Re: [R] nested design
I would like to apply a nested ANOVA on my dataset, but I cannot find a
satisfying answer on how to implement it in R.
The simplest formula for a two-level nested design is resp~fac1/fac2
All of the models you list are equivalent to this after allowing for the fact
that R drops duplicated model terms. For example, fac1+fac1/fac2 expands to
fac1 + fac1 + fac1:fac2 ... which reduces to fac1+fac1:fac2.
All this is specified in some detail in ?formula.
S Ellison
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[R] nested design
Dear useRs, I would like to apply a nested ANOVA on my dataset, but I cannot find a satisfying answer on how to implement it in R. For example, fac2 is nested within fac1: df - data.frame(resp=rnorm(12), fac1=rep(LETTERS[1:2],each=6), fac2=rep(letters[1:6],each=2)) I have found three different ways that are said to be nested designs and I cannot understand whether they do the same or not. They all give similar results with this example but it might not always be the case. 1) following: http://www.personal.psu.edu/mar36/stat_461/nested/nested_designs.html summary(aov(resp~fac1+fac1/fac2, data=df)) 2) following: http://www.zoology.unimelb.edu.au/stats/Worksheets/nested%20two-way%20anova%20curdies.pdf summary(aov(resp~fac1+fac2%in%fac1, data=df)) This notation is very intuitive to me. 3) following: http://cran.r-project.org/doc/contrib/Vikneswaran-ED_companion.pdf summary(aov(resp~fac1+fac1:fac2, data=df)) For me, the : specifies the interaction. Is this then analogous since in a nested design the levels of fac2 are different in each level of fac1? So my questions are: Are there differences between these notations? If yes, which ones? And then, which notation should I prefer? And if they are identical, then why are there 3 (or more) ways to do it? Is there a reason not to have a single implementation? Thank you in advance, Ivan -- Ivan Calandra University of Franche-Comté Laboratoire Chrono-Environnement Bureau ATER -107L 16, Route de Gray 25030 Besançon Cedex, France ivan.calan...@univ-fcomte.fr +33 (0) 381 66 20 60 http://chrono-environnement.univ-fcomte.fr/spip.php?article1830 __ R-help@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.
[R] Nested design
Dear R-users, I have the following problem. I have performed an experiment for which I gathered a lot of data which I now want to test. The problem is that I cannot find an appropriate test in R (I am a starter) and someone might give me a hand. This is what I have done: Across three sites (Site), I have laid out five transects (Trans)...meaning five transects in each sites. In each transect I have five Microhabitats (MH) which should be regarded as subplots (I think). In each transect, every MH has the same position (so they are not randomized). I now want to test the effect of Site and MH (nested in Trans) on my response variables. This is what I do now: model-aov(Response~Site*MH+error(Trans/MH)) I get the following output: Error: Trans Df Sum Sq Mean Sq Site 1 0.030294 0.030294 Error: Trans:MH Df Sum Sq Mean Sq Site 1 10.8367 10.8367 MH3 0.2836 0.0945 Error: Within Df Sum Sq Mean Sq F valuePr(F) Site 2 0.92504 0.46252 11.7304 5.880e-05 *** MH 4 1.86688 0.46672 11.8370 5.645e-07 *** Site:MH8 1.17041 0.14630 3.7105 0.001615 ** Residuals 54 2.12917 0.03943 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 How do I read this? Any help appreciated! BTW: I also tried the lme function: model-lme(Response~Site*MH, random=~1|Trans/MH) but then the output is really complicated. - Dr. Bjorn JM Robroek Ecology and Biodiversity Group Institute of Environmental Biology, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands Email address: b.j.m.robr...@uu.nl http://www.researcherid.com/rid/C-4379-2008 Tel: +31-(0)30-253 6091 -- View this message in context: http://r.789695.n4.nabble.com/Nested-design-tp3557404p3557404.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
Re: [R] Nested design
Hi: Essentially, you are asking for free statistical advice, which is not within the intended scope of R-help. It's always better to consult with someone locally, and as luck would have it, your university apparently provides free statistical consulting for faculty and grad students: http://www.uu.nl/faculty/socialsciences/EN/organisation/Departments/methodologystatistics/consultation/Pages/default.aspx I would suggest that you contact someone there and have a face-to-face discussion rather than a possibly extended back-and-forth on the Net. Dennis On Sat, May 28, 2011 at 6:09 AM, unpeatable bjorn.robr...@gmail.com wrote: Dear R-users, I have the following problem. I have performed an experiment for which I gathered a lot of data which I now want to test. The problem is that I cannot find an appropriate test in R (I am a starter) and someone might give me a hand. This is what I have done: Across three sites (Site), I have laid out five transects (Trans)...meaning five transects in each sites. In each transect I have five Microhabitats (MH) which should be regarded as subplots (I think). In each transect, every MH has the same position (so they are not randomized). I now want to test the effect of Site and MH (nested in Trans) on my response variables. This is what I do now: model-aov(Response~Site*MH+error(Trans/MH)) I get the following output: Error: Trans Df Sum Sq Mean Sq Site 1 0.030294 0.030294 Error: Trans:MH Df Sum Sq Mean Sq Site 1 10.8367 10.8367 MH 3 0.2836 0.0945 Error: Within Df Sum Sq Mean Sq F value Pr(F) Site 2 0.92504 0.46252 11.7304 5.880e-05 *** MH 4 1.86688 0.46672 11.8370 5.645e-07 *** Site:MH 8 1.17041 0.14630 3.7105 0.001615 ** Residuals 54 2.12917 0.03943 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 How do I read this? Any help appreciated! BTW: I also tried the lme function: model-lme(Response~Site*MH, random=~1|Trans/MH) but then the output is really complicated. - Dr. Bjorn JM Robroek Ecology and Biodiversity Group Institute of Environmental Biology, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands Email address: b.j.m.robr...@uu.nl http://www.researcherid.com/rid/C-4379-2008 Tel: +31-(0)30-253 6091 -- View this message in context: http://r.789695.n4.nabble.com/Nested-design-tp3557404p3557404.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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. __ R-help@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.
Re: [R] Nested design
Dear Dennis, In my opinion I am not at all asking for any stats help, just a question how to read this output. Thanks, Bjorn - Dr. Bjorn JM Robroek Ecology and Biodiversity Group Institute of Environmental Biology, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands Email address: b.j.m.robr...@uu.nl http://www.researcherid.com/rid/C-4379-2008 Tel: +31-(0)30-253 6091 -- View this message in context: http://r.789695.n4.nabble.com/Nested-design-tp3557404p3557472.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
Re: [R] Nested design
Hi, If you are not asking for stats help, then do you understand the model and are just confused by how R labels it? We can help match R's labels to the ones you are used to, if you tell us what you are used to. Cheers, Josh On Sat, May 28, 2011 at 6:54 AM, unpeatable bjorn.robr...@gmail.com wrote: Dear Dennis, In my opinion I am not at all asking for any stats help, just a question how to read this output. Thanks, Bjorn - Dr. Bjorn JM Robroek Ecology and Biodiversity Group Institute of Environmental Biology, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands Email address: b.j.m.robr...@uu.nl http://www.researcherid.com/rid/C-4379-2008 Tel: +31-(0)30-253 6091 -- View this message in context: http://r.789695.n4.nabble.com/Nested-design-tp3557404p3557472.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@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.
Re: [R] Nested design
Date: Sat, 28 May 2011 09:33:03 -0700 From: jwiley.ps...@gmail.com To: bjorn.robr...@gmail.com CC: r-help@r-project.org Subject: Re: [R] Nested design Hi, If you are not asking for stats help, then do you understand the model and are just confused by how R labels it? We can help match R's labels to the ones you are used to, if you tell us what you are used to. I would not suggest as a rule to use a tool to validate itself but you can use R to make sure your interpretation of other R output is right by giving contrived datasets to the analysis package and see what you get back. Comparison can be to examples from text book or your own paper and pencil analysis. This is also a good way to learn things from basic terms to things like sign or unit conventions in different fields etc. You can generate samples from normal distro and feed that to the questionable package to see what comes back. Cheers, Josh On Sat, May 28, 2011 at 6:54 AM, unpeatable wrote: Dear Dennis, In my opinion I am not at all asking for any stats help, just a question how to read this output. Thanks, Bjorn - Dr. Bjorn JM Robroek Ecology and Biodiversity Group Institute of Environmental Biology, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands Email address: b.j.m.robr...@uu.nl http://www.researcherid.com/rid/C-4379-2008 Tel: +31-(0)30-253 6091 -- View this message in context: http://r.789695.n4.nabble.com/Nested-design-tp3557404p3557472.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@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. __ R-help@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.
[R] nested design
This is a nested design where team is nested in group. Method is fixed, while team and group are random. Is this the correct R code for this? gunload.aov - aov(rounds ~ method+group + Error((team %in% group)/method),data=gunload, qr=T) -- View this message in context: http://n4.nabble.com/nested-design-tp1569449p1569449.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
