rocThresholds: Display rate classification performance with thresholds...

Description Usage Arguments Value See Also Examples

Description

Display rate classification performance with thresholds visible at x-axis

A method to visualize the performance in the classification of synthesis, degradation and processing rates based on the comparison of the original simulated rates and the one obtained by the function modelRates. For each rate, classification performance is measured in terms of sensitivity and specificity using a ROC curve analysis. False negatives (FN) represent cases where the rate is identified as constant while it was simulated as varying. False positives (FP) represent cases where INSPEcT identified a rate as varying while it was simulated as constant. On the contrary, true positives (TP) and negatives (TN) are cases of correct classification of varying and constant rates, respectively. Consequently, at increasing brown p-values different sensitivity and specificity can be achieved.

Usage

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rocThresholds(object, object2, cTsh = NULL, bTsh = NULL, xlim = c(1e-05,
  1))

## S4 method for signature 'INSPEcT_model,INSPEcT_model'
rocThresholds(object, object2,
  cTsh = NULL, bTsh = NULL, xlim = c(1e-05, 1))

## S4 method for signature 'INSPEcT_model,INSPEcT'
rocThresholds(object, object2, cTsh = NULL,
  bTsh = NULL, xlim = c(1e-05, 1))

Arguments

object

An object of class INSPEcT_model, with true rates

object2

An object of class INSPEcT or INSPEcT_model, with modeled rates

cTsh

A numeric representing the threshold for the chi-squared test to consider a model as valid

bTsh

A numeric representing the threshold for the Brown's method to consider a rate as varying

xlim

A numeric representing limits for the x-axis (default is c(1-e-5,1))

Value

None

See Also

makeSimModel, makeSimDataset, rocCurve

Examples

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data('nascentInspObj', package='INSPEcT')	

simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
 
newTpts<-simRates@params$tpts
nascentInspObj_sim3<-makeSimDataset(object=simRates
                                   ,tpts=newTpts
                                   ,nRep=3
                                   ,NoNascent=FALSE
                                   ,seed=1)
nascentInspObj_sim3<-modelRates(nascentInspObj_sim3[1:10]
                               ,seed=1)

rocThresholds(simRates[1:10],nascentInspObj_sim3,bTsh=c(.01,.01,.05),cTsh=.1)

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.