From Torsten.Hothorn@rzmail.uni-erlangen.de  Mon Dec  2 09:40:07 2002
From: Torsten.Hothorn@rzmail.uni-erlangen.de (Torsten Hothorn)
Date: Mon Dec  2 09:40:07 2002
Subject: [Rd] generating contrast names
In-Reply-To: <5.1.0.14.2.20021201114748.01dcd870@mcmail.cis.mcmaster.ca>
Message-ID: <Pine.LNX.4.21.0212020931530.485-100000@artemis>


> Dear R-devel list members,
> 
> I'd like to suggest a more flexible procedure for generating contrast 
> names. I apologise for a relatively long message -- I want my proposal to 
> be clear.
> 
> I've never liked the current approach. For example, the names generated by 
> contr.treatment paste factor to level names with no separation between the 
> two; contr.sum simply numbers contrasts (I recall an exchange on the list 
> about this question); none of contr.* explicitly indicates what kind of 
> contrasts are generated. There are ways around these problems -- e.g., 
> beginning level names with an uppercase character -- but in my experience 
> it's common to see things like "regionmidwest".
> 
> I propose that the current behaviour remain the default, but that the 
> contr.* functions use optional "prefix" and "suffix" characters around 
> level names (or their equivalent) and an optional identifier string to 
> indicate what kind of contrasts are generated. As well, I propose that 
> contr.sum optionally identify contrasts by level names. All of these 
> behaviours could be controlled by options which, if unset, would produce 
> the current behaviour. There might be problems with my implementation of 
> these ideas, or with the ideas themselves -- but I expect that these will 
> arise in discussion. (Of course, there's nothing to prevent me from using 
> the functions that I show below, but I thought that these questions might 
> be of more general interest.)
> 

very interesting suggestion. We had the same problem within the multcomp
package and we decided to paste the factor names, levels and kind of
contrasts used into one single name where possible, for example Dunnett: 

> ci <- simint(minutes ~ blanket, data=recovery, conf.level=0.9,
+       alternative="less",eps=0.0001)
> summary(ci)

        Simultaneous 90% confidence intervals: Dunnett contrasts

Call: 
simint.formula(formula = minutes ~ blanket, data = recovery,
    conf.level = 0.9, alternative = "less", eps = 1e-04)

         Dunnett contrasts for factor blanket

Contrast matrix:
                      blanketb0 blanketb1 blanketb2 blanketb3
blanketb1-blanketb0 0        -1         1         0         0
blanketb2-blanketb0 0        -1         0         1         0
blanketb3-blanketb0 0        -1         0         0         1

where the factor is `blanket' at levels b0,b1,b2,b3. Of course this is
restricted to simple contrasts (like the difference here) but breaks for
more complicated situations (tetrade constrasts for example).

best,

Torsten




> Here, for example, are rewrites of contr.treatment and contr.sum (renamed 
> contr.Treatment and contr.Sum because of name-space issues) that implement 
> my suggestions, together with illustrations of their use:
> 
> ------------------------------------------------------------------------------------------------------------------------------
> 
>      contr.Treatment <- function (n, base = 1, contrasts = TRUE) {
>          if (is.numeric(n) && length(n) == 1)
>              levs <- 1:n
>          else {
>              levs <- n
>              n <- length(n)
>          }
>          lev.opt <- getOption("decorate.factor.levels")
>          pre <- if (is.null(lev.opt)) "" else lev.opt[1]
>          suf <- if (is.null(lev.opt)) "" else lev.opt[2]
>          dec <- getOption("decorate.contr.Treatment")
>          dec <- if (is.null(dec)) "" else dec
>          contr.names <- paste(pre, dec, levs, suf, sep="")
>          contr <- array(0, c(n, n), list(levs, contr.names))
>          diag(contr) <- 1
>          if (contrasts) {
>              if (n < 2)
>                  stop(paste("Contrasts not defined for", n - 1, "degrees of 
> freedom"))
>              if (base < 1 | base > n)
>                  stop("Baseline group number out of range")
>              contr <- contr[, -base, drop = FALSE]
>          }
>          contr
>      }
> 
>      contr.Sum <- function (n, contrasts = TRUE)
>      {
>          if (length(n) <= 1) {
>              if (is.numeric(n) && length(n) == 1 && n > 1)
>                  levels <- 1:n
>              else stop("Not enough degrees of freedom to define contrasts")
>          }
>          else levels <- n
>          lenglev <- length(levels)
>          lev.opt <- getOption("decorate.factor.levels")
>          pre <- if (is.null(lev.opt)) "" else lev.opt[1]
>          suf <- if (is.null(lev.opt)) "" else lev.opt[2]
>          dec <- getOption("decorate.contr.Sum")
>          dec <- if (is.null(dec)) "" else dec
>          show.lev <- getOption("contr.Sum.show.levels")
>          contr.names <- if ((!is.null(show.lev)) && show.lev) paste(pre, 
> dec, levels, suf, sep="")
>          if (contrasts) {
>              cont <- array(0, c(lenglev, lenglev - 1), list(levels,
>                  contr.names[-lenglev]))
>              cont[col(cont) == row(cont)] <- 1
>              cont[lenglev, ] <- -1
>          }
>          else {
>              cont <- array(0, c(lenglev, lenglev), list(levels, levels))
>              cont[col(cont) == row(cont)] <- 1
>          }
>          cont
>      }
> 
>      > library(car)
>         . . .
> 
>      > data(Prestige)
>      > attach(Prestige)
>      > contrasts(type) <- "contr.Treatment"
>      >
>      > lm(prestige ~ (income + education)*type) # default behaviour
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type)
> 
>      Coefficients:
>          (Intercept)              income           education 
> typeprof              typewc
>              2.275753            0.003522            1.713275 
> 15.351896          -33.536652
>      income:typeprof       income:typewc  education:typeprof 
> education:typewc
>              -0.002903           -0.002072            1.387809 
> 4.290875
> 
>      >
>      > options(decorate.factor.levels=c("[", "]")) # using brackets
>      > lm(prestige ~ (income + education)*type)
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type)
> 
>      Coefficients:
>              (Intercept)                income             education 
>      type[prof]              type[wc]
>                  2.275753              0.003522              1.713275 
>        15.351896            -33.536652
>      income:type[prof]       income:type[wc]  education:type[prof] 
> education:type[wc]
>              -0.002903             -0.002072              1.387809 
>      4.290875
> 
>      >
>      > options(decorate.contr.Treatment="T.") # naming contrast type
>      > lm(prestige ~ (income + education)*type)
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type)
> 
>      Coefficients:
>              (Intercept)                  income               education 
>          type[T.prof]
>                  2.275753                0.003522                1.713275 
>              15.351896
>                  type[T.wc]     income:type[T.prof]       income:type[T.wc] 
>   education:type[T.prof]
>                  -33.536652               -0.002903               -0.002072 
>                 1.387809
>      education:type[T.wc]
>                  4.290875
> 
>      >
>      > options(decorate.contr.Treatment=NULL)
>      > options(decorate.factor.levels=c("#", "")) # alternate style, using hash
>      > lm(prestige ~ (income + education)*type)
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type)
> 
>      Coefficients:
>              (Intercept)               income            education 
>    type#prof              type#wc
>              2.275753             0.003522             1.713275 
> 15.351896           -33.536652
>      income:type#prof       income:type#wc  education:type#prof 
> education:type#wc
>              -0.002903            -0.002072             1.387809 
>   4.290875
> 
>      >
>      > lm(prestige ~ (income + education)*type, 
> contrasts=list(type="contr.Sum")) # default behaviour
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type, contrasts = 
> list(type = "contr.Sum"))
> 
>      Coefficients:
>          (Intercept)           income        education            type1 
>         type2     income:type1     income:type2
>          -3.785832         0.001864         3.606169         6.061585 
>   21.413481         0.001658        -0.001244
>      education:type1  education:type2
>          -1.892895        -0.505086
> 
>      >
>      > options(contr.Sum.show.levels=TRUE)
>      > options(decorate.factor.levels=c("[", "]"))
>      > options(decorate.contr.Sum="S.")  # showing levels, brackets, 
> contrast type
>      > lm(prestige ~ (income + education)*type, 
> contrasts=list(type="contr.Sum"))
> 
>      Call:
>      lm(formula = prestige ~ (income + education) * type, contrasts = 
> list(type = "contr.Sum"))
> 
>      Coefficients:
>              (Intercept)                  income               education 
>            type[S.bc]
>                  -3.785832                0.001864                3.606169 
>                6.061585
>              type[S.prof]       income:type[S.bc]     income:type[S.prof] 
>   education:type[S.bc]
>                  21.413481                0.001658               -0.001244 
>               -1.892895
>      education:type[S.prof]
>                  -0.505086
> 
> ------------------------------------------------------------------------------------------------------------------------------
> 
> I look forward to people's comments.
>   John
> -----------------------------------------------------
> John Fox
> Department of Sociology
> McMaster University
> Hamilton, Ontario, Canada L8S 4M4
> email: jfox@mcmaster.ca
> phone: 905-525-9140x23604
> web: www.socsci.mcmaster.ca/jfox
> -----------------------------------------------------
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> http://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>



[Rd] generating contrast names
Torsten Hothorn