DoseFinding (version 0.6-3)

planMM: Calculate optimal contrasts and critical value for MCP test

Description

Calculates the optimal model contrasts, the critical value and the contrast correlation matrix, i.e. the quantities necessary to conduct a multiple contrast test for a given candidate set of dose-response models (see also MCPtest).

Usage

planMM(models, doses, n, off = 0.1 * max(doses), scal = 1.2 * max(doses),
       std = TRUE, alpha = 0.025, alternative = c("one.sided", "two.sided"),
       direction = c("increasing", "decreasing"),
       control = mvtnorm.control(), cV = TRUE, muMat = NULL, vCov = NULL)

Arguments

models

A list of candidate models

doses

A numeric vector giving the doses to be administered.

n

The vector of sample sizes per group. In case just one number is specified, it is assumed that all group sample sizes are equal to this number.

off

Offset parameter for the linear in log model (default 10 perc of the maximum dose).

scal

Scale parameter for the beta model (default 20 perc. larger than maximum dose).

std

Optional logical indicating, whether standardized version of the models should be assumed.

alpha

Level of significance (default: 0.025)

alternative

Character determining the type of alternative used for the multiple contrast trend test. When muMat is specified or std = F, this argument is ignored.

direction

Character determining the trend direction of the data, which one wants to investigate (e.g., if one wants to investigate whether the response gets larger with increasing dose direction should be equal to "increasing").

control

A list of options for the pmvt and qmvt functions as produced by mvtnorm.control

cV

Logical indicating whether critical value should be calculated

muMat

An optional matrix with means in the columns and given dimnames (dose levels and names of contrasts). If specified the models argument should not be specified, see examples below.

vCov

Covariance matrix of mean vectors assumed for calculation of optimal contrasts. When vCov is given it is assumed that the estimates are asymptotically normal.

Value

• An object of class planMM with the following components:
• contMat
  Matrix of optimal contrasts.
• critVal
  The critical value for the test (if calculated)
• muMat
  Matrix of (non-normalized) model means
• corMat
  Matrix of the contrast correlations.

References

Bornkamp B., Pinheiro J. C., and Bretz, F. (2009). MCPMod: An R Package for the Design and Analysis of Dose-Finding Studies, Journal of Statistical Software, 29(7), 1--23 Bretz, F., Pinheiro, J., and Branson, M. (2005), Combining Multiple Comparisons and Modeling Techniques in Dose-Response Studies, Biometrics, 61, 738--748 Pinheiro, J. C., Bornkamp, B., and Bretz, F. (2006). Design and analysis of dose finding studies combining multiple comparisons and modeling procedures, Journal of Biopharmaceutical Statistics, 16, 639--656

See Also

critVal, MCPtest

Examples

## Example from JBS paper
doses <- c(0,10,25,50,100,150)
models <- list(linear = NULL, emax = 25,                               
               logistic = c(50, 10.88111), exponential= 85,            
               betaMod=matrix(c(0.33,2.31,1.39,1.39), byrow=TRUE, nrow=2))
plM <- planMM(models, doses, n = rep(50,6), alpha = 0.05, scal=200)
plot(plM)

## example, where means are directly specified
## doses   
dvec <- c(0, 10, 50, 100)
## mean vectors
mu1 <- c(1, 2, 2, 2)
mu2 <- c(1, 1, 2, 2)
mu3 <- c(1, 1, 1, 2)
mMat <- cbind(mu1, mu2, mu3)
dimnames(mMat)[[1]] <- dvec
planMM(muMat = mMat, doses = dvec, n = 30)