MCPAN (version 1.1-21)

poly3test: Approximate simultaneous test for poly-3-adjusted tumour rates

Description

P-value of maximum test and adjusted p-values for M contrasts of I groups in a one-way layout. Based on approximation of the true distribution of the M test statistics by an M-variate normal distribution.

Usage

poly3test(time, status, f, type = "Dunnett",
 cmat = NULL, method = "BP", alternative = "two.sided",
dist="MVN", k=3, …)

Arguments

time

a numeric vector of times of death of the individuals

status

a logical (or numeric, consisting of 0,1 only) vector giving the tumour status at time of death of each individual, where TRUE (1) = tumour present, FALSE (0) = no tumour present

f

a factor of the same length as time, status, giving the levels of a grouping variable in a one-way layout

type

a character string specifying the contrast type

cmat

an optional user defined contrast matrix of dimension MxI

method

a single charcter string, specifying the method for adjustment, with options: "BP" (Bailer Portier: assuming poly-3-adjusted rates are binomial variables), "BW" (Bieler, Williams: delta method as in Bieler-Williams (1993)) "ADD1" (as Bailer Portier, including an add1-adjustment on the raw tumour rates) "ADD2" (as Bailer Portier, including an add2-adjustment on the raw tumour rates following Agresti Caffo (2000) for binomials)

alternative

a character string specifying the direction of the alternative hypothesis

dist

a character string, where "MVN" invokes the computation of p-values using the multivariate normal distribution, and "N" invokes use p-value computation using the univariate normal distribution

k

a single numeric value, the exponent to calculate survival adjusted proportions according to Bailer and Portier (1988), defaults to 3

…

further arguments to be passed; currently only base, to choose the control group with type="Dunnett"

Value

An object of class "poly3test", a list containing:

teststat

a numeric vector of teststatistics of length M

pval

a single numeric p-value, the p-value of the maximum test (minimum p-value)

p.val.adj

a vector of length M, the adjusted p-values of the single contrasts

alternative

a single character vector, as the input

dist

a character string specifying which distribution

time

as input

status

as input

f

as input

method

as input

cmat

used contrast matrix

sample.est

a list containing sample estimates

Details

Testversion.

References

Assumptions corresponding to the poly-k-adjustment:

Bailer, J.A. and Portier, C.J. (1988): Effects of treatment-induced mortality and tumor-induced mortality on tests for carcinogenicity in small samples. Biometrics 44, 417-431.

Peddada, S.D., Dinse, G.E., and Haseman, J.K. (2005): A survival-adjusted quantal response test for comparing tumor incidence rates. Applied Statistics 54, 51-61.

Statistical procedures and characterization of coverage probabilities are described in: Sill, M. (2007): Approximate simultaneous confidence intervals for multiple comparisons of binomial proportions. Master thesis, Institute of Biostatistics, Leibniz University Hannover.

Examples

# NOT RUN {
# poly-3-adjusted tumour rates with a potential
# down-turn effect for the highest dose group "4":

data(methyl)

# many-to-one:
methylD<-poly3test(time=methyl$death, status=methyl$tumour,
 f=methyl$group, type = "Dunnett", method = "ADD1")

methylD

# Williams-Contrast:
methylW<-poly3test(time=methyl$death, status=methyl$tumour,
 f=methyl$group, type = "Williams", method = "ADD1", alternative="greater" )

methylW

# Changepoint-Contrast:
methylCh<-poly3test(time=methyl$death, status=methyl$tumour,
 f=methyl$group, type = "Change", method = "ADD1", alternative="greater" )

methylCh

# }