Description Usage Arguments Details Value Author(s) References See Also
Computes a standarized or a signpermutation based version of either the Single Tree Measure, the Quantitative Response Measure, or the Multiple Tree Measure.
1 2 3 4  vim.norm(object, mu = 0)
vim.signperm(object, mu = 0, n.perm = 10000, n.subset = 1000,
version = 1, adjust = "bonferroni", rand = NA)

object 
either the output of 
mu 
a nonnegative numeric value against which the importances are tested. See 
n.perm 
the number of sign permutations used in 
n.subset 
an integer specifying how many permutations should be considered at once. 
version 
either 
adjust 
character vector naming the method with which the raw permutation based
pvalues are adjusted for multiplicity. If 
rand 
an integer for setting the random number generator in a reproducible case. 
In both vim.norm
and vim.signperm
, a paired tstatistic is computed for each
prime implicant, where the numerator is given by VIM  mu
with VIM being the
single or the multiple tree importance, and the denominator is the corresponding standard
error computed by employing the B
improvements of the considered prime implicant
in the B
logic regression models, where VIM is the mean over these
B
improvements.
Note that in the case of a quantitative response, such a standardization is not necessary.
Thus, vim.norm
returns a warning when the response is quantitative, and vim.signperm
does not divide VIM  mu
by its sample standard error.
Using mu = 0
might lead to calling a prime implicant important, even though it actually
shows only improvements of 1 or 0. When considering the prime implicants, it might be therefore
be helpful to set mu
to a value slightly larger than zero.
In vim.norm
, the value of this tstatistic is returned as the standardized importance
of a prime implicant. The larger this value, the more important is the prime implicant. (This applies
to all importance measures – at least for those contained in this package.) Assuming normality,
a possible threshold for a prime implicant to be considered as important is the 1  0.05 / m quantile
of the tdistribution with B  1 degrees of freedom, where m is the number of prime implicants.
In vim.signperm
, the sign permutation is used to determine n.perm
permuted values of the
onesample tstatistic, and to compute the raw pvalues for each of the prime implicants. Afterwards,
these pvalues are adjusted for multiple comparisons using the method specified by adjust
.
The permutation based importance of a prime implicant is then given by 1  these adjusted pvalues.
Here, a possible threshold for calling a prime implicant important is 0.95.
An object of class logicFS
containing
primes 
the prime implicants, 
vim 
the respective importance of the prime implicants, 
prop 
NULL, 
type 
the type of model (1: classification, 2: linear regression, 3: logistic regression), 
param 
further parameters (if 
mat.imp 
NULL, 
measure 
the name of the used importance measure, 
useN 
the value of 
threshold 
the threshold suggested in 
mu 

Holger Schwender, [email protected]
Schwender, H., Ruczinski, I., Ickstadt, K. (2011). Testing SNPs and Sets of SNPs for Importance in Association Studies. Biostatistics, 12, 1832.
logic.bagging
, logicFS
,
vim.logicFS
, vim.chisq
, vim.ebam
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