-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net]
Sent: 24. november 2008 17:11
To: BXC (Bendix Carstensen)
Cc: r-sig-epi at stat.math.ethz.ch
Subject: Re: [R-sig-Epi] Epidemiology Task View
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