updateModel.Bin: Update the IDI/NRI-based model using new data or new...

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

Update the IDI/NRI-based model using new data or new threshold values

Description

This function will take the frequency-ranked set of variables and will generate a new model with terms that meet either the integrated discrimination improvement (IDI), or the net reclassification improvement (NRI), threshold criteria.

Usage

	updateModel.Bin(Outcome,
	            covariates = "1",
	            pvalue = c(0.025, 0.05),
	            VarFrequencyTable, 
	            variableList,
	            data,
	            type = c("LM", "LOGIT", "COX"), 
	            lastTopVariable = 0,
	            timeOutcome = "Time",
	            selectionType = c("zIDI","zNRI"),
	            maxTrainModelSize = 0,
	            zthrs = NULL
	            )

Arguments

Outcome	The name of the column in data that stores the variable to be predicted by the model
covariates	A string of the type "1 + var1 + var2" that defines which variables will always be included in the models (as covariates)
pvalue	The maximum p-value, associated to either IDI or NRI, allowed for a term in the model
VarFrequencyTable	An array with the ranked frequencies of the features, (e.g. the ranked.var value returned by the ForwardSelection.Model.Bin function)
variableList	A data frame with two columns. The first one must have the names of the candidate variables and the other one the description of such variables
data	A data frame where all variables are stored in different columns
type	Fit type: Logistic ("LOGIT"), linear ("LM"), or Cox proportional hazards ("COX")
lastTopVariable	The maximum number of variables to be tested
timeOutcome	The name of the column in data that stores the time to event (needed only for a Cox proportional hazards regression model fitting)
selectionType	The type of index to be evaluated by the improveProb function (Hmisc package): z-score of IDI or of NRI
maxTrainModelSize	Maximum number of terms that can be included in the model
zthrs	The z-thresholds estimated in forward selection

Value

final.model	An object of class lm, glm, or coxph containing the final model
var.names	A vector with the names of the features that were included in the final model
formula	An object of class formula with the formula used to fit the final model
z.selectionType	A vector in which each term represents the z-score of the index defined in selectionType obtained with the Full model and the model without one term

Author(s)

Jose G. Tamez-Pena and Antonio Martinez-Torteya

See Also

updateModel.Res

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