjusted p-values.

Usage

gMCP(graph, pvalues, test, correlation, alpha=0.05, 
	     approxEps=TRUE, eps=10^(-3), ..., useC=FALSE, 
	     verbose=FALSE, keepWeights=TRUE, adjPValues=TRUE)

Arguments

graph

A graph of class graphMCP.

pvalues

A numeric vector specifying the p-values for the sequentially rejective MTP.

test

If test is set to "Simes" the weighted Simes test will be performed for each subset of hypotheses. Further alternatives will be added in the future.

correlation

Correlation matrix, if the tests are correlated. Also valid are strings like "Dunnett", "Tukey", "Sequen", "AVE", "Changepoint", "Williams", "Marcus", "McDermott", "UmbrellaWilliams", "GrandMean". In this case please add a numeric para

alpha

A numeric specifying the maximal allowed type one error rate.

approxEps

A boolean specifying whether epsilon values should be substituted with the value given in the paramenter eps.

eps

A numeric scalar specifying a value for epsilon edges.

...

Test specific arguments can be given here.

useC

Logical scalar. If TRUE neither adjusted p-values nor intermediate graphs are returned, but the calculation is sped up by using code written in C. THIS CODE IS NOT FOR PRODUCTIVE USE YET! If approxEps is FALSE and the graph

verbose

Logical scalar. If TRUE verbose output is generated during sequentially rejection steps.

keepWeights

Logical scalar. If FALSE the weight of a node without outgoing edges is set to 0 if it is removed. Otherwise it keeps its weight.

adjPValues

Logical scalar. If FALSE no adjusted p-values will be calculated. Especially for the weighted Simes test this will result in significantly less calculations in most cases.

Value

• An object of class gMCPResult, more specifically a list with elements
• graphs
  list of graphs
• pvalues
  p-values
• rejected
  logical whether hyptheses could be rejected
• adjPValues
  adjusted p-values

Details

For details see the given references.

References

Frank Bretz, Willi Maurer, Werner Brannath, Martin Posch: A graphical approach to sequentially rejective multiple test procedures. Statistics in Medicine 2009 vol. 28 issue 4 page 586-604. http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf

Bretz F., Posch M., Glimm E., Klinglmueller F., Maurer W., Rohmeyer K. (2011): Graphical approaches for multiple endpoint problems using weighted Bonferroni, Simes or parametric tests - to appear.

Strassburger K., Bretz F.: Compatible simultaneous lower confidence bounds for the Holm procedure and other Bonferroni based closed tests. Statistics in Medicine 2008; 27:4914-4927.

Hommel G., Bretz F., Maurer W.: Powerful short-cuts for multiple testing procedures with special reference to gatekeeping strategies. Statistics in Medicine 2007; 26:4063-4073.

Guilbaud O.: Simultaneous confidence regions corresponding to Holm's stepdown procedure and other closed-testing procedures. Biometrical Journal 2008; 50:678-692.

See Also

graphMCP graphNEL

Examples

g <- BonferroniHolm(5)

gMCP(g, pvalues=c(0.01, 0.02, 0.04, 0.04, 0.7))