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kruskal wallis post hoc?
7 messages · Mario Garrido, Tal Galili, Iasonas Lamprianou +2 more
Try to use "kruskalmc" in the package pgirmess I give one of my results
kruskal.test(rojos~mes)
Kruskal-Wallis chi-squared = 132.3091, df = 3, p-value < 2.2e-16
kruskalmc(rojos~mes)
Multiple comparison test after Kruskal-Wallis
p.value: 0.05
Comparisons
obs.dif critical.dif difference
abril-julio 134.52815 56.84018 TRUE
abril-junio 53.42185 58.73584 FALSE
abril-mayo 58.96383 59.73167 FALSE
julio-junio 187.95000 44.40539 TRUE
julio-mayo 75.56432 45.71446 TRUE
junio-mayo 112.38568 48.05106 TRUE
-----
Mario Garrido Escudero
PhD student
Dpto. de Biolog?a Animal, Ecolog?a, Parasitolog?a, Edafolog?a y Qca. Agr?cola
Universidad de Salamanca
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The Kruskal-Wallis test is a special case of the proportional odds ordinal logistic model. You can get any contrast you want by testing regression coefficients. In a couple of weeks the rms package's contrast function will allow for individual confidence intervals of effects that together have a 0.05 type I error, by using the multcomp package (called automatically from contrast.rms). Frank Iasonas Lamprianou wrote
Thank you for the result, I will have a look at the link. ? Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus
________________________________ From: Tal Galili <tal.galili@> To: Iasonas Lamprianou <lamprianou@> Cc: "r-help@" <r-help@> Sent: Thursday, 12 January 2012, 10:48 Subject: Re: [R] kruskal wallis post hoc? Hi?Iasonas , This is a stat question and not an R question. But the general answer is that it could happen :) The R question would have been if their is a Tukey HSD for kruskel.test,
the answer is yes:
http://stats.stackexchange.com/questions/17342/is-there-a-nonparametric-equivalent-of-tukey-hsd But if you didn't get any significant result from the pairwise comparison,
I would say that the post hoc correction wouldn't help you (it could be that the reason for this significance is based on some weird contrast...)
Best, Tal ----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili@ |? 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
---------------------------------------------------------------------------------------------- On Thu, Jan 12, 2012 at 8:35 AM, Iasonas Lamprianou <lamprianou@>
wrote:
Dear all,
I run a kruskal wallis test and found significant results. Then, I
conducted all pairwise comparisons and found no significant results. Could anyone please give me a hint as to why this happens or redirect me towards a specific web page where I can find more info? (I used alpha=5% and made no bonferroni or other correction for the pairwise comparisons)
Thank you ? Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus ? ? ? ?[[alternative HTML version deleted]]
______________________________________________ R-help@ 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.
[[alternative HTML version deleted]]
______________________________________________ R-help@ 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.
----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/kruskal-wallis-post-hoc-tp4288008p4288894.html Sent from the R help mailing list archive at Nabble.com.
On Jan 12, 2012, at 14:11 , Frank Harrell wrote:
The Kruskal-Wallis test is a special case of the proportional odds ordinal logistic model.
Eh? Can you elaborate on that? I would expect that at best it is equivalent to some _test_ in a polr-type model. It is never really clear what the model is when some groups are different and others not.
You can get any contrast you want by testing regression coefficients. In a couple of weeks the rms package's contrast function will allow for individual confidence intervals of effects that together have a 0.05 type I error, by using the multcomp package (called automatically from contrast.rms). Frank Iasonas Lamprianou wrote
Thank you for the result, I will have a look at the link. Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus
________________________________ From: Tal Galili <tal.galili@> To: Iasonas Lamprianou <lamprianou@> Cc: "r-help@" <r-help@> Sent: Thursday, 12 January 2012, 10:48 Subject: Re: [R] kruskal wallis post hoc? Hi Iasonas , This is a stat question and not an R question. But the general answer is that it could happen :) The R question would have been if their is a Tukey HSD for kruskel.test,
the answer is yes:
http://stats.stackexchange.com/questions/17342/is-there-a-nonparametric-equivalent-of-tukey-hsd But if you didn't get any significant result from the pairwise comparison,
I would say that the post hoc correction wouldn't help you (it could be that the reason for this significance is based on some weird contrast...)
Best, Tal ----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili@ | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
---------------------------------------------------------------------------------------------- On Thu, Jan 12, 2012 at 8:35 AM, Iasonas Lamprianou <lamprianou@>
wrote:
Dear all,
I run a kruskal wallis test and found significant results. Then, I
conducted all pairwise comparisons and found no significant results. Could anyone please give me a hint as to why this happens or redirect me towards a specific web page where I can find more info? (I used alpha=5% and made no bonferroni or other correction for the pairwise comparisons)
Thank you
Dr. Iasonas Lamprianou
Department of Social and Political Sciences
University of Cyprus
[[alternative HTML version deleted]]
______________________________________________ R-help@ 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. [[alternative HTML version deleted]] ______________________________________________ R-help@ 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. ----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/kruskal-wallis-post-hoc-tp4288008p4288894.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.
Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
Peter, The score test from the P.O. model for the global null hypothesis (k-1 degrees of freedom for comparing k groups) is almost exactly the Kruskal-Wallis test statistic. For the case where k=2 (Wilcoxon test) the numerator of the score test is exactly the numerator of the Wilcoxon-Mann-Whitney U test. Frank Peter Dalgaard-2 wrote
On Jan 12, 2012, at 14:11 , Frank Harrell wrote:
The Kruskal-Wallis test is a special case of the proportional odds ordinal logistic model.
Eh? Can you elaborate on that? I would expect that at best it is equivalent to some _test_ in a polr-type model. It is never really clear what the model is when some groups are different and others not.
You can get any contrast you want by testing regression coefficients. In a couple of weeks the rms package's contrast function will allow for individual confidence intervals of effects that together have a 0.05 type I error, by using the multcomp package (called automatically from contrast.rms). Frank Iasonas Lamprianou wrote
Thank you for the result, I will have a look at the link. Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus
________________________________ From: Tal Galili <tal.galili@> To: Iasonas Lamprianou <lamprianou@> Cc: "r-help@" <r-help@> Sent: Thursday, 12 January 2012, 10:48 Subject: Re: [R] kruskal wallis post hoc? Hi Iasonas , This is a stat question and not an R question. But the general answer is that it could happen :) The R question would have been if their is a Tukey HSD for kruskel.test,
the answer is yes:
http://stats.stackexchange.com/questions/17342/is-there-a-nonparametric-equivalent-of-tukey-hsd But if you didn't get any significant result from the pairwise comparison,
I would say that the post hoc correction wouldn't help you (it could be that the reason for this significance is based on some weird contrast...)
Best, Tal ----------------Contact
Details:-------------------------------------------------------
Contact me: Tal.Galili@ | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
---------------------------------------------------------------------------------------------- On Thu, Jan 12, 2012 at 8:35 AM, Iasonas Lamprianou <lamprianou@>
wrote:
Dear all,
I run a kruskal wallis test and found significant results. Then, I
conducted all pairwise comparisons and found no significant results. Could anyone please give me a hint as to why this happens or redirect me towards a specific web page where I can find more info? (I used alpha=5% and made no bonferroni or other correction for the pairwise comparisons)
Thank you
Dr. Iasonas Lamprianou
Department of Social and Political Sciences
University of Cyprus
[[alternative HTML version deleted]]
______________________________________________ R-help@ 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. [[alternative HTML version deleted]] ______________________________________________ R-help@ 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. ----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/kruskal-wallis-post-hoc-tp4288008p4288894.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@ 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.
-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes@ Priv: PDalgd@
______________________________________________ R-help@ 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.
----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/kruskal-wallis-post-hoc-tp4288008p4290363.html Sent from the R help mailing list archive at Nabble.com.