ethz.ch/mailman/listinfo/r-sig-mixed-models
Also check the latest documentation for lme4 and the lmer()
and lmer2() functions at
http://cran.r-project.org/
in the
Packages ... lme4
pages.
Hope this helps
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia
omewhat related to your situation,
and it has plenty of good references
Application of Shrinkage Techniques in Logistic Regression Analysis: A Case
Study
E. W. Steyerberg
Statistica Neerlandica, 2001, vol. 55, issue 1, pages 76-88
Steven McKinney
Statistician
Molecular Oncology and Breast
") :
undefined columns selected
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base
Hi Bert,
> -Original Message-
> From: Bert Gunter [mailto:[EMAIL PROTECTED]
> Sent: Fri 8/3/2007 3:19 PM
> To: Steven McKinney; r-help@stat.math.ethz.ch
> Subject: RE: [R] FW: Selecting undefined column of a data frame (was
> [BioC]read.phenoData vs read.Annotated
oding/debugging implications, and as you
point out,
"[.data.frame is one of the most complex functions in R"
so please bear with me. This change in behaviour has
taken away a side-effect debugging tool, discussed below.
>
>
> On Fri, 3 Aug 2007, Steven McKinney wrote:
> -Original Message-
> From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
> Sent: Fri 8/3/2007 1:05 PM
> To: Steven McKinney
> Cc: r-help@stat.math.ethz.ch
> Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC]
> read.phenoData vs read.Annotated
er than after?
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Fri 8/3/2007 12:25 PM
To: Steven McKinney
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC]
read.phenoData vs read.AnnotatedDataFrame)
You a
erpc-apple-darwin8.9.1
locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
"base"
other attached packages:
UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
"base"
other attached packages:
plotrix lme4 Matr
>-Original Message-
>From: [EMAIL PROTECTED] on behalf of Am Stat
>Sent: Wed 8/1/2007 2:19 PM
>To: r-help@stat.math.ethz.ch
>Subject: [R] Extracting a website text content using R
>Dear useR,
>Just wandering whether it is possible that there is any function in R could
>let me get the t
del
> model.matrix(~ A * B - B, df)
(Intercept) Aa Ax:Bb Aa:Bb
1 1 1 0 1
2 1 1 0 0
3 1 0 0 0
4 1 0 0 0
attr(,"assign")
[1] 0 1 2 2
attr(,"contrasts")
attr(,"contrasts")$A
[1]
powerpc-apple-darwin8.9.1
locale:
C
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
other attached packages:
lme4 Matrix lattice
"0.997
B
20 10.6319798 BB
> lm(y ~ grp2, data = mydata)
Call:
lm(formula = y ~ grp2, data = mydata)
Coefficients:
(Intercept)grp2A
10.66 -10.17
>
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
}
> Y
A B C
3 1 4 3
7 3 2 2
9 3 3 3
6 2 1 2
5 2 1 1
1 1 2 1
2 1 3 2
8 3 1 1
4 2 3 3
> oY <- order(Y$A)
> Y[oY,]
A B C
3 1 4 3
1 1 2 1
2 1 3 2
6 2 1 2
5 2 1 1
4 2 3 3
7 3 2 2
9 3 3 3
8 3 1 1
>
HTH
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
Briti
rms =1)
> ## how to extract a = 10 from data.ppr?
> data.ppr$yb
[1] 9.973964
> a <- 210
> data$z <- evalq(a + atan (x + y) + rnorm (n), data)
> data.ppr <- ppr(z ~ x + y, data=data, nterms =1)
> data.ppr$yb
[1] 209.9773
>
HTH
Steven McKinney
Statistician
Molecular
score
cat("\nIterations:", object$iter[1], "outer,", object$iter[2],
"Newton-Raphson\n")
if (length(print2)) {
for (i in 1:length(print2)) cat("", print2[i], "\n")
}
if (is.null(object$df))
df <- s
quot;grDevices" "utils" "datasets" "methods"
[7] "base"
other attached packages:
DBI
"0.1-12"
>
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: [EMAIL
E
5 TRUE FALSE TRUE TRUE FALSE
6 FALSE TRUE TRUE FALSE FALSE
> mydata.df[is.na(mydata.df)] <- 0
> mydata.df
V1 V2 V3 V4 V5
1 1 0 1 1 1
2 1 0 0 0 1
3 0 0 1 0 0
4 0 0 0 0 1
5 0 1 0 0 1
6 1 0 0 1 1
>
Steven McKinney
Statistician
Molecular Oncology and Br
e able
to identify nodes deeper in the tree. This is aided
by having access to internal node labels/names and being
able to extract internal nodes by those labels/names.
Best
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centr
of the graphical codes, left-arrow mutated to the
underscore of ASCII-1967. It may have had earlier,
or other, meanings, but for some early programming
languages it was "assignment", eg.
c ? b + a
"C is assigned the sum of B and A".
Steven McKinney
Statistician
Mo
ean=0, sd=1)
>
> x2=rnorm(25, mean=0, sd=1)
> y2=dnorm(x2, mean=0, sd=1)
> plot(x1, y1, type='p', xlim=range(x1,x2), ylim=range(y1, y2), xlab='x',
> ylab='y')
> points(x2, y2, type='p', col="red", xlab='x', ylab=&#
Whereas "R" is very generic,
"CRAN" is much less so.
I've had very good luck adding CRAN
to my search terms, e.g. try to Google
cran 3d scatterplot
This produces all R-related hits on
the first Google page.
Hope this helps
Steven McKinney
Statistician
Molecular O
If users post a bug or problem issue to an R-based news group
(R-devel, R-help, BioC - though BioC is far more forgiving)
they get yelled at for not reading the posting guide
and FAQ.
"Please *_do_* read the FAQ, the posting guide, ..."
the yellers do say. So I read the BioC FAQ and it says...
iting, I see the original
copy. But if I reinvoke the editor via fixInNamespace(),
I do see my modification.
Where is my copy residing? How do I push it out
to replace the exported copy?
Is this the proper way to modify a package function?
Are there other ways? I've searched webpages, R news
and use to create an aCGH object.
Any info appreciated.
Best
Steve McKinney
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
[EMAIL PROTECTED]
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