\name{sensitivity}
\alias{sensitivity}
\alias{sensitivity.default}
\alias{sensitivity.table}
\alias{sensitivity.matrix}
\alias{specificity}
\alias{specificity.default}
\alias{specificity.table}
\alias{specificity.matrix}
\alias{posPredValue}
\alias{posPredValue.default}
\alias{posPredValue.table}
\alias{posPredValue.matrix}
\alias{negPredValue}
\alias{negPredValue.default}
\alias{negPredValue.table}
\alias{negPredValue.matrix}
\title{Calculate sensitivity, specificity and predictive values}
\description{
 These functions calculate the sensitivity, specificity or predictive values of a measurement system compared to a 
  reference results (the truth or a gold standard). The measurement and "truth" 
  data must have the same two possible outcomes and one of the outcomes 
  must be thought of as a "positive" results.
 
 The sensitivity is defined as the proportion of positive results out of the number of
 samples which were actually positive. When there are no positive results, sensitivity is
 not defined and a value of \code{NA} is returned. Similarly, when there are no negative 
 results, specificity is not defined and a value of \code{NA} is returned. Similar 
 statements are true for predictive values.
 
 The positive predictive value is defined as the percent of  predicted positives that 
 are actually positive while the negative predictive value is defined as the percent 
 of  negative positives that are actually negative.
}
\usage{
sensitivity(data, ...)
\method{sensitivity}{default}(data, reference, positive = levels(reference)[1], na.rm = TRUE, ...)
\method{sensitivity}{table}(data, positive = rownames(data)[1], ...)
\method{sensitivity}{matrix}(data, positive = rownames(data)[1], ...)

specificity(data, ...)
\method{specificity}{default}(data, reference, negative = levels(reference)[-1], na.rm = TRUE, ...)
\method{specificity}{table}(data, negative = rownames(data)[-1], ...)
\method{specificity}{matrix}(data, negative = rownames(data)[-1], ...)

posPredValue(data, ...)
\method{posPredValue}{default}(data, reference, positive = levels(reference)[1], 
             prevalence = NULL, ...)
\method{posPredValue}{table}(data, positive = rownames(data)[1], prevalence = NULL, ...)
\method{posPredValue}{matrix}(data, positive = rownames(data)[1], prevalence = NULL, ...)

negPredValue(data, ...)
\method{negPredValue}{default}(data, reference, negative = levels(reference)[2], 
             prevalence = NULL, ...)
\method{negPredValue}{table}(data, negative = rownames(data)[-1], prevalence = NULL, ...)
\method{negPredValue}{matrix}(data, negative = rownames(data)[-1], prevalence = NULL, ...)

}

\arguments{
  \item{data}{for the default functions, a factor containing the discrete measurements. For the \code{table} or \code{matrix} functions, a table or matric object, respectively.}
  \item{reference}{a factor containing the reference values}
  \item{positive}{a character string that defines the factor level corresponding to 
  the "positive" results}
  \item{negative}{a character string that defines the factor level corresponding to 
  the "negative" results}  
  \item{prevalence}{a numeric value for the rate of the "positive" class of the data}
  \item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds}
  \item{...}{not currently used}
}

\details{
Suppose a 2x2 table with notation

 \tabular{rcc}{
                    \tab Reference \tab          \cr
         Predicted  \tab Event     \tab No Event \cr
         Event      \tab A         \tab B        \cr
         No Event   \tab C         \tab D        \cr
       }

The formulas used here are:
\deqn{Sensitivity = A/(A+C)}
\deqn{Specificity = D/(B+D)}
\deqn{Prevalence = (A+C)/(A+B+C+D)}
\deqn{PPV = (sensitivity * Prevalence)/((sensitivity*Prevalence) + ((1-specificity)*(1-Prevalence)))}
\deqn{NPV = (specificity * (1-Prevalence))/(((1-sensitivity)*Prevalence) + ((specificity)*(1-Prevalence)))}

See the references for discussions of the statistics.
}

\value{
   A number between 0 and 1 (or NA).
}

\author{Max Kuhn}
\references{Kuhn, M. (2008), ``Building predictive models in R using the caret package, '' \emph{Journal of Statistical Software}, (\url{http://www.jstatsoft.org/v28/i05/}).

Altman,  D.G., Bland,  J.M. (1994) ``Diagnostic tests 1: sensitivity and specificity,'' \emph{British Medical Journal}, vol 308, 1552.

Altman,  D.G., Bland,  J.M. (1994) ``Diagnostic tests 2: predictive values,'' \emph{British Medical Journal}, vol 309, 102. 
}
\seealso{\code{\link{confusionMatrix}}}

\examples{
\dontrun{
###################
## 2 class example

lvs <- c("normal", "abnormal")
truth <- factor(rep(lvs, times = c(86, 258)),
                levels = rev(lvs))
pred <- factor(
               c(
                 rep(lvs, times = c(54, 32)),
                 rep(lvs, times = c(27, 231))),               
               levels = rev(lvs))

xtab <- table(pred, truth)

sensitivity(pred, truth)
sensitivity(xtab)
posPredValue(pred, truth)
posPredValue(pred, truth, prevalence = 0.25)

specificity(pred, truth)
negPredValue(pred, truth)
negPredValue(xtab)
negPredValue(pred, truth, prevalence = 0.25)


prev <- seq(0.001, .99, length = 20)
npvVals <- ppvVals <- prev  * NA
for(i in seq(along = prev))
  {
    ppvVals[i] <- posPredValue(pred, truth, prevalence = prev[i])
    npvVals[i] <- negPredValue(pred, truth, prevalence = prev[i])
  }

plot(prev, ppvVals,
     ylim = c(0, 1),
     type = "l",
     ylab = "",
     xlab = "Prevalence (i.e. prior)")
points(prev, npvVals, type = "l", col = "red")
abline(h=sensitivity(pred, truth), lty = 2)
abline(h=specificity(pred, truth), lty = 2, col = "red")
legend(.5, .5,
       c("ppv", "npv", "sens", "spec"),
       col = c("black", "red", "black", "red"),
       lty = c(1, 1, 2, 2))

###################
## 3 class example

library(MASS)

fit <- lda(Species ~ ., data = iris)
model <- predict(fit)$class

irisTabs <- table(model, iris$Species)

## When passing factors, an error occurs with more
## than two levels
sensitivity(model, iris$Species)

## When passing a table, more than two levels can
## be used
sensitivity(irisTabs, "versicolor")
specificity(irisTabs, c("setosa", "virginica"))
}
}
\keyword{manip}
