RE: [R] Adding labels to variables
References: <[EMAIL PROTECTED]> X-Mailer: VM 7.18 under Emacs 21.3.1 Reply-To: Martin Maechler <[EMAIL PROTECTED]> FCC: ~maechler/F/out --text follows this line-- > "AustinM" == Austin, Matt <[EMAIL PROTECTED]> > on Tue, 24 Aug 2004 22:15:15 -0700 writes: AustinM> Check out the Hmisc library. It's a *package*, not a library ! Note that there are also the "comment" and "comment<-" function pair (in R's base) that you could use : > x <- 1:10 > comment(x) <- "this is the price of the R stock" > x [1] 1 2 3 4 5 6 7 8 9 10 > comment(x) [1] "this is the price of the R stock" > comment(x+4) [1] "this is the price of the R stock" [these are probably among the oldest R (non-S) functions, maybe not known for this reason, and not really used in other public functions AFAIK] Martin Maechler AustinM> -Original Message- AustinM> [mailto:[EMAIL PROTECTED] Behalf Of Neil Leonard AustinM> Sent: Tuesday, August 24, 2004 22:0 PM AustinM> To: [EMAIL PROTECTED] AustinM> Subject: [R] Adding labels to variables AustinM> Hi, AustinM> Is it possible to add labels to variables in R (so AustinM> as to have a better description of what the AustinM> variables represent)? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Adding labels to variables
Neil Leonard tartarus.uwa.edu.au> writes: : Is it possible to add labels to variables in R (so as to have a better : description of what the variables represent)? One can add arbitrarily named attributes to objects. For example, we can add an attribute which we shall call memo to object z: R> z <- 3 R> attr(z,"memo") <- "very important number" R> # sometime later R> z [1] 3 attr(,"memo") [1] "very important number" __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Adding labels to variables
Check out the Hmisc library. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Neil Leonard Sent: Tuesday, August 24, 2004 22:0 PM To: [EMAIL PROTECTED] Subject: [R] Adding labels to variables Hi, Is it possible to add labels to variables in R (so as to have a better description of what the variables represent)? Thanks, Neil __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Adding labels to variables
Hi, Is it possible to add labels to variables in R (so as to have a better description of what the variables represent)? Thanks, Neil __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Boxplot across levels of a factor
Thank you: works like a charm. Paul > -Original Message- > From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] > Sent: Tuesday, August 24, 2004 2:28 AM > To: Paul Boutros > Cc: R-Help > Subject: Re: [R] Boxplot across levels of a factor > > > On Tue, 24 Aug 2004, Paul Boutros wrote: > > > Hello, > > > > I have a data-frame in which one-column is a factor: > > > > > str(data); > > `data.frame': 194 obs. of 8 variables: > > $ Type : Factor w/ 3 levels "Nuclear-Rec..",..: 1 2 2 > 2 2 2 2 2 2 2 > > ... > > $ Locus: num 0.000571 0.004000 0.001429 0.004857 0.007429 ... > > > > And I'd like to make a boxplot of the data$Locus values, where > each level of > > the factor gets its own box-and-whiskers plot. I'm weak in R, > but I thought > > there might be some shortcut to automating this instead of just > creating a > > new data-structure with all the separate values? > > There are two. The simpler is > > boxplot(Locus ~ Type, data=data) > > and you can also use > > with(data, boxplot(split(Locus, Type))) > > (split() does automate the construction of a suitable data structure.) > > -- > 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 > __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] stem() bug?
First, I'm curious. Is there any reason why the leaves are squished together with no delimeters? Second, the crucial point that seems to be missing from the stem help page (and one I can't glean without going through the code) is how bins are determined. If that can be explained to the reader, the explanation of scale follows naturally. Third, feel free to incorporate the following text into the help page as necessary; I've tried to make it helpful (but clarity is obviously in the eye of the beholder). stem produces a stem-and-leaf plot of the elements in x. Each element is placed in a bin ranging [low, high); that is, if y is an element, it is placed in the bin iff low <= element < high. The size of the bin is determined by... . The stem that is listed for the bin is not necessarily the stem of all (or any) of the leaves in the bin; the true stems must be equal to or higher than the listed stems, but they will all be smaller than the lowerst stem of the next highest bin. (Observe how the bin for the stem 4 changes with the two examples below.) Leaves are ordered within a bin. If leaves seem unordered (e.g., 4 | 0306), then the scale of the plot may be too compressed: that bin contains leaves from multiple different stems. The parameter scale can be used to expand the scale of the plot. Arguments x a numeric vector. scale This controls the number of bins. A value of scale=2 will cause the plot to be twice as long as the default by using roughly twice as many bins. width The desired width of the plot, in characters. atom a tolerance [This needs better text.] Examples stem(c(30, 32, 50, 52, 60, 62, 70, 72, 80, 82)) stem(c(30, 32, 50, 52, 60, 62, 70, 72, 80, 82), scale=2) Original Message Follows From: Prof Brian Ripley <[EMAIL PROTECTED]> To: Ramzi Nahhas <[EMAIL PROTECTED]> CC: [EMAIL PROTECTED], <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> Subject: Re: [R] stem() bug? Date: Tue, 24 Aug 2004 09:17:08 +0100 (BST) It is as intended. The answer is correct but your interpretation of it is not, and the help page is woefully lacking. Note that the bins in your problem are [20, 40), [40, 60), [60, 80) and [80, 100) and they are correctly labelled. In such bins e.g. 20 and 30 are both represented in the same way. Does stem(seq(30, 92, 5)) help you see the pattern? Please would one of those bemoaning R's documentation recently submit to R-bugs an enhanced help page for stem? On Tue, 24 Aug 2004, Ramzi Nahhas wrote: > > Is the following a bug with stem() or is there something else that I am > missing? I ran stem() on the vector x below and got stem(x-10) instead of > stem(x). If I subtract 1 from x, I get a correct answer. If I add 1 to x, I > still get a wrong answer. If I add 10 to x, I get a correct answer. I'm not > sure what to make of this, other than to think it is a bug. > > Can anyone tell me if this is a bug? > > I am running R 1.9.1 on Windows XP (SP2). > > Sincerely, > Ramzi Nahhas > > PS In your reply, please copy me at [EMAIL PROTECTED] as I am not > subscribed to this list. Thank you. > > > x > [1] 30 70 90 75 70 95 75 70 60 55 > > stem(x) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 0 > 4 | 5 > 6 | 55 > 8 | 05 > > > stem(x-1) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 9 > 4 | 49 > 6 | 99944 > 8 | 94 > > > stem(x+1) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 1 > 4 | 6 > 6 | 66 > 8 | 16 > > > stem(x+10) > > The decimal point is 1 digit(s) to the right of the | > >4 | 0 >6 | 50 >8 | 00055 > 10 | 05 > > --- > > > > > > [[alternative HTML version deleted]] > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] analyzing cluster sample
I am analyzing a survey where ~20,000 cases were sampled in ~1000 clusters. I would like to analyze the data using, for example, gam. What is the best way to account for the clustering? I've tried including the cluster ID as a factor in the model formula, but the default response is to try and estimate the unique effect of each cluster, which given 1000 clusters is impossibly time consuming. What I want instead is an estimate of the variance due to clusters, or perhaps an intraclass correlation, and cluster-adjusted standard errors for the effects of other variables in the model. I expect I can account for clustering by using lme with clusters as a random effect, but then I can't use the flexible smooths available in gam. If it's not possible to get both clustering and smooths, I may use gam and adjust the standard errors using an estimate of the design effect. Many thanks for any advice, Paul Paul von Hippel Department of Sociology / Initiative in Population Research Ohio State University __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bug or no?
Note that R requires that anything placed AFTER the ...
to be matched exactly so one can force exact matching
on sb by putting it after the ... like this:
R> temp<-function(...,sb) print(sb)
R> temp(2,s=3)
Error in print(sb) : Argument "sb" is missing, with no default
Chuck Cleland optonline.net> writes:
:
: I don't think it's a bug, it's partial matching of
: argument names. To avoid it, use exact argument names in
: your call to the function:
:
: temp(sb=2,s=3)
: [1] 2
:
:From the R language definition:
:
: "Argument matching: Formal arguments are matched to supplied
: arguments first by exact matching on tags, then by partial
: matching on tags, and finally by positional matching."
:
: http://cran.r-project.org/doc/contrib/R_language.pdf
:
: Richard Morey wrote:
: > The following code prints [1] 2, as it should
: >
: > temp<-function(ab,...){
: > print(ab)
: > }
: > temp(2,s=3)
: >
: > However, this code prints [1] 3:
: >
: > temp<-function(sb,...){
: > print(sb)
: > }
: > temp(2,s=3)
: >
: > It should still print [1] 2. It appears
: > that if a variable in ... begins with the same letter as another variable,
: > the value in the variable in ... overwrites the value in the variable with
: > the same first letter.
: >
: > I didn't see this bug reported elsewhere.
: >
: > Richard Morey
: >
: > Is this a bug or am I missing something?
: >
: > output of R.version
: > platform i686-pc-linux-gnu
: > arch i686
: > os linux-gnu
: > system i686, linux-gnu
: > status
: > major1
: > minor9.1
: > year 2004
: > month06
: > day 21
: > language R
: >
: >
:
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Re: [R] bug or no?
I don't think it's a bug, it's partial matching of
argument names. To avoid it, use exact argument names in
your call to the function:
temp(sb=2,s=3)
[1] 2
From the R language definition:
"Argument matching: Formal arguments are matched to supplied
arguments first by exact matching on tags, then by partial
matching on tags, and finally by positional matching."
http://cran.r-project.org/doc/contrib/R_language.pdf
Richard Morey wrote:
The following code prints [1] 2, as it should
temp<-function(ab,...){
print(ab)
}
temp(2,s=3)
However, this code prints [1] 3:
temp<-function(sb,...){
print(sb)
}
temp(2,s=3)
It should still print [1] 2. It appears
that if a variable in ... begins with the same letter as another variable,
the value in the variable in ... overwrites the value in the variable with
the same first letter.
I didn't see this bug reported elsewhere.
Richard Morey
Is this a bug or am I missing something?
output of R.version
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major1
minor9.1
year 2004
month06
day 21
language R
--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 452-1424 (M, W, F)
fax: (917) 438-0894
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Re: [R] bug or no?
Richard Morey wrote:
The following code prints [1] 2, as it should
temp<-function(ab,...){
print(ab)
}
temp(2,s=3)
However, this code prints [1] 3:
temp<-function(sb,...){
print(sb)
}
temp(2,s=3)
It should still print [1] 2. It appears
that if a variable in ... begins with the same letter as another variable,
the value in the variable in ... overwrites the value in the variable with
the same first letter.
I didn't see this bug reported elsewhere.
Richard Morey
Is this a bug or am I missing something?
You are missing something. Mainly, reading section 4.3 of "R Language
Definition", which should come with your distribution or is accessible
from CRAN.
http://cran.r-project.org/doc/manuals/R-lang.pdf
--sundar
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[R] bug or no?
The following code prints [1] 2, as it should
temp<-function(ab,...){
print(ab)
}
temp(2,s=3)
However, this code prints [1] 3:
temp<-function(sb,...){
print(sb)
}
temp(2,s=3)
It should still print [1] 2. It appears
that if a variable in ... begins with the same letter as another variable,
the value in the variable in ... overwrites the value in the variable with
the same first letter.
I didn't see this bug reported elsewhere.
Richard Morey
Is this a bug or am I missing something?
output of R.version
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major1
minor9.1
year 2004
month06
day 21
language R
--
Richard Morey
Graduate Research Assistant, Cognition and Neuroscience
University of Missouri-Columbia
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[R] R/S-plus Course***September, 2004***R/Splus Fundamentals and Programming Techniques
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce August 2004 2-day "R/S-plus Fundamentals and Programming Techniques". Washington, DC --> September, 23-24 Chicago, IL--> September, 16-17 Interested in our R/Splus Advanced Programming course? Please email us! 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. We will perform basic statistics 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) Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Visit us: www.xlsolutions-corp.com/training.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] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] "how to set the number format to pure numeric?" was SOLVED
Thank you for your kind help. I am done now. regards, lichi __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (no subject)
Looks like there might have been some truncation of Jonathon Baron's message. Here's one way of computing the sample mode of a vector. > set.seed(1) > x <- sample(1:5,20,rep=T) > x [1] 2 2 3 5 2 5 5 4 4 1 2 1 4 2 4 3 4 5 2 4 > table(x) x 1 2 3 4 5 2 6 2 6 4 > names(which.max(table(x))) [1] "2" > Note that this method returns the first max value in the case of ties. hope this helps, Tony Plate At Tuesday 11:01 AM 8/24/2004, Jonathan Baron wrote: On 08/24/04 13:50, Paolo Tommasini wrote: >Hi my name is Paolo Tommasini does anyone know how to compute a "mode" >( most frequent element ) for a distribution ? which.max -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to set the number format to pure numeric?
lichi shi <[EMAIL PROTECTED]> wrote: > I want to export a numeric matrix in pure numeric format, i.e. I want > 0.0001 to appear as "0.0001". But it seems the default setting for > write.table is scientific notation, i.e. it will appear as "1e-04". how > to set the number format to pure numeric? Try: R> options(scipen=99) which sets a very high SCIentific notation PENalty. -- -- David Brahm ([EMAIL PROTECTED]) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] apply ( , , table)
apply() tries to be a bit smart about what it does (sometimes maybe too smart), but it actually is pretty useful a lot of the time. It's extremely widely used, so changing the behavior is not an option -- changing the behavior would break a lot of existing code. (Personally, I'd prefer it if apply() put its dimensions back together in a slightly more intelligent way, i.e., if apply(x, 1, c) and apply(x, 2, c) returned the same thing, but apply is how it is.) In situations where you don't want apply() to try to construct a matrix from your results, you can wrap the results in a list, to force apply() to return just a list of results, e.g. (the outer "lapply()" strips off an unnecessary level of list depth): > b2 <- lapply(apply (a, 1, function(x) list(table(x))), "[[", 1) > length(b2) [1] 4 > b2[[1]] x 1 2 6 7 2 1 1 1 > attributes(b2[[1]]) $dim [1] 4 $dimnames $dimnames$x [1] "1" "2" "6" "7" $class [1] "table" Your particular case might benefit from more information given to table, which allows it to provide results in a more uniform format, e.g.: > b1 <- apply (a, 1, function(x) table(factor(x, levels=0:9))) > b1 [,1] [,2] [,3] [,4] 00100 12112 21001 30100 40220 50011 61001 71000 80010 90000 > hope this helps, Tony Plate At Tuesday 10:42 AM 8/24/2004, [EMAIL PROTECTED] wrote: a <- matrix (c( 7, 1, 1, 2, 6, 3, 4, 0, 1, 4, 5, 1, 8, 4, 4, 6, 1, 1, 2, 5), nrow=4, byrow=TRUE) b <- apply (a, 1, table) "apply" documentation says clearly that if the rows of the result of FUN are the same length, then an array will be returned. And column-major would be the appropriate order in R. But "b" above is pretty opaque compared to what one would expect, and what one would get from "apply ( , , table)" if the rows were not of equal length. One needs to do something like n <- matrix (apply (a, 1, function (x) unique (sort (x))), nrow=nrow(a)) to get the corresponding "names" of "b" to figure out the counts. Denis White __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] mode of a distribution - was (no subject)
Perhaps a time out might be helpful. ?which.max will produce the location (index) of the maximum of a numeric vector, but Paolo doesn't want that. He wants the location of the most frequent observation which would be the maximum of the probability density, which he doesn't have. It would be useful to estimate what kind of density represents the data and then, given this, determine its interesting statistics, including the mode. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 503-217-5849 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jonathan Baron Sent: Tuesday, August 24, 2004 1:01 PM To: Paolo Tommasini Cc: [EMAIL PROTECTED] Subject: Re: [R] (no subject) On 08/24/04 13:50, Paolo Tommasini wrote: >Hi my name is Paolo Tommasini does anyone know how to compute a "mode" >( most frequent element ) for a distribution ? which.max -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] (no subject)
No, this is not quite right: which.max -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ You need to be more careful 1. For a continuous distribution, the mode is ** not ** the most frequent value (this has no meaning) -- it is the maximum of the density function. So you must fit a density function and then estimate the mode, perhaps by using which.max() on a discretization of the fitted density. Or, if you have the fitted density in closed form (and it is unimodal) you can use calculus. 2. For a discrete distribution, which could be the sample empirical distribution,use which.max(table()). -- Bert Gunter __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] The "Green" Book?
Thank you for your perspective . . . I see what you mean, and that's actually
more or less how I had interpreted Professor Ripley's remarks. I'll have to
investigate further the advantages of using S4 classes in my work. I suspect
they'll eventually prove their worth. Thanks again for the clarification. SC
Quoting "Liaw, Andy" <[EMAIL PROTECTED]>:
> Sam,
>
> What BDR meant (I believe) is that it depends on _how_ you intend to use R,
> not what your background is. If you are going to develop code using the new
> S4 classes, the green book will be relevant. If you are going to use R for
> data analysis, there's probably little to gain by reading the green book.
>
> Best,
> Andy
>
> > -Original Message-
> > From: [EMAIL PROTECTED]
> > [mailto:[EMAIL PROTECTED] On Behalf Of Sam Chapman
> > Sent: Monday, August 23, 2004 10:16 AM
> > To: Prof Brian Ripley
> > Cc: Thomas Lumley; [EMAIL PROTECTED]
> > Subject: Re: [R] The "Green" Book?
> >
> >
> > Thank you for your responses. I should have mentioned that I
> > am new to R, but
> > not to programming. Nevertheless, the insights are valued and
> > appreciated!
> >
> >
> > Quoting Prof Brian Ripley <[EMAIL PROTECTED]>:
> >
> > > On Fri, 20 Aug 2004, Thomas Lumley wrote:
> > >
> > > > On Fri, 20 Aug 2004, Sam Chapman wrote:
> > > >
> > >
> > > [A quote from `An Introduction to R' has been excised here]
> > >
> > > > > There is no mention of 'Programming with Data: A Guide
> > to the S Language'
> > > by
> > > > > John M. Chambers. Is this newest ("Green") book also
> > suitable as a
> > > reference
> > > > > for R? Thank you for your time and attention!
> > > > >
> > > >
> > > > Yes. The system implemented in the "methods" package is
> > not identical to
> > > > that in the Green Book, but it's pretty similar.
> > >
> > > Well, it is suitable as reference for programmers using the
> > "methods"
> > > package in R, not quite the question asked. At the level of `An
> > > Introduction to R' it is not really a suitable reference as
> > it has limited
> > > coverage at that level. (The Green Book itself recommends
> > other books for
> > > end users.)
> > >
> > > --
> > > 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
> > >
> > >
> >
> >
> > Sincerely,
> >
> > Sam Chapman
> >
> > __
> > [EMAIL PROTECTED] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> >
> >
>
>
> --
> Notice: This e-mail message, together with any attachments, contains
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Sincerely,
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Re: [R] (no subject)
On 08/24/04 13:50, Paolo Tommasini wrote: >Hi my name is Paolo Tommasini does anyone know how to compute a "mode" >( most frequent element ) for a distribution ? which.max -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
Hi my name is Paolo Tommasini does anyone know how to compute a "mode" ( most frequent element ) for a distribution ? thanks __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] apply ( , , table)
a <- matrix (c( 7, 1, 1, 2, 6, 3, 4, 0, 1, 4, 5, 1, 8, 4, 4, 6, 1, 1, 2, 5), nrow=4, byrow=TRUE) b <- apply (a, 1, table) "apply" documentation says clearly that if the rows of the result of FUN are the same length, then an array will be returned. And column-major would be the appropriate order in R. But "b" above is pretty opaque compared to what one would expect, and what one would get from "apply ( , , table)" if the rows were not of equal length. One needs to do something like n <- matrix (apply (a, 1, function (x) unique (sort (x))), nrow=nrow(a)) to get the corresponding "names" of "b" to figure out the counts. Denis White __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] firewall or proxy problems
Sergio Anguissola wrote:
Hi, I right now installed the R and then I tried to download and install the
get bioC package, but I receive an error message saying that the software
couldn't connect trough the port 80. I went to the FAQ and I found that I
have to type somewhere -internet 2
So you are on Windows?
You are going to *invoke* R the way mentioned there. Just change the
link that calls R in the described manner (BTW: it says "--internet2"!).
If you don't know how to change a link, please contact local Windows
support.
Uwe Ligges
, but I couldn't understand when and
where, could you help me?
Thanks.
Sergio.
Sergio Anguissola Ph.D
Dept. of Physiology
RCSI, Education & Research Center
Smurfit Building, Beaumont Hospital
Dublin 9
Republic of Ireland
Tel: 01-809-3861
Fax: 01-809-3837
Email: [EMAIL PROTECTED]
This email and any files transmitted with it are confidentia...{{dropped}}
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Re: [R] how to in XML on windows XP for R 1.9.1
On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote:
> Hello, Uwe,
> Thank you all for your reply!
> I installed binary packages XML_0.97.0.zip by "Install package(s) from local zip
> file" and followed instruction in the doc:
That's not the instructions in the README!
> you will have to add the XML/libs
> directory to your path. Putting them into the
> directory which contains Rgui.exe and Rterm.exe for this
> version of R is probably best.
> I then put add the XML/libs directory to director rw1091/bin, but it still gave
> messagae like this:
What it actually says is
but to use it in R, you will have to add the XML/libs
directory to your path or copy the files
libxml2.dll zlib.dll iconv.dll
to a directory in your path. Putting them into the
directory which contains Rgui.exe and Rterm.exe for this
version of R is probably best.
and there are no such files in the distribution.
> > library("XML")
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
> "C:/PROGRA~1/R/rw1091/library/XML/libs/XML.dll":
> LoadLibrary failure: The specified module could not be found.
> Error in library("XML") : package/namespace load failed
> What should I do now?
Asking Uwe questions about a package his ReadMe explicitly says he does
not support is unfair.
Since XML_0.97-0 is not a CRAN package, please ask its author
directly. It depends on a libxml2.dll (etc) he has not included.
[This is part of the reason why I statically link libxml into the port of
XML that I make available. Another is that with a dynamic link the
internet connection possibilities do not work correctly, at least when I
build it.
Another issue is that you need different builds for different versions of
R, and www.omegahat.org/RSXML does not say which it was built for.]
> Josh
> Quoting Uwe Ligges <[EMAIL PROTECTED]>:
>
> > Prof Brian Ripley wrote:
> > > On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote:
> > >
> > >
> > >>I tried two ways to install Package:XML on windows xp for R 1.9.1, all
> > failed.
> > >
> > >
> > > But you did not read the ReadMe's.
> > >
> > > Do read the ReadMe at http://cran.r-project.org/bin/windows/contrib/1.9.
> >
> > Additionally, after you have got the right package, read the docs how to
> > install binary packages from the local hard disc.
> >
> > Uwe Ligges
> >
>
> __
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
--
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] firewall or proxy problems
Hi, I right now installed the R and then I tried to download and install the
get bioC package, but I receive an error message saying that the software
couldn't connect trough the port 80. I went to the FAQ and I found that I
have to type somewhere -internet 2, but I couldn't understand when and
where, could you help me?
Thanks.
Sergio.
Sergio Anguissola Ph.D
Dept. of Physiology
RCSI, Education & Research Center
Smurfit Building, Beaumont Hospital
Dublin 9
Republic of Ireland
Tel: 01-809-3861
Fax: 01-809-3837
Email: [EMAIL PROTECTED]
This email and any files transmitted with it are confidentia...{{dropped}}
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Re: [R] how to in XML on windows XP for R 1.9.1
[EMAIL PROTECTED] wrote:
Hello, Uwe,
Thank you all for your reply!
I installed binary packages XML_0.97.0.zip
Hear, hear. To my knowledge, there are the versions
0.94-1 and 0.95-6 of XML available at the URL given in the ReadMe cited
by Brian Ripley. Note that this ReadMe points to
http://www.stats.ox.ac.uk/pub/RWin/ !!!
Uwe Ligges
> by "Install package(s) from local zip
file" and followed instruction in the doc:
you will have to add the XML/libs
directory to your path. Putting them into the
directory which contains Rgui.exe and Rterm.exe for this
version of R is probably best.
I then put add the XML/libs directory to director rw1091/bin, but it still gave
messagae like this:
library("XML")
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
"C:/PROGRA~1/R/rw1091/library/XML/libs/XML.dll":
LoadLibrary failure: The specified module could not be found.
Error in library("XML") : package/namespace load failed
What should I do now?
Josh
Quoting Uwe Ligges <[EMAIL PROTECTED]>:
Prof Brian Ripley wrote:
On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote:
I tried two ways to install Package:XML on windows xp for R 1.9.1, all
failed.
But you did not read the ReadMe's.
Do read the ReadMe at http://cran.r-project.org/bin/windows/contrib/1.9.
Additionally, after you have got the right package, read the docs how to
install binary packages from the local hard disc.
Uwe Ligges
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Re: [R] how to set the number format to pure numeric?
On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote: > I want to export a numeric matrix in pure numeric format, i.e. I want > 0.0001 to appear as "0.0001". But it seems the default setting for > write.table is scientific notation, i.e. it will appear as "1e-04". how to > set the number format to pure numeric? Thank you very much for your help. It's not the default, BTW. Try 0.002, say. See ?options and look at `scipen' to alter the rules. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to in XML on windows XP for R 1.9.1
Hello, Uwe,
Thank you all for your reply!
I installed binary packages XML_0.97.0.zip by "Install package(s) from local zip
file" and followed instruction in the doc:
you will have to add the XML/libs
directory to your path. Putting them into the
directory which contains Rgui.exe and Rterm.exe for this
version of R is probably best.
I then put add the XML/libs directory to director rw1091/bin, but it still gave
messagae like this:
> library("XML")
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
"C:/PROGRA~1/R/rw1091/library/XML/libs/XML.dll":
LoadLibrary failure: The specified module could not be found.
Error in library("XML") : package/namespace load failed
What should I do now?
Josh
Quoting Uwe Ligges <[EMAIL PROTECTED]>:
> Prof Brian Ripley wrote:
> > On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote:
> >
> >
> >>I tried two ways to install Package:XML on windows xp for R 1.9.1, all
> failed.
> >
> >
> > But you did not read the ReadMe's.
> >
> > Do read the ReadMe at http://cran.r-project.org/bin/windows/contrib/1.9.
>
> Additionally, after you have got the right package, read the docs how to
> install binary packages from the local hard disc.
>
> Uwe Ligges
>
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[R] how to set the number format to pure numeric?
Hello, I want to export a numeric matrix in pure numeric format, i.e. I want 0.0001 to appear as "0.0001". But it seems the default setting for write.table is scientific notation, i.e. it will appear as "1e-04". how to set the number format to pure numeric? Thank you very much for your help. cheers, lichi shi __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ROracle and vector elements
Hi Laura, Sorry for the delay, but I was away and I'm finally catching up... I do have a windows binary at http://stat.bell-labs.com/RS-DBI/download/ but note that you need to have the Oracle's client software. Hope this helps, -- David Laura Holt wrote: > Hi there! > > Is ROracle available for Windows, please? > > I found a download site, but it's really for UNIX/Linux. > > Here is a "thought question", please: Why do the vector elements start at > location 1 rather than zero, as C does? > > Thanks in advance! > > R Version 1.9.1 Windows > Sincerely, > Laura Holt > mailto: [EMAIL PROTECTED] > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- David A. James Statistics Research, Room 2C-253Phone: (908) 582-3082 Bell Labs, Lucent Technologies Fax:(908) 582-3340 Murray Hill, NJ 09794-0636 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rgl installation problems
It is indeed the following problem. I used the RPM installation as of July 20, 2004
and had the same problem installing rgl. After fixing the following line in the
Makeconf file ("-share" is missing), the installation of rgl went successfully.
>This is a little strange. I'm now building RPMS for older Red Hat versions on FC2
>using a tool called Mach. There is a possibility that
>there is some configuration problem, but I can't see it. As Brian has pointed out,
>you are missing the crucial "-shared" flag when building
>the shared library for rgl. This comes from the line
>
>SHLIB_CXXLDFLAGS = -shared
>
>in the file /usr/lib/R/etc/Makeconf. This is present in my latest RPM for Red Hat (
>R-1.9.1-0.fdr.2.rh90.i386.rpm ) so I don't know why it
>isn't working for you.
>>Here's what should happen on RH9 (with the latest libpng and gcc in /usr/local/lib)
>>
>>g++ -shared -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o
>>pixmap.o gui.o api.o device.o devicemanager.o rglview.o scene.o
>>glgui.o -L/usr/X11R6/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lpng12 -lz -lm
>>-lstdc++ -lX11 -lXext -lGL -lGLU -lpng12 -lz -lm
>>Note that he had no --shared but did have crt1.o, that is was trying to build a
>>standalone executable and not a shared object.
>>Something is wrong with the R installation's rules to make shared libraries.
>>On Fri, 25 Jun 2004, Duncan Murdoch wrote:
>> On Fri, 25 Jun 2004 17:36:30 +, "E GCP" <[EMAIL PROTECTED]> wrote :
>>
>> >Hi!
>> >
>> >I'm new to R, but have worked with Splus before. I installed several
>> >packages in R (R-1.9.1) without problems, but when I try to install rgl
>> >(rgl_0.64-13.tar.gz). I get the following, and the package does not install.
>> >Any help would be greatly appreciated. I'm running R in redhat 9.
>>
>> The missing reference R_InputHandlers is declared in the
>> $RHOME/src/include/R_ext/eventloop.h file, and I believe is compiled
>> into the library R_X11 (with some extension). You don't seem to have
>> that in the list of libraries:
>>
>> >g++ -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o
>> >pixmap.o
>> >gui.o api.o device.o devicemanager.o rglview.o scene.o glgui.o
>> >-L/usr/X11R6/lib
>> >-L/usr/lib -lstdc++ -lX11 -lXext -lGL -lGLU -lpng
>> >/usr/lib/gcc-lib/i386-redhat-linux/3.2.2/../../../crt1.o(.text+0x18): In
>> >functio
>> >n `_start':
>> >../sysdeps/i386/elf/start.S:77: undefined reference to `main'
>> >x11lib.o(.text+0x84): In function `set_R_handler':
>> >/tmp/R.INSTALL.8663/rgl/src/x11gui.h:33: undefined reference to
>> >`R_InputHandlers
>>
>> I don't know what you'll need to do to fix this, since I'm using
>> Windows, so none of this stuff happens there, and I could be
>> completely wrong about it.
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Re: [R] how to in XML on windows XP for R 1.9.1
On Tue, 24 Aug 2004 [EMAIL PROTECTED] wrote: > I tried two ways to install Package:XML on windows xp for R 1.9.1, all failed. But you did not read the ReadMe's. Do read the ReadMe at http://cran.r-project.org/bin/windows/contrib/1.9. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to in XML on windows XP for R 1.9.1
Dear R experts:
I tried two ways to install Package:XML on windows xp for R 1.9.1, all failed.
Messages are given as bellows:
1> download from CRAN
> install.packages("XML", CRAN = getOption("CRAN"),
+ contriburl = contrib.url("http://cran.r-project.org";),
+ available = NULL, destdir = NULL,
+ installWithVers = FALSE)
trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 20065 bytes
opened URL
downloaded 19Kb
Warning message:
No package "XML" on CRAN. in: download.packages(pkgs, destdir = tmpd, available
= available,
2> Download binary code XML_0.97.0.zip from http://www.omegahat.org/RSXML/
unzipt to goXML directory:
> install.packages("C:/goXML/XML")
trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 20065 bytes
opened URL
downloaded 19Kb
Warning message:
No package "C:/goXML/XML" on CRAN. in: download.packages(pkgs, destdir = tmpd,
available = available,
Could you please help me install it sucessfully?
Thank you for your hellp!
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RE: [R] Maxima/minima of loess line?
On Tue, 2004-08-24 at 15:23, Liaw, Andy wrote: > Just take range() of the fitted loess values. > Or if you really want to investigate the *line* instead of some random *points*, you may need something like: > optimize(function(x, mod) predict(mod, data.frame(speed=x)), c(0,20), maximum=TRUE, mod=cars.lo) $maximum [1] 19.5 $objective [1] 56.44498 This elaborates the ?loess example with the result object cars.lo (and, of course is a bad example since the fit is monotone and solutions is forced to the margin). Use maximum=FALSE for *a* minimum. If you have several predictors, you either need to supply constant values for those in optimize, or for simultaneous search in all use optim or nlm. cheers, jari oksanen > > > From: Fredrik Karlsson > > > > Dear list, > > > > I've produced a loess line that I would like to investigate > > in terms of > > local/global maxima and minima. How would you do this? > > > > Thank you in advance. > > > > /Fredrik Karlsson > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Jari Oksanen <[EMAIL PROTECTED]> __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Maxima/minima of loess line?
Just take range() of the fitted loess values. Andy > From: Fredrik Karlsson > > Dear list, > > I've produced a loess line that I would like to investigate > in terms of > local/global maxima and minima. How would you do this? > > Thank you in advance. > > /Fredrik Karlsson __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] help with knn from class library
> From: Martin Olivier > > Hi all, > > I made some computations with the knn function from the class library. > If I execute this function several times (with the same parameters k, > training set and test set), I obtain different results. > I don't understand why the results for my test set are > different. Could > you give me some explanations? > Is the solution for a k-nearest-neighbor classifier unique? Could it be that you have ties in the data? There's a `use.all' argument: use.all: controls handling of ties. If true, all distances equal to the 'k'th largest are included. If false, a random selection of distances equal to the 'k'th is chosen to use exactly 'k' neighbours. So you may want to try that. The other thing to try is to set.seed() before calling knn(). Andy > Best regards. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help with knn from class library
Hi all, I made some computations with the knn function from the class library. If I execute this function several times (with the same parameters k, training set and test set), I obtain different results. I don't understand why the results for my test set are different. Could you give me some explanations? Is the solution for a k-nearest-neighbor classifier unique? Best regards. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Run function in BATCH mode?
[EMAIL PROTECTED] wrote:
Hi,
I am working on a shell script where i need to start a R function defined in a
script. I know how to run the script; with
R CMD BATCH script
which would be equal to
source("script") in R.
But how do I run a function(param) of that script in the BATCH mode?
Thanks in advance.
__
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Say you have a function MyFoo defined in foo.R then you create a file
call.R that sources foo.r (source("foo.R")) and calls your function by,
e.g., MyFoo(a, b, x).
Then just say "R CMD BATCH call.R" ...
Uwe Ligges
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[R] Run function in BATCH mode?
Hi,
I am working on a shell script where i need to start a R function defined in a
script. I know how to run the script; with
R CMD BATCH script
which would be equal to
source("script") in R.
But how do I run a function(param) of that script in the BATCH mode?
Thanks in advance.
__
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[R] Run function in BATCH mode?
Hi,
I am working on a shell script where i need to start a R function defined in a
script. I know how to run the script; with
R CMD BATCH script
which would be equal to
source("script") in R.
But how do I run a function(param) of that script in the BATCH mode?
Thanks in advance.
__
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[R] Maxima/minima of loess line?
Dear list, I've produced a loess line that I would like to investigate in terms of local/global maxima and minima. How would you do this? Thank you in advance. /Fredrik Karlsson __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Test of significance in estimation of correlation coefficients
On Tue, 24 Aug 2004, Jonathan Baron wrote: > BTW, there is a small bug in the documentation for cor: cor.test > is no longer in the ctest package, but in stats. Your information is not up to date: that page has been changed in R-patched and R-devel. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Test of significance in estimation of correlation coefficients
On 08/24/04 15:05, Vikas Rawal wrote: >I estimated spearman's correlation coefficient using cor(). How do I >test for significance? cor.test You could find this many ways, but one is to look at the help document for cor. cor.test is listed is at the bottom. In general, it is a good idea to look at help before posting here. BTW, there is a small bug in the documentation for cor: cor.test is no longer in the ctest package, but in stats. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Test of significance in estimation of correlation coefficients
I estimated spearman's correlation coefficient using cor(). How do I test for significance? Vikas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] rgdal under windows?
Success! I'm pleased to inform that Roger's recipe worked a treat for compiling rgdal_0.2-7 in conjunction with gdal-1.2.1 and proj-4.4.8. Using MinGW-3.1.0 with MYS-1.0.8 on an xp pro box (SP1) Proj-4 compiled straight out of the box. Gdal needed a couple of minor tweaks wrt how the boolean type is defined. I suspect that gcc is being strict about name spaces. My hack was an explicit typedef in jpeglib.h: typedef unsigned char boolean; and to comment out the definition in jmorecfg.h After that it was plain sailing except for the curious behaviour of the MinGW dlltool.exe which refused to to pick up R.dll unless it was given the full path _irrespective_ of what was placed in $PATH. Big thanks to Roger and Brian for their helpful advice. Complicated? Not if you learn to read! Cheers, Ben -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: 19 August 2004 19:27 To: Prof Brian Ripley Cc: Benjamin Lloyd-Hughes; [EMAIL PROTECTED] Subject: Re: [R] rgdal under windows? On Thu, 19 Aug 2004, Prof Brian Ripley wrote: > On Thu, 19 Aug 2004, Benjamin Lloyd-Hughes wrote: > > > Has anyone had any joy getting the rgdal package to compile under windows? > > First you need to meet the system requirements: > > SystemRequirements: GDAL library from > http://www.remotesensing.org/gdal/download.html > > Since that has build instructions which say > > GDAL can be built on Windows using MS VC++ 6.x and MS Visual Studio .NET > (C++) at the DOS command line. > > you will first need to get a copy of DOS and those compilers. (I suspect > they mean the Windows command prompt, but they don't seem to know the > difference which is not confidence-inspiring. I also suspect they mean > `or' not `and'.) Then you will have to fathom out how to link against a > VC++ DLL which since this C++ is very unlikely to work with MinGW. So you > probably need to make the package's rgdal.dll under VC++ -- see > README.packages. > > I have tried and failed to make GDAL with MinGW. > > > I've been trying with MinGW using Duncan Murdoch's Rtools but to no avail. > > Do read README.packages and follow the advice at the top. You don't have > the (mis-attributed) tools in your path. But that is probably the least > of your potential problems. > Exactly. The closest anyone has got so far is Hisaji Ono, who used MSYS (http://www.mingw.org/) to build PROJ.4 and GDAL (GDAL depends on PROJ.4, PROJ.4 needs a PATH to metadata files for projection and transformation), and then hand-pasted the paths to the GDAL headers and library into src/Makevars, running Rcmd INSTALL rgdal at the Windows command prompt as usual. All of this can be repeated, but is not portable, and does not suit the very valuable standard binary package build system for Windows. Roughly: 1. Download everything you need to build source packages under Windows and make sure it works; 2. Download MSYS and make sure it works; 3. Download the GDAL and PROJ.4 source tarballs, and possibly other libraries you want to use with GDAL, and *within MSYS* untar, ./configure with the appropriate arguments, at least make but maybe also make install - now leave MSYS; 4. Download the rgdal source package, and *at the Windows command prompt* untar it, change the name of configure to something else, create src/Makevars manually from src/Makevars.in, insert the correct values of: PKG_CPPFLAGS as -I, PKG_LIBS as -L< ... GDAL libraries> -lgdal, run Rcmd INSTALL rgdal (better first Rcmd check rgdal), and repeat until all the problems are resolved. 5. The installation should work locally, but some paths are compiled into the resulting *.dll, so it will, most likely, not be portable. Both Hisaji and I were surprised that this actually seemed to work (as of late Autumn last year for the versions of MinGW and MSYS available then; further fragility is introduced by much of GDAL being written in C++); it is not wholly impossible that it could be made available portably as a Windows binary with an installer, but not through the regular R binary package repositories. > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to get Dunnett's table value?
Hi, I want to retrieve a value in the Dunnett's tables. I know the comparisons type, the percent of level,the number of traitments and the degrees of freedom. Is there a function to retrieve this value with this? Laurent Houdusse Analyste Programmeur __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] stem() bug?
It is as intended. The answer is correct but your interpretation of it is not, and the help page is woefully lacking. Note that the bins in your problem are [20, 40), [40, 60), [60, 80) and [80, 100) and they are correctly labelled. In such bins e.g. 20 and 30 are both represented in the same way. Does stem(seq(30, 92, 5)) help you see the pattern? Please would one of those bemoaning R's documentation recently submit to R-bugs an enhanced help page for stem? On Tue, 24 Aug 2004, Ramzi Nahhas wrote: > > Is the following a bug with stem() or is there something else that I am > missing? I ran stem() on the vector x below and got stem(x-10) instead of > stem(x). If I subtract 1 from x, I get a correct answer. If I add 1 to x, I > still get a wrong answer. If I add 10 to x, I get a correct answer. I'm not > sure what to make of this, other than to think it is a bug. > > Can anyone tell me if this is a bug? > > I am running R 1.9.1 on Windows XP (SP2). > > Sincerely, > Ramzi Nahhas > > PS In your reply, please copy me at [EMAIL PROTECTED] as I am not > subscribed to this list. Thank you. > > > x > [1] 30 70 90 75 70 95 75 70 60 55 > > stem(x) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 0 > 4 | 5 > 6 | 55 > 8 | 05 > > > stem(x-1) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 9 > 4 | 49 > 6 | 99944 > 8 | 94 > > > stem(x+1) > > The decimal point is 1 digit(s) to the right of the | > > 2 | 1 > 4 | 6 > 6 | 66 > 8 | 16 > > > stem(x+10) > > The decimal point is 1 digit(s) to the right of the | > >4 | 0 >6 | 50 >8 | 00055 > 10 | 05 > > --- > > > > > > [[alternative HTML version deleted]] > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] do linux-version r has gui?
R-cmdr package is nice R-gui. Help.start() work if your browser support java script, then I think you haven't a java-plugin installed on your browser Best regards! A.S. Alessandro Semeria Models and Simulations Laboratory Montecatini Environmental Research Center (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] stem() bug?
Is the following a bug with stem() or is there something else that I am missing? I ran stem() on the vector x below and got stem(x-10) instead of stem(x). If I subtract 1 from x, I get a correct answer. If I add 1 to x, I still get a wrong answer. If I add 10 to x, I get a correct answer. I'm not sure what to make of this, other than to think it is a bug. Can anyone tell me if this is a bug? I am running R 1.9.1 on Windows XP (SP2). Sincerely, Ramzi Nahhas PS In your reply, please copy me at [EMAIL PROTECTED] as I am not subscribed to this list. Thank you. > x [1] 30 70 90 75 70 95 75 70 60 55 > stem(x) The decimal point is 1 digit(s) to the right of the | 2 | 0 4 | 5 6 | 55 8 | 05 > stem(x-1) The decimal point is 1 digit(s) to the right of the | 2 | 9 4 | 49 6 | 99944 8 | 94 > stem(x+1) The decimal point is 1 digit(s) to the right of the | 2 | 1 4 | 6 6 | 66 8 | 16 > stem(x+10) The decimal point is 1 digit(s) to the right of the | 4 | 0 6 | 50 8 | 00055 10 | 05 --- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Boxplot across levels of a factor
On Tue, 24 Aug 2004, Ivar Herfindal wrote:
> I think Paul wanted one plot for each box, not all boxes in one plot (sorry
> if I misunderstand).
>
> One way to solve this can be like this:
>
> par(mfrow=c(1,3))
> with(data, by(1:nrow(data), Type, function(x) boxplot(Locus[x]~data[x]))
Actually, that does not come close to working. Did you try it?
(Please read the documentation for by().) The following does work
by(data, Type, function(x) boxplot(x$Locus,
main=paste("Type", unique(x$Type
but that would be a very unusual plot, and one in which the three plots
had different scalings so the boxplots could not be compared.
For something like that, lattice's bwplot is a better option.
bwplot(Locus ~ Type, data=data) 1 panel
bwplot(Locus ~ factor(rep(1, 182)) | Type, data=data) 3 panels
>
> Hope this works for you.
>
> Ivar
>
> On Tue, 24 Aug 2004 07:27:57 +0100 (BST), Prof Brian Ripley
> <[EMAIL PROTECTED]> wrote:
>
> > On Tue, 24 Aug 2004, Paul Boutros wrote:
> >
> >> Hello,
> >>
> >> I have a data-frame in which one-column is a factor:
> >>
> >> > str(data);
> >> `data.frame': 194 obs. of 8 variables:
> >> $ Type : Factor w/ 3 levels "Nuclear-Rec..",..: 1 2 2 2 2 2 2 2
> >> 2 2
> >> ...
> >> $ Locus: num 0.000571 0.004000 0.001429 0.004857 0.007429 ...
> >>
> >> And I'd like to make a boxplot of the data$Locus values, where each
> >> level of
> >> the factor gets its own box-and-whiskers plot. I'm weak in R, but I
> >> thought
> >> there might be some shortcut to automating this instead of just creating
> >> a
> >> new data-structure with all the separate values?
> >
> > There are two. The simpler is
> >
> > boxplot(Locus ~ Type, data=data)
> >
> > and you can also use
> >
> > with(data, boxplot(split(Locus, Type)))
> >
> > (split() does automate the construction of a suitable data structure.)
> >
>
>
>
>
--
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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