Re: [R] LSD, HSD,...
On Tue, 17 Jul 2007, John Maindonald wrote: follow-on rant Stepwise regression variable selection methods make multiple post hoc comparisons. The Some do, but step() (the only way offered in base R) does not test at all. number of comparisons may be very large, vastly more than the half-dozen post-hoc comparisons that are common in an experimental design context. There is a disconnect here. The multiple testing issue is noted in pretty much every discussion of analysis of experimental data, but not commonly mentioned (at least in older texts) in discussions of stepwise regression, best subsets and related regression approaches. One reason for this silence may be that there is no ready HSD-like fix. The SEs and t-statistics that lm() gives for the finally selected model can be grossly optimistic. Running the analysis with the same model matrix, but with y-values that are noise, can give a useful wake-up call. Predictions from any single model will also have 'optimistic' standard errors. The major problem is attempting to select a single model and there is also a problem with assuming the model to be true (which Huber-White so-called 'sandwich' estimators try to avoid, and robust fitting does so more comprehensively). If you really want to assess uncertainty you need to take into account that the models are false and that several models may capture different aspects of the data and so be false in different ways. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 16 Jul 2007, at 8:00 PM, Simon Blomberg wrote: If you have a priori planned comparisons, you can just test those using linear contrasts, with no need to correct for multiple testing. If you do not, and you are relying on looking at the data and analysis to tell you which treatment means to compare, and you are considering several tests, then you should consider correcting for multiple testing. There is a large literature on the properties of the various tests. (Tukey HSD usually works pretty well for me.) rant Why do people design experiments with a priori hypotheses in mind, yet test them using post hoc comparison procedures? It's as if they are afraid to admit that they had hypotheses to begin with! Far better to test what you had planned to test using the more powerful methods for planned comparisons, and leave it at that. /rant On Mon, 2007-07-16 at 09:52 +0200, Adrian J. Montero Calvo wrote: Hi, I'm designing a experiment in order to compare the growing of several clones of a tree specie. It will be a complete randomized block design. How can I decide what model of mean comparision to choose? LSD, HSD,TukeyHSD, Duncan,...? Thanks in advance __ R-help@stat.math.ethz.ch 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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au __ R-help@stat.math.ethz.ch 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
Re: [R] LSD, HSD,...
Dear Adrain, You can see the library agricolae for the functions LSD.test, HSD.test, and Waller.test for Waller-Duncan. The criterion is that LSD is more used for few treatments and HSD for many treatments (more than 5) the test of Waller is Bayes and minimizes the two types of error (I or II). In experiment with clones, we prefer Waller-Duncan. Felipe de Mendiburu Statistician. International Potato Center Lima-Peru -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Adrian J. Montero Calvo Sent: Monday, July 16, 2007 2:52 AM To: r-help@stat.math.ethz.ch Subject: [R] LSD, HSD,... Hi, I'm designing a experiment in order to compare the growing of several clones of a tree specie. It will be a complete randomized block design. How can I decide what model of mean comparision to choose? LSD, HSD,TukeyHSD, Duncan,...? Thanks in advance __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] LSD, HSD,...
Hi, I'm designing a experiment in order to compare the growing of several clones of a tree specie. It will be a complete randomized block design. How can I decide what model of mean comparision to choose? LSD, HSD,TukeyHSD, Duncan,...? Thanks in advance __ R-help@stat.math.ethz.ch 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.
Re: [R] LSD, HSD,...
If you have a priori planned comparisons, you can just test those using linear contrasts, with no need to correct for multiple testing. If you do not, and you are relying on looking at the data and analysis to tell you which treatment means to compare, and you are considering several tests, then you should consider correcting for multiple testing. There is a large literature on the properties of the various tests. (Tukey HSD usually works pretty well for me.) rant Why do people design experiments with a priori hypotheses in mind, yet test them using post hoc comparison procedures? It's as if they are afraid to admit that they had hypotheses to begin with! Far better to test what you had planned to test using the more powerful methods for planned comparisons, and leave it at that. /rant On Mon, 2007-07-16 at 09:52 +0200, Adrian J. Montero Calvo wrote: Hi, I'm designing a experiment in order to compare the growing of several clones of a tree specie. It will be a complete randomized block design. How can I decide what model of mean comparision to choose? LSD, HSD,TukeyHSD, Duncan,...? Thanks in advance __ R-help@stat.math.ethz.ch 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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@stat.math.ethz.ch 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.
Re: [R] LSD, HSD,...
follow-on rant Stepwise regression variable selection methods make multiple post hoc comparisons. The number of comparisons may be very large, vastly more than the half-dozen post-hoc comparisons that are common in an experimental design context. There is a disconnect here. The multiple testing issue is noted in pretty much every discussion of analysis of experimental data, but not commonly mentioned (at least in older texts) in discussions of stepwise regression, best subsets and related regression approaches. One reason for this silence may be that there is no ready HSD-like fix. The SEs and t-statistics that lm() gives for the finally selected model can be grossly optimistic. Running the analysis with the same model matrix, but with y-values that are noise, can give a useful wake-up call. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 16 Jul 2007, at 8:00 PM, Simon Blomberg wrote: If you have a priori planned comparisons, you can just test those using linear contrasts, with no need to correct for multiple testing. If you do not, and you are relying on looking at the data and analysis to tell you which treatment means to compare, and you are considering several tests, then you should consider correcting for multiple testing. There is a large literature on the properties of the various tests. (Tukey HSD usually works pretty well for me.) rant Why do people design experiments with a priori hypotheses in mind, yet test them using post hoc comparison procedures? It's as if they are afraid to admit that they had hypotheses to begin with! Far better to test what you had planned to test using the more powerful methods for planned comparisons, and leave it at that. /rant On Mon, 2007-07-16 at 09:52 +0200, Adrian J. Montero Calvo wrote: Hi, I'm designing a experiment in order to compare the growing of several clones of a tree specie. It will be a complete randomized block design. How can I decide what model of mean comparision to choose? LSD, HSD,TukeyHSD, Duncan,...? Thanks in advance __ R-help@stat.math.ethz.ch 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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au __ R-help@stat.math.ethz.ch 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.
