getVar.Bin: Analysis of the effect of each term of a binary...

In FRESA.CAD: Feature Selection Algorithms for Computer Aided Diagnosis

Analysis of the effect of each term of a binary classification model by analysing its reclassification performance

Description

This function provides an analysis of the effect of each model term by comparing the binary classification performance between the Full model and the model without each term. The model is fitted using the train data set, but probabilities are predicted for the train and test data sets. Reclassification improvement is evaluated using the improveProb function (Hmisc package). Additionally, the integrated discrimination improvement (IDI) and the net reclassification improvement (NRI) of each model term are reported.

Usage

	getVar.Bin(object,
	                       data,
	                       Outcome = "Class", 
	                       type = c("LOGIT", "LM", "COX"),
	                       testData = NULL,
	                       callCpp=TRUE)

Arguments

object	An object of class lm, glm, or coxph containing the model to be analysed
data	A data frame where all variables are stored in different columns
Outcome	The name of the column in data that stores the variable to be predicted by the model
type	Fit type: Logistic ("LOGIT"), linear ("LM"), or Cox proportional hazards ("COX")
testData	A data frame similar to data, but with a data set to be independently tested. If NULL, data will be used.
callCpp	is set to true it will use the c++ implementation of improvement.

Value

z.IDIs	A vector in which each term represents the z-score of the IDI obtained with the Full model and the model without one term
z.NRIs	A vector in which each term represents the z-score of the NRI obtained with the Full model and the model without one term
IDIs	A vector in which each term represents the IDI obtained with the Full model and the model without one term
NRIs	A vector in which each term represents the NRI obtained with the Full model and the model without one term
testData.z.IDIs	A vector similar to z.IDIs, where values were estimated in testdata
testData.z.NRIs	A vector similar to z.NRIs, where values were estimated in testdata
testData.IDIs	A vector similar to IDIs, where values were estimated in testdata
testData.NRIs	A vector similar to NRIs, where values were estimated in testdata
uniTrainAccuracy	A vector with the univariate train accuracy of each model variable
uniTestAccuracy	A vector with the univariate test accuracy of each model variable

Author(s)

Jose G. Tamez-Pena and Antonio Martinez-Torteya

References

Pencina, M. J., D'Agostino, R. B., & Vasan, R. S. (2008). Evaluating the added predictive ability of a new marker: from area under the ROC curve to reclassification and beyond. Statistics in medicine 27(2), 157-172.

See Also

getVar.Res

FRESA.CAD documentation built on Nov. 25, 2023, 1:07 a.m.