[R] mimic SPSS contingency table results

[David Winsemius]

On Jul 8, 2010, at 5:55 AM, Petr PIKAL wrote:

> Thanks,
>
> now I have to think it over how to explain it to statistics  
> analphabet and
> to transfer to measured data. Is there any "simple theory for dummies"
> book to look into?

The Wikipedia entry for "positive predictive value" looks pretty  
standard. The way tests were often developed with the goal of  
estimating sensitivity and spcificity corresponds to case-control  
sampling strategies. This  effectively removes the capacity to  
estimate performance of test in the population.

-- 
David.

>
> Best regards
> Petr
>
>
>
> r-help-bounces at r-project.org napsal dne 08.07.2010 11:33:45:
>
>> Dear Petr,
>> the ppv / npv are the conditional probabilities beeing ill/not ill
>> having a positive/negative test result.
>> So the ppv is the proportion of correct positive tests of all  
>> positive
>> tests and respectively the npv the proportion of true negative  
>> tests of
>> all negative tests.
>> Alternatively, you can use Bayes theorem
>> PPV = P(D+|T+) = sensitivity*prevalence/(sensitivity*prevalence +
>> (1-specificity)*(1-prevalence))
>> D+ disease, T+ stands for "positive Test".
>>
>> With this, you can either use a normal approximation for a CI:
>> ppv+-1.96*sqrt( ppv*(1-ppv)/(# pos. tests)) or exact binomial  
>> confidence
>> limits,
>>
>> binom.test(number of true positive,number positive Tests)
>>
>> This works for all other proportions as well, eg sensitivity=P(T+|D 
>> +) :
>>
>> p<-15/24   #sensitivity
>> p+qnorm(.975)*c(-1,1)*sqrt(p*(1-p)/24)
>> binom.test(15,24)
>>
>> hth.
>>
>> Am 08.07.2010 10:59, schrieb Petr PIKAL:
>>> Dear all
>>>
>>> Seems that puzzles always come in packs. I was asked to help with  
>>> some
>
>>> statistics in blood analysis. (You can not refuse your wife's asks
> :-).
>>>
>>> She has contingency table for values IgVH mutation and ZAP  
>>> expression.
> I
>>> can do chi-square test (in R) and get a results, and with some
> literature
>>> I can try explain them. However she found an article in which they  
>>> use
>
>>> SPSS and use gamma-squared test?? Resulting p-value is different  
>>> from
> R
>>> chi square and seems to be close to fisher.test.
>>>
>>> They also get percentages for sensitivity and specificity with 95%
>>> confidence interval for these percentages and here I am lost. Also
>>> something called positive or negative predictive value is  
>>> something I
> do
>>> not know how to get from contingency table.
>>>
>>> Is it possible to get this in R? Where to look?
>>>
>>> Here are data
>>> mat <- matrix(c(22,7,9,15), 2,2)
>>>
>>>> From that matrix they get:
>>>
>>> positive statistical association between columns (IgVH mutation
> status)
>>> and rows (ZAP expression) with p=0.005
>>> which is close to fisher.test
>>>
>>> They also get sensitivity and specificity for prediction 62.5% (CI:
> 41-84)
>>> and 76% (CI: 59-93) respectively and positive predictive value 68%
> (CI:
>>> 46-90) and negative predictive value 71% (CI: 53-89)
>>>
>>> It seems that dividing observed value by marginal value is close but
>>> ***how I can get confidence intervals***?
>>> 22/31 resp. 15/22 or 22/29 resp. 15/24
>>>
>>> Any hint or explanation would be greatly appreciated.
>>>
>>> Best regards
>>> Petr
>>>
>>> chisq.test(mat)
>>>
>>>        Pearson's Chi-squared test with Yates' continuity correction
>>>
>>> data:  mat
>>> X-squared = 6.4582, df = 1, p-value = 0.01104
>>>
>>> fisher.test(mat)
>>>
>>>        Fisher's Exact Test for Count Data
>>>
>>> data:  mat
>>> p-value = 0.006152
>>> alternative hypothesis: true odds ratio is not equal to 1
>>> 95 percent confidence interval:
>>>  1.391323 20.407944
>>> sample estimates:
>>> odds ratio
>>>  5.057521
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> -- 
>> Eik Vettorazzi
>> Institut für Medizinische Biometrie und Epidemiologie
>> Universitätsklinikum Hamburg-Eppendorf
>>
>> Martinistr. 52
>> 20246 Hamburg
>>
>> T ++49/40/7410-58243
>> F ++49/40/7410-57790
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
West Hartford, CT