[R-sig-Epi] Problem with DiagnosisMed package

[David Winsemius]

On Feb 1, 2010, at 4:10 PM, Amy Mikhail wrote:

> Dear R epidemiologists,
>
> I have been trying to find the simplest possible way to:
>
> (a) Create contingency tables,

?xtabs

> (b) Perform a chi square or fisher exact test on those contingency  
> tables,
> and

?chisq.test
?fisher.test


> (c) Determine sensitivity, specificity and predictive values etc  
> from a
> rapid test compared to gold standard.

Those concepts are more typically used with a continuous test result  
such as hemoglobin or ALT that is predicting a "diagnosis". The ROC  
plotting facilities in the Epi package are quite good if that were the  
data situation.


>
> More on my contingency table problem later, but for now problem (c):
>
> I tried to use the DiagnosisMed package, since by the description it  
> seemed
> I could use my two variables (gold standard test results and results  
> of test
> being evaluated) directly with the function (i.e. no need to make a  
> 2x2
> table first since the function would do this as well).
>
> I carefully coded my gold standard and test results as "positive" and
> "negative", and removed all NAs.  I converted both columns from  
> character to
> factors (which now had 2 levels).
>
> Then I tried this:
>
> diagnosis(ref, r1a)

No experience with that package.

>
> where ref is my gold standard and r1a is my test being evaluated.
>
> I got this error:
>
> Error in uniroot(function(or) { :
>  f() values at end points not of opposite sign
>
> I can't understand why - the data is as clean as a whistle.  Here is  
> the
> summary, fyi (six tests are being evaluated against one gold  
> standard):
>
> summary(analc)
>       ref            r1a            r1b            r2a
> r2b            r3a            r3b
> negative: 18   negative: 19   negative: 19   negative: 36    
> negative: 33
> negative: 23   negative: 22
> positive:202   positive:201   positive:201   positive:184   positive: 
> 187
> positive:197   positive:198
>
> Did I misunderstand?  Does the diagnosis function require a 2x2  
> table as
> input?
>
> Many thanks,
> Amy
-- 

David Winsemius, MD
Heritage Laboratories
West Hartford, CT