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R: McNemar Test for Comparison of Sensitivities and...

sesp.mcnemar

R Documentation

McNemar Test for Comparison of Sensitivities and Specificities

Description

Performs a McNemar Test for comparison of sensitivities and specificities of two binary diagnostic tests in a paired study design.

Usage

sesp.mcnemar(tab)

Arguments

tab

An object of class tab.paired.

Details

The test is performed as described by McNemar (1947).

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`), the `test.statistic` 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`), the `test.statistic` and the corresponding `p.value`.
`method`	The name of the method used to compare sensitivity and specificity, here “`mcnemar`”.

References

McNemar, Q. (1947). Note on the sampling error of the difference between correlated proportions or percentages. Psychometrika, 12(2):153-7.

Examples

data(Paired1) # Hypothetical study data
ftable(Paired1)
paired.layout <- tab.paired(d=d, y1=y1, y2=y2, data=Paired1)
paired.layout 
mcnem.results <- sesp.mcnemar(paired.layout)
str(mcnem.results)
mcnem.results
mcnem.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.mcnemar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sesp.mcnemar
> ### Title: McNemar Test for Comparison of Sensitivities and Specificities
> ### Aliases: sesp.mcnemar
> 
> ### ** 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

> mcnem.results <- sesp.mcnemar(paired.layout)
> str(mcnem.results)
List of 3
 $ sensitivity:List of 5
  ..$ test1         : num 0.88
  ..$ test2         : num 0.756
  ..$ diff          : num -0.124
  ..$ test.statistic: num 31.4
  ..$ p.value       : num 2.14e-08
 $ specificity:List of 5
  ..$ test1         : num 0.678
  ..$ test2         : num 0.797
  ..$ diff          : num 0.119
  ..$ test.statistic: num 12.8
  ..$ p.value       : num 0.000344
 $ method     : chr "mcnemar"
> mcnem.results
$sensitivity
$sensitivity$test1
[1] 0.8802661

$sensitivity$test2
[1] 0.7560976

$sensitivity$diff
[1] -0.1241685

$sensitivity$test.statistic
[1] 31.36

$sensitivity$p.value
[1] 2.143518e-08


$specificity
$specificity$test1
[1] 0.6781609

$specificity$test2
[1] 0.7969349

$specificity$diff
[1] 0.1187739

$specificity$test.statistic
[1] 12.81333

$specificity$p.value
[1] 0.0003441579


$method
[1] "mcnemar"

> mcnem.results$sensitivity["p.value"]
$p.value
[1] 2.143518e-08

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