MultAdjProc {Mediana}

MultAdjProc object

Description

This function creates an object of class MultAdjProc which can be added to objects of class AnalysisModel, MultAdj or MultAdjStrategy.

Usage

MultAdjProc(proc, par = NULL, tests = NULL)

Arguments

proc

defines a multiplicity adjustment procedure.

par

defines the parameters of the multiplicity adjustment procedure (optional).

tests

defines the tests taken into account in the multiplicity adjustment procedure.

Details

Objects of class MultAdjProc are used in objects of class AnalysisModel to specify a Multiplicity Adjustment Procedure that will be applied to the statistical tests to protect the overall Type I error rate. Several objects of class MultAdjProc can be added to an object of class AnalysisModel, using the '+' operator or by grouping them into a MultAdj object.

proc argument defines the multiplicity adjustment procedure. Several procedures are already implemented in the Mediana package (listed below, along with the required or optional parameters to specify in the par argument):

• BonferroniAdj: Bonferroni procedure. Optional parameter: weight.

• HolmAdj: Holm procedure. Optional parameter: weight.

• HochbergAdj: Hochberg procedure. Optional parameter: weight.

• HommelAdj: Hommel procedure. Optional parameter: weight.

• FixedSeqAdj: Fixed-sequence procedure.

• ChainAdj: Family of chain procedures. Required parameters: weight and transition.

• FallbackAdj: Fallback procedure. Required parameters: weight.

• NormalParamAdj: Parametric multiple testing procedure derived from a multivariate normal distribution. Required parameter: corr. Optional parameter: weight.

• ParallelGatekeepingAdj: Family of parallel gatekeeping procedures. Required parameters: family, proc, gamma.

• MultipleSequenceGatekeepingAdj: Family of multiple-sequence gatekeeping procedures. Required parameters: family, proc, gamma.

• MixtureGatekeepingAdj: Family of mixture-based gatekeeping procedures. Required parameters: family, proc, gamma, serial, parallel.

If no tests are defined, the multiplicity adjustment procedure will be applied to all tests defined in the AnalysisModel.

References

http://gpaux.github.io/Mediana/

See Also

See Also MultAdj, MultAdjStrategy and AnalysisModel.

Examples

# Parameters of the chain procedure (fixed-sequence procedure)
# Vector of hypothesis weights
chain.weight = c(1, 0)
# Matrix of transition parameters
chain.transition = matrix(c(0, 1,
                            0, 0), 2, 2, byrow = TRUE)

# Analysis model
analysis.model = AnalysisModel() +
  MultAdjProc(proc = "ChainAdj",
              par = parameters(weight = chain.weight,
                               transition = chain.transition)) +
  Test(id = "PFS test",
       samples = samples("Plac PFS", "Treat PFS"),
       method = "LogrankTest") +
  Test(id = "OS test",
       samples = samples("Plac OS", "Treat OS"),
       method = "LogrankTest")