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Re: st: Cut-off point for ROC curve using parametric and non-parametric method


From   Pham Ngoc Minh <phamngocm@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: Cut-off point for ROC curve using parametric and non-parametric method
Date   Mon, 21 Jan 2013 22:25:18 +0900

Dear Roger,
Thank you very much for your helpful suggestion. While I am reading
how to use -somersd- package for estimating Youden index, I found
-senspec- package convenient to calculate sensitivity (sn) and
specificity (sp). However, I'm not sure about programs below are
accurate for estimating age-adjusted sn and sp and their subsequent
youden index.

logit metabo bmi age
predict p if e(sample)
senspec metabo p, sensitivity(sn) specificity(sp)
gen youdenid= sn-(1-sp)
egen youdenidmax= max(youdenid)
gen distance = sqrt((1-sn)^2 + (1-sp)^2)
egen mindistance = min(distance)
/* Identify cut-off point */
list sn sp  youdenidmax   distance bmi if abs(youdenid -youdenidmax)<0.000001
list sn sp  youdenid     mindistance bmi  if abs(distance -
mindistance)<0.000001

And evaluating threshold of BMI based on Youden index or shortest
distance from the curve to upper-left corner.

I'd appreciate your responses to ensure the above commands.
sincerely,
Pham Ngoc Minh

On Mon, Jan 21, 2013 at 1:30 AM, Roger B. Newson
<r.newson@imperial.ac.uk> wrote:
> If your aim is to estimate the Youden index, then you can use the -somersd-
> package, which you can download from SSC. The Youden index is an alternative
> name for Somers' D between 2 binary variables. The -somersd- package can
> also be used, together with -lincom-, to calculate the difference between 2
> Youden indices for 2 diagnostic tests for the same disease.
>
> I hope this helps.
>
> Best wishes
>
> Roger
>
> Roger B Newson BSc MSc DPhil
> Lecturer in Medical Statistics
> Respiratory Epidemiology and Public Health Group
> National Heart and Lung Institute
> Imperial College London
> Royal Brompton Campus
> Room 33, Emmanuel Kaye Building
> 1B Manresa Road
> London SW3 6LR
> UNITED KINGDOM
> Tel: +44 (0)20 7352 8121 ext 3381
> Fax: +44 (0)20 7351 8322
> Email: r.newson@imperial.ac.uk
> Web page: http://www.imperial.ac.uk/nhli/r.newson/
> Departmental Web page:
> http://www1.imperial.ac.uk/medicine/about/divisions/nhli/respiration/popgenetics/reph/
>
> Opinions expressed are those of the author, not of the institution.
>
>
> On 19/01/2013 03:38, Pham Ngoc Minh wrote:
>>
>> Dear Statalist,
>>
>> I want to construct age-adjusted (age is a continuous variable) optimal
>> cut-off points for body mass index (bmi)  and waist circumference (wc) in
>> determining metabolic syndrome (metabo) for a large study. My question is
>> how can I calculate sensitivity and specificity for bmi and wc with
>> adjustment for age, based on which I can calculate Youden index. For
>> non-parametric method, I know only about using command: roctab metabo bmi,
>> detail or senspec metabo bmi, se(varname1) spe(varname2)  (without
>> covariate adjustment). Moreover, how can I calculate age-adjusted
>> sensitivity and specificity using parametric ROC analysis. It is because
>>   using non-parametric method showed P less than 0.01, although AUC for
>> bmi and wc was somewhat similar.
>> Thank you for your guidance in advance.
>>
>> Pham Ngoc Minh
>> Thai Nguyen University Faculty of Public Health, Vietnam
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