[R] Sensitivity and Specificity

[greg holly]

THanks Michael for this.This is much appreciated. So, how can I estimate
the sensitivity and  specificity after having the prediction on testing
data. Any thoughts?

Kind regards,
Greg



On Mon, Oct 24, 2022 at 12:10 PM Michael Dewey <lists using dewey.myzen.co.uk>
wrote:

> So predict is a one-dimensional vector of predictions but you are
> treating it as a two-dimensional matrix (presumably you think those are
> the totals).
>
> Michael
>
> On 24/10/2022 16:50, greg holly wrote:
> > Hi Michael,
> >
> > I appreciate your writing. Here are what I have after;
> >
> >  > predict_testing <- ifelse(predict > 0.5,1,0)
> >  >
> >  > head(predict)
> >           1          2          3          5          7          8
> > 0.29006984 0.28370507 0.10761993 0.02204224 0.12873872 0.08127920
> >  >
> >  > # Sensitivity and Specificity
> >  >
> >  >
> >
> sensitivity<-(predict_testing[2,2]/(predict_testing[2,2]+predict_testing[2,1]))*100
> > Error in predict_testing[2, 2] : incorrect number of dimensions
> >  > sensitivity
> > function (data, ...)
> > {
> >      UseMethod("sensitivity")
> > }
> > <bytecode: 0x000002082a2f01d8>
> > <environment: namespace:caret>
> >  >
> >  >
> >
> specificity<-(predict_testing[1,1]/(predict_testing[1,1]+predict_testing[1,2]))*100
> > Error in predict_testing[1, 1] : incorrect number of dimensions
> >  > specificity
> > function (data, ...)
> > {
> >      UseMethod("specificity")
> > }
> > <bytecode: 0x000002082a2fa600>
> > <environment: namespace:caret>
> >
> > On Mon, Oct 24, 2022 at 10:45 AM Michael Dewey <lists using dewey.myzen.co.uk
> > <mailto:lists using dewey.myzen.co.uk>> wrote:
> >
> >     Rather hard to know without seeing what output you expected and what
> >     error message you got if any but did you mean to summarise your
> >     variable
> >     predict before doing anything with it?
> >
> >     Michael
> >
> >     On 24/10/2022 16:17, greg holly wrote:
> >      > Hi all R-Help ,
> >      >
> >      > After partitioning my data to testing and training (please see
> >     below), I
> >      > need to estimate the Sensitivity and Specificity. I failed. It
> >     would be
> >      > appropriate to get your help.
> >      >
> >      > Best regards,
> >      > Greg
> >      >
> >      >
> >      > inTrain <- createDataPartition(y=data$case,
> >      >                                 p=0.7,
> >      >                                 list=FALSE)
> >      > training <- data[ inTrain,]
> >      > testing  <- data[-inTrain,]
> >      >
> >      > attach(training)
> >      > #model training and prediction
> >      > data_training <- glm(case ~ age+BMI+Calcium+Albumin+meno_1, data =
> >      > training, family = binomial(link="logit"))
> >      >
> >      > predict <- predict(data_training, data_predict = testing, type =
> >     "response")
> >      >
> >      > predict_testing <- ifelse(predict > 0.5,1,0)
> >      >
> >      > # Sensitivity and Specificity
> >      >
> >      >
> >
>  sensitivity<-(predict_testing[2,2]/(predict_testing[2,2]+predict_testing[2,1]))*100
> >      >   sensitivity
> >      >
> >      >
> >
>  specificity<-(predict_testing[1,1]/(predict_testing[1,1]+predict_testing[1,2]))*100
> >      >   specificity
> >      >
> >      >       [[alternative HTML version deleted]]
> >      >
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> >
> >     --
> >     Michael
> >     http://www.dewey.myzen.co.uk/home.html
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> >
> >
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