# Re: [R] contr.treatments query

From: Ted Harding <Ted.Harding_at_manchester.ac.uk>
Date: Tue, 20 May 2008 10:14:30 +0100 (BST)

On 20-May-08 06:10:48, Prof Brian Ripley wrote:

```>>From ?contrasts

> Usage:

>       contrasts(x, how.many) <- value
```
> ...
> how.many: How many contrasts should be made. Defaults to one less than
> the number of levels of 'x'. This need not be the same as
> the number of columns of 'ctr'.
>
> so that is 2 in your example, and it takes the first 2 of the 3 you
> supplied.
> (The posting guide does ask you to read the help before posting.)

I had read it (and other), and it did not help me. The point of my query was not the fact of getting 2 columns; I was expecting that. The point was the difference, after

N<-factor(sample(c(1,2,3),1000,replace=TRUE))

between

[A]
contr.treatment(3, base=1, contrasts=TRUE)

```  #   2 3
# 1 0 0
# 2 1 0
# 3 0 1

```

i.e. omitting "level 1" as implied by

"contr <- contr[, -base, drop = FALSE]"

in the code for contr.treatment(), and the result of

[B]
contrasts(N)<-contr.treatment(3, base=1, contrasts=FALSE)   contrasts(N)

```  #   1 2
# 1 1 0
# 2 0 1
# 3 0 0

```

i.e. omitting "level 3", despite having had the contrasts assigned from exactly the same expression as in [A].

Possibly Bill Venables' comments may contain the clue; but I would need to experiment to see whether that it is fact the root cause.

With thanks,
Ted.

```>> Hi Folks,
>> I'm a bit puzzled by the following (example):
>>
>> N<-factor(sample(c(1,2,3),1000,replace=TRUE))
>> unique(N)
>> # [1] 3 2 1
>> # Levels: 1 2 3
>>
>> So far so good. Now:
>>
>> contrasts(N)<-contr.treatment(3, base=1, contrasts=FALSE)
>> contrasts(N)
>> #   1 2
>> # 1 1 0
>> # 2 0 1
>> # 3 0 0
>>
>> whereas:
>>
>> contr.treatment(3, base=1, contrasts=FALSE)
>> #   1 2 3
>> # 1 1 0 0
>> # 2 0 1 0
>> # 3 0 0 1
>>
>> contr.treatment(3, base=1, contrasts=TRUE)
>> #   2 3
>> # 1 0 0
>> # 2 1 0
>> # 3 0 1
>>
>> I can follow the last two fine -- they are what is implied
>> by the code for contr.treatment().
>>
>> Likewise:
>>
>> contrasts(factor(Nlevs <-c(1,2,3)))
>> #   2 3
>> # 1 0 0
>> # 2 1 0
>> # 3 0 1
>>
>> But why the different result when applied to N?
>>
>> With thanks,
>> Ted.
>>
>> --------------------------------------------------------------------
>> E-Mail: (Ted Harding) <Ted.Harding_at_manchester.ac.uk>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 20-May-08                                       Time: 01:12:30
>> ------------------------------ XFMail ------------------------------
>>
>> ______________________________________________
>> R-help_at_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, ripley@stats.ox.ac.uk
> 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_at_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.

E-Mail: (Ted Harding) <Ted.Harding_at_manchester.ac.uk> Fax-to-email: +44 (0)870 094 0861
```Date: 20-May-08                                       Time: 10:14:26
------------------------------ XFMail ------------------------------

______________________________________________
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