[R] Contrasts for a data
Bert Gunter
gunter.berton at gene.com
Fri Feb 8 23:20:21 CET 2013
Rail is an ordered factor. ?ordered for details.
Default contrasts for an ordered factor are orthogonal polynomials.
See: https://stat.ethz.ch/pipermail/r-help/2007-January/123268.html
and
http://www.ats.ucla.edu/stat/r/library/contrast_coding.htm#ORTHOGONAL
-- Bert
On Fri, Feb 8, 2013 at 1:36 PM, jing tang <gimmytang at gmail.com> wrote:
> Hi,
> I am using a data called Rail in the nlme package. The data contains two
> variables: Rail and Travel.
>>Rail
> Grouped Data: travel ~ 1 | Rail
> Rail travel
> 1 1 55
> 2 1 53
> 3 1 54
> 4 2 26
> 5 2 37
> 6 2 32
> 7 3 78
> 8 3 91
> 9 3 85
> 10 4 92
> 11 4 100
> 12 4 96
> 13 5 49
> 14 5 51
> 15 5 50
> 16 6 80
> 17 6 85
> 18 6 83
>>Rail$Rail
>>[1] 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6
>>Levels: 2 < 5 < 1 < 6 < 3 < 4
>
> Then I used the contrasts function as:
>>contrasts(Rail$Rail)
> And it returns with some strange continuous values:
> .L .Q .C ^4 ^5
> [1,] -0.5976143 0.5455447 -0.3726780 0.1889822 -0.06299408
> [2,] -0.3585686 -0.1091089 0.5217492 -0.5669467 0.31497039
> [3,] -0.1195229 -0.4364358 0.2981424 0.3779645 -0.62994079
> [4,] 0.1195229 -0.4364358 -0.2981424 0.3779645 0.62994079
> [5,] 0.3585686 -0.1091089 -0.5217492 -0.5669467 -0.31497039
> [6,] 0.5976143 0.5455447 0.3726780 0.1889822 0.06299408
>
> I am expecting to see 0s and 1s in the contrast, but it may be due to the
> order of the factor levels for Rail variable?
>
> Best,
> Jing
>
> [[alternative HTML version deleted]]
>
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--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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