Dear Christophe and Ben,
Also see the car package for replacements for contr.treatment(),
contr.sum(), and contr.helmert() -- e.g., help("contr.Sum", package="car").
These functions have been in the car package for more than two decades,
and AFAIK, no one uses them (including myself). I didn't write a
replacement for contr.poly() because the current coefficient labeling
seemed reasonably transparent.
Best,
John
--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/
--
On 2024-06-17 4:29 p.m., Ben Bolker wrote:
Caution: External email.
It's sorta-kinda-obliquely-partially documented in the examples:
zapsmall(cP <- contr.poly(3)) # Linear and Quadratic
output:
.L .Q
[1,] -0.7071068 0.4082483
[2,] 0.0000000 -0.8164966
[3,] 0.7071068 0.4082483
FWIW the faux package provides better-named alternatives.
On 2024-06-17 4:25 p.m., Christophe Dutang wrote:
Thanks for your reply.
It might good to document the naming convention in ?contrasts. It is
hard to understand .L for linear, .Q for quadratic, .C for cubic and
^n for other degrees.
For contr.sum, we could have used .Sum<level1>, .Sum<level2>…
Maybe the examples ?model.matrix should use names in dd objects so
that we observe when names are dropped.
Kind regards, Christophe
Le 14 juin 2024 à 11:45, peter dalgaard <pda...@gmail.com> a écrit :
You're at the mercy of the various contr.XXX functions. They may or
may not set the colnames on the matrices that they generate.
The rationales for (not) setting them is not perfectly transparent,
but you obviously cannot use level names on contr.poly, so it uses
.L, .Q, etc.
In MASS, contr.sdif is careful about labeling the columns with the
levels that are being diff'ed.
For contr.treatment, there is a straightforward connection to 0/1
dummy variables, so level names there are natural.
One could use levels in contr.sum and contr.helmert, but it might
confuse users that comparisons are with the average of all levels or
preceding levels. (It can be quite confusing when coding is +1 for
male and -1 for female, so that the gender difference is twice the
coefficient.)
-pd
On 14 Jun 2024, at 08:12 , Christophe Dutang <duta...@gmail.com> wrote:
Dear list,
Changing the default contrasts used in glm() makes me aware how
model.matrix() set column names.
With default contrasts, model.matrix() use the level values to name
the columns. However with other contrasts, model.matrix() use the
level indexes. In the documentation, I don’t see anything in the
documentation related to this ? It does not seem natural to have
such a behavior?
Any comment is welcome.
An example is below.
Kind regards, Christophe
#example from ?glm
counts <- c(18,17,15,20,10,20,25,13,12)
outcome <- paste0("O", gl(3,1,9))
treatment <- paste0("T", gl(3,3))
X3 <- model.matrix(counts ~ outcome + treatment)
X4 <- model.matrix(counts ~ outcome + treatment, contrasts =
list("outcome"="contr.sum"))
X5 <- model.matrix(counts ~ outcome + treatment, contrasts =
list("outcome"="contr.helmert"))
#check with original factor
cbind.data.frame(X3, outcome)
cbind.data.frame(X4, outcome)
cbind.data.frame(X5, outcome)
#same issue with glm
glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())
glm.D94 <- glm(counts ~ outcome + treatment, family = poisson(),
contrasts = list("outcome"="contr.sum"))
glm.D95 <- glm(counts ~ outcome + treatment, family = poisson(),
contrasts = list("outcome"="contr.helmert"))
coef(glm.D93)
coef(glm.D94)
coef(glm.D95)
#check linear predictor
cbind(X3 %*% coef(glm.D93), predict(glm.D93))
cbind(X4 %*% coef(glm.D94), predict(glm.D94))
-------------------------------------------------
Christophe DUTANG
LJK, Ensimag, Grenoble INP, UGA, France
ILB research fellow
Web: http://dutangc.free.fr
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd....@cbs.dk Priv: pda...@gmail.com
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of
working hours.
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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