[R] Populate matrix from data.frame
Dear all,
I have a data frame
a - data.frame(cbind(x=c('a','a','a','b','c'),
y=c('a','b','c','d','e'),z=c(1,2,3,4,5)))
a
x y z
1 a a 1
2 a b 2
3 a c 3
4 b d 4
5 c e 5
and a matrix
mm - matrix(0,5,5)
colnames(mm) - c('a','b','c','d','e')
rownames(mm) - c('a','b','c','d','e')
mm
a b c d e
a 0 0 0 0 0
b 0 0 0 0 0
c 0 0 0 0 0
d 0 0 0 0 0
e 0 0 0 0 0
How to populate matrix in a way that first column of data frame 'a'
correspond to rownames(mm), second column to colnames(mm) and the third
column is the element of matrix 'mm'?
Thanks in advance,
Andrej
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Re: [R] no applicable method
On Wed, 27 Jun 2007, Kyle Ellrott wrote: I'm getting started in R, and I'm trying to use one of the gradient boosting packages, mboost. I'm already installed the package with install.packages(mboost) and loaded it with library(mboost). My problem is that when I attempt to call glmboost, I get a message that Error in glmboost() : no applicable method for glmboost . Does anybody have an idea of what kind of problem this is indicative of? The wrong class of input object 'x'. The help page for glmboost is written obscurely, but it seems to imply that it has methods for 'formula' and 'matrix'. Perhaps you passed a data frame? PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. is pertinent. With an example and its output we would have been much better placed to help you. -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
Re: [R] Populate matrix from data.frame
On Thu, 28 Jun 2007, Andrej Kastrin wrote:
Dear all,
I have a data frame
a - data.frame(cbind(x=c('a','a','a','b','c'),
y=c('a','b','c','d','e'),z=c(1,2,3,4,5)))
a
x y z
1 a a 1
2 a b 2
3 a c 3
4 b d 4
5 c e 5
and a matrix
mm - matrix(0,5,5)
colnames(mm) - c('a','b','c','d','e')
rownames(mm) - c('a','b','c','d','e')
mm
a b c d e
a 0 0 0 0 0
b 0 0 0 0 0
c 0 0 0 0 0
d 0 0 0 0 0
e 0 0 0 0 0
How to populate matrix in a way that first column of data frame 'a'
correspond to rownames(mm), second column to colnames(mm) and the third
column is the element of matrix 'mm'?
mm[cbind(a$x, a$y)] - a$z
Please read about the forms of indexing matrices in 'An Introduction to
R'.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] : regular expressions: escaping a dot
What's really the problem with: regexpr( '\.odt$', Yodt, perl=TRUE ) Warning: '\.' is an unrecognized escape in a character string Warning: unrecognized escape removed from \.odt$ [1] 5 attr(,match.length) [1] 4 I know that I could use: regexpr( '[.]odt$', Yodt, perl=TRUE ) But it seems to me that the first expression is also an accepted regular expression in accordance with perl. Regards - Wolfram __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] : regular expressions: escaping a dot
Wolfram Fischer wrote: What's really the problem with: regexpr( '\.odt$', Yodt, perl=TRUE ) Warning: '\.' is an unrecognized escape in a character string Warning: unrecognized escape removed from \.odt$ [1] 5 attr(,match.length) [1] 4 I know that I could use: regexpr( '[.]odt$', Yodt, perl=TRUE ) But it seems to me that the first expression is also an accepted regular expression in accordance with perl. In R you have to escape the \. From the help page of regexpr: ## Double all 'a' or 'b's; \ must be escaped, i.e., 'doubled' gsub(([ab]), \\1_\\1_, abc and ABC) HTH, Tobias -- Tobias Verbeke - Consultant Business Decision Benelux Rue de la révolution 8 1000 Brussels - BELGIUM +32 499 36 33 15 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re : restructuring matrix
se reshape package Justin BEM Elève Ingénieur Statisticien Economiste BP 294 Yaoundé. Tél (00237)9597295. - Message d'origine De : yoo [EMAIL PROTECTED] À : r-help@stat.math.ethz.ch Envoyé le : Jeudi, 28 Juin 2007, 2h15mn 52s Objet : Re: [R] restructuring matrix Yea... let's say I constructed a matrix with rownames/colnames be those unique elements.. then what should I do? I don't want to do mapply, etc to find the field.. I'm wondering if there's a smarter way using row/col.. etc... Thanks! Moshe Olshansky-2 wrote: If your original matrix is A then unique(A$People) and unique(A$Desc) will produce a vector of different people and a vector of different descriptions. --- yoo [EMAIL PROTECTED] wrote: Hi all, let's say I have matrix PeopleDescValue Mary Height50 Mary Weight 100 FannyHeight 60 Fanny Height200 Is there a quick way to form the following matrix? People HeightWeight Mary 50 100 Fanny 60200 (Assuming I don't know the length of people/desc and let's say these are characters matrix.. I tried play with row(), col(), etc.. but I don't seem to find like a duplicate match function... I'm trying to write some one/two liner that convert my resulting matrix to vector and pick the appropriate fields.. etc ) Thanks! -- View this message in context: http://www.nabble.com/restructuring-matrix-tf3991741.html#a11334950 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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. -- View this message in context: http://www.nabble.com/restructuring-matrix-tf3991741.html#a11335437 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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. _ Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
[R] Meta-Analysis of proportions
Dear colleagues, I'm conducting a meta-analysis of studies evaluating adherence of HIV-positive drug users into AIDS treatment, therefore I'm looking for some advice and syntax suggestion for running the meta-regression using proportions, not the usual OR/RR frequently used on RCT studies. Have already searched already several handbooks, R-manuals, mailing lists, professors, but... not clue at all... Does anyone have already tried this? A colleague of mine recently published a similar study on JAMA, but he used OpenBUGS - a software I'm not familiar with... If there is any tip/suggestion for a possible syntax, could someone send me? I need to finish this paper before my PhD qualify, but I'm completely stuck... So, any tip will be more than welcome...I will really appreciate it!!! Thanks in advance and congrats on the amazing mailing-list. Bests from Rio de Janeiro, Brazil. Monica Monica Malta Researcher Oswaldo Cruz Foundation - FIOCRUZ Social Science Department - DCS/ENSP Rua Leopoldo Bulhoes, 1480 - room 905 Manguinhos Rio de Janeiro - RJ 21041-210 Brazil phone +55.21.2598-2715 fax +55.21.2598-2779 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] : regular expressions: escaping a dot
On Thu, 28 Jun 2007, Wolfram Fischer wrote: What's really the problem with: regexpr( '\.odt$', Yodt, perl=TRUE ) Warning: '\.' is an unrecognized escape in a character string Warning: unrecognized escape removed from \.odt$ [1] 5 attr(,match.length) [1] 4 I know that I could use: regexpr( '[.]odt$', Yodt, perl=TRUE ) But it seems to me that the first expression is also an accepted regular expression in accordance with perl. This is explained in ?regexp (in the See Also of ?regexpr): Patterns are described here as they would be printed by 'cat': _do remember that backslashes need to be doubled when entering R character strings from the keyboard_. and in the R FAQ and -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
Re: [R] Meta-Analysis of proportions
OpenBUGS should be something related to Bayesian statistics. You may refer to Chapter 12 of Handbook http://cran.r-project.org/doc/vignettes/HSAUR/Ch_meta_analysis.pdf It talks about meta-regression. On 6/28/07, Monica Malta [EMAIL PROTECTED] wrote: Dear colleagues, I'm conducting a meta-analysis of studies evaluating adherence of HIV-positive drug users into AIDS treatment, therefore I'm looking for some advice and syntax suggestion for running the meta-regression using proportions, not the usual OR/RR frequently used on RCT studies. Have already searched already several handbooks, R-manuals, mailing lists, professors, but... not clue at all... Does anyone have already tried this? A colleague of mine recently published a similar study on JAMA, but he used OpenBUGS - a software I'm not familiar with... If there is any tip/suggestion for a possible syntax, could someone send me? I need to finish this paper before my PhD qualify, but I'm completely stuck... So, any tip will be more than welcome...I will really appreciate it!!! Thanks in advance and congrats on the amazing mailing-list. Bests from Rio de Janeiro, Brazil. Monica Monica Malta Researcher Oswaldo Cruz Foundation - FIOCRUZ Social Science Department - DCS/ENSP Rua Leopoldo Bulhoes, 1480 - room 905 Manguinhos Rio de Janeiro - RJ 21041-210 Brazil phone +55.21.2598-2715 fax +55.21.2598-2779 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- The scientists of today think deeply instead of clearly. One must be sane to think clearly, but one can think deeply and be quite insane. Nikola Tesla http://www.macgrass.com __ R-help@stat.math.ethz.ch 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.
Re: [R] Populate matrix from data.frame
You need some caution with Brian's solution as it
depends on the matrix being in the same order as
the factors in the data frame.
a - data.frame(cbind(x=c('a','a','a','b','c'),
y=c('a','b','c','d','e'),z=c(1,2,3,4,5)))
mm - matrix(0,5,5)
colnames(mm) - c('a','b','c','d','e')
rownames(mm) - c('a','b','c','d','e')
pp - mm[5:1, 5:1]
mm[cbind(a$x, a$y)] - a$z # desired result
pp[cbind(a$x, a$y)] - a$z # not desired result
It would be nice if the following worked:
mm[cbind(as.character(a$x), as.character(a$y))] - a$z
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Prof Brian Ripley wrote:
On Thu, 28 Jun 2007, Andrej Kastrin wrote:
Dear all,
I have a data frame
a - data.frame(cbind(x=c('a','a','a','b','c'),
y=c('a','b','c','d','e'),z=c(1,2,3,4,5)))
a
x y z
1 a a 1
2 a b 2
3 a c 3
4 b d 4
5 c e 5
and a matrix
mm - matrix(0,5,5)
colnames(mm) - c('a','b','c','d','e')
rownames(mm) - c('a','b','c','d','e')
mm
a b c d e
a 0 0 0 0 0
b 0 0 0 0 0
c 0 0 0 0 0
d 0 0 0 0 0
e 0 0 0 0 0
How to populate matrix in a way that first column of data frame 'a'
correspond to rownames(mm), second column to colnames(mm) and the third
column is the element of matrix 'mm'?
mm[cbind(a$x, a$y)] - a$z
Please read about the forms of indexing matrices in 'An Introduction to
R'.
__
R-help@stat.math.ethz.ch 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.
[R] maximum difference between two ECDF's
Hello,
I have a vector of samples x of length N. Associated with each
sample x_i is a certain weight w_i. All the weights are in another
vector w of the same length N.
I have another vector of samples y of length n (small n). All
these samples have equal weights 1/n. The ECDF of these samples
is defined as for example at
http://en.wikipedia.org/wiki/Empirical_distribution_function and
I can compute it using the ecdf() function in R.
I define the 'ECDF' of the samples x with their associated
weights in the following way:
F_N(x) = 1/N * sum_{i=1}^{N}w_i * Indicator(x_i = x)
(does this 'ECDF' have another name???)
So it's basically the same formula as the one on the above URL, but the
only difference is that I multiply the indicator function for x_i with
the weight w_i.
Now suppose F_n(x) is the ECDF of the n samples with equal
weights 1/n, and F_N(x) is the 'ECDF' of the other samples with
their associated weights.
What I now would like to compute is the maximum difference
between these two, so:
max(abs(F_N(x)-F_n(x)))
So it's like computing the Kolmogorov-Smirnov statistic of two
discrete CDF's.
If i didn't have these weights, or if one of the two was a
continuous CDF, then I could simply use the ks.test() function.
However, my situation is different... my first set of samples has
associated weights and therefore the 'ECDF' has a slightly
different definition.
How can I compute max(abs(F_N(x)-F_n(x))) ? Do there exist
standard functions for this?
Thanks,
Bart
--
Share what you know. Learn what you don't.
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[R] Repeat if
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not known
as a variable. But I don´t know how to say that it is a variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to do
this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] compare 2 vectors
Dear all, I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) So I would like to have the vector b without the same values as vector a. Kind regards, João Fadista [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not known
as a variable. But I don´t know how to say that it is a variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to do
this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] compare 2 vectors
On 6/28/07, João Fadista [EMAIL PROTECTED] wrote: I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) b[!(b %in% intersect(a,b))] See ?intersect -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] compare 2 vectors
setdiff(b, a) 2007/6/28, João Fadista [EMAIL PROTECTED]: Dear all, I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) So I would like to have the vector b without the same values as vector a. Kind regards, João Fadista [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Antonio, Fabio Di Narzo Ph.D. student at Department of Statistical Sciences University of Bologna, Italy __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Thanks that was really a quick answer.
It works but I get this warning message anyway:
1: kein nicht-fehlendes Argument für min; gebe Inf zurück (None not-
lacking argument for min; give Inf back)
2: kein nicht-fehlendes Argument für max; gebe -Inf zurück
what does this mean?
Greeting and thanks for your help!
Birgit
Am 28.06.2007 um 12:05 schrieb Jacques VESLOT:
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not
known as a variable. But I don´t know how to say that it is a
variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to
do this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
-
---
__
R-help@stat.math.ethz.ch 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.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] compare 2 vectors
setdiff(b,a) is even simpler. On 6/28/07, Christophe Pallier [EMAIL PROTECTED] wrote: On 6/28/07, João Fadista [EMAIL PROTECTED] wrote: I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) b[!(b %in% intersect(a,b))] See ?intersect -- Christophe Pallier (http://www.pallier.org) -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Hi
I think a for loop would be more what you want.
Something along the lines of:
V-list(a=c(1,2,3), b=c(2,3,4)) # list of 2 vectors
for ( i in 1:2 ) { # 2 vectors (replace with 85 ...)
print(range (V[i], na.rm = TRUE))
}
Regards
JS
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Birgit Lemcke
Sent: 28 June 2007 10:48
To: R Hilfe
Subject: [R] Repeat if
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
__
R-help@stat.math.ethz.ch 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.
[R] using self-written functions
Hi, I am pretty new to R, so I apologize for the obvious question. I have worked with R for a few months now and in the process have written several functions that I frequently use in various data analysis projects. I tend to give each project a directory of its own and set the working directory to that. Since there are several tasks that need to be accomplished in many of my projects, I frequently want to use functions I have written previously. My question is, how do I get access to them? The way I do it now is copy the relevant code to the script file of the project I am working on at the time and then run it so as to make the functions available. But that seems to be unnecessarily cumbersome. I used to work a lot with gauss, which had the opportunity of putting one's own functions is one directory and gauss would then have that directory in its search path always. How can I access my own functions in R without having to copy-paste them everytime and run them manually so I can call them later? Do I need to learn how to write a package and attach the package to make the functions available at all times? Is there another way? thanks, James [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Your V1 to V85 are probably coming from a data.frame, aren't they?
If yes, and if this data.frame is named 'a', you can use 'sapply(a,range)'
Otherwise, see ?get (get(paste(V,1,sep=)) returns V1)
Christophe
On 6/28/07, Birgit Lemcke [EMAIL PROTECTED] wrote:
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not known
as a variable. But I don´t know how to say that it is a variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to do
this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
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Re: [R] compare 2 vectors
look at setdiff(), e.g., setdiff(b, a) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: João Fadista [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Thursday, June 28, 2007 11:55 AM Subject: [R] compare 2 vectors Dear all, I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) So I would like to have the vector b without the same values as vector a. Kind regards, João Fadista [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch 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.
[R] prior covariance in Mclust
Hello, I'm trying to use Mclust to fit a Gaussian Mixture Model to a mulitdimensional data set. Because of the specific source of my data, I know that all components have the same variance and that the covariance between dimensions is zero (modelname=VII). Furthermore, I have a reliable estimate of the variance of the components. I want to to use this estimate as a prior in mclust, hoping that exploiting this knowledge will yield better estimates of the number of components and their means (which are the unknowns). First I have a general question: Is this a sensible thing to do? As far as I can see (which might be not too far), this will indeed lead to more robust estimates. But is this true? Another question concerns the practical side of things. How can I do this in mclust? I've read through the manual but this leaves me uncertain about the exact implementation (and earlier posts about this problem seem not to have been answered by the mailing list). If specifying a prior for the covariance matrix is possible (and sensible) in mclust, could someone provide an example of how to specify a prior on the covariance matrix? Thank you, Dieter __ R-help@stat.math.ethz.ch 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.
Re: [R] compare 2 vectors
Christophe Pallier wrote: On 6/28/07, João Fadista [EMAIL PROTECTED] wrote: I would like to take out the values from one vector that are equal to the values in another vector. Example: a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b_noRepeats = c(10,20) b[!(b %in% intersect(a,b))] See ?intersect Hi, There is also a pretty useful operator %w/o% in the help page of %in%. see : ?`%in%` a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b %w/o% a [1] 10 20 Cheers, Romain -- Mango Solutions data analysis that delivers Tel: +44(0) 1249 467 467 Fax: +44(0) 1249 467 468 Mob: +44(0) 7813 526 123 __ R-help@stat.math.ethz.ch 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.
[R] aov and lme differ with interaction in oats example of MASS?
Dear R-Community! The example oats in MASS (2nd edition, 10.3, p.309) is calculated for aov and lme without interaction term and the results are the same. But I have problems to reproduce the example aov with interaction in MASS (10.2, p.301) with lme. Here the script: library(MASS) library(nlme) options(contrasts = c(contr.treatment, contr.poly)) # aov: Y ~ N + V oats.aov - aov(Y ~ N + V + Error(B/V), data = oats, qr = T) summary(oats.aov) # now lme oats.lme-lme(Y ~ N + V, random = ~1 | B/V, data = oats) anova(oats.lme, type=m) # Ok! # aov:Y ~ N * V + Error(B/V) oats.aov2 - aov(Y ~ N * V + Error(B/V), data = oats, qr = T) summary(oats.aov2) # now lme - my trial! oats.lme2-lme(Y ~ N * V, random = ~1 | B/V, data = oats) anova(oats.lme2, type=m) # differences!!! (except of interaction term) My questions: 1) Is there a possibility to reproduce the result of aov with interaction using lme? 2) If not, which result of the above is the correct one for the oats example? Thanks a lot! Karl __ Alles was der Gesundheit und Entspannung dient. BE A BETTER MEDIZINMANN! www.yahoo.de/clever __ R-help@stat.math.ethz.ch 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.
Re: [R] using self-written functions
One quick and dirty way is to put all your functions inside a file, say
/home/me/R/myfuncs.R, and add the following line at the beginning of your
scripts:
source('/home/me/R/myfuncs.R')
This is dirty because if you need to change the location of this file, your
scripts will cease to work.
Alternatively, you can add this command to your Rprofile (see the Annex B of
An introduction to R Invoking R)
Christophe
On 6/28/07, R. Leenders [EMAIL PROTECTED] wrote:
Hi, I am pretty new to R, so I apologize for the obvious question.
I
have worked with R for a few months now and in the process have written
several functions that I frequently use in various data analysis
projects. I tend to give each project a directory of its own and set
the working directory to that.
Since there are several tasks that
need to be accomplished in many of my projects, I frequently want to
use functions I have written previously. My question is, how do I get
access to them? The way I do it now is copy the relevant code to the
script file of the project I am working on at the time and then run it
so as to make the functions available. But that seems to be
unnecessarily cumbersome. I used to work a lot with gauss, which had
the opportunity of putting one's own functions is one directory and
gauss would then have that directory in its search path always. How can
I access my own functions in R without having to copy-paste them
everytime and run them manually so I can call them later? Do I need to
learn how to write a package and attach the package to make the
functions available at all times? Is there another way?
thanks, James
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Christophe Pallier (http://www.pallier.org)
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and provide commented, minimal, self-contained, reproducible code.
[R] Writing - specyfic format
Hi all, I have a trouble - I need to write file in a very specyfic format. I have two vectors which different lengths and one data.frame (or matrix). I want to write it to *.txt file in following way: 1st row of file is my 1st vector (separate by spacebar) 2nd row of file is 2nd vector (also separate by spacebar) Rest of this file should be a matrix with elements separated by tab. For example: a=1, 2, 3, b=4, 5, c=[1, 2, 3, 4, 5, 6; 7, 8, 9, 10, 11, 12,] and I want to have file (it have to be .txt file) like: 1 2 3 4 5 1 2 3 4 5 6 7 8 9 10 1112 This thing have to be done automaticly from R. Is it possible? Thank you in advance -- View this message in context: http://www.nabble.com/Writing---specyfic-format-tf3994017.html#a11341784 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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.
Re: [R] using self-written functions
On Thu, 2007-06-28 at 17:29 +0800, R. Leenders wrote: Hi, I am pretty new to R, so I apologize for the obvious question. I have worked with R for a few months now and in the process have written several functions that I frequently use in various data analysis projects. I tend to give each project a directory of its own and set the working directory to that. Since there are several tasks that need to be accomplished in many of my projects, I frequently want to use functions I have written previously. My question is, how do I get access to them? The way I do it now is copy the relevant code to the script file of the project I am working on at the time and then run it so as to make the functions available. But that seems to be unnecessarily cumbersome. I used to work a lot with gauss, which had the opportunity of putting one's own functions is one directory and gauss would then have that directory in its search path always. How can I access my own functions in R without having to copy-paste them everytime and run them manually so I can call them later? Do I need to learn how to write a package and attach the package to make the functions available at all times? Is there another way? Building a package is one way, and not that difficult once you've read the Writing R Extensions manual. An alternative is to have a directory where you keep R function scripts. Put your functions in here in text files with say a .R extension. Then in R you can source one or more of these R scripts as required, using the source() function. Say you have a directory, myScripts at the base of file system (/home/user say on Linux or C:\ on Windows). in this directory there is a file called my_r_function.R. To use this script/function in an R session, you would issue: ## replace /home/user/ with what ever is the correct path for your ## system source(/home/user/myScripts/my_r_function.R) Which would make available to your current session any functions defined in my_r_function.R. Read ?source for more information. HTH G thanks, James [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch 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.
Re: [R] compare 2 vectors
Romain Francois wrote: There is also a pretty useful operator %w/o% in the help page of %in%. see : ?`%in%` a - c(1,2,3,4,5,6,7,8,9) b - c(3,10,20,5,6) b %w/o% a [1] 10 20 I don't like the example. It's not obvious, in the expression... x[!x %in% y] ... that this is the same as x[!(x %in% y)] and not x[(!x) %in% y] Alberto Monteiro __ R-help@stat.math.ethz.ch 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.
Re: [R] lme correlation structures
Thanks for your help. I can weight the variances in the 2 groups using weights, as in lme(Y~1+time+sex+age, random=~1|indv, correlation=corAR1(form=~time|indv), weights=varIdent(form=~1|sex),method=ML) but what I would like is to have a different phi estimate for each gender, not just different variances. Will track down a copy of the Pinheiro and Bates book... On 6/27/07, Bert Gunter [EMAIL PROTECTED] wrote: Please read ?lme carefully -- the info you seek is there. In particular, the weights argument for changing variance weighting by covariates and the correlation argument for specifying correlation structures. Pinheiro and Bates's MIXED EFFECT MODELS IN S... is the canonical reference (which you should get if you want to use R as you said) that exposits the ideas at greater length. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gareth Hughes Sent: Wednesday, June 27, 2007 7:50 AM To: r-help@stat.math.ethz.ch Subject: [R] lme correlation structures Hi all, I've been using SAS proc mixed to fit linear mixed models and would like to be able to fit the same models in R. Two things in particular: 1) I have longitudinal data and wish to allow for different repeated measures covariance parameter estimates for different groups (men and women), each covariance matrix having the same structure. In proc mixed this would be done by specifying group= in the REPEATED statement. Is this simple to do in R? (I've tried form=~time|indv/sex for example but this doesn't seem to do the job). 2) I've read that other correlation structures can be specified. Does anyone have any examples of how toeplitz or (first-order) ante-dependence structures can be specified? Many thanks, Gareth __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] Meta-Analysis of proportions
Monica Malta wrote: Dear colleagues, I'm conducting a meta-analysis of studies evaluating adherence of HIV-positive drug users into AIDS treatment, therefore I'm looking for some advice and syntax suggestion for running the meta-regression using proportions, not the usual OR/RR frequently used on RCT studies. Have already searched already several handbooks, R-manuals, mailing lists, professors, but... not clue at all... Does anyone have already tried this? A colleague of mine recently published a similar study on JAMA, but he used OpenBUGS - a software I'm not familiar with... If there is any tip/suggestion for a possible syntax, could someone send me? I need to finish this paper before my PhD qualify, but I'm completely stuck... So, any tip will be more than welcome...I will really appreciate it!!! Thanks in advance and congrats on the amazing mailing-list. Specifying adherence as the effect size, if you can also specify a sampling variance perhaps you can use a tool like mima (http://www.wvbauer.com/downloads/mima_tutorial.pdf). For example, working with logits rather than proportions directly, consider the following example data: df ntot nadhere mod prop logitse 1 100 76 0 0.760 -1.1526795 0.2341463 2 125 98 0 0.784 -1.2891306 0.2173501 350 37 0 0.740 -1.0459686 0.3224127 4 200 159 0 0.795 -1.3553321 0.1751557 5 150 114 0 0.760 -1.1526795 0.1911796 680 56 1 0.700 -0.8472979 0.2439749 7 160 113 1 0.7062500 -0.8772402 0.1735688 8 200 130 1 0.650 -0.6190392 0.1482498 9 120 75 1 0.625 -0.5108256 0.1885618 10 105 78 1 0.7428571 -1.0608720 0.2232879 Then do the meta-regression as follows: source(http://www.wvbauer.com/downloads/mima.ssc;) with(df, mima(yi=logit, vi=se, mods=mod)) Estimate of (Residual) Heterogeneity: 0 Test for (Residual) Heterogeneity: QE = 1.2419 df = 8 p-value = 0.9962 Parameter Estimates: [,1] intrcpt -1.2161 mods 0.4520 Variance-Covariance Matrix of Parameter Estimates: intrcptmods intrcpt 0.0436 -0.0436 mods-0.0436 0.0815 Omnibus Test of all Moderators: QME = 2.5058 df = 1 p-value = 0.1134 Individual Moderator Tests: estimate SEzval pvalCI_LCI_U intrcpt -1.2161 0.2089 -5.8213 0. -1.6256 -0.8067 mods 0.4520 0.2856 1.5830 0.1134 -0.1077 1.0117 Bests from Rio de Janeiro, Brazil. Monica Monica Malta Researcher Oswaldo Cruz Foundation - FIOCRUZ Social Science Department - DCS/ENSP Rua Leopoldo Bulhoes, 1480 - room 905 Manguinhos Rio de Janeiro - RJ 21041-210 Brazil phone +55.21.2598-2715 fax +55.21.2598-2779 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch 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.
[R] R 2.5.1 is released
I've rolled up R-2.5.1.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs and platform issues. See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.5.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: a8efde35b940278de19730d326f58449 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 24ad9647e525609bce11f6f6ff9eac2d FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL f04bdfaf8b021d046b8040c8d21dad41 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 162f6d5a1bd7c60fd652145e050f3f3c R-2.5.1.tar.gz 162f6d5a1bd7c60fd652145e050f3f3c R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 4eaf8a3e428694523edc16feb0140206 THANKS Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.5.1 NEW FEATURES o density(1:20, bw = SJ) now works as bw.SJ() now tries a larger search interval than the default (lower, upper) if it does not find a solution within the latter. o The output of library() (no arguments) is now sorted by library trees in the order of .libPaths() and not alphabetically. o R_LIBS_USER and R_LIBS_SITE feature possible expansion of specifiers for R version specific information as part of the startup process. o C-level warning calls now print a more informative context, as C-level errors have for a while. o There is a new option rl_word_breaks to control the way the input line is tokenized in the readline-based terminal interface for object- and file-name completion. This allows it to be tuned for people who use their space bar vs those who do not. The default now allows filename-completion with +-* in the filenames. o If the srcfile argument to parse() is not NULL, it will be added to the result as a srcfile attribute. o It is no longer possible to interrupt lazy-loading (which was only at all likely when lazy-loading environments), which would leave the object being loaded in an unusable state. This is a temporary measure: error-recovery when evaluating promises will be tackled more comprehensively in 2.6.0. INSTALLATION o 'make check' will work with --without-iconv, to accommodate building on AIX where the system iconv conflicts with libiconv and is not compatible with R's requirements. o There is support for 'DESTDIR': see the R-admin manual. o The texinfo manuals are now converted to HTML with a style sheet: in recent versions of makeinfo the markup such as @file was being lost in the HTML rendering. o The use of inlining has been tweaked to avoid warnings from gcc = 4.2.0 when compiling in C99 mode (which is the default from configure). BUG FIXES o as.dendrogram() failed on objects of class dendrogram. o plot(type =s) (or S) with many (hundreds of thousands) of points could overflow the stack. (PR#9629) o Coercing an S4 classed object to matrix (or other basic class) failed to unset the S4 bit. o The 'useS4' argument of print.default() had been broken by an unrelated change prior to 2.4.1. This allowed print() and show() to bounce badly constructed S4 objects between themselves indefinitely. o Prediction of the seasonal component in HoltWinters() was one step out at one point in the calculations. decompose() incorrectly computed the 'random' component for a multiplicative fit. o Wildcards work again in unlink() on Unix-alikes (they did not in 2.5.0). o When qr() used pivoting, the coefficient names in qr.coef() were not pivoted to match. (PR#9623) o UseMethod() could crash R if the first argument was not a character string. o R and Rscript on Unix-alikes were not accepting spaces in -e arguments (even if quoted). o Hexadecimal integer constants (e.g. 0x10L) were not being parsed correctly on platforms where the C function atof did not accept hexadecimal prefixes (as required by C99, but not implemented in MinGW as used by R on Windows). (PR#9648) o libRlapack.dylib on Mac OS X had no version information and sometimes an invalid identification name. o Rd conversion of \usage treated '\\' as a single backslash in all but latex: it now acts consistently with the other verbatim-like environments (it was never 'verbatim'
Re: [R] : regular expressions: escaping a dot
Prof Brian Ripley wrote: This is explained in ?regexp (in the See Also of ?regexpr): Patterns are described here as they would be printed by 'cat': _do remember that backslashes need to be doubled when entering R character strings from the keyboard_. and in the R FAQ and Hmm, that's not actually correct, is it? Perhaps this is better ...entering R character string literals (i.e., between quote symbols.) The counterexample would be readLines() \\abc [1] abc (of course it is more important to get people to read the documentation at all...) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
you may have a vector with only NA values in it...
max(c(NA,NA), na.rm=T)
[1] -Inf
Warning message:
aucun argument pour max ; -Inf est renvoyé
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Thanks that was really a quick answer.
It works but I get this warning message anyway:
1: kein nicht-fehlendes Argument für min; gebe Inf zurück (None
not-lacking argument for min; give Inf back)
2: kein nicht-fehlendes Argument für max; gebe -Inf zurück
what does this mean?
Greeting and thanks for your help!
Birgit
Am 28.06.2007 um 12:05 schrieb Jacques VESLOT:
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not
known as a variable. But I don´t know how to say that it is a
variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to
do this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailto:R-help@stat.math.ethz.ch 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.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] aov and lme differ with interaction in oats example of MASS?
Karl Knoblick wrote: Dear R-Community! The example oats in MASS (2nd edition, 10.3, p.309) is calculated for aov and lme without interaction term and the results are the same. But I have problems to reproduce the example aov with interaction in MASS (10.2, p.301) with lme. Here the script: library(MASS) library(nlme) options(contrasts = c(contr.treatment, contr.poly)) # aov: Y ~ N + V oats.aov - aov(Y ~ N + V + Error(B/V), data = oats, qr = T) summary(oats.aov) # now lme oats.lme-lme(Y ~ N + V, random = ~1 | B/V, data = oats) anova(oats.lme, type=m) # Ok! # aov:Y ~ N * V + Error(B/V) oats.aov2 - aov(Y ~ N * V + Error(B/V), data = oats, qr = T) summary(oats.aov2) # now lme - my trial! oats.lme2-lme(Y ~ N * V, random = ~1 | B/V, data = oats) anova(oats.lme2, type=m) # differences!!! (except of interaction term) My questions: 1) Is there a possibility to reproduce the result of aov with interaction using lme? 2) If not, which result of the above is the correct one for the oats example? The issue is that you are using marginal tests which will do strange things when contrasts are not coded right, and in particular treatment contrasts are not. Switch to e.g. contr.helmert and the results become similar. Marginal tests of main effects in the presence of interaction is not necessarily a good idea and they have been debated here and elsewhere a number of times before. People don't agree entirely, but the dividing line is essentially whether it is uniformly or just mostly a bad idea. It is essentially the discussion of type III SS. fortune(type III) Some of us feel that type III sum of squares and so-called ls-means are statistical nonsense which should have been left in SAS. -- Brian D. Ripley s-news (May 1999) Thanks a lot! Karl __ Alles was der Gesundheit und Entspannung dient. BE A BETTER MEDIZINMANN! www.yahoo.de/clever __ R-help@stat.math.ethz.ch 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. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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.
[R] Help in Bootstrapping
I have a time series (count) data.. Can you tell me the command for the parametric bootstrapping. My parameters are var to mean ratio and mean run length... -- [EMAIL PROTECTED] Regina M.Verghis, [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] aov and lme differ with interaction in oats example of MASS?
On Thu, 28 Jun 2007, Karl Knoblick wrote: Dear R-Community! The example oats in MASS (2nd edition, 10.3, p.309) is calculated for aov and lme without interaction term and the results are the same. But I have problems to reproduce the example aov with interaction in MASS (10.2, p.301) with lme. Here the script: library(MASS) library(nlme) options(contrasts = c(contr.treatment, contr.poly)) That is the problem. You need true contrasts, so use contr.helmert. When I did so I got the same results from lme and aov for the anovas. The question of what a 'marginal' AoV means without orthogonality is moot. The sequential version is fine here. # aov: Y ~ N + V oats.aov - aov(Y ~ N + V + Error(B/V), data = oats, qr = T) summary(oats.aov) # now lme oats.lme-lme(Y ~ N + V, random = ~1 | B/V, data = oats) anova(oats.lme, type=m) # Ok! # aov:Y ~ N * V + Error(B/V) oats.aov2 - aov(Y ~ N * V + Error(B/V), data = oats, qr = T) summary(oats.aov2) # now lme - my trial! oats.lme2-lme(Y ~ N * V, random = ~1 | B/V, data = oats) anova(oats.lme2, type=m) # differences!!! (except of interaction term) My questions: 1) Is there a possibility to reproduce the result of aov with interaction using lme? 2) If not, which result of the above is the correct one for the oats example? Thanks a lot! Karl -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
[R] Installing an old package in R-2.4.1
I am new to R. We have a binary package that was not maintained for about a year, and the original maintainer is not around anymore. The package used to work in R-1.5.1. I used the following steps to install this package in R-2.4 on WinXP: Started the GUI Went into the menu Packages and selected Install packages from local zip files Clicked on the zip file with the package, and clicked Open R responded with the message Updating HTML package descriptions. I can see the package files in the library subdirectory of R installation: cd c:/program files/R/R-2.4.1/library find . -name 'Rproj' -print ./file72ae2cd6/Rproj ./file72ae2cd6/Rproj/help/Rproj ./file72ae2cd6/Rproj/R/Rproj ./Rproj ./Rproj/help/Rproj ./Rproj/R/Rproj ( Please don't get confused by the UNIX-style paths, I am using cygwin shell on Windows ). However when I go to Packages-Load package menu, the Rproj package is not listed there. How would I find out what went wrong? Thanks, Vlad __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Birgit Lemcke wrote: Thanks that was really a quick answer. It works but I get this warning message anyway: 1: kein nicht-fehlendes Argument f�r min; gebe Inf zur�ck (None not- lacking argument for min; give Inf back) 2: kein nicht-fehlendes Argument f�r max; gebe -Inf zur�ck what does this mean? Same as this max(c(NA, NA), na.rm=T) [1] -Inf Warning message: no non-missing arguments to max; returning -Inf which is related to the issues of empty sum(), prod(), any(), and all() in that it allows a consistent concatenation rule: max(c(x1,x2)) == max(max(x1), max(x2)) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Thats not the case.
I have two vectosr with a lot of NAs, but not only NAs.
But nevertheless as i saw the results are accurate.
Birgit
Am 28.06.2007 um 15:17 schrieb Jacques VESLOT:
you may have a vector with only NA values in it...
max(c(NA,NA), na.rm=T)
[1] -Inf
Warning message:
aucun argument pour max ; -Inf est renvoyé
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Thanks that was really a quick answer.
It works but I get this warning message anyway:
1: kein nicht-fehlendes Argument für min; gebe Inf zurück (None
not-lacking argument for min; give Inf back)
2: kein nicht-fehlendes Argument für max; gebe -Inf zurück
what does this mean?
Greeting and thanks for your help!
Birgit
Am 28.06.2007 um 12:05 schrieb Jacques VESLOT:
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not
known as a variable. But I don´t know how to say that it is a
variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way
to do this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
[[alternative HTML version deleted]]
---
-
__
R-help@stat.math.ethz.ch mailto:R-help@stat.math.ethz.ch
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.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Hello John,
I tried this code. But I got only the ranges of V1 and V2 what is
easily understandable.
Do I have to write in all 85 vectors in the first line?
V-list(a=c(V1), b=c(V2))
for ( i in 1:85 ) { # 2 vectors (replace with 85 ...)
+ print(range (V[i], na.rm = TRUE))
+ }
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
But thanks anyway.
Greetings
Birgit
Am 28.06.2007 um 12:23 schrieb john seers ((IFR)):
Hi
I think a for loop would be more what you want.
Something along the lines of:
V-list(a=c(1,2,3), b=c(2,3,4)) # list of 2 vectors
for ( i in 1:2 ) { # 2 vectors (replace with 85 ...)
print(range (V[i], na.rm = TRUE))
}
Regards
JS
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Birgit Lemcke
Sent: 28 June 2007 10:48
To: R Hilfe
Subject: [R] Repeat if
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Thanks Christophe,
I received already an answer with a similar suggestion.
But thanks for your answer.
Birgit
Am 28.06.2007 um 12:34 schrieb Christophe Pallier:
Your V1 to V85 are probably coming from a data.frame, aren't they?
If yes, and if this data.frame is named 'a', you can use 'sapply
(a,range)'
Otherwise, see ?get (get(paste(V,1,sep=)) returns V1)
Christophe
On 6/28/07, Birgit Lemcke [EMAIL PROTECTED] wrote:
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not known
as a variable. But I don´t know how to say that it is a variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to do
this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
--
Christophe Pallier (http://www.pallier.org)
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Hello Patrick,
this does not work and gives following warning message:
for(i in 1:85) range(get(paste(V, i, sep=)), na.rm=TRUE)
Warning messages:
1: kein nicht-fehlendes Argument für min; gebe Inf zurück
2: kein nicht-fehlendes Argument für max; gebe -Inf zurück
This works but also with the warning message:
Vranges - array(NA, c(85, 2))
for(i in 1:85) Vranges[i,] - range(get(paste(V, i, sep=)),
na.rm=TRUE)
Greetings
Birgit
Am 28.06.2007 um 12:27 schrieb Patrick Burns:
In your code the 'range' call is only seen when i is 85.
I think the following is what you want:
for(i in 1:85) range(get(paste(V, i, sep=)), na.rm=TRUE)
Except that nothing is done with the results of 'range'. More
likely is:
Vranges - array(NA, c(85, 2))
for(i in 1:85) Vranges[i,] - range(get(paste(V, i, sep=)),
na.rm=TRUE)
See S Poetry for details.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Birgit Lemcke wrote:
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not
known as a variable. But I don´t know how to say that it is a
variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way to
do this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
-
---
__
R-help@stat.math.ethz.ch 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.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] : regular expressions: escaping a dot
On Thu, 28 Jun 2007, Peter Dalgaard wrote: Prof Brian Ripley wrote: This is explained in ?regexp (in the See Also of ?regexpr): Patterns are described here as they would be printed by 'cat': _do remember that backslashes need to be doubled when entering R character strings from the keyboard_. and in the R FAQ and Hmm, that's not actually correct, is it? Perhaps this is better ...entering R character string literals (i.e., between quote symbols.) The counterexample would be readLines() \\abc [1] abc (of course it is more important to get people to read the documentation at all...) The definition of 'character string' used throughout the help is your 'character string literal', as distinct from an element of a character vector. -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
[R] Adding different output to different lattice panels
I would like to add a reference line to lattice graphs, with the reference line
being different according to the factor level.
Example : Draw 3 dotplots for a,b and c factors, and then add an
horizontal line at y=10 for panel a, y=8 for panel b and y=6 for panel 4
I tried the code below, but this draw all three reference lines for each panel.
How do I index the current panel to chose the right reference vector value ?
dat-data.frame(id=rep(c(a,b,c),4),val=1:12,quand=rep(c(t1,t2,t3,t4),each=3))
ref-c(10,8,6)
plot.new()
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref)
})
print(datplot)
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Repeat if
Hi Birgit
No, you do not have to write all 85 vectors in the first line. I just did not
fully appreciate what you were trying to do.
You could use the get option as was suggested somewhere else.
So, if your vectors are V1 to V2 (i.e. 85) say, something like:
V1-c(1,2,3)
V2-c(5,2,7)
...
V-paste(V, 1:2, sep=)
for ( i in 1:length(V) ) {
print(range (get(V[i]), na.rm = TRUE))
}
Regards
JS
---
Web sites:
www.ifr.ac.uk
www.foodandhealthnetwork.com
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Birgit Lemcke
Sent: 28 June 2007 15:12
To: john seers (IFR)
Cc: R Hilfe
Subject: Re: [R] Repeat if
Hello John,
I tried this code. But I got only the ranges of V1 and V2 what is easily
understandable.
Do I have to write in all 85 vectors in the first line?
V-list(a=c(V1), b=c(V2))
for ( i in 1:85 ) { # 2 vectors (replace with 85 ...)
+ print(range (V[i], na.rm = TRUE))
+ }
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, , na.rm=T),
sep=
But thanks anyway.
Greetings
Birgit
Am 28.06.2007 um 12:23 schrieb john seers ((IFR)):
Hi
I think a for loop would be more what you want.
Something along the lines of:
V-list(a=c(1,2,3), b=c(2,3,4)) # list of 2 vectors
for ( i in 1:2 ) { # 2 vectors (replace with 85 ...)
print(range (V[i], na.rm = TRUE))
}
Regards
JS
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Birgit Lemcke
Sent: 28 June 2007 10:48
To: R Hilfe
Subject: [R] Repeat if
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
[R] align() function missing in R ?
Dear list members, I switched from Splus to R a few years ago and so far found no functionality missing. However, I am struggling to find the equivalent align() function for time series. I did find some reduced functionality such as alignDailySeries in package:fCalendar but the full capability of aligning two timeseries seems to be missing. Could this be true ? I am sure there must be a need for this useful function. Any help would be greatly appreciated. Thanks ! Markus __ R-help@stat.math.ethz.ch 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.
[R] embedFonts() and bounding box
Dear R gurus I have a question regarding the function embedFonts(). I assume the in that function which calls gs, the bounding box of the eps file is changed. Is that by intention? Do I have call explicitly some gs-options to avoid it and if yes, how? Thank you very much for your help. Best regards, Christoph Buser ## R example postscript(test.eps, width = 14, height = 8, onefile = FALSE, horizontal=FALSE, paper=special) plot(1:10) dev.off() embedFonts(file = test.eps, outfile = test1.eps) -- Christoph Buser [EMAIL PROTECTED] Seminar fuer Statistik, LEO C13 ETH Zurich 8092 Zurich SWITZERLAND phone: x-41-44-632-4673 fax: 632-1228 http://stat.ethz.ch/~buser/ __ R-help@stat.math.ethz.ch 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.
Re: [R] Adding different output to different lattice panels
On 6/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I would like to add a reference line to lattice graphs, with the reference line being different according to the factor level. Example : Draw 3 dotplots for a,b and c factors, and then add an horizontal line at y=10 for panel a, y=8 for panel b and y=6 for panel 4 It's quite easy to do this with ggplot2 (http://had.co.nz/ggplot2) - see http://had.co.nz/ggplot2/geom_vline.html for examples of both common and specific reference lines. Hadley __ R-help@stat.math.ethz.ch 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.
Re: [R] TukeyHSD
Are you sure that Tukey's HSD (or any other usual multiple comparison procedure) applies to within-subject factors? I do not have my stats books (e.g. Winer or Kirk) to check. You can get some output with: TukeyHSD(aov(hand:gaze+subject)) (assuming you ant to compare the cells defined by hand:gaze) but I am not sure wheter this is meaningful/correct in the context of the within-subject design. (Actually, I write this email because I am interested to know whether it is a legitimate approach or not.) Christophe On 6/28/07, Patrick Bedard [EMAIL PROTECTED] wrote: Hello everyone, So I ran an anova with aov and then I want to run post-hoc comparisons but keep receiving this message : no applicable method for TukeyHSD Here is my code: d-read.table(d.txt) d Obs subj Hand GazeRT 11 s111 401.4 22 s211 363.3.. summary(ano - aov(RT~(Hand*Gaze)+Error(subj/(Hand*Gaze)),data=d )) This seems to work fine, but then I use fm1Tukey=TukeyHSD(fm1,Hand) ; fm1Tukey And receive no applicable method for TukeyHSD I can¹t seem to find the error nor anyone ever answering that question which seems to pop-up here and there on other websites (eg, Nabble) Tnaks in advance for your help, __ Patrick Bédard Ph.D. Dept. of Neuroscience Brown University [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Repeat if
Sorry Jacques and all the other helpful people!
I made a mistake because I didn´t realize that I have a vector only
containing NAs. That happened during standardization and i didn´t
check this.
I apologize for that.
Greetings
Birgit
Am 28.06.2007 um 15:17 schrieb Jacques VESLOT:
you may have a vector with only NA values in it...
max(c(NA,NA), na.rm=T)
[1] -Inf
Warning message:
aucun argument pour max ; -Inf est renvoyé
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Thanks that was really a quick answer.
It works but I get this warning message anyway:
1: kein nicht-fehlendes Argument für min; gebe Inf zurück (None
not-lacking argument for min; give Inf back)
2: kein nicht-fehlendes Argument für max; gebe -Inf zurück
what does this mean?
Greeting and thanks for your help!
Birgit
Am 28.06.2007 um 12:05 schrieb Jacques VESLOT:
sapply(1:85, function(i) eval(parse(text=paste(range(V, i, ,
na.rm=T), sep=
Jacques VESLOT
INRA - Biostatistique Processus Spatiaux
Site Agroparc 84914 Avignon Cedex 9, France
Tel: +33 (0) 4 32 72 21 58
Fax: +33 (0) 4 32 72 21 84
Birgit Lemcke a écrit :
Hello,
(Power Book G4, Mac OS X, R 2.5.0)
I would like to repeat the function range for 85 Vectors (V1-V85).
I tried with this code:
i-0
repeat {
+ i-i+1
+ if (i85) next
+ range (Vi, na.rm = TRUE)
+ if (i==85) break
+ }
I presume that the Vi is wrong, because in this syntax i is not
known as a variable. But I don´t know how to say that it is a
variable here.
Would be nice if somebody could help me.
Perhaps I´m thinking too complicated and there is an easier way
to do this.
Thanks in advance
Greetings
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
[[alternative HTML version deleted]]
---
-
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posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
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Re: [R] TukeyHSD
TukeyHSD takes an aov object, not an aovlist object. The result of aov() with an Error() term is an aovlist object. In the HH package, see ?MMC for an example of how to work around this limitation. See the maiz example. Rich __ R-help@stat.math.ethz.ch 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.
[R] R.matlab questions
Hello:
Two questions about R.matlab:
1. How to break a hung R-Matlab connection?
2. How to execute R.matlab commands from within a function?
BREAKING AN R-Matlab CONNECTION
Sometimes an attempted R.matlab command locks up my computer. The
standard R break process interrupts the R command. However, when I do
that, the command to Matlab is still pending, and I don't know an easy
way to interrupt that. A simple, self-contained example appears below.
The easiest way I've found so far to interrupt Matlab is to quit R.
This will finally release Matlab.
CALLING R.matlab FUNCTIONS FROM WITHIN A FUNCTION
An R.matlab function call that works as a direct R command hangs for
me when executed within an R function. A simple, self-contained example
appears below.
How can I work around this?
Thanks,
Spencer Graves
Using Matlab 7.3.0 (R2006b) under Windows XP Pro.
sessionInfo()
R version 2.5.0 (2007-04-23)
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 packages:
[1] splines stats graphics grDevices utils datasets
[7] methods base
other attached packages:
R.matlab R.oo fda zoo
1.1.3 1.2.7 1.2.1 1.3-1
###
#EXAMPLE: CALLING R.matlab FROM WITHIN A FUCTION?
# 1. library(R.matlab)
library(R.matlab)
# 2. Create a Matlab client object to support communications
(matlab - Matlab())
# Optionally set setVerbose(..., -2) to get max info
setVerbose(matlab, -2)
# 3. Start Matlab
# 4. Ask Matlab to become a slave
#Matlab MatlabServer
# 5. Open the connection from R to MatlabServer
(isOpenMatlab - open(matlab))
# NOTE: If Matlab is not frozen:
#R close(matlab)
# returns local control to Matlab.
# Control of Matlab can be returned to R at any time
# by repeating steps 4 5.
# 6. matlab.compute.a
compute - evaluate(matlab, a = 1+2)
(a0 - getVariable(matlab, a))
# The above works fine for me.
# 7. R.matlab.compute.a function
R.matlab.compute.a - function(text=a=1+2, matlabClient=matlab){
# text = a Matlab expression that stores 'a'
ev0 - evaluate(matlabClient, text)
getVariable(matlabClient, a)
}
# The following locks up both R and Matlab for me:
R.matlab.compute.a()
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Re: [R] Adding different output to different lattice panels
On 6/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
I would like to add a reference line to lattice graphs, with the reference
line
being different according to the factor level.
Example : Draw 3 dotplots for a,b and c factors, and then add an
horizontal line at y=10 for panel a, y=8 for panel b and y=6 for panel
4
I tried the code below, but this draw all three reference lines for each
panel.
How do I index the current panel to chose the right reference vector value ?
dat-data.frame(id=rep(c(a,b,c),4),val=1:12,quand=rep(c(t1,t2,t3,t4),each=3))
ref-c(10,8,6)
plot.new()
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref)
})
print(datplot)
dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h = ref[packet.number()])
})
(Things are more complicated if you have more than one conditioning variable.)
-Deepayan
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Re: [R] Writing - specyfic format
jastar [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Hi all,
I have a trouble - I need to write file in a very specyfic format.
I have two vectors which different lengths and one data.frame (or matrix).
I want to write it to *.txt file in following way:
1st row of file is my 1st vector (separate by spacebar)
2nd row of file is 2nd vector (also separate by spacebar)
Rest of this file should be a matrix with elements separated by tab.
For example: a=1, 2, 3, b=4, 5, c=[1, 2, 3, 4, 5, 6;
7, 8, 9, 10, 11, 12,]
and I want to have file (it have to be .txt file) like:
1 2 3
4 5
1 2 3 4 5 6
7 8 9 10 1112
This thing have to be done automaticly from R.
Is it possible?
Try this:
a - 1:3
b - 4:5
c - matrix(1:12, 2,6, byrow=TRUE)
outFile - file(SpecificFormat.txt, w)
cat(paste(a, sep= ), \n, file=outFile)
cat(paste(b, sep= ), \n, file=outFile)
for (j in 1:nrow(c))
{
cat(paste(c[j,], collapse=\t), \n, file=outFile)
}
close(outFile)
Resulting output file (with spaces or tabs as specified):
1 2 3
4 5
1 2 3 4 5 6
7 8 9 10 11 12
[But I normally avoid tabs since you cannot see them easily with many
editors.]
efg
Earl F. Glynn
Stowers Institute for Medical Research
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[R] Method dispatch in functions?
Hi, Could someone point me in the right direction for documentation on the following question? Let's say I have two objects a and b of classes A and B, respectively. Now let's say I write a function foo that does something similar to objects of type A and B. Basically I want to overload the function in C++ talk, so if I give foo and object of type A something (and this is my question) dispatches the call to, say, foo.A, and if I give foo and object of type B something dispatches the call to, say, foo.B. I want to write foo.A and foo.B. How to I perform the method dispatch? From what I understand there are two ways in R: S3 and S4. What is the simple S3 way? Thanks! Jack. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
[R] Error en assign(mname, def, where)
Hi R users, I am working with the fda package but when I call the function pca.fd I obtain a message error, which I cann't identify. The error say That : error in assihn(mname,def,where), is not possible to add links to a blockade enviroment. The orther that I'm writting is: cp1 - pca.fd(ind.fd1,nharm=3) and before it I can to plot the functional data object ind.fd1. ¿Have anybody seen this error or any similar message?, ¿Any idea? Thancks for your help -- View this message in context: http://www.nabble.com/Error-en-assign%28mname%2C-def%2C-where%29-tf3995432.html#a11346689 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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.
Re: [R] Meta-Analysis of proportions
At 09:58 28/06/2007, Chung-hong Chan wrote: OpenBUGS should be something related to Bayesian statistics. You may refer to Chapter 12 of Handbook http://cran.r-project.org/doc/vignettes/HSAUR/Ch_meta_analysis.pdf It talks about meta-regression. On 6/28/07, Monica Malta [EMAIL PROTECTED] wrote: Dear colleagues, I'm conducting a meta-analysis of studies evaluating adherence of HIV-positive drug users into AIDS treatment, therefore I'm looking for some advice and syntax suggestion for running the meta-regression using proportions, not the usual OR/RR frequently used on RCT studies. Monica, you have a number of options. 1 - weight each study equally 2 - weight each individual equally 3 - use the usual inverse variance procedure, possibly transforming the proportions first 4 - something else I have not though of You could do 3 using rmeta which is available from CRAN. Programming 1 or 2 is straightforward. Of course, you do need to decide which corresponds to your scientific question. Have already searched already several handbooks, R-manuals, mailing lists, professors, but... not clue at all... Does anyone have already tried this? A colleague of mine recently published a similar study on JAMA, but he used OpenBUGS - a software I'm not familiar with... If there is any tip/suggestion for a possible syntax, could someone send me? I need to finish this paper before my PhD qualify, but I'm completely stuck... So, any tip will be more than welcome...I will really appreciate it!!! Thanks in advance and congrats on the amazing mailing-list. Bests from Rio de Janeiro, Brazil. Monica Monica Malta Researcher Oswaldo Cruz Foundation - FIOCRUZ Social Science Department - DCS/ENSP Rua Leopoldo Bulhoes, 1480 - room 905 Manguinhos Rio de Janeiro - RJ 21041-210 Brazil phone +55.21.2598-2715 fax +55.21.2598-2779 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- The scientists of today think deeply instead of clearly. One must be sane to think clearly, but one can think deeply and be quite insane. Nikola Tesla http://www.macgrass.com Michael Dewey [EMAIL PROTECTED] http://www.aghmed.fsnet.co.uk/home.html __ R-help@stat.math.ethz.ch 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.
[R] R function command on a list
Hello R:
I am working with a self-defined function and I wish to subject a list
(t) to this function. My list is a list of tables:
$rs7609589
2/2 2/4 4/4 2/2 2/4 4/4
89 188 87 89 188 87
$rs3909907
1/1 1/4 4/4
94 178 92
$rs12748004
0/0 1/3 3/3
37 150 177
$rs6695928
2/2 2/4 4/4
35 129 200
My function looks as follows:
delete_nocall_listoftables-function(i){
names-names(i)
i
if (names[1] == 0/0){
i[-(1:1)]
}else{
i
}
}
Within the function, how can I access the table name of a given element (e.g.
$rs3909907)? Using names(i) I get the header of the table...
Thanking you!
Georg.
[[alternative HTML version deleted]]
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[R] TukeyHSD
Hello everyone, So I ran an anova with aov and then I want to run post-hoc comparisons but keep receiving this message : no applicable method for TukeyHSD Here is my code: d-read.table(d.txt) d Obs subj Hand GazeRT 11 s111 401.4 22 s211 363.3.. summary(ano - aov(RT~(Hand*Gaze)+Error(subj/(Hand*Gaze)),data=d )) This seems to work fine, but then I use fm1Tukey=TukeyHSD(fm1,Hand) ; fm1Tukey And receive no applicable method for TukeyHSD I can¹t seem to find the error nor anyone ever answering that question which seems to pop-up here and there on other websites (eg, Nabble) Tnaks in advance for your help, __ Patrick Bédard Ph.D. Dept. of Neuroscience Brown University [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] R function command on a list
Try whit rownames.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/06/07, G E [EMAIL PROTECTED] wrote:
Hello R:
I am working with a self-defined function and I wish to subject a list
(t) to this function. My list is a list of tables:
$rs7609589
2/2 2/4 4/4 2/2 2/4 4/4
89 188 87 89 188 87
$rs3909907
1/1 1/4 4/4
94 178 92
$rs12748004
0/0 1/3 3/3
37 150 177
$rs6695928
2/2 2/4 4/4
35 129 200
My function looks as follows:
delete_nocall_listoftables-function(i){
names-names(i)
i
if (names[1] == 0/0){
i[-(1:1)]
}else{
i
}
}
Within the function, how can I access the table name of a given element (
e.g.
$rs3909907)? Using names(i) I get the header of the table...
Thanking you!
Georg.
[[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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[R] stack multiple plots on one page
Hi All, I typed pairs to see its code but did not get what I want. How do I see its code? What I am trying to do, is to stack about 10 scatter plots on one page as the way pairs does. I have about 150 variables in my table. Instead of plotting 150X150 pairs using pairs, I only need to plot 10 pairs. Thanks. jiong The email message (and any attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message (and any attachments). Thank You. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] stack multiple plots on one page
https://svn.r-project.org/R/branches/R-2-5-branch/src/library/graphics/R/pairs.R -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 28/06/07, Jiong Zhang, PhD [EMAIL PROTECTED] wrote: Hi All, I typed pairs to see its code but did not get what I want. How do I see its code? What I am trying to do, is to stack about 10 scatter plots on one page as the way pairs does. I have about 150 variables in my table. Instead of plotting 150X150 pairs using pairs, I only need to plot 10 pairs. Thanks. jiong The email message (and any attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message (and any attachments). Thank You. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
[R] Evaluating predictive power with no intercept-statistics question - not R question
I realize that the following has been talked about on this list many
times before in some related way but I
am going to ask for help anyway because I still don't know what to do.
Suppose I have no intercept models such as the following :
Y = B*X_1 + error
Y = B*X_2 + error
Y = B*X_3 + error
Y = B*X_4 + error
and I run regressions on each ( over the same sample of Y ) and now I
want to evaluate which X has the greatest predictive power.
I'm fairly certain that R squared is not applicable because of the lack
of an intercept but I was wondering what was ?
Any references to this particular problem or suggestions are
appreciated. I honestly believe that including an intercept is incorrect
For my particular problem. Thanks.
Maybe I could put all the X's in one regression and some kind of
topdownselect or StepAIC algorithm for example ? Thanks.
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
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[R] Course in Boston** R/Splus Fundamentals and Programming Techniques
XLSolutions Corporation (www.xlsolutions-corp.com) is making a last call for our July 2007 R/S-plus Fundamentals and Programming Techniques : www.xlsolutions-corp.com/Rfund.htm In Boston *** July 16 - 17, 2007 Reserve your seat now at the early bird rates! Payment due AFTER the class Course Description: This two-day beginner to intermediate R/S-plus course focuses on a broad spectrum of topics, from reading raw data to a comparison of R and S. We will learn the essentials of data manipulation, graphical visualization and R/S-plus programming. We will explore statistical data analysis tools,including graphics with data sets. How to enhance your plots, build your own packages (librairies) and connect via ODBC,etc. We will perform some statistical modeling and fit linear regression models. Participants are encouraged to bring data for interactive sessions With the following outline: - An Overview of R and S - Data Manipulation and Graphics - Using Lattice Graphics - A Comparison of R and S-Plus - How can R Complement SAS? - Writing Functions - Avoiding Loops - Vectorization - Statistical Modeling - Project Management - Techniques for Effective use of R and S - Enhancing Plots - Using High-level Plotting Functions - Building and Distributing Packages (libraries) - Connecting; ODBC, Rweb, Orca via sockets and via Rjava Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/courselist.htm Please let us know if you and your colleagues are interested in this classto take advantage of group discount. Register now to secure your seat! Interested in R/Splus Advanced course? email us. Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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.
Re: [R] stack multiple plots on one page
or just type: pairs.default b On Jun 28, 2007, at 2:36 PM, Henrique Dallazuanna wrote: https://svn.r-project.org/R/branches/R-2-5-branch/src/library/ graphics/R/pairs.R -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 28/06/07, Jiong Zhang, PhD [EMAIL PROTECTED] wrote: Hi All, I typed pairs to see its code but did not get what I want. How do I see its code? What I am trying to do, is to stack about 10 scatter plots on one page as the way pairs does. I have about 150 variables in my table. Instead of plotting 150X150 pairs using pairs, I only need to plot 10 pairs. Thanks. jiong The email message (and any attachments) is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message (and any attachments). Thank You. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] no applicable method
You actually got it right. I didn't realize there was a difference between a data frame and matrix. What is the difference any way? Seems like all two dimensional arrays should be equivalent. Kyle On Wed, 27 Jun 2007, Kyle Ellrott wrote: I'm getting started in R, and I'm trying to use one of the gradient boosting packages, mboost. I'm already installed the package with install.packages(mboost) and loaded it with library(mboost). My problem is that when I attempt to call glmboost, I get a message that Error in glmboost() : no applicable method for glmboost . Does anybody have an idea of what kind of problem this is indicative of? The wrong class of input object 'x'. The help page for glmboost is written obscurely, but it seems to imply that it has methods for 'formula' and 'matrix'. Perhaps you passed a data frame? PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. is pertinent. With an example and its output we would have been much better placed to help you. -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
Re: [R] R function command on a list
Thank you Henrique,
rownames also gives me the header of the table, but not the name of the
list-element...
Any other idea?
Wishing you a good day, Georg.
**
Georg Ehret
Johns Hopkins University
Baltimore
On 6/28/07, Henrique Dallazuanna [EMAIL PROTECTED] wrote:
Try whit rownames.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/06/07, G E [EMAIL PROTECTED] wrote:
Hello R:
I am working with a self-defined function and I wish to subject a
list
(t) to this function. My list is a list of tables:
$rs7609589
2/2 2/4 4/4 2/2 2/4 4/4
89 188 87 89 188 87
$rs3909907
1/1 1/4 4/4
94 178 92
$rs12748004
0/0 1/3 3/3
37 150 177
$rs6695928
2/2 2/4 4/4
35 129 200
My function looks as follows:
delete_nocall_listoftables-function(i){
names-names(i)
i
if (names[1] == 0/0){
i[-(1:1)]
}else{
i
}
}
Within the function, how can I access the table name of a given element
( e.g.
$rs3909907)? Using names(i) I get the header of the table...
Thanking you!
Georg.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Loading problem with XML_1.9
Weijun -- If memory is a problem, you might try using the 'handler' argument of xmlTreeParse. This provides access to each node as it is processed, so that you can, for instance, choose to ignore nodes, or save only numeric values, or ... I'm not sure whether the entire document is read into a C 'external pointer', or whether the savings is just in the R representation of the document. Also, depending on how you use the resulting document, you might want to watch out for the memory leak mentioned in http://www.omegahat.org/RSXML/Changes Martin Luo Weijun [EMAIL PROTECTED] writes: Hello all, I have loading problem with XML_1.9 under 64 bit R2.3.1, which I got from http://R.research.att.com/. XML_1.9 works fine under 32 bit R2.5.0. I thought that could be installation problem, and I tried install.packages or biocLite, every time the package installed fine, except some warning messages below: ld64 warning: in /usr/lib/libxml2.dylib, file does not contain requested architecture ld64 warning: in /usr/lib/libz.dylib, file does not contain requested architecture ld64 warning: in /usr/lib/libiconv.dylib, file does not contain requested architecture ld64 warning: in /usr/lib/libz.dylib, file does not contain requested architecture ld64 warning: in /usr/lib/libxml2.dylib, file does not contain requested architecture Here is the error messages I got, when XML is loaded: library(XML) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/local/lib64/R/library/XML/libs/XML.so': dlopen(/usr/local/lib64/R/library/XML/libs/XML.so, 6): Symbol not found: _xmlMemDisplay Referenced from: /usr/local/lib64/R/library/XML/libs/XML.so Expected in: flat namespace Error: .onLoad failed in 'loadNamespace' for 'XML' Error: package/namespace load failed for 'XML' I understand that it has been pointed out that Sys.getenv(PATH) needs to be revised in the file XML/R/zzz.R, but I canâ�t even find that file under XML/R/ directory. Does anybody have any idea what might be the problem, and how to solve it? Thanks a lot! BTW, the reason I need to use R64 is that I have memory limitation issue with R 32 bit version when I load some very large XML trees. Session information sessionInfo() Version 2.3.1 Patched (2006-06-27 r38447) powerpc64-apple-darwin8.7.0 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base Weijun __ R-help@stat.math.ethz.ch 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. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-help@stat.math.ethz.ch 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.
[R] Function call within a function.
I am trying to call a funtion within another function
and I clearly am misunderstanding what I should do.
Below is a simple example.
I know lstfun works on its own but I cannot seem to
figure out how to get it to work within ukn. Basically
I need to create the variable nts. I have probably
missed something simple in the Intro or FAQ.
Any help would be much appreciated.
EXAMPLE
---
# create data.frame
cata - c( 1,1,6,1,1,4)
catb - c( 1,2,3,4,5,6)
id - c('a', 'b', 'b', 'a', 'a', 'b')
dd1 - data.frame(id, cata,catb)
# function to create list from data.frame
lstfun - function(file, alpha , beta ) {
cda - subset(file, file[,1] == alpha)
cdb - subset (file, file[,1]== beta)
list1 - list(cda,cdb)
}
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
mysum - nam1[,3]*5
return(mysum)
}
results - ukn(dd1, a, b, nts$cda)
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Re: [R] Error en assign(mname, def, where)
Hi Martin, Could you please provide a minimal replicable example so that we can investigate further. Thanks, Hadley On 6/28/07, Martín Gastón [EMAIL PROTECTED] wrote: Hi R users, I am working with the fda package but when I call the function pca.fd I obtain a message error, which I cann't identify. The error say That : error in assihn(mname,def,where), is not possible to add links to a blockade enviroment. The orther that I'm writting is: cp1 - pca.fd(ind.fd1,nharm=3) and before it I can to plot the functional data object ind.fd1. ¿Have anybody seen this error or any similar message?, ¿Any idea? Thancks for your help -- View this message in context: http://www.nabble.com/Error-en-assign%28mname%2C-def%2C-where%29-tf3995432.html#a11346689 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] R function command on a list
Perhaps, you can get the name of list element whit:
unlist(lapply(list_name, rownames))
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/06/07, Georg Ehret [EMAIL PROTECTED] wrote:
Thank you Henrique,
rownames also gives me the header of the table, but not the name of the
list-element...
Any other idea?
Wishing you a good day, Georg.
**
Georg Ehret
Johns Hopkins University
Baltimore
On 6/28/07, Henrique Dallazuanna [EMAIL PROTECTED] wrote:
Try whit rownames.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/06/07, G E [EMAIL PROTECTED] wrote:
Hello R:
I am working with a self-defined function and I wish to subject a
list
(t) to this function. My list is a list of tables:
$rs7609589
2/2 2/4 4/4 2/2 2/4 4/4
89 188 87 89 188 87
$rs3909907
1/1 1/4 4/4
94 178 92
$rs12748004
0/0 1/3 3/3
37 150 177
$rs6695928
2/2 2/4 4/4
35 129 200
My function looks as follows:
delete_nocall_listoftables-function(i){
names-names(i)
i
if (names[1] == 0/0){
i[-(1:1)]
}else{
i
}
}
Within the function, how can I access the table name of a given
element
( e.g.
$rs3909907)? Using names(i) I get the header of the table...
Thanking you!
Georg.
[[alternative HTML version deleted]]
__
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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.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] mixed-effects model using lmer
Hello R-users, I have been trying to fit what I think is a simple mixed-effects model using lmer (from lme4), but I've run into some difficulty that I have not been able to resolve using the existing archives or Pinheiro and Bates (2000). I am measuring populations (of birds) which change with time at a number of different sites. These sites are grouped into regions. Sites are not measured with any regularity, so each site has a different number of observations. I want to treat the effect of year (i.e. the rate of population change) as a fixed effect which is modeled separately for each region, but I want to allow sites within regions to be random effects. I've come up with the following model, but I'm not sure its correct. Any help would be most appreciated. fit-lmer(log.count~site+month+year:region-1+(year:region-1|site)) What my variables mean: log.count=log(count) site=factor for the different sites, each site is associated with exactly one region month=fixed effect for the month of the survey year:region = allows me to model different year effects for each region Each site should have a completely separate intercept, so I have chosen to suppress the intercept and use all the factors of site instead. The difficulty is, of course, with the last term. I want to have sites vary randomly *within* a region, but I don't want them to vary randomly throughout all the regions, i.e. I want the random effects to sum to zero for each region separately. My output looks like (using the display() function from Gelman and Hill (2007)): *** lmer(formula = log.count ~ site + month + year:region - 1 + (year:region - 1 | site)) coef.est coef.se siteAITC 7.25 0.15 siteALMI 4.57 0.29 siteBENE 5.98 0.29 siteBOOT 7.08 0.17 siteBROW 6.47 0.14 (I cut some out here for space) siteUSEF 6.97 0.21 siteWATE 7.38 0.15 siteYANK 8.31 0.11 monthJAN -0.15 0.07 monthNOV -0.01 0.07 year:regionNE -0.16 0.12 year:regionNW 0.04 0.01 year:regionSH 0.02 0.02 year:regionSW 0.07 0.01 Error terms: Groups Name Std.Dev. Corr site year:regionNE 0.12 year:regionNW 0.03 0.00 year:regionSH 0.00 0.00 0.00 year:regionSW 0.00 0.00 0.00 0.00 Residual 0.26 --- number of obs: 110, groups: site, 23 AIC = 157.8, DIC = -72.6 deviance = 3.6 The coefficients look totally reasonable given all the analysis I've already done on the system. My confusion comes about when I look at the random effects using ranef(fit) and se.ranef(fit): ranef(fit) An object of class ranef.lmer [[1]] year:regionNE year:regionNW year:regionSH year:regionSW AITC 0.0e+00 0.0e+00 5.8e-10 0.0e+00 ALMI 0.0e+00 -2.3e-04 0.0e+00 0.0e+00 BENE 0.0e+00 -2.1e-17 0.0e+00 0.0e+00 BOOT 0.0e+00 0.0e+00 0.0e+00 -2.4e-09 BROW 3.0e-15 0.0e+00 0.0e+00 0.0e+00 BRYE 0.0e+00 -1.3e-02 0.0e+00 0.0e+00 BRYS 0.0e+00 -8.9e-17 0.0e+00 0.0e+00 CUVE 0.0e+00 -1.7e-02 0.0e+00 0.0e+00 DAMO 0.0e+00 -5.0e-03 0.0e+00 0.0e+00 DANC 0.0e+00 -5.2e-03 0.0e+00 0.0e+00 DOBE 0.0e+00 8.1e-04 0.0e+00 0.0e+00 GEOR 0.0e+00 -9.3e-03 0.0e+00 0.0e+00 HANN 0.0e+00 0.0e+00 3.2e-10 0.0e+00 HERO -6.3e-16 0.0e+00 0.0e+00 0.0e+00 JOUG 0.0e+00 -2.3e-02 0.0e+00 0.0e+00 MADD 7.3e-16 0.0e+00 0.0e+00 0.0e+00 MOOT 0.0e+00 0.0e+00 0.0e+00 8.7e-11 NEKO 0.0e+00 -2.1e-03 0.0e+00 0.0e+00 PETE 0.0e+00 0.0e+00 0.0e+00 2.5e-09 PLEN 0.0e+00 0.0e+00 0.0e+00 -2.0e-10 USEF 0.0e+00 5.6e-02 0.0e+00 0.0e+00 WATE 0.0e+00 1.8e-02 0.0e+00 0.0e+00 YANK 0.0e+00 0.0e+00 -9.0e-10 0.0e+00 se.ranef(fit) $site year:regionNE year:regionNW year:regionSH year:regionSW AITC 0.1200.0296 5.8e-06 5.8e-06 ALMI 0.1200.0204 5.8e-06 5.8e-06 BENE 0.1200.0196 5.8e-06 5.8e-06 BOOT 0.1200.0296 5.8e-06 5.8e-06 BROW 0.0160.0296 5.8e-06 5.8e-06 BRYE 0.1200.0144 5.8e-06 5.8e-06 BRYS 0.1200.0231 5.8e-06 5.8e-06 CUVE 0.1200.0136 5.8e-06 5.8e-06 DAMO 0.1200.0086 5.8e-06 5.8e-06 DANC
[R] sampling question
I am interested in locating a script to implement a sampling scheme that would basically make it more likely that a particular observation is chosen based on a weight associated with the observation. I am trying to select a sample of ~30 census blocks from each ZIP code area based on the proportion of women in a ZCTA living in a particular block. I want to make it more likely that a block will be chosen if the proportion of women in a patient's age group in a particular block is high. Any ideas are appreciated! __ R-help@stat.math.ethz.ch 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.
[R] applying max elementwise to two vectors
All, Is there one liner way to obtain the max per observation for two vectors? I looked at apply and lapply but it seems that groundwork would have to be done before applying either of those. The code below does it but seems like overkill. Thanks! Dave x = rnorm(10) y = rnorm(10) ind = which(x y) z = x z[ind] - y[ind] ## z now contains the max's __ R-help@stat.math.ethz.ch 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.
[R] Wilcoxon Rank Sum Test.
Dear, I'm using R software to evaluate Wilcoxon Rank Sum Test and I' getting one Warning message as this: C1dea_com [1] 1.000 0.345 0.200 0.208 0.508 0.480 0.545 0.563 0.451 0.683 0.380 0.913 1.000 0.506 C1dea_sem [1] 1.000 0.665 0.284 0.394 0.509 0.721 0.545 0.898 0.744 0.683 0.382 0.913 1.000 0.970 wilcox.test(C1dea_sem,C1dea_com, paired = TRUE, alternative = two.sided) Wilcoxon signed rank test with continuity correction data: C1dea_sem and C1dea_com V = 45, p-value = 0.009152 alternative hypothesis: true mu is not equal to 0 Warning message: Cannot compute exact p-value with zeroes in: wilcox.test.default(C1dea_sem, C1dea_com, paired = TRUE, alternative = two.sided) What is happening? Best Regards, Marcus Vinicius [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Sweave bug? when writing figures / deleting variable in chunk
Thanks to the four distinguished R'ers who answered. I have used
Sweave intensively for over a year, and have poured through all the
doc. as well as the help archives, and could find nothing on this. It
is now well known to me! since it bit me, but it did cost me a day
of head-scratching and putting it in the shortest possible form for
the list (the original example where this happened was a lot more
complicated). Perhaps it could be documented in Sweave-
manual-20060104.pdf or its successor?
Now I see the reasoning behind it, thanks. I had already determined
the work-around. The problem is that I distribute the Tangled .R
files along with the Sweaved PDF doc, so that students etc. can run
the code. Anything unintuitive in the code confuses people. In this
case I think it's good pratice to delete temporary variables right
after they are no longer needed (as in my original example), so
that's why I want to put it in the same chunk.
Having said that, I am a Sweave devotee, it has radically improved my
productivity in writing R-based tech. notes.
David Rossiter
ITC Enschede (NL)
On 27 Jun2007, at 21:34, Achim Zeileis wrote:
On Wed, 27 Jun 2007 21:06:04 -0400 D G Rossiter wrote:
I have found a quite strange (to me) behaviour in Sweave. It only
occurs in the following situation:
1. define a variable in one chunk
2. use it within a subsequent figure-generating chunk
3. delete it at the end of that same chunk
Then the Sweave driver chokes, not finding the variable name when
generating the figure
Sweave() executes figure chunks more than once because they might
also create printed output. If you create both EPS and PDF
graphics, it
executes them three times (print + EPS + PDF). Hence, data
manipulations should be avoided in figure chunks.
I was also once bitten by this when I permuted columns of a table
prior
to plotting and never obtained the desired order...
Fritz, maybe this is worth an entry in the FAQ?
Z
Example:
% document bug2.Rnw
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\SweaveOpts{eps=false}
=
sel - 1:5
@
fig=T=
plot(trees[sel,])
rm(sel)
@
\end{document}
Try to sweave:
Sweave(bug2.Rnw)
Writing to file bug2.tex
Processing code chunks ...
1 : echo term verbatim
2 : echo term verbatim pdf
Error: no function to return from, jumping to top level
Error in plot(trees[sel, ]) : error in evaluating the argument 'x'
in selecting a method for function 'plot'
Error in driver$runcode(drobj, chunk, chunkopts) :
Error in plot(trees[sel, ]) : error in evaluating the
argument 'x' in selecting a method for function 'plot'
The generated .tex is complete up through the rm() but no figure is
generated. The file bug2-002.pdf is incomplete (corrupt).
...
\begin{Schunk}
\begin{Sinput}
plot(trees[sel, ])
rm(sel)
\end{Sinput}
\end{Schunk}
The following ALL eliminate the problem:
0. Executing the code directly, also with ESS
1. fig=F
2. moving rm(sel) to a separate, later code chunk
3. Stangle the source and then source it
4. don't use a variable, i.e. in this case: plot(trees[1:5,])
It seems that Sweave is executing the rm(sel) before it uses it in
the trees[sel,].
Technical details: R 2.5.0, Mac OS X 10.4.10, PPC
Same behaviour in stand-alone R for Mac and for R within Aquamacs
using ESS
Workaround: I am putting any deletions into a later code chunk. This
only has the disadvantage of making more chunks, so now that I know
what's happening it's no big deal. But it's driving me crazy... am I
missing something? Thanks!
D. G. Rossiter
Senior University Lecturer
Department of Earth Systems Analysis
International Institute for Geo-Information Science and Earth
Observation (ITC)
Hengelosestraat 99
PO Box 6, 7500 AA Enschede, The Netherlands
Phone: +31-(0)53 4874 499
Fax: +31-(0)53 4874 336
mailto:rossiter--at--itc.nl, Internet: http://www.itc.nl/personal/
rossiter
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave bug? when writing figures / deleting variable in chunk
On Thu, 28 Jun 2007 08:14:44 -0400, D G Rossiter (DGR) wrote: Thanks to the four distinguished R'ers who answered. I have used Sweave intensively for over a year, and have poured through all the doc. as well as the help archives, and could find nothing on this. It is now well known to me! since it bit me, but it did cost me a day of head-scratching and putting it in the shortest possible form for the list (the original example where this happened was a lot more complicated). Sorry! Perhaps it could be documented in Sweave- manual-20060104.pdf or its successor? Yes, I'll put it in ASAP. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.stat.uni-muenchen.de/~leisch __ R-help@stat.math.ethz.ch 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.
[R] Changing graphics height when using grid and lattice
Hi,
I have recently been playing with the grid package in an attempt to create
some pages containing multiple lattice plots on the same page. However, when
I specify a grid layout with different widths, such as:
pushViewport(viewport(layout = grid.layout(1, 2, unit(c(2, 1), null
the individual graphs do not end up as the same height - which is a feature
I would prefer to have.
A complete example is as follows:
### Start of example
library(lattice)
library(Hmisc)
library(grid)
# Incidence data
testData - data.frame(
strata = rep(c(CHF : Yes, CHF : No), each = 20),
ae = rep(paste(Adverse Event, 1:10), each = 2),
trt = rep(c(Active, Placebo), 20),
pct = runif(40, 1, 30)
)
# RR data
testData2 - data.frame(
strata = rep(c(CHF : Yes, CHF : No), each = 10),
ae = paste(Adverse Event, 1:10),
rr = runif(20, 0.5, 5)
)
testData2$lower = testData2$rr / 2
testData2$upper = testData2$rr * 2
# Combined plot
testPlots - function(relativeWidth)
{
plot1- dotplot(
ae ~ pct | strata,
groups = trt,
data = testData,
layout = c(1, 2),
xlab = Percent,
auto.key = list(space = top, columns = 2)
)
plot2 - Dotplot(
ae ~ Cbind(rr, log10(lower), log10(upper)) | strata,
data = testData2,
panel = function(...)
{
panel.Dotplot(...)
panel.abline(v = 0, col = 'red', lty = 2)
},
layout = c(1, 2),
scales = list(
x = list(log = T, at = c(0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32)),
y = list(draw = F)
),
xlab = Relative Risk with 95% CI,
ylab = ,
key = list(text = list())
)
grid.newpage()
pushViewport(viewport(layout = grid.layout(2, 1, heights = unit(c(1, 6),
null
pushViewport(viewport(layout.pos.col = 1, layout.pos.row = 1))
grid.text(Analysis of Relative Risks of various Adverse Events)
upViewport()
pushViewport(viewport(layout.pos.col = 1, layout.pos.row = 2))
### Change the relative width of the 2 presented graphics
pushViewport(viewport(layout = grid.layout(1, 2, unit(c(relativeWidth, 1),
null
pushViewport(viewport(layout.pos.col = 1, layout.pos.row = 1))
print(plot1, newpage = F)
upViewport()
pushViewport(viewport(layout.pos.col = 2, layout.pos.row = 1))
print(plot2, newpage = F)
upViewport()
}
# Everything is fine, both graphs maintain the same y-axis
testPlots(1)
# The second graph is now taller than the first one
win.graph()
testPlots(3)
# End of example
I've been through the documentation of both lattice and grid, and I have not
been able to find the answer. I would appreciate any solution!
Regards,
James Price.
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Re: [R] Wilcoxon Rank Sum Test.
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marcus Vinicius Sent: Thursday, June 28, 2007 1:32 PM To: r-help@stat.math.ethz.ch Subject: [R] Wilcoxon Rank Sum Test. Dear, I'm using R software to evaluate Wilcoxon Rank Sum Test and I' getting one Warning message as this: C1dea_com [1] 1.000 0.345 0.200 0.208 0.508 0.480 0.545 0.563 0.451 0.683 0.380 0.913 1.000 0.506 C1dea_sem [1] 1.000 0.665 0.284 0.394 0.509 0.721 0.545 0.898 0.744 0.683 0.382 0.913 1.000 0.970 wilcox.test(C1dea_sem,C1dea_com, paired = TRUE, alternative = two.sided) Wilcoxon signed rank test with continuity correction data: C1dea_sem and C1dea_com V = 45, p-value = 0.009152 alternative hypothesis: true mu is not equal to 0 Warning message: Cannot compute exact p-value with zeroes in: wilcox.test.default(C1dea_sem, C1dea_com, paired = TRUE, alternative = two.sided) What is happening? Best Regards, Marcus Vinicius Marcus, It means that you have one or more pairs of observations (5 in your case) where the difference is 0. The wilcox.test can only compute an approximate p-value under these circumstances. Hope this is helpful, Dan Daniel J. Nordlund Research and Data Analysis Washington State Department of Social and Health Services Olympia, WA 98504-5204 __ R-help@stat.math.ethz.ch 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.
Re: [R] applying max elementwise to two vectors
On Thu, 28 Jun 2007 16:19:39 -0400, Afshartous, David [EMAIL PROTECTED] wrote: All, Is there one liner way to obtain the max per observation for two vectors? I looked at apply and lapply but it seems that groundwork would have to be done before applying either of those. The code below does it but seems like overkill. Thanks! Dave x = rnorm(10) y = rnorm(10) ind = which(x y) z = x z[ind] - y[ind] ## z now contains the max's ?pmax -- Seb __ R-help@stat.math.ethz.ch 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.
Re: [R] sampling question
The sample function has a prob argument that determines the probabilities of each element being sampled, put your proportion of women in there and see if that works for you. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kirsten Beyer Sent: Thursday, June 28, 2007 2:00 PM To: r-help@stat.math.ethz.ch Subject: [R] sampling question I am interested in locating a script to implement a sampling scheme that would basically make it more likely that a particular observation is chosen based on a weight associated with the observation. I am trying to select a sample of ~30 census blocks from each ZIP code area based on the proportion of women in a ZCTA living in a particular block. I want to make it more likely that a block will be chosen if the proportion of women in a patient's age group in a particular block is high. Any ideas are appreciated! __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] Function call within a function.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of John Kane
Sent: Thursday, June 28, 2007 12:04 PM
To: R R-help
Subject: [R] Function call within a function.
I am trying to call a funtion within another function
and I clearly am misunderstanding what I should do.
Below is a simple example.
I know lstfun works on its own but I cannot seem to
figure out how to get it to work within ukn. Basically
I need to create the variable nts. I have probably
missed something simple in the Intro or FAQ.
Any help would be much appreciated.
EXAMPLE
--
-
# create data.frame
cata - c( 1,1,6,1,1,4)
catb - c( 1,2,3,4,5,6)
id - c('a', 'b', 'b', 'a', 'a', 'b')
dd1 - data.frame(id, cata,catb)
# function to create list from data.frame
lstfun - function(file, alpha , beta ) {
cda - subset(file, file[,1] == alpha)
cdb - subset (file, file[,1]== beta)
list1 - list(cda,cdb)
}
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
mysum - nam1[,3]*5
return(mysum)
}
results - ukn(dd1, a, b, nts$cda)
John,
The first problem I see is one of scope. nts$cda refers to an object called
nts which does not exist in the calling environment (it is local to the
function ukn). So trying to call ukn() with nts results in an error. Second,
even if you pass the name of the object, you will not be able to use it in
ukn() in the manner that you are trying. Your ukn() function definition also
requires that it know the inner workings of function lstfun(). Functions
generally shouldn't require knowing how other functions work, they should only
rely on what value is returned.
You can get what you want by redefining ukn in the following way
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
mysum - nts[[nam1]][,3]*5
return(mysum)
}
And change the function call to
results - ukn(dd1, a, b, 1)
This still leaves the functions coupled in a way that I don't like, but I'm not
a good enough R programmer to solve that problem at the moment. Maybe someone
else will come along with a better solution.
Hope this is helpful,
Dan
Daniel J. Nordlund
Research and Data Analysis
Washington State Department of Social and Health Services
Olympia, WA 98504-5204
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Re: [R] applying max elementwise to two vectors
thanks all. yes, pmax(x,y) gets it straight away. sorry for missing this when I checked the docs. -Original Message- From: Greg Snow [mailto:[EMAIL PROTECTED] Sent: Thursday, June 28, 2007 5:26 PM To: Afshartous, David; r-help@stat.math.ethz.ch Subject: RE: [R] applying max elementwise to two vectors Are you looking for pmax? (look at the help ?pmax and the examples and see if that does what you want). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Afshartous, David Sent: Thursday, June 28, 2007 2:20 PM To: r-help@stat.math.ethz.ch Subject: [R] applying max elementwise to two vectors All, Is there one liner way to obtain the max per observation for two vectors? I looked at apply and lapply but it seems that groundwork would have to be done before applying either of those. The code below does it but seems like overkill. Thanks! Dave x = rnorm(10) y = rnorm(10) ind = which(x y) z = x z[ind] - y[ind] ## z now contains the max's __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] applying max elementwise to two vectors
Please... use and **read** the docs: ?max --- pmax Bert Gunter -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Afshartous, David Sent: Thursday, June 28, 2007 1:20 PM To: r-help@stat.math.ethz.ch Subject: [R] applying max elementwise to two vectors All, Is there one liner way to obtain the max per observation for two vectors? I looked at apply and lapply but it seems that groundwork would have to be done before applying either of those. The code below does it but seems like overkill. Thanks! Dave x = rnorm(10) y = rnorm(10) ind = which(x y) z = x z[ind] - y[ind] ## z now contains the max's __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] Wilcoxon Rank Sum Test.
On Thu, 28 Jun 2007 14:18:52 -0700 Nordlund, Dan (DSHS/RDA) wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marcus Vinicius Sent: Thursday, June 28, 2007 1:32 PM To: r-help@stat.math.ethz.ch Subject: [R] Wilcoxon Rank Sum Test. Dear, I'm using R software to evaluate Wilcoxon Rank Sum Test and I' getting one Warning message as this: C1dea_com [1] 1.000 0.345 0.200 0.208 0.508 0.480 0.545 0.563 0.451 0.683 0.380 0.913 1.000 0.506 C1dea_sem [1] 1.000 0.665 0.284 0.394 0.509 0.721 0.545 0.898 0.744 0.683 0.382 0.913 1.000 0.970 wilcox.test(C1dea_sem,C1dea_com, paired = TRUE, alternative = two.sided) Wilcoxon signed rank test with continuity correction data: C1dea_sem and C1dea_com V = 45, p-value = 0.009152 alternative hypothesis: true mu is not equal to 0 Warning message: Cannot compute exact p-value with zeroes in: wilcox.test.default(C1dea_sem, C1dea_com, paired = TRUE, alternative = two.sided) What is happening? Best Regards, Marcus Vinicius Marcus, It means that you have one or more pairs of observations (5 in your case) where the difference is 0. The wilcox.test can only compute an approximate p-value under these circumstances. ...while wilcox.exact() from package exactRankTests can evaluate the permutation distribution correctly. Z Hope this is helpful, Dan Daniel J. Nordlund Research and Data Analysis Washington State Department of Social and Health Services Olympia, WA 98504-5204 __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] Adding different output to different lattice panels
Selon [EMAIL PROTECTED]:
On 6/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
I would like to add a reference line to lattice graphs, with the reference
line
being different according to the factor level.
Example : Draw 3 dotplots for a,b and c factors, and then add an
horizontal line at y=10 for panel a, y=8 for panel b and y=6 for panel
4
I tried the code below, but this draw all three reference lines for each
panel.
How do I index the current panel to chose the right reference vector value
?
dat-data.frame(id=rep(c(a,b,c),4),val=1:12,quand=rep(c(t1,t2,t3,t4),each=3))
ref-c(10,8,6)
plot.new()
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref)
})
print(datplot)
dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h = ref[packet.number()])
})
(Things are more complicated if you have more than one conditioning
variable.)
-Deepayan
I tried you solution, but the following error appears when I print(datplot):
Erreur dans as.numeric(h) : impossible de trouver la fonction packet.number
I have lattice and grid libraries loaded. The exact code I use is
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref[packet.number()])
})
print(datplot)
What do I do wrong ?
Note : I usually need to use the indirect datplot-dotplot(... and then
print(datplot) when I store my code in a file and use it through
source(myfile.R). The direct dotplot(... does not open a device whereas it
does if I type directly dotplot(... at the R command line...
Is this normal ?
--
Alexandre Salvador
Tel: +33(0)6.8214.7733
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Re: [R] Adding different output to different lattice panels
Selon Deepayan Sarkar [EMAIL PROTECTED]:
On 6/28/07, Alexandre Salvador [EMAIL PROTECTED] wrote:
Selon [EMAIL PROTECTED]:
On 6/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
I would like to add a reference line to lattice graphs, with the
reference
line
being different according to the factor level.
Example : Draw 3 dotplots for a,b and c factors, and then add an
horizontal line at y=10 for panel a, y=8 for panel b and y=6 for
panel
4
I tried the code below, but this draw all three reference lines for
each
panel.
How do I index the current panel to chose the right reference vector
value
?
dat-data.frame(id=rep(c(a,b,c),4),val=1:12,quand=rep(c(t1,t2,t3,t4),each=3))
ref-c(10,8,6)
plot.new()
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref)
})
print(datplot)
dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h = ref[packet.number()])
})
(Things are more complicated if you have more than one conditioning
variable.)
-Deepayan
I tried you solution, but the following error appears when I
print(datplot):
Erreur dans as.numeric(h) : impossible de trouver la fonction
packet.number
I have lattice and grid libraries loaded. The exact code I use is
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref[packet.number()])
})
print(datplot)
What do I do wrong ?
You are using a very old version of R (or at least old enough that the
packet.number number didn't exist). You haven't told us what version
you are using.
I would encourage you to upgrade, but this might work for now:
dotplot(val~quand|id,data=dat,
panel=function(..., panel.number){
panel.dotplot(...)
panel.abline(h = ref[panel.number])
})
Note : I usually need to use the indirect datplot-dotplot(... and then
print(datplot) when I store my code in a file and use it through
source(myfile.R). The direct dotplot(... does not open a device whereas
it
does if I type directly dotplot(... at the R command line...
Is this normal ?
Yes, and a FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
-Deepayan
Works all right,
I use Version 2.3.1 (2006-06-01)
I'll upgrade to the newer versions...
Thanks very much,
Cheers
--
Alexandre Salvador
Tel: +33(0)6.8214.7733
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Re: [R] applying max elementwise to two vectors
Are you looking for pmax? (look at the help ?pmax and the examples and see if that does what you want). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Afshartous, David Sent: Thursday, June 28, 2007 2:20 PM To: r-help@stat.math.ethz.ch Subject: [R] applying max elementwise to two vectors All, Is there one liner way to obtain the max per observation for two vectors? I looked at apply and lapply but it seems that groundwork would have to be done before applying either of those. The code below does it but seems like overkill. Thanks! Dave x = rnorm(10) y = rnorm(10) ind = which(x y) z = x z[ind] - y[ind] ## z now contains the max's __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] Writing - specyfic format
That's exactly what I need.
Thank's a lot!!
Earl F. Glynn wrote:
jastar [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Hi all,
I have a trouble - I need to write file in a very specyfic format.
I have two vectors which different lengths and one data.frame (or
matrix).
I want to write it to *.txt file in following way:
1st row of file is my 1st vector (separate by spacebar)
2nd row of file is 2nd vector (also separate by spacebar)
Rest of this file should be a matrix with elements separated by tab.
For example: a=1, 2, 3, b=4, 5, c=[1, 2, 3, 4, 5, 6;
7, 8, 9, 10, 11, 12,]
and I want to have file (it have to be .txt file) like:
1 2 3
4 5
1 2 3 4 5 6
7 8 9 10 1112
This thing have to be done automaticly from R.
Is it possible?
Try this:
a - 1:3
b - 4:5
c - matrix(1:12, 2,6, byrow=TRUE)
outFile - file(SpecificFormat.txt, w)
cat(paste(a, sep= ), \n, file=outFile)
cat(paste(b, sep= ), \n, file=outFile)
for (j in 1:nrow(c))
{
cat(paste(c[j,], collapse=\t), \n, file=outFile)
}
close(outFile)
Resulting output file (with spaces or tabs as specified):
1 2 3
4 5
1 2 3 4 5 6
7 8 9 10 11 12
[But I normally avoid tabs since you cannot see them easily with many
editors.]
efg
Earl F. Glynn
Stowers Institute for Medical Research
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Re: [R] Function call within a function.
Dear John,
Perhaps I am mistaken in what you are trying to accomplish but it seems like
what is required is that you call lstfun() outside of ukn(). [and remove the
call to lstfun() in ukn()].
nts - lstfun(myfile, aa, bb)
results - ukn(dd1, a, b, nts$cda)
Alternatively, you can eliminate the fourth argument in ukn() and assign (via
'-') the results of lstfun() to 'nam1' within ukn() instead of saving to
'nts'...
--- John Kane [EMAIL PROTECTED] wrote:
I am trying to call a funtion within another function
and I clearly am misunderstanding what I should do.
Below is a simple example.
I know lstfun works on its own but I cannot seem to
figure out how to get it to work within ukn. Basically
I need to create the variable nts. I have probably
missed something simple in the Intro or FAQ.
Any help would be much appreciated.
EXAMPLE
---
# create data.frame
cata - c( 1,1,6,1,1,4)
catb - c( 1,2,3,4,5,6)
id - c('a', 'b', 'b', 'a', 'a', 'b')
dd1 - data.frame(id, cata,catb)
# function to create list from data.frame
lstfun - function(file, alpha , beta ) {
cda - subset(file, file[,1] == alpha)
cdb - subset (file, file[,1]== beta)
list1 - list(cda,cdb)
}
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
mysum - nam1[,3]*5
return(mysum)
}
results - ukn(dd1, a, b, nts$cda)
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Re: [R] Function call within a function.
The problem isn't the function call.
First, list1 returned by lstfun does not name its elements so nts$cda
won't work. See code change in lstfun.
Second, specifying nts$cda as the nam1 argument tells R to look for
the nts object in the environment in which ukn is called. However,
the nts object is not created in the parent environment, it is created
in the ukn's environment.
Third, nam1[,3] should be nam1[2] as there is no third element to this
list (although and this doesn't resolve the environment issue).
I've modified your code below to work, but there are better ways to go
about this. Thomas Lumley has a famous quote regarding parse. See
http://tolstoy.newcastle.edu.au/R/e2/help/07/01/8059.html among
others.
I was once referred to Patrick Burns' S Poetry to learn about the
eval(parse(text=))) paradigm which was very helpful. You may also
want to brush up on environments (see ?environment) to learn more
about lexical scoping.
Hope this helps.
-jason
#MODIFIED CODE
# create data.frame
cata - c( 1,1,6,1,1,4)
catb - c( 1,2,3,4,5,6)
id - c('a', 'b', 'b', 'a', 'a', 'b')
dd1 - data.frame(id, cata,catb)
# function to create list from data.frame
lstfun - function(file, alpha , beta ) {
cda - subset(file, file[,1] == alpha)
cdb - subset (file, file[,1]== beta)
### CODE ADDED HERE
list1 - list(cda=cda,cdb=cdb)
}
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
### CODE ADDED HERE
mysum - eval(parse(text=nam1))
#mysum - nam1[,3]*5
return(mysum)
}
results - ukn(dd1, a, b, nts$cda) ### modified how called.
- Original Message -
From: John Kane [EMAIL PROTECTED]
To: R R-help r-help@stat.math.ethz.ch
Sent: Thursday, June 28, 2007 12:03 PM
Subject: [R] Function call within a function.
I am trying to call a funtion within another function
and I clearly am misunderstanding what I should do.
Below is a simple example.
I know lstfun works on its own but I cannot seem to
figure out how to get it to work within ukn. Basically
I need to create the variable nts. I have probably
missed something simple in the Intro or FAQ.
Any help would be much appreciated.
EXAMPLE
---
# create data.frame
cata - c( 1,1,6,1,1,4)
catb - c( 1,2,3,4,5,6)
id - c('a', 'b', 'b', 'a', 'a', 'b')
dd1 - data.frame(id, cata,catb)
# function to create list from data.frame
lstfun - function(file, alpha , beta ) {
cda - subset(file, file[,1] == alpha)
cdb - subset (file, file[,1]== beta)
list1 - list(cda,cdb)
}
# funtion to operate on list
ukn - function(file, alpha, beta, nam1){
aa - alpha
bb - beta
myfile - file
nts - lstfun(myfile, aa, bb)
mysum - nam1[,3]*5
return(mysum)
}
results - ukn(dd1, a, b, nts$cda)
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Re: [R] Adding different output to different lattice panels
On 6/28/07, Alexandre Salvador [EMAIL PROTECTED] wrote:
Selon [EMAIL PROTECTED]:
On 6/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
I would like to add a reference line to lattice graphs, with the reference
line
being different according to the factor level.
Example : Draw 3 dotplots for a,b and c factors, and then add an
horizontal line at y=10 for panel a, y=8 for panel b and y=6 for panel
4
I tried the code below, but this draw all three reference lines for each
panel.
How do I index the current panel to chose the right reference vector value
?
dat-data.frame(id=rep(c(a,b,c),4),val=1:12,quand=rep(c(t1,t2,t3,t4),each=3))
ref-c(10,8,6)
plot.new()
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref)
})
print(datplot)
dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h = ref[packet.number()])
})
(Things are more complicated if you have more than one conditioning
variable.)
-Deepayan
I tried you solution, but the following error appears when I print(datplot):
Erreur dans as.numeric(h) : impossible de trouver la fonction
packet.number
I have lattice and grid libraries loaded. The exact code I use is
datplot-dotplot(val~quand|id,data=dat,panel=function(...){
panel.dotplot(...)
panel.abline(h=ref[packet.number()])
})
print(datplot)
What do I do wrong ?
You are using a very old version of R (or at least old enough that the
packet.number number didn't exist). You haven't told us what version
you are using.
I would encourage you to upgrade, but this might work for now:
dotplot(val~quand|id,data=dat,
panel=function(..., panel.number){
panel.dotplot(...)
panel.abline(h = ref[panel.number])
})
Note : I usually need to use the indirect datplot-dotplot(... and then
print(datplot) when I store my code in a file and use it through
source(myfile.R). The direct dotplot(... does not open a device whereas it
does if I type directly dotplot(... at the R command line...
Is this normal ?
Yes, and a FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
-Deepayan
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Re: [R] sampling question
Lets assume your zcta data looks like this
set.seed(12345) ## temporary for reproducibility
zcta - data.frame( zipcode=LETTERS[1:5], prop=runif(5) )
zcta
zipcode prop
1 A 0.7209039
2 B 0.8757732
3 C 0.7609823
4 D 0.8861246
5 E 0.4564810
This says that 72.1% of the population in zipcode A is female, ..., and
45.6% in zipcode E is female.
Now suppose you sampled 20 people and you recorded the zipcode (and
other variables) and stored in 'samp'
samp - data.frame( id=1:20,
zipcode=LETTERS[ sample(1:5, 20, replace=TRUE) ])
Now, I am not sure what you want to do. But I could see two possible
meanings from your message.
1) If you want to sample 10 observation, with each observation weighted
INDEPENDENTLY by the proportion of women in its zipcode, try something
like the following. The problem with this option is that it depends on
the prevalence of the zipcodes of the observations.
comb - merge( samp, zcta, all.x=T )
comb - comb[ order(comb$id), ]
comb[ sample( comb$id, 10, prob=comb$prop ), ]
2) If you want to sample x% in each zipcode, where x is the proportion
of women in that zipcode. Then this is what I would call stratified
sampling. Try this:
tmp - split( samp, samp$zipcode )
out - NULL
for( z in names(tmp) ){
df - tmp[[z]]
p - zcta[ zcta$zipcode == z, prop ]
out[[z]] - df[ sample( 1:nrow(df), p*nrow(df) ), ]
}
do.call(rbind, out)
You probably need a variant of these but if you need further help, you
will need to provide more information and better yet examples.
Regards, Adai
Kirsten Beyer wrote:
I am interested in locating a script to implement a sampling scheme
that would basically make it more likely that a particular observation
is chosen based on a weight associated with the observation. I am
trying to select a sample of ~30 census blocks from each ZIP code area
based on the proportion of women in a ZCTA living in a particular
block. I want to make it more likely that a block will be chosen if
the proportion of women in a patient's age group in a particular block
is high. Any ideas are appreciated!
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[R] exaustive subgrouping or combination
Waverley [EMAIL PROTECTED] asked: Dear Colleagues, I am looking for a package or previous implemented R to subgroup and exaustively divide a vector of squence into 2 groups. -- Waverley @ Palo Alto Google [R] Generating all possible partitions and you will find some R code from 2002 or so. David Duffy. -- | David Duffy (MBBS PhD) ,-_|\ | email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v __ R-help@stat.math.ethz.ch 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.
Re: [R] Changing graphics height when using grid and lattice
On 6/28/07, Jim Price [EMAIL PROTECTED] wrote: Hi, I have recently been playing with the grid package in an attempt to create some pages containing multiple lattice plots on the same page. However, when I specify a grid layout with different widths, such as: pushViewport(viewport(layout = grid.layout(1, 2, unit(c(2, 1), null the individual graphs do not end up as the same height - which is a feature I would prefer to have. The default padding between components of a graph is defined as a proportion of the plot area. In particular, it's unit(0.01, snpc), which makes it the same on both axes. The problem is that when you have two grid viewports, unit(0.01, snpc) may give different physical length. One option is to set all paddings to 0, which can be done with myLatticeSettings - function() list(layout.heights = list(top.padding = 0, main.key.padding = 0, key.axis.padding = 0, axis.xlab.padding = 0, xlab.key.padding = 0, key.sub.padding = 0, bottom.padding = 0), layout.widths = list(left.padding = 0, key.ylab.padding = 0, ylab.axis.padding = 0, axis.key.padding = 0, right.padding = 0) ) trellis.par.set(myLatticeSettings()) This may not be what you want, so another option is to set the paddings to something absolute; e.g. myLatticeOptions - function() list(layout.heights = list(top.padding = list(x = 1, units = mm, data = NULL), main.key.padding = list(x = 1, units = mm, data = NULL), key.axis.padding = list(x = 1, units = mm, data = NULL), axis.xlab.padding = list(x = 1, units = mm, data = NULL), xlab.key.padding = list(x = 1, units = mm, data = NULL), key.sub.padding = list(x = 1, units = mm, data = NULL), bottom.padding = list(x = 1, units = mm, data = NULL)), layout.widths = list(left.padding = list(x = 1, units = mm, data = NULL), key.ylab.padding = list(x = 1, units = mm, data = NULL), ylab.axis.padding = list(x = 1, units = mm, data = NULL), axis.key.padding = list(x = 1, units = mm, data = NULL), right.padding = list(x = 1, units = mm, data = NULL)) ) lattice.options(myLatticeOptions()) I'm not particularly attached to the snpc solution, so I may change them at some point. -Deepayan __ R-help@stat.math.ethz.ch 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.
[R] logistic regression and dummy variable coding
Hello everyone, I have a variable with several categories and I want to convert this into dummy variables and do logistic regression on it. I used model.matrix to create dummy variables but it always picked the smallest one as the reference. For example, model.matrix(~.,data=as.data.frame(letters[1:5])) will code 'a' as '0 0 0 0'. But I want to code another category as reference, say 'b'. How to do it in R using model.matrix? Is there other way to do it if model.matrix has no such functionality? Thanks! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] logistic regression and dummy variable coding
On Thu, 2007-06-28 at 18:16 -0500, Bingshan Li wrote: Hello everyone, I have a variable with several categories and I want to convert this into dummy variables and do logistic regression on it. I used model.matrix to create dummy variables but it always picked the smallest one as the reference. For example, model.matrix(~.,data=as.data.frame(letters[1:5])) will code 'a' as '0 0 0 0'. But I want to code another category as reference, say 'b'. How to do it in R using model.matrix? Is there other way to do it if model.matrix has no such functionality? Thanks! See ?relevel Note that this (creating dummy variables) will be done automatically in R's modeling functions, which default to treatment contrasts on factors. model.matrix() is used internally by model functions such as glm(). For example using a single factor: FL - factor(letters[1:5]) FL [1] a b c d e Levels: a b c d e contrasts(FL) b c d e a 0 0 0 0 b 1 0 0 0 c 0 1 0 0 d 0 0 1 0 e 0 0 0 1 FL.b - relevel(FL, b) FL.b [1] a b c d e Levels: b a c d e contrasts(FL.b) a c d e b 0 0 0 0 a 1 0 0 0 c 0 1 0 0 d 0 0 1 0 e 0 0 0 1 See ?contrasts and the Statistical Models section in An Introduction to R. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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.
Re: [R] logistic regression and dummy variable coding
NewVar - relevel( factor(OldVar), ref = b) should create a dummy variable, and change the reference category for the model. Reza On 6/28/07, Bingshan Li [EMAIL PROTECTED] wrote: Hello everyone, I have a variable with several categories and I want to convert this into dummy variables and do logistic regression on it. I used model.matrix to create dummy variables but it always picked the smallest one as the reference. For example, model.matrix(~.,data=as.data.frame(letters[1:5])) will code 'a' as '0 0 0 0'. But I want to code another category as reference, say 'b'. How to do it in R using model.matrix? Is there other way to do it if model.matrix has no such functionality? Thanks! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
Re: [R] logistic regression and dummy variable coding
Hi All, Now it works. Thanks for all your answers and the explanations are very clear. Bingshan On Jun 28, 2007, at 7:44 PM, Seyed Reza Jafarzadeh wrote: NewVar - relevel( factor(OldVar), ref = b) should create a dummy variable, and change the reference category for the model. Reza On 6/28/07, Bingshan Li [EMAIL PROTECTED] wrote: Hello everyone, I have a variable with several categories and I want to convert this into dummy variables and do logistic regression on it. I used model.matrix to create dummy variables but it always picked the smallest one as the reference. For example, model.matrix(~.,data=as.data.frame(letters[1:5])) will code 'a' as '0 0 0 0'. But I want to code another category as reference, say 'b'. How to do it in R using model.matrix? Is there other way to do it if model.matrix has no such functionality? Thanks! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
