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Last data update: 2014.03.03

R: Exact Binomial Test for Differences in Sensitivity and...

sesp.exactbinom

R Documentation

Exact Binomial Test for Differences in Sensitivity and Specificity

Description

Performs an exact binomial test for differences in sensitivity and specificity of two binary diagnostic tests in a paired study design.

Usage

sesp.exactbinom(tab)

Arguments

tab

An object of class tab.paired.

Details

The function performs a standard exact binomial test.

An exact binomial test is recommended when the number of patients with differing results for test 1 and test 2 (discordant pairs) is small, i.e. <20 (Zhou et al., 2011).

Value

A list containing:

`sensitivity`	A list containing `test1` (sensitivity of test 1), `test2` (specificity of test 2), `diff` (the difference in sensitivity, computed as `test2 - test1`) and the corresponding `p.value`.
`specificity`	A list containing `test1` (specificity of test 1), `test2` (specificity of test 2), `diff` (the difference in specificity, computed as `test2 - test1`) and the corresponding `p.value`.
`method`	The name of the method used to compare sensitivity and specificity, here “exactbinom”.

References

Zhou, X., Obuchowski, N., and McClish, D. (2011). Statistical Methods in Diagnostic Medicine. Wiley Series in Probability and Statistics. John Wiley & Sons, Hoboken, New Jersey, 2nd edition.

Examples

data(Paired1) # Hypothetical study data
ftable(Paired1)
paired.layout <- tab.paired(d=d, y1=y1, y2=y2, data=Paired1)
paired.layout 
exact.results <- sesp.exactbinom(paired.layout)
str(exact.results)
exact.results
exact.results$sensitivity["p.value"]

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DTComPair)
Loading required package: gee
Loading required package: PropCIs
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/DTComPair/sesp.exactbinom.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sesp.exactbinom
> ### Title: Exact Binomial Test for Differences in Sensitivity and
> ###   Specificity
> ### Aliases: sesp.exactbinom
> 
> ### ** Examples
> 
> data(Paired1) # Hypothetical study data
> ftable(Paired1)
     y2   0   1
d y1           
0 0     155  22
  1      53  31
1 0      32  22
  1      78 319
> paired.layout <- tab.paired(d=d, y1=y1, y2=y2, data=Paired1)
> paired.layout 
Two binary diagnostic tests (paired design)

Test1: 'y1'
Test2: 'y2'

Diseased:
           Test1 pos. Test1 neg. Total
Test2 pos.        319         22   341
Test2 neg.         78         32   110
Total             397         54   451

Non-diseased:
           Test1 pos. Test1 neg. Total
Test2 pos.         31         22    53
Test2 neg.         53        155   208
Total              84        177   261

> exact.results <- sesp.exactbinom(paired.layout)
> str(exact.results)
List of 3
 $ sensitivity:List of 4
  ..$ test1  : num 0.88
  ..$ test2  : num 0.756
  ..$ diff   : num -0.124
  ..$ p.value: num 1.59e-08
 $ specificity:List of 4
  ..$ test1  : num 0.678
  ..$ test2  : num 0.797
  ..$ diff   : num 0.119
  ..$ p.value: num 0.00045
 $ method     : chr "exactbinom"
> exact.results
$sensitivity
$sensitivity$test1
[1] 0.8802661

$sensitivity$test2
[1] 0.7560976

$sensitivity$diff
[1] -0.1241685

$sensitivity$p.value
[1] 1.590533e-08


$specificity
$specificity$test1
[1] 0.6781609

$specificity$test2
[1] 0.7969349

$specificity$diff
[1] 0.1187739

$specificity$p.value
[1] 0.000449648


$method
[1] "exactbinom"

> exact.results$sensitivity["p.value"]
$p.value
[1] 1.590533e-08

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>