Re: [R] dependent p.values in R
dear michael thanks for your input i do agree in visual tests (indeed a recent paper in TAS=http://amstat.tandfonline.com/doi/abs/10.1080/00031305.2015.1077728 ) as a matter of fact, the test i'm after is simply for comparative purposes with some visualisation techniques best f Fernando Marmolejo-Ramos Postdoctoral Fellow Gösta Ekman Laboratory Department of Psychology Stockholm University Frescati Hagväg 9A, Stockholm 114 19 Sweden ph = +46 08-16 46 07 website = http://sites.google.com/site/fernandomarmolejoramos/ From: Michael Friendly <frien...@yorku.ca> Sent: Sunday, 10 July 2016 7:51 PM To: Fernando Marmolejo Ramos; Marc Girondot; r-help@r-project.org Subject: Re: dependent p.values in R Hello Fernando First, ask yourself what Gosta Ekman would have said if you asked him this question. He would have asked "does it make any difference to your conclusion?" He might also have asked you "Did you do a visual test?" Plot your data as a QQ plot or density plot? If the test doesn't make a difference in conclusions, it is a waste of your time (and ours) to worry about how to cite a 'combined p.value' (if such an animal exists), presumably to more decimal places than is worth worrying about. If the test *does* make a difference about normality, then ask yourself does the degree of non-normality impede my substantive conclusions. HTH, -ichael On 7/10/16 3:39 AM, Fernando Marmolejo Ramos wrote: > hi marc > > say i have a vector with some x number of observations > > x = c(23, 56, 123, . ) > > and i want to know how normal it is > > as there are many normality tests, i want to combine their p.values > > so, suppose i use shapiro.wilk, anderson darling and jarque bera and each > will give a pvalue > > i could simply average those p,values but to my knowledge that approach is > biased > > so i thought, in the same way there is a method to combine independent > pvalues (e.g. stouffer method); is there a way to combine dependent pvalues? > > best > > f > > > Fernando Marmolejo-Ramos > Postdoctoral Fellow > Gösta Ekman Laboratory > Department of Psychology > Stockholm University > Frescati Hagväg 9A, Stockholm 114 19 > Sweden > > ph = +46 08-16 46 07 > website = http://sites.google.com/site/fernandomarmolejoramos/ > > > > > From: Marc Girondot <marc.giron...@u-psud.fr> > Sent: Sunday, 10 July 2016 8:25 AM > To: r-help@r-project.org; Fernando Marmolejo Ramos > Subject: Re: [R] dependent p.values > > Le 09/07/2016 à 17:17, Fernando Marmolejo Ramos a écrit : >> hi all >> >> >> does any one know a method to combine dependent p.values? >> >> > First, it is a stats question and not a R question. So you could have > better chance to ask this in stackexchange forum. > Second, your question is difficult to answer without context: why > p.values are dependent ? Do they come from the same dataset ? Or are > they linked by an external source ? For both these situations, combining > dependent p.values seems strange for me. > When you will ask question in stackexchange, be more precise. > Sincerely, > Marc Girondot > > -- > __ > Marc Girondot, Pr > > Laboratoire Ecologie, Systématique et Evolution > Equipe de Conservation des Populations et des Communautés > CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079 > Bâtiment 362 > 91405 Orsay Cedex, France > > Tel: 33 1 (0)1.69.15.72.30 Fax: 33 1 (0)1.69.15.73.53 > e-mail: marc.giron...@u-psud.fr > Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html > Skype: girondot > > __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] dependent p.values in R
Hello Fernando First, ask yourself what Gosta Ekman would have said if you asked him this question. He would have asked "does it make any difference to your conclusion?" He might also have asked you "Did you do a visual test?" Plot your data as a QQ plot or density plot? If the test doesn't make a difference in conclusions, it is a waste of your time (and ours) to worry about how to cite a 'combined p.value' (if such an animal exists), presumably to more decimal places than is worth worrying about. If the test *does* make a difference about normality, then ask yourself does the degree of non-normality impede my substantive conclusions. HTH, -ichael On 7/10/16 3:39 AM, Fernando Marmolejo Ramos wrote: hi marc say i have a vector with some x number of observations x = c(23, 56, 123, . ) and i want to know how normal it is as there are many normality tests, i want to combine their p.values so, suppose i use shapiro.wilk, anderson darling and jarque bera and each will give a pvalue i could simply average those p,values but to my knowledge that approach is biased so i thought, in the same way there is a method to combine independent pvalues (e.g. stouffer method); is there a way to combine dependent pvalues? best f Fernando Marmolejo-Ramos Postdoctoral Fellow Gösta Ekman Laboratory Department of Psychology Stockholm University Frescati Hagväg 9A, Stockholm 114 19 Sweden ph = +46 08-16 46 07 website = http://sites.google.com/site/fernandomarmolejoramos/ From: Marc Girondot <marc.giron...@u-psud.fr> Sent: Sunday, 10 July 2016 8:25 AM To: r-help@r-project.org; Fernando Marmolejo Ramos Subject: Re: [R] dependent p.values Le 09/07/2016 à 17:17, Fernando Marmolejo Ramos a écrit : hi all does any one know a method to combine dependent p.values? First, it is a stats question and not a R question. So you could have better chance to ask this in stackexchange forum. Second, your question is difficult to answer without context: why p.values are dependent ? Do they come from the same dataset ? Or are they linked by an external source ? For both these situations, combining dependent p.values seems strange for me. When you will ask question in stackexchange, be more precise. Sincerely, Marc Girondot -- __ Marc Girondot, Pr Laboratoire Ecologie, Systématique et Evolution Equipe de Conservation des Populations et des Communautés CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079 Bâtiment 362 91405 Orsay Cedex, France Tel: 33 1 (0)1.69.15.72.30 Fax: 33 1 (0)1.69.15.73.53 e-mail: marc.giron...@u-psud.fr Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html Skype: girondot __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] dependent p.values in R
Fernando Marmolejo Ramos psychology.su.se> writes: > > hi marc > > say i have a vector with some x number of observations > > x = c(23, 56, 123, . ) > > and i want to know how normal it is > > as there are many normality tests, i want to combine their p.values > > so, suppose i use shapiro.wilk, anderson darling and >jarque bera and each will give a pvalue > > i could simply average those p,values but to my knowledge >that approach is biased > > so i thought, in the same way there is a method to combine >independent pvalues (e.g. stouffer method); is > there a way to combine dependent pvalues? > > best > > f > Yikes. There is extensive discussion, e.g. at http://tinyurl.com/normtests , that suggests that much of the time (if not always) formal statistical hypothesis tests for normality are misguided. Combining p-values from different tests feels like compounding the issue. In any case, I would definitely say that this a question for CrossValidated (http://stats.stackexchange.com), rather than r-help ... Ben Bolker __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] dependent p.values in R
hi marc say i have a vector with some x number of observations x = c(23, 56, 123, . ) and i want to know how normal it is as there are many normality tests, i want to combine their p.values so, suppose i use shapiro.wilk, anderson darling and jarque bera and each will give a pvalue i could simply average those p,values but to my knowledge that approach is biased so i thought, in the same way there is a method to combine independent pvalues (e.g. stouffer method); is there a way to combine dependent pvalues? best f Fernando Marmolejo-Ramos Postdoctoral Fellow Gösta Ekman Laboratory Department of Psychology Stockholm University Frescati Hagväg 9A, Stockholm 114 19 Sweden ph = +46 08-16 46 07 website = http://sites.google.com/site/fernandomarmolejoramos/ From: Marc Girondot <marc.giron...@u-psud.fr> Sent: Sunday, 10 July 2016 8:25 AM To: r-help@r-project.org; Fernando Marmolejo Ramos Subject: Re: [R] dependent p.values Le 09/07/2016 à 17:17, Fernando Marmolejo Ramos a écrit : > hi all > > > does any one know a method to combine dependent p.values? > > First, it is a stats question and not a R question. So you could have better chance to ask this in stackexchange forum. Second, your question is difficult to answer without context: why p.values are dependent ? Do they come from the same dataset ? Or are they linked by an external source ? For both these situations, combining dependent p.values seems strange for me. When you will ask question in stackexchange, be more precise. Sincerely, Marc Girondot -- __ Marc Girondot, Pr Laboratoire Ecologie, Systématique et Evolution Equipe de Conservation des Populations et des Communautés CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079 Bâtiment 362 91405 Orsay Cedex, France Tel: 33 1 (0)1.69.15.72.30 Fax: 33 1 (0)1.69.15.73.53 e-mail: marc.giron...@u-psud.fr Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html Skype: girondot __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
