Dear GMM, > -----Original Message----- > From: Manzoni, GianMauro [mailto:gm.manz...@auxologico.it] > Sent: July-30-12 9:49 AM > To: John Fox > Cc: r-help@r-project.org; Greg Snow > Subject: Re: [R] MANOVA polynomial contrasts > > Dear Prof. John Fox, > thus all I should do to test quadratic and cubic effects is to change the second > argument of the linearHypothesis() function, right? > So, for testing the cubic effect: > > linearHypothesis (mod, "f.C")
Yes, but wouldn't it have been faster simply to try it? Also see ?linearHypothesis. > > Is there a chapter or paragragh about contrasts in your book "An R > companion for applied regression"? There are discussions of contrasts and of linear hypotheses about coefficients, though not in the context of *multivariate* linear models; that's the subject of an on-line appendix, at < http://socserv.socsci.mcmaster.ca/jfox/Books/Companion/appendix/Appendix-Mul tivariate-Linear-Models.pdf>. Best, John > > Best regards, > GMM > > 2012/7/30 John Fox <j...@mcmaster.ca> > > > Dear Gian Mauro, > > > On Mon, 30 Jul 2012 14:44:44 +0200 > "Manzoni, GianMauro" <gm.manz...@auxologico.it> wrote: > > Dear Prof. John Fox, > > thank you very much for your suggestions. > > However, I still do not know how to use the contrasts after > generating them. > > Once I generate the matrix with the polynomial contrasts, what are > the > > following steps toward the statistical test? > > > Here's a contrived example, which uses the Anova() and > linearHypothesis() functions in the car package: > > ----- snip ------ > > > Y <- matrix(rnorm(300), 100, 3) > > colnames(Y) <- c("y1", "y2", "y3") > > f <- ordered(sample(letters[1:4], 100, replace=TRUE)) > > (mod <- lm(Y ~ f)) > > Call: > lm(formula = Y ~ f) > > Coefficients: > y1 y2 y3 > (Intercept) 0.06514 -0.01683 -0.13787 > f.L -0.37837 0.18309 0.29736 > f.Q -0.02102 -0.39894 0.08455 > f.C 0.05898 0.09358 -0.17634 > > > Anova(mod) > > Type II MANOVA Tests: Pillai test statistic > Df test stat approx F num Df den Df Pr(>F) > f 3 0.11395 1.2634 9 288 0.2566 > > > linearHypothesis(mod, "f.L") > > Sum of squares and products for the hypothesis: > y1 y2 y3 > y1 3.607260 -1.745560 -2.834953 > y2 -1.745560 0.844680 1.371839 > y3 -2.834953 1.371839 2.227995 > > Sum of squares and products for error: > y1 y2 y3 > y1 86.343376 -8.054928 -3.711756 > y2 -8.054928 95.473020 2.429151 > y3 -3.711756 2.429151 89.593163 > > Multivariate Tests: > Df test stat approx F num Df den Df Pr(>F) > Pillai 1 0.0648520 2.172951 3 94 0.096362 . > Wilks 1 0.9351480 2.172951 3 94 0.096362 . > Hotelling-Lawley 1 0.0693495 2.172951 3 94 0.096362 . > Roy 1 0.0693495 2.172951 3 94 0.096362 . > --- > Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > > ----- snip ------ > > You could do similar tests for the quadratic and cubic contrasts. > > I hope this helps, > > John > > ------------------------------------------------ > John Fox > Sen. William McMaster Prof. of Social Statistics > Department of Sociology > McMaster University > Hamilton, Ontario, Canada > http://socserv.mcmaster.ca/jfox/ > > > > > A whole example would be very useful. > > > > Thank you very much in advance! > > > > Best regards, > > Gian Mauro Manzoni > > > > > > > > 2012/7/25 John Fox <j...@mcmaster.ca> > > > > > Dear Gian, > > > > > > How contrasts are created by default is controlled by the > contrasts option: > > > > > > > getOption("contrasts") > > > unordered ordered > > > "contr.treatment" "contr.poly" > > > > > > So, unless you've changed this option, contr.poly() will be used to > > > generate orthogonal polynomial contrasts for an ordered factor, > and you > > > therefore need do nothing special to get this result. For example: > > > > > > > (f <- ordered(sample(letters[1:3], 10, replace=TRUE))) > > > [1] c c a a c c b c a c > > > Levels: a < b < c > > > > > > > round(contrasts(f), 4) > > > .L .Q > > > [1,] -0.7071 0.4082 > > > [2,] 0.0000 -0.8165 > > > [3,] 0.7071 0.4082 > > > > > > For more information, see section 11 on statistical models in the > manual > > > "An Introduction to R," which is part of the standard R > distribution, and > > > in particular sections 11.1 and 11.1.1. > > > > > > I hope that this clarifies the issue. > > > > > > Best, > > > John > > > > > > ------------------------------------------------ > > > John Fox > > > Sen. William McMaster Prof. of Social Statistics > > > Department of Sociology > > > McMaster University > > > Hamilton, Ontario, Canada > > > http://socserv.mcmaster.ca/jfox/ > > > > > > On Wed, 25 Jul 2012 11:58:30 +0200 > > > "Manzoni, GianMauro" <gm.manz...@auxologico.it> wrote: > > > > Dear Greg Snow, > > > > thank you very much for your suggestions. However, I need an > example in > > > > order to understand fully. > > > > I was told that, given the ordinal factor, I do not need to specify > the > > > > contr.poly function because R does it automatically. > > > > However, I don not know if I have to add an argument into the > > > manova/anova > > > > function or something else. > > > > Please write me an illustrative example. > > > > Many thanks. > > > > > > > > Best regards, > > > > Gian Mauro Manzoni > > > > > > > > 2012/7/25 Greg Snow <538...@gmail.com> > > > > > > > > > You should not need to write them yourself. Look at the > contr.poly > > > > > function along with the C function (Note uppercase C) or the > contrasts > > > > > function. > > > > > > > > > > > > > > > On Monday, July 23, 2012, Manzoni, GianMauro wrote: > > > > > > > > > >> Dear all, > > > > >> I am quite new to R and I am having trouble writing the > polynomial > > > > >> contrasts for an ordinal factor in MANOVA. > > > > >> # I have a model such as this > > > > >> fit<-manova(cbind(Y1,Y2,Y3)~Groups,data=Events) # where > groups is an > > > > >> ordinal factor with 4 levels > > > > >> # how to set polynomial contrasts for the "Groups" factor ? > > > > >> > > > > >> Thank you very much in advance for any help! > > > > >> > > > > >> Best regards, > > > > >> Mauro > > > > >> > > > > >> -- > > > > >> Dr. Gian Mauro Manzoni > > > > >> PhD, PsyD > > > > >> Psychology Research Laboratory > > > > >> San Giuseppe Hospital > > > > >> Istituto Auxologico Italiano > > > > >> Verbania - Italy > > > > >> e-mail: gm.manz...@auxologico.it > > > > >> cell. phone +39 338 4451207 <tel:%2B39%20338%204451207> > > > > >> Tel. +39 0323 514278 <tel:%2B39%200323%20514278> > > > > >> > > > > >> [[alternative HTML version deleted]] > > > > >> > > > > >> ______________________________________________ > > > > >> 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. > > > > >> > > > > > > > > > > > > > > > -- > > > > > Gregory (Greg) L. Snow Ph.D. > > > > > 538...@gmail.com > > > > > > > > > > > > > > > > > > > > > -- > > > > Dr. Gian Mauro Manzoni > > > > PhD, PsyD > > > > Psychology Research Laboratory > > > > San Giuseppe Hospital > > > > Istituto Auxologico Italiano > > > > Verbania - Italy > > > > e-mail: gm.manz...@auxologico.it > > > > cell. phone +39 338 4451207 <tel:%2B39%20338%204451207> > > > > Tel. +39 0323 514278 <tel:%2B39%200323%20514278> > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > ______________________________________________ > > > > 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. > > > > > > > > > > > > > > > -- > > Dr. Gian Mauro Manzoni > > PhD, PsyD > > Psychology Research Laboratory > > San Giuseppe Hospital > > Istituto Auxologico Italiano > > Verbania - Italy > > e-mail: gm.manz...@auxologico.it > > cell. phone +39 338 4451207 <tel:%2B39%20338%204451207> > > Tel. +39 0323 514278 <tel:%2B39%200323%20514278> > > > > > > -- > Dr. Gian Mauro Manzoni > PhD, PsyD > Psychology Research Laboratory > San Giuseppe Hospital > Istituto Auxologico Italiano > Verbania - Italy > e-mail: gm.manz...@auxologico.it > cell. phone +39 338 4451207 > Tel. +39 0323 514278 ______________________________________________ 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.
