- effect.size
The effect size (mean over standard deviation) for test statistics
having non-zero means. Assumed to be a constant (in magnitude) over
non-zero mean test statistics.
- n.sample
The number of experimental replicates.
- r.1
The proportion of simultaneous tests that are non-centrally located
- alpha
The upper bound on the probability that the FDP exceeds delta.
- delta
The exceedance thresh-hold for the FDP tail probability control method
(BHFDX or Romano) \(P\{ FDP > \delta \} < \alpha\). The default
value is \(\alpha\).
- groups
The number of experimental groups to compare. Default value is 2.
- N.tests
The number of simultaneous hypothesis tests.
- type
A character string specifying, in the groups=2 case, whether the
test is 'paired', 'balanced', or 'unbalanced' and in the case when
groups >=3, whether the test is 'balanced' or 'unbalanced'. The
default in all cases is 'balanced'. Left unspecified in the one
sample (groups=1) case.
- grpj.per.grp1
Required when type="unbalanced", specifies the group 0 to
group 1 ratio in the two group case, and in the case of 3 or more
groups, the group j to group 1 ratio, where group 1 is the group
with the largest effect under the alternative hypothesis.
- corr.struct
Specifies a block correlation structure between test
statistics which is used in both the simulation routine, and in the
computations based upon asymptotic approximation, e.g. the AFDX
control and the ATPP method. Its form is specified via the following
named elements.
"type": "CS-Blocks" for compound symmetry within blocks or
"Toeplitz-Blocks" for toeplitz within blocks.
"block.size": the size of the correlated blocks
"rho": When type="CS-Blocks", then 'rho' is a correlation of length 1
when type="Toeplitz-Blocks", then 'rho' is a vector of
correlations of length 'block.size' - 1
- control
Optionally, a list with components with the following components:
'groups', used when distop=3 (F-dist), specifying number of groups.
'tol' is a convergence criterion used in iterative methods
which is set to 1e-8 by default
'max.iter' is an iteration limit, set to 20 for the iterated
function limit and 1000 for all others by default
'sim.level' sim level 2 results in more detail at the expense of
slightly more computational time.
'low.power.stop' in simulation option, will result in an error message if
the power computed via FixedPoint method is too low, which
result in no solution for the BHFDX option. Default setting
is TRUE. Set to FALSE to over-ride.
'FDP.meth.thresh' fine-tunes the 'Auto' voodoo (see above). Leave
this alone.
'verb' vebosity level.
- formula
Optionally, the function can be used to _estimate_ f*
from a given dataset of sorted p-values. In this case we specify
formula, which is a formula of the form pval~1 where 'pval'
is the name of the p-value variable in the dataset, dataset
(see
- data
The name of the dataset.
- distopt
Test statistic distribution in among null and
alternatively distributed sub-populations.
distopt=0 gives normal (2 groups), distop=1 gives t- (2 groups)
and distopt=2 gives F- (2+ groups)