Generalized Score Statistic for Comparison of Predictive Values

Performs a test for differences in (positive and negative) predictive values of two binary diagnostic tests using a generalized score statistic proposed by Leisenring, Alonzo and Pepe (2000).

Usage

pv.gs(tab)

Arguments

tab

An object of class tab.paired.

Value

A list containing:

ppv

A list with test1 (the positive predictive value of test 1), test2 (the positive predictive value of test 2), diff (the difference in positive predictive values, computed as test2 - test1), the test.statistic and the corresponding p.value.

npv

A list with test1 (the negative predictive value of test 1), test2 (the negative predictive value of test 2), diff (the difference in negative predictive values, computed as test2 - test1), the test.statistic and the corresponding p.value.

method

The name of the method used to compare predictive values, here “generalized score statistic (gs)”.

References

Leisenring, W., Alonzo, T., and Pepe, M. S. (2000). Comparisons of predictive values of binary medical diagnostic tests for paired designs. Biometrics, 56(2):345-51.

See also

pv.wgs and pv.rpv.

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
#> 
gs.results <- pv.gs(paired.layout)
str(gs.results)
#> List of 3
#>  $ ppv   : Named num [1:5] 0.8254 0.8655 0.0401 5.7112 0.0169
#>   ..- attr(*, "names")= chr [1:5] "test1" "test2" "diff" "test.statistic" ...
#>  $ npv   : Named num [1:5] 7.66e-01 6.54e-01 -1.12e-01 1.78e+01 2.47e-05
#>   ..- attr(*, "names")= chr [1:5] "test1" "test2" "diff" "test.statistic" ...
#>  $ method: chr "generalized score statistic (gs)"
gs.results
#> $ppv
#>          test1          test2           diff test.statistic        p.value 
#>     0.82536383     0.86548223     0.04011841     5.71124070     0.01685662 
#> 
#> $npv
#>          test1          test2           diff test.statistic        p.value 
#>   7.662338e-01   6.540881e-01  -1.121457e-01   1.778567e+01   2.472383e-05 
#> 
#> $method
#> [1] "generalized score statistic (gs)"
#> 
gs.results$ppv["p.value"]
#>    p.value 
#> 0.01685662