[R-sig-Epi] Epidemiology Task View

[David Winsemius]

Thanks, Bendix;

I haven't been involved in teaching R and so have not gone looking for  
stuff I don't use. I think my suggestion to add links to functions or  
packages with ability to create ROC curves should be taken in the  
spirit of responding to Neil's request for ideas about this notion:  
"Thus I feel that it would be useful to mention which functions within  
a given package are useful for a particular task." My personal hope  
would be that the ROC producing functions which label the cutpoints on  
the curves by default should be given favorable notice. The widespread  
practice of publishing ROC curves which do not have cutpoint labels  
should be deplored.

I just looked at the Distributions Task View (prompted by the  
announcement of a revision). I notice that it first listed the  
facilities in its domain that are part of the base R and  later had  
sections for available packages that extended the functionality.

If such an organization were chosen, I would nominate mantelhaen.test  
as a base "epi" function of at least classical epidemiologic note.

http://sekhon.berkeley.edu/stats/html/mantelhaen.test.html
(It is interesting that so many other elaborations of that function  
have been written in the epi-packages.)

The coin package deserves mention for its provision of "exact" tests.

In searching further on the extensions or elaborations of the Mantel- 
Haenszel test I also found the package MDD (minimal detectable  
difference) and TSHRC (two stage hazard rate comparison) which look  
worthy of inclusion.

Because their vignettes start out with longitudinal data analysis and  
also include a chapter on meta-analysis as well as many worked  
examples of meat-and-potatoes methods in epidemiology, I think the  
HSAUR package and accompanying vignettes could have separate links.
http://cran.r-project.org/web/packages/HSAUR/
http://cran.r-project.org/web/packages/HSAUR/vignettes/

Best;
David Winsemius, MD, MPH
Heritage Labs


On Nov 24, 2008, at 3:20 AM, BXC (Bendix Carstensen) wrote:

> In the Epi package is a function ROC.
> Bendix
>
>> -----Original Message-----
>> From: r-sig-epi-bounces at stat.math.ethz.ch
>> [mailto:r-sig-epi-bounces at stat.math.ethz.ch] On Behalf Of
>> David Winsemius
>> Sent: 24. november 2008 05:52
>> To: r-sig-epi at stat.math.ethz.ch
>> Subject: Re: [R-sig-Epi] Epidemiology Task View
>>
>> Dear EpidemiRogists;
>>
>> " ... this I now have the following categories with suggested
>> packages...
>>
>> Case-Control : Epi, epiR epibasic, epicalc, epitools Cohort :
>> Epi epiR, epibasic epicalc epitools Incidence/Mortality :
>> Demography : demogR   "
>>
>>
>> I notice that there were no suggested entries for
>> Incidence/Mortality.
>> I would have thought that glm (for Poisson regression),
>> survival, and Harrell's Design/Hmisc packages would fit
>> there, although I also saw that there are also plans for a
>> cross-reference to the Survival Task View. I do not see a
>> problem in having some overlap with other Task Views at least
>> in "obvious" slots.
>>
>> I have also notice that analysis of ROC curves comes up in
>> r-help fairly commonly. I am not a big fan of these and do
>> not have any recommendations to propose as a result, but
>> maybe some notice of the potential problems could surround
>> references to packages that offer that desired facility?
>>
>> --
>> David Winsemius, MD
>> Heritage Labs
>>
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>>