Description Usage Arguments Author(s) References See Also Examples

The sampSize function implements a bisection search algorithm for sample size calculation. The user can hand over a general target function (via targFunc) that is then iterated so that a certain target is achieved. The sampSizeMCT is a convenience wrapper of sampSize for multiple contrast tests using the power as target function.

The targN functions calculates a general target function for different given sample sizes. The powN function is a convenience wrapper of targN for multiple contrast tests using the power as target function.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
sampSize(upperN, lowerN = floor(upperN/2), targFunc, target,
tol = 0.001, alRatio, Ntype = c("arm", "total"),
verbose = FALSE)
sampSizeMCT(upperN, lowerN = floor(upperN/2), ..., power, sumFct = mean,
tol = 0.001, alRatio, Ntype = c("arm", "total"),
verbose = FALSE)
targN(upperN, lowerN, step, targFunc, alRatio,
Ntype = c("arm", "total"), sumFct = c("min", "mean", "max"))
powN(upperN, lowerN, step, ..., alRatio,
Ntype = c("arm", "total"), sumFct = c("min", "mean", "max"))
## S3 method for class 'targN'
plot(x, superpose = TRUE, line.at = NULL,
xlab = NULL, ylab = NULL, ...)
``` |

`upperN, lowerN` |
Upper and lower bound for the target sample
size. |

`step` |
Only needed for functions targN and powN. Stepsize
for the sample size at which the target function is calculated. The
steps are calculated via |

`targFunc, target` |
The target function needs to take as an input the vector of sample
sizes in the different dose groups. For sampSize it needs to
return a univariate number. For function targN it should
return a numerical vector. |

`tol` |
A positive numeric value specifying the tolerance level for the bisection search algorithm. Bisection is stopped if the targFunc value is within tol of target. |

`alRatio` |
Vector describing the relative patient allocations to the dose groups up to proportionality, e.g. rep(1, length(doses)) corresponds to balanced allocations. |

`Ntype` |
One of "arm" or "total". Determines, whether the sample size in the smallest arm or the total sample size is iterated in bisection search algorithm. |

`verbose` |
Logical value indicating if a trace of the iteration progress of the bisection search algorithm should be displayed. |

`...` |
Arguments directly passed to the The placAdj argument needs to be FALSE (which is the default value for this argument). If sample size calculations are desired for a placebo-adjusted formulation use sampSize or targN directly. In case For a homoscedastic normally distributed response variable only sigma needs to be specified, as the sample size n is iterated in the different powMCT calls. |

`power, sumFct` |
power is a numeric defining the desired summary power to achieve (in sampSizeMCT). sumFct needs to be a function that combines the power values under the different alternatives into one value (in sampSizeMCT). |

`x, superpose, line.at, xlab, ylab` |
arguments for the plot method of targN and powN, additional arguments are passed down to the low-level lattice plotting routines. |

Jose Pinheiro, Bjoern Bornkamp

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | ```
## sampSize examples
## first define the target function
## first calculate the power to detect all of the models in the candidate set
fmodels <- Mods(linear = NULL, emax = c(25),
logistic = c(50, 10.88111), exponential=c(85),
betaMod=matrix(c(0.33,2.31,1.39,1.39), byrow=TRUE, nrow=2),
doses = c(0,10,25,50,100,150), placEff=0, maxEff=0.4,
addArgs = list(scal=200))
## contrast matrix to use
contMat <- optContr(fmodels, w=1)
## this function calculates the power under each model and then returns
## the average power under all models
tFunc <- function(n){
powVals <- powMCT(contMat, altModels=fmodels, n=n, sigma = 1,
alpha=0.05)
mean(powVals)
}
## assume we want to achieve 80% average power over the selected shapes
## and want to use a balanced allocations
## Not run:
sSize <- sampSize(upperN = 80, targFunc = tFunc, target=0.8,
alRatio = rep(1,6), verbose = TRUE)
sSize
## Now the same using the convenience sampSizeMCT function
sampSizeMCT(upperN=80, contMat = contMat, sigma = 1, altModels=fmodels,
power = 0.8, alRatio = rep(1, 6), alpha = 0.05)
## Alternatively one can also specify an S matrix
## covariance matrix in one observation (6 total observation result in a
## variance of 1 in each group)
S <- 6*diag(6)
## this uses df = Inf, hence a slightly smaller sample size results
sampSizeMCT(upperN=500, contMat = contMat, S=S, altModels=fmodels,
power = 0.8, alRatio = rep(1, 6), alpha = 0.05, Ntype = "total")
## targN examples
## first calculate the power to detect all of the models in the candidate set
fmodels <- Mods(linear = NULL, emax = c(25),
logistic = c(50, 10.88111), exponential=c(85),
betaMod=matrix(c(0.33,2.31,1.39,1.39), byrow=TRUE, nrow=2),
doses = c(0,10,25,50,100,150), placEff=0, maxEff=0.4,
addArgs = list(scal=200))
## corresponding contrast matrix
contMat <- optContr(fmodels, w=1)
## define target function
tFunc <- function(n){
powMCT(contMat, altModels=fmodels, n=n, sigma = 1, alpha=0.05)
}
powVsN <- targN(upperN = 100, lowerN = 10, step = 10, tFunc,
alRatio = rep(1, 6))
plot(powVsN)
## the same can be achieved using the convenience powN function
## without the need to specify a target function
powN(upperN = 100, lowerN=10, step = 10, contMat = contMat,
sigma = 1, altModels = fmodels, alpha = 0.05, alRatio = rep(1, 6))
## End(Not run)
``` |

DoseFinding documentation built on Jan. 5, 2018, 1:05 a.m.

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