Anne sent me off-line the error message.
============ error message starts here ==========
This error message:
"Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 Error in
`[.default`(xj, i) : type 'closure' d'indice incorrect"
appears after the following R codes:
library(gee)
attach(geefile) # stored in some spss directory
geereg <- gee(outcome ~ trial + group + trial*group + trial*group*beckce
+ trial*group*beckref, id = subject, data = geefile, na.omit, tol =
0.001, maxiter = 25, family = binomial, corstr = "exchangeable", silent
= TRUE)
The following command would have allowed me to modify the power so as to
obtain the sample size I have:
lmmpower(geereg, pct.change = 0.10, t = seq(0,6,3), power = 0.80)
================ end ===============
I am not an expert on R programming but in my experience that error has
meant that I was including as a parameter something which was not of the
type which the program expected. I would suggest as a first step not
using attach() at all and instead using data=geefile in the call to gee
or investigating the with() command if it does not allow a data parameter.
On 27/08/2019 12:25, Michael Dewey wrote:
Dear Anne
Can you resend the eror message which you accidentally sent only to me
please?
Michael
On 27/08/2019 08:02, CHATTON Anne wrote:
Dear Michael,
Thanks a lot for your suggestion. This is what I am trying to do with
R (longpower and gee packages). But I am getting stuck with a
confusing error message sent earlier I don't understand.
Best,
Anne
-----Message d'origine-----
De : Michael Dewey [mailto:li...@dewey.myzen.co.uk]
Envoyé : lundi, 26 août 2019 18:29
À : Marc Schwartz <marc_schwa...@me.com>; CHATTON Anne
<anne.chat...@hcuge.ch>
Cc : R-help <r-help@r-project.org>
Objet : Re: [R] Code modification for post-hoc power
Dear Anne
In addition to Marc's comments if you are forced to do this then,
assuming your package computes sample size from power then just feed
it a range of powers and find the one for which it calculates the
sample size you had. There is a more elegant way to do this using
uniroot but brute force should work.
Michael
On 26/08/2019 13:42, Marc Schwartz via R-help wrote:
On Aug 26, 2019, at 6:24 AM, CHATTON Anne via R-help
<r-help@r-project.org> wrote:
Hello everybody,
I am trying to accommodate the R codes provided by Donohue for
sample size calculation in the package "longpower" with lmmpower
function to estimate the post-hoc power (asked by a reviewer) of a
binary GEE model with a three-way interaction (time x condition x
continuous predictor) given a fixed sample size. In other words
instead of the sample size I would like to estimate the power of my
study.
Could anyone please help me to modify these codes as to obtain the
power I'm looking for.
I would really appreciate receiving any feedback on this subject.
Yours sincerely,
Anne
Hi,
Three comments:
1. Don't calculate post hoc power. Do a Google search and you will
find a plethora of papers and discussions on why not, including these:
The Abuse of Power: The Pervasive Fallacy of Power Calculations
for Data Analysis
The American Statistician, February 2001, Vol. 55, No. 1
https://www.vims.edu/people/hoenig_jm/pubs/hoenig2.pdf
Post Hoc Power: Tables and Commentary
https://stat.uiowa.edu/sites/stat.uiowa.edu/files/techrep/tr378.pdf
Observed power, and what to do if your editor asks for post-hoc
power analyses
http://daniellakens.blogspot.com/2014/12/observed-power-and-what-to-do
-if-your.html
Retraction Watch:
Statisticians clamor for retraction of paper by Harvard
researchers they say uses a “nonsense statistic”
https://retractionwatch.com/2019/06/19/statisticians-clamor-for-retrac
tion-of-paper-by-harvard-researchers-they-say-uses-a-nonsense-statisti
c/
PubPeer Comments on the paper cited in the above RW post:
https://pubpeer.com/publications/4399282A80691D9421B497E8316CF6
A discussion on Frank's Data Methods forum also related to the
same paper cited above:
"Observed Power" and other "Power" Issues
https://discourse.datamethods.org/t/observed-power-and-other-power-iss
ues/731/30
2. If you are still compelled (voluntarily or involuntarily), you may
want to review the vignette for the longpower package which may have
some insights, and/or contact the package maintainer for additional
guidance on how to structure the code. See the vignette here:
https://cran.r-project.org/web/packages/longpower/vignettes/longpower.
pdf
3. Don't calculate post hoc power.
Regards,
Marc Schwartz
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