Further to Duncan's comments, you can control factor codings via options(contrasts=), by setting contrasts() on the factor and via C(). This does enable you to code an ordered factor as a linear term, for example.
The only place I know that this is discussed in any detail is in Bill Venables' account in MASS chapter 6. On Sat, 5 Jan 2008, Duncan Murdoch wrote: > On 05/01/2008 7:16 PM, David Winsemius wrote: >> David Winsemius <[EMAIL PROTECTED]> wrote in >> news:[EMAIL PROTECTED]: >> >>> I have a variable which is roughly age categories in decades. In the >>> original data, it came in coded: >>>> str(xxx) >>> 'data.frame': 58271 obs. of 29 variables: >>> $ issuecat : Factor w/ 5 levels "0 - 39","40 - 49",..: 1 1 1 >>> 1... >>> snip >>> >>> I then defined issuecat as ordered: >>>> xxx$issuecat<-as.ordered(xxx$issuecat) >>> When I include issuecat in a glm model, the result makes me think I >>> have asked R for a linear+quadratic+cubic+quartic polynomial fit. >>> The results are not terribly surprising under that interpretation, >>> but I was hoping for only a linear term (which I was taught to >>> call a "test of trend"), at least as a starting point. >>> >>>> age.mdl<-glm(actual~issuecat,data=xxx,family="poisson") >>>> summary(age.mdl) >>> Call: >>> glm(formula = actual ~ issuecat, family = "poisson", data = xxx) >>> >>> Deviance Residuals: >>> Min 1Q Median 3Q Max >>> -0.3190 -0.2262 -0.1649 -0.1221 5.4776 >>> >>> Coefficients: >>> Estimate Std. Error z value Pr(>|z|) >>> (Intercept) -4.31321 0.04865 -88.665 <2e-16 *** >>> issuecat.L 2.12717 0.13328 15.960 <2e-16 *** >>> issuecat.Q -0.06568 0.11842 -0.555 0.579 >>> issuecat.C 0.08838 0.09737 0.908 0.364 >>> issuecat^4 -0.02701 0.07786 -0.347 0.729 >>> >>> This also means my advice to a another poster this morning may have >>> been misleading. I have tried puzzling out what I don't understand >>> by looking at indices or searching in MASSv2, the Blue Book, >>> Thompson's application of R to Agresti's text, and the FAQ, so far >>> without success. What I would like to achieve is having the lowest >>> age category be a reference category (with the intercept being the >>> log-rate) and each succeeding age category be incremented by 1. The >>> linear estimate would be the log(risk-ratio) for increasing ages. I >>> don't want the higher order polynomial estimates. Am I hoping for >>> too much? >>> >> >> I acheived what I needed by: >> >>> xxx$agecat<-as.numeric(xxx$issuecat) >>> xxx$agecat<-xxx$agecat-1 >> >> The results look quite sensible: >>> exp.mdl<-glm(actual~gendercat+agecat+smokecat, data=xxx, >> family="poisson", offset=expected) >>> summary(exp.mdl) >> >> Call: >> glm(formula = actual ~ gendercat + agecat + smokecat, family = >> "poisson", >> data = xxx, offset = expected) >> >> Deviance Residuals: >> Min 1Q Median 3Q Max >> -0.5596 -0.2327 -0.1671 -0.1199 5.2386 >> >> Coefficients: >> Estimate Std. Error z value Pr(>|z|) >> (Intercept) -5.89410 0.11009 -53.539 < 2e-16 *** >> gendercatMale 0.29660 0.06426 4.615 3.92e-06 *** >> agecat 0.66143 0.02958 22.360 < 2e-16 *** >> smokecatSmoker 0.22178 0.07870 2.818 0.00483 ** >> smokecatUnknown 0.02378 0.08607 0.276 0.78233 >> >> I remain curious about how to correctly control ordered factors, or I >> should just simply avoid them. > > If you're using a factor, R generally assumes you mean each level is a > different category, so you get levels-1 parameters. If you don't want > this, you shouldn't use a factor: convert to a numeric scale, just as > you did. > > Duncan Murdoch > > ______________________________________________ > 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. > -- 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, UK Fax: +44 1865 272595 ______________________________________________ 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.
