logicFS (version 1.42.0)

vim.input: VIM for Inputs

Description

Quantifies the importance of each input variable occuring in at least one of the logic regression models found in the application of logic.bagging.

Usage

vim.input(object, useN = NULL, iter = NULL, prop = TRUE, standardize = NULL, mu = 0, addMatImp = FALSE, prob.case = 0.5, rand = NA)

Arguments

object
an object of class logicBagg, i.e.\ the output of logic.bagging
useN
logical specifying if the number of correctly classified out-of-bag observations should be used in the computation of the importance measure. If FALSE, the proportion of correctly classified oob observations is used instead. If NULL (default), then the specification of useN in object is used.
iter
integer specifying the number of times the values of the considered variable are permuted in the computation of its importance. If NULL (default), the values of the variable are not permuted, but the variable is removed from the model.
prop
should the proportion of logic regression models containing the respective variable also be computed?
standardize
should a standardized version of the importance measure for a set of variables be returned? By default, standardize = TRUE is used in the classification and the (multinomial) logistic regression case, and standarize is set to FALSE in the linear regression case. For details, see mu.
mu
a non-negative numeric value. Ignored if standardize = FALSE. Otherwise, a t-statistic for testing the null hypothesis that the importance of the respective variable is equal to mu is computed.
addMatImp
should the matrix containing the improvements due to each of the variables in each of the logic regression models be added to the output?
prob.case
a numeric value between 0 and 1. If the logistic regression approach of logic regression has been used in logic.bagging, then an observation will be classified as a case (or more exactly, as 1), if the class probability of this observation is larger than prob.case. Otherwise, prob.case is ignored.
rand
an integer for setting the random number generator in a reproducible case.

Value

An object of class logicFS containing
vim
the importances of the variables,
prop
the proportion of logic regression models containing the respective variable (if prop = TRUE) or NULL (if prop = FALSE),
primes
the names of the variables,
type
the type of model (1: classification, 2:linear regression, 3: logistic regression),
param
further parameters (if addInfo = TRUE in the previous call of logic.bagging),
mat.imp
either a matrix containing the improvements due to the variables for each of the models (if addMatImp = TRUE), or NULL (if addMatImp = FALSE),
measure
the name of the used importance measure,
useN
the value of useN,
threshold
NULL if standardize = FALSE, otherwise the $1-0.05/m$ quantile of the t-distribution with $B-1$ degrees of freedom, where $m$ is the number of variables and $B$ is the number of logic regression models composing object,
mu
mu (if standardize = TRUE), or NULL (otherwise),
iter
iter.

References

Schwender, H., Ruczinski, I., Ickstadt, K. (2011). Testing SNPs and Sets of SNPs for Importance in Association Studies. Biostatistics, 12, 18-32.

See Also

logic.bagging, logicFS, vim.logicFS, vim.set, vim.ebam, vim.chisq