Re: [R] uniform integer RNG 0 to t inclusive
Prof Ripley,
You are absolutely correct, this code will not work at all - for
starters, M isn't correctly initialized, etc. I edited my code in
tinn-r and never ran it before posting... my apologies, I always seem
to be too quick off the mark to reply - despite the 4*runif(1)
suggestion in the posting guide...
I hadn't realized before what significant difference the replace=TRUE
would make to the runtime... Now I can just use the sample() code you
suggested and remove my runif() code altogether, as sample(t+1, 1,
replace=TRUE) - 1 will work fine with t <- 2e9 which is considerably
more that I need.
Thanks again to both Prof Ripley and Duncan Murdoch,
Sean O'Riordain
affiliation <- NULL
On 19/09/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> On Tue, 19 Sep 2006, Sean O'Riordain wrote:
>
> > Hi Duncan,
> >
> > Thanks for that. In the light of what you've suggested, I'm now using
> > the following:
> >
> > # generate a random integer from 0 to t (inclusive)
> > if (t < 1000) { # to avoid memory problems...
> >M <- sample(t, 1)
> > } else {
> >while (M > t) {
> > M <- as.integer(urand(1,min=0, max=t+1-.Machine$double.eps))
> >}
> > }
>
> sample(t, 1) is a sample from 1:t, not 0:t.
>
> You need
>
> sample(t+1, 1, replace=TRUE) - 1
>
> which works in all cases up to INT_MAX-1, and beyond that you need to
> worry about the resolution of the RNG (and to use floor not as.integer).
>
> There is no such thing as urand in base R
>
> >
> > cheers and Thanks,
> > Sean
> >
> > On 18/09/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> >> On 9/18/2006 3:37 AM, Sean O'Riordain wrote:
> >>> Good morning,
> >>>
> >>> I'm trying to concisely generate a single integer from 0 to n
> >>> inclusive, where n might be of the order of hundreds of millions.
> >>> This will however be used many times during the general procedure, so
> >>> it must be "reasonably efficient" in both memory and time... (at some
> >>> later stage in the development I hope to go vectorized)
> >>>
> >>> The examples I've found through searching RSiteSearch() relating to
> >>> generating random integers say to use : sample(0:n, 1)
> >>> However, when n is "large" this first generates a large sequence 0:n
> >>> before taking a sample of one... this computer doesn't have the memory
> >>> for that!
> >>
> >> You don't need to give the whole vector: just give n, and you'll get
> >> draws from 1:n. The man page is clear on this.
> >>
> >> So what you want is sample(n+1, 1) - 1. (Use "replace=TRUE" if you want
> >> a sample bigger than 1, or you'll get sampling without replacement.)
> >>>
> >>> When I look at the documentation for runif(n, min, max) it states that
> >>> the generated numbers will be min <= x <= max. Note the "<= max"...
> >>
> >> Actually it says that's the range for the uniform density. It's silent
> >> on the range of the output. But it's good defensive programming to
> >> assume that it's possible to get the endpoints.
> >>
> >>>
> >>> How do I generate an x such that the probability of being (the
> >>> integer) max is the same as any other integer from min (an integer) to
> >>> max-1 (an integer) inclusive... My attempt is:
> >>>
> >>> urand.int <- function(n,t) {
> >>> as.integer(runif(n,min=0, max=t+1-.Machine$double.eps))
> >>> }
> >>> # where I've included the parameter n to help testing...
> >>
> >> Because of rounding error, t+1-.Machine$double.eps might be exactly
> >> equal to t+1. I'd suggest using a rejection method if you need to use
> >> this approach: but sample() is better in the cases where as.integer()
> >> will work.
> >>
> >> Duncan Murdoch
> >>>
> >>> is floor() "better" than as.integer?
> >>>
> >>> Is this correct? Is the probability of the integer t the same as the
> >>> integer 1 or 0 etc... I have done some rudimentary testing and this
> >>> appears to work, but power being what it is, I can't see how to
> >>> realistically test this hypothesis.
> >>>
> >>> Or is there a a better way of doing this?
> >>>
> >>> I'm trying to implement an
Re: [R] uniform integer RNG 0 to t inclusive
Hi Duncan,
Thanks for that. In the light of what you've suggested, I'm now using
the following:
# generate a random integer from 0 to t (inclusive)
if (t < 1000) { # to avoid memory problems...
M <- sample(t, 1)
} else {
while (M > t) {
M <- as.integer(urand(1,min=0, max=t+1-.Machine$double.eps))
}
}
cheers and Thanks,
Sean
On 18/09/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> On 9/18/2006 3:37 AM, Sean O'Riordain wrote:
> > Good morning,
> >
> > I'm trying to concisely generate a single integer from 0 to n
> > inclusive, where n might be of the order of hundreds of millions.
> > This will however be used many times during the general procedure, so
> > it must be "reasonably efficient" in both memory and time... (at some
> > later stage in the development I hope to go vectorized)
> >
> > The examples I've found through searching RSiteSearch() relating to
> > generating random integers say to use : sample(0:n, 1)
> > However, when n is "large" this first generates a large sequence 0:n
> > before taking a sample of one... this computer doesn't have the memory
> > for that!
>
> You don't need to give the whole vector: just give n, and you'll get
> draws from 1:n. The man page is clear on this.
>
> So what you want is sample(n+1, 1) - 1. (Use "replace=TRUE" if you want
> a sample bigger than 1, or you'll get sampling without replacement.)
> >
> > When I look at the documentation for runif(n, min, max) it states that
> > the generated numbers will be min <= x <= max. Note the "<= max"...
>
> Actually it says that's the range for the uniform density. It's silent
> on the range of the output. But it's good defensive programming to
> assume that it's possible to get the endpoints.
>
> >
> > How do I generate an x such that the probability of being (the
> > integer) max is the same as any other integer from min (an integer) to
> > max-1 (an integer) inclusive... My attempt is:
> >
> > urand.int <- function(n,t) {
> > as.integer(runif(n,min=0, max=t+1-.Machine$double.eps))
> > }
> > # where I've included the parameter n to help testing...
>
> Because of rounding error, t+1-.Machine$double.eps might be exactly
> equal to t+1. I'd suggest using a rejection method if you need to use
> this approach: but sample() is better in the cases where as.integer()
> will work.
>
> Duncan Murdoch
> >
> > is floor() "better" than as.integer?
> >
> > Is this correct? Is the probability of the integer t the same as the
> > integer 1 or 0 etc... I have done some rudimentary testing and this
> > appears to work, but power being what it is, I can't see how to
> > realistically test this hypothesis.
> >
> > Or is there a a better way of doing this?
> >
> > I'm trying to implement an algorithm which samples into an array,
> > hence the need for an integer - and yes I know about sample() thanks!
> > :-)
> >
> > { incidentally, I was surprised to note that the maximum value
> > returned by summary(integer_vector) is "pretty" and appears to be
> > rounded up to a "nice round number", and is not necessarily the same
> > as max(integer_vector) where the value is large, i.e. of the order of
> > say 50 million }
> >
> > Is version etc relevant? (I'll want to be portable)
> >> version _
> > platform i386-pc-mingw32
> > arch i386
> > os mingw32
> > system i386, mingw32
> > status
> > major 2
> > minor 3.1
> > year 2006
> > month 06
> > day01
> > svn rev38247
> > language R
> > version.string Version 2.3.1 (2006-06-01)
> >
> > Many thanks in advance for your help.
> > Sean O'Riordain
> > affiliation <- NULL
> >
> > __
> > 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.
>
>
__
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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] uniform integer RNG 0 to t inclusive
Good morning,
I'm trying to concisely generate a single integer from 0 to n
inclusive, where n might be of the order of hundreds of millions.
This will however be used many times during the general procedure, so
it must be "reasonably efficient" in both memory and time... (at some
later stage in the development I hope to go vectorized)
The examples I've found through searching RSiteSearch() relating to
generating random integers say to use : sample(0:n, 1)
However, when n is "large" this first generates a large sequence 0:n
before taking a sample of one... this computer doesn't have the memory
for that!
When I look at the documentation for runif(n, min, max) it states that
the generated numbers will be min <= x <= max. Note the "<= max"...
How do I generate an x such that the probability of being (the
integer) max is the same as any other integer from min (an integer) to
max-1 (an integer) inclusive... My attempt is:
urand.int <- function(n,t) {
as.integer(runif(n,min=0, max=t+1-.Machine$double.eps))
}
# where I've included the parameter n to help testing...
is floor() "better" than as.integer?
Is this correct? Is the probability of the integer t the same as the
integer 1 or 0 etc... I have done some rudimentary testing and this
appears to work, but power being what it is, I can't see how to
realistically test this hypothesis.
Or is there a a better way of doing this?
I'm trying to implement an algorithm which samples into an array,
hence the need for an integer - and yes I know about sample() thanks!
:-)
{ incidentally, I was surprised to note that the maximum value
returned by summary(integer_vector) is "pretty" and appears to be
rounded up to a "nice round number", and is not necessarily the same
as max(integer_vector) where the value is large, i.e. of the order of
say 50 million }
Is version etc relevant? (I'll want to be portable)
> version _
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
>
Many thanks in advance for your help.
Sean O'Riordain
affiliation <- NULL
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] subsetting a data set
Hi Graham, Try creating a new column with the two levels that you want... something along the lines of (warning untested!!!) GQ1[(GQ1$Status == "Expert) | (GQ1$Status == "Ecol"),]$newColumn <- "AllEcol" GQ1[GQ1$Status == "Stake",]$newColumn <- "Stake" and then do the by(GQ1[,"Max"], list(GQ1$NewColumn), summary) when in doubt... break the problem into smaller chunks... :-) cheers, Sean On 08/09/06, Graham Smith <[EMAIL PROTECTED]> wrote: > Petr, > > Thanks again, but the data is GQ1, Max is a variable (column) > > So I have used > > by(GQ1[,"Max"], list(GQ1$Status), summary) > > Which is very good, and is better than the way I did it before by > summarising for each status level individually, but that still isn't combing > the data for Status == "Expert" and Status = "Ecol" > > So at the moment the status variable has 3 levels Expert, Ecol and Stake, > > I want to analsye that at two levels: Expert and Ecol combined into a new > level called "AllEcol" and the exsiting level "Stake" > > It is this combining the levels that has got me stuck. > > Thanks again, > > Graham > > On 08/09/06, Petr Pikal <[EMAIL PROTECTED]> wrote: > > > > Sorry, I did not notice that in your case Max is not a function but > > your data. So probably > > > > by(Max[, your.columns], list(Max$status), summary) > > > > is maybe what you want. > > HTH > > Petr > > > > > > On 8 Sep 2006 at 10:31, Petr Pikal wrote: > > > > From: "Petr Pikal" <[EMAIL PROTECTED]> > > To: "Graham Smith" <[EMAIL PROTECTED]>, > > r-help@stat.math.ethz.ch > > Date sent: Fri, 08 Sep 2006 10:31:12 +0200 > > Priority: normal > > Subject:Re: [R] subsetting a data set > > > > > Hi > > > > > > I am not sure if your Max is the same as max so I am not sure what you > > > exactly want from your data. However you shall consult ?tapply, ?by, > > > ?aggregate and maybe also ?"[" together with chapter 2 in intro manual > > > in docs directory. > > > > > > aggregate(data[, some.columns], list(data$factor1, data$factor2), max) > > > > > > will give you maximum for specified columns based on spliting the data > > > according to both factors > > > > > > Also connection summary with max is not common and I wonder what is > > > your output in this case. I believe that there are six same numbers. > > > However R is case sensitive and maybe Max does something different > > > from max. In my case it throws an error. > > > > > > HTH > > > Petr > > > > > > On 8 Sep 2006 at 8:06, Graham Smith wrote: > > > > > > Date sent:Fri, 8 Sep 2006 08:06:16 +0100 > > > From: "Graham Smith" <[EMAIL PROTECTED]> > > > To: r-help@stat.math.ethz.ch > > > Subject: [R] subsetting a data set > > > > > > > I have a data set called GQ1, which has 20 variables one of which is > > > > a factor called Status at thre levels "Expert", "Ecol" and "Stake" > > > > > > > > I have managed to evaluate some of the data split by status using > > > > commands like: > > > > > > > > summary (Max[Status=="Ecol"]) > > > > > > > > BUT how do I produce asummary for Ecol and Expert combined, the > > > > only example I can find suggsts I could use > > > > > > > > summary (Max[Status=="Ecol"& Status=="Expert"]) but that doesn't > > > > work. > > > > > > > > Additionally on the same vein, if I cannot work out how to create a > > > > new data set that would contain all the data for all the variables > > > > but only for the data where Status = Ecol, or where status equalles > > > > Ecol and Expert. > > > > > > > > I know this is yet again a very simple problem, but I really can't > > > > find the solution in the help or the books I have. > > > > > > > > Many thanks, > > > > > > > > Graham > > > > > > > > [[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. > > > > > > Petr Pikal > > > [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. > > > > Petr Pikal > > [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 ht
Re: [R] how to the p-values or t-values from the lm's results
Hi there Zhang,
While there might be a better way... an ugly but generic way of
accessing this type of information is to use str() and a little
experimentation... here is a little history() of what I did to find
it...
a
str(a)
str(logr)
a[[1]]
a[[2]]
a[[3]]
a[[4]]
a[[4]][[1]]
a[[4]][1,]
a[[4]][,4]
and hey presto... we have it... :-)
now if I actually understood what was going on here I'd probably be
faster... but it is pretty generic and you can almost always get at
those things using this technique... no doubt somebody with more
knowledge will explain why it works :-)
cheers,
Sean
On 20/08/06, zhijie zhang <[EMAIL PROTECTED]> wrote:
> Dear friends,
> After running the lm() model, we can get summary resluts like the
> following:
> Coefficients:
>Estimate Std. Error t value Pr(>|t|)
> x1 0.115620.10994 1.052 0.2957
> x2 -0.138790.09674 -1.435 0.1548
> x3 0.010510.09862 0.107 0.9153
> x4 0.141830.08471 1.674 0.0975 .
> x5 0.189950.10482 1.812 0.0732 .
> x6 0.248320.10059 2.469 0.0154 *
> x7 -0.044250.11008 -0.402 0.6886
> x8 0.051460.10290 0.500 0.6182
> -
> **the program maybe :
> data<-matrix(rnorm(900),ncol=9) #9variables,1dependent var,8independent
> data<-data.frame(data)
> names(data)<-c('y','x1','x2','x3','x4','x5','x6','x7','x8')
> logr<-lm(y~x1+x2+x3+x4+x5+x6+x7+x8-1,data)
> a<-summary(logr)
>
> Could i extract the p-values or t-values from the a$Coefficients, i searched
> the attributes(a), but don't find the options,how to do that?
> Thanks very much!
>
> --
> Kind Regards,
> Zhi Jie,Zhang ,
>
> [[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.
>
__
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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] String manipulation and formatting
Does it have to be a stop char ".", or could it be a separate
parameter, i.e. put in a comma, then the 10 becomes an integer...
s/
On 18/07/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> On Tue, 18 Jul 2006, Bashir Saghir (Aztek Global) wrote:
>
> > Thanks to Richard, Gabor and Marc for some nice solutions to my request.
> >
> > I have a new problem:
> >
> > > xify(30.10)
> > [1] "X.X"
> > > xify(30.11)
> > [1] "XXX.XXX"
> >
> > The problem originates from:
> >
> > > as.numeric(unlist(strsplit(as.character(15.10), "\\.")))
> > [1] 15 1
> > > as.numeric(unlist(strsplit(as.character(15.11), "\\.")))
> > [1] 15 11
> >
> > It seems to boils down to:
> >
> > > as.character(15.10)
> > [1] "15.1"
> >
> > A simple solution is:
> >
> > > xify("15.10")
> > [1] "X.XX"
> >
> > I was wondering if there is a simple way for xify to see the zero of the 10
> > without having to force the user to add quotes around the format?
>
> No, as the parser has converted '15.10' to a numeric constant.
>
> What is the problem with asking users to enter strings as strings?
>
> --
> 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.
>
__
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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] Generating random normal distribution with mean 0 and standard deviation 1
?rnorm On 14/07/06, Neuro LeSuperHéros <[EMAIL PROTECTED]> wrote: > Hello, > > This must be really simple, but I can't find it on R Site search. I need to > generate a random normally distributed series with mean 0 and sd 1. In > Matlab, this code is randn(n). > > The closest I found is runif(20,-1,1) but this forces a maximum and a > minimum, and there's no way to specify a standard deviation of 1. > > >sd(runif(20,-1,1)) > [1] 0.578164 > > __ > 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 > __ 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
Re: [R] References verifying accuracy of R for basic statisticalcalculations and tests
Please don't shoot!
q: would it be a good idea to use these datasets as a basis for some
regression tests?
Sean
On 14/07/06, Rau, Roland <[EMAIL PROTECTED]> wrote:
> Hi,
> > [mailto:[EMAIL PROTECTED] On Behalf Of Corey Powell
> >
> > Do you know of any references that verify the accuracy of R
> > for basic statistical calculations and tests. The results of
> > these studies should indicate that R results are the same as
> > the results of other statistical packages to a certain number
> > of decimal places on some benchmark calculations.
>
> I don't know of any references, but maybe you can somehow "verify the
> accuracy of R" by running some analysis with the "NIST Statistical
> Reference Datasets"; the URL is http://www.itl.nist.gov/div898/strd/
> So maybe you can run the analyses mentioned there and say that R
> (hopefully) returned the correct results.
>
> Hope this helps,
> Roland
>
> --
> This mail has been sent through the MPI for Demographic Rese...{{dropped}}
>
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>
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Re: [R] PowerPoint
or try win.metafile() if i'm in a hurry, (in windows) i just right click on the graph and select "Copy as Metafile" and paste directly into powerpoint... Sean On 23/06/06, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > Note that jpg, bmp and png are in less desirable bit mapped formats whereas > eps is in a more desirable vector format (magnification and shrinking does > not involve loss of info) and so would be preferable from a quality > viewpoint. See: > http://www.stc-saz.org/resources/0203_graphics.pdf > > On 6/23/06, Doran, Harold <[EMAIL PROTECTED]> wrote: > > Use the functions in library(grDevices) for jpeg, bmp, or png formats. > > Or, you can use postscript() for an eps file. Of course, I personally > > think tex files make for much better looking presentations if you can be > > persuaded. > > > > Harold > > > > > > > -Original Message- > > > From: [EMAIL PROTECTED] > > > [mailto:[EMAIL PROTECTED] On Behalf Of Marc Bernard > > > Sent: Friday, June 23, 2006 7:28 AM > > > To: r-help@stat.math.ethz.ch > > > Subject: [R] PowerPoint > > > > > > Dear All, > > > > > > I am looking for the best way to use graphs from R (like > > > xyplot, curve ...) for a presentation with powerpoint. I > > > used to save my plot as pdf and after to copy them as image > > > in powerpoint but the quality is not optimal by so doing. > > > > > > Another completely independent question is the following: > > > when I use "main" in the xyplot, the main title is very > > > close to my plot, i.e. no ligne separate the main and the > > > plot. I would like my title to be well distinguished from the plots. > > > > > > I would be grateful for any improvements... > > > > > > Many thanks, > > > > > > Bernard, > > > > > > > > > > > > > > > - > > > > > > [[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 > > > > > > > __ > > 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 > > > > __ > 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 > __ 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
Re: [R] how to successfully remove missing values for a repeated measures analysis
Spencer,
A number of times I've been wrecking my head trying to solve a
problem, and when I thought I'd tried everything possible (all the
docs that I can think of, web searches etc...) I start re-reading the
posting guide (I've no idea how many times I've read it now)... and 9
times out of 10, the answer is there for me... :-)
Like yesterday... I had forgotten about the posting-guide (why Sean?
why?) and I was trying to get windows to startup with a default entry
for CRAN so I don't have to select *everytime*... which was starting
to annoy me... a lot... eventually after running out of options I
started down the posting guide route... and it turns out I've been
starting using "--vanilla", so I turned that off and hey presto... it
worked... :-)
Takeaway... now I read the posting guide earlier in the problem
solving process :-)
cheers,
Sean
On 20/06/06, Spencer Graves <[EMAIL PROTECTED]> wrote:
> I don't see enough information for me to diagnose the problem. If
> it were my problem, I'd print out some assessment of the results of
> every step you've described below. This should expose the step in which
> things disappear.
>
> Hope this helps.
> Spencer Graves
> p.s. I almost never attach a data.frame. It can be done, but I just
> find the mechanisms too subtle for my brain. I use "with" routinely,
> but I know I can't include an assignment inside "with", because "with"
> creates a frame and then discards it after it's done. Anything I
> created inside "with" gets thereby discarded.
>
> p.p.s. If you'd like more help from this listserve, PLEASE do read the
> posting guide! "www.R-project.org/posting-guide.html". People who
> follow that posting guide seem more likely to solve their own problems
> in the process of preparing a question for the listserve. If that
> fails, they are more likely to get a useful reply quickly. Clean, crisp
> questions sometimes generate a feeding frenzy of replies. Questions
> that are harder to understand often get ignored.
>
> Bob Green wrote:
> > Hello ,
> >
> > I am hoping for some advice. I want to run a repeated measures ANOVA. The
> > primary problem is that my attempt to remove missing values created a
> > dataset of missing values.
> >
> > The data set consists of 92 rows (1 row per participant) x 186 variables.
> >
> > The steps of the analysis undertaken are outlined below (#). Any assistance
> > is appreciated in relation to how to remove the missing values so the
> > analysis is run. Feedback regarding the prior steps is also welcomed .
> >
> > Bob Green
> >
> >
> >
> > #Step 1
> >
> > study1dat <- read.csv("c:\\study1.csv",header=T)
> > attach (study1dat)
> >
> > outcome <- c(t1frq, t2frq,t3frq,t4frq)
> > grp <- factor( rep(group, 2,length=368) )
> > time <- gl(4,92,length=368)
> > subject <- gl(92,1,length=368)
> > data.frame(subject, grp, time, outcome)
> >
> > # there are 3 missing values in $outcome
> >
> > #Step 2 - create a new data frame removing missing values from variable
> > $outcome
> >
> > d2<-study1dat[!is.na(outcome),]
> >
> > #the previous step generates NA values.
> >
> > #Step 3 detach original data set & attach dataset without missing values
> > detach(study1dat)
> >
> > attach(d2)
> >
> > The following object(s) are masked _by_ .GlobalEnv : time
> > The following object(s) are masked from package:datasets
> > : sleep
> >
> > #Step 4 run analysis
> >
> > library(nlme)
> > anova(lme(outcome ~ grp * time, random = ~ 1 | subject))
> >
> > #The data is the format below
> >
> > subject grp time outcome
> > 1 1 01 4
> > 2 2 01 3
> > 3 3 01 7
> > 4 4 01 0
> > 5 5 01 1
> > 6 6 01 7
> > 7 7 01 7
> > 8 8 01 7
> > 9 9 01 7
> > 10 10 01 5
> >
> > __
> > 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
>
> __
> 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
>
__
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
Re: [R] can I call user-created functions without source() ?
Indeed, some folk say that the documentation should be written before the code... Sean On 19/06/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > 2. If you use the package system, you will be encouraged to create man > pages for your functions. This is work, but I think it pays off in the > end. I often find that when I document a function I realize an error in > the design, and I end up improving it. It's also useful to have > documentation for functions that you don't use every day, or when using > functions written by someone else. > > Duncan Murdoch __ 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
Re: [R] Qurey : How to add trendline( st. line) in Graph
lines(predict(lm(g~f))~f,lty=2) or if its a curvy line you're looking for... lines(predict(loess(g~f))~f,lty=3) On 19/06/06, priti desai <[EMAIL PROTECTED]> wrote: > How to add trendline (i.e. straight line passing through maximum points) > in graph. > I have worked on the data given below. > Please tell me how to add trendline in the graph. > > The script is as follows > > === start > > > # The data is as follows > > data <- c( 0.01, 0.02, 0.04, 0.13, 0.17 , 0.19 , 0.21 , 0.27 , 0.27 , > 0.28, 0.29, 0.37, >0.41, 0.49, 0.51, 0.52, 0.54, 0.57, 0.62, 0.63, 0.68, > 0.73, 0.74, 0.79, >0.81, 0.81, 0.82, 0.86, 0.94, 0.96, 1.02, 1.10, 1.10, > 1.20, 1.29, 1.36, >1.40, 1.41, 1.44, 1.45, 1.62, 1.67, 1.69, 1.78, 1.82, > 2.11, 2.13, 2.14, >2.24, 2.29, 2.34, 2.40, 2.46, 2.70, 2.83, 2.98, 3.00, > 3.30, 3.53, 3.70, >3.86, 3.90, 3.91, 3.98, 5.01, 5.23, 6.05, 6.12, 10.41, > 10.73) > > # P-P plot > average <- mean(data) > lambda<- (1/average) > e <- c(1:70) > f <- c((e-.5)/70) > Fx<- c(1 - exp(-lambda*data)) > g <- sort(Fx) > plot(f,g) > > = end > > > Awaiting your positive reply. > > Regards. > Priti. > > __ > 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 > __ 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
Re: [R] a question about a simply figure
Hi Zhang Jian, If I say plot(t$no,t$leiji), then the lower bound is "neatly" set at about 25... (I'm not sure how I can measure the bounds on the current plot - but I'm sure it can be found!) You can set the bounds on the y-axis to be between 0 and 100 by saying plot(fre$no,fre$leiji,ylim=c(0,100)) cheers, Sean On 02/06/06, zhang jian <[EMAIL PROTECTED]> wrote: > I think there is a question in R. I donot know the reason. > This is my data about comulative percentage figure. The result is not right. > > The first point (no=1,leiji=26.94350) in the plot figure was showen in a > lower location. Why? > Thanks ! > > > fre >no leiji > 1 1 26.94350 > 2 2 46.86401 > 3 3 60.59032 > 4 4 72.17355 > 5 5 77.85521 > 6 6 82.05853 > 7 7 85.56495 > 8 8 87.64378 > 9 9 89.42997 > 10 10 91.01150 > 11 11 92.32409 > 12 12 93.48106 > 13 13 94.62618 > 14 14 95.47530 > 15 15 96.25000 > 16 16 96.71516 > 17 17 97.14648 > 18 18 97.51522 > 19 19 97.86367 > 20 20 98.10217 > 21 21 98.32544 > 22 22 98.51658 > 23 23 98.69756 > 24 24 98.85995 > 25 25 99.00372 > 26 26 99.11874 > 27 27 99.22192 > 28 28 99.32510 > 29 29 99.42659 > 30 30 99.49932 > 31 31 99.56360 > 32 32 99.61265 > 33 33 99.66001 > 34 34 99.70737 > 35 35 99.75304 > 36 36 99.79702 > 37 37 99.83424 > 38 38 99.86130 > 39 39 99.88836 > 40 40 99.91373 > 41 41 99.93572 > 42 42 99.95264 > 43 43 99.96448 > 44 44 99.97294 > 45 45 99.97970 > 46 46 99.98647 > 47 47 99.99154 > 48 48 99.99493 > 49 49 99.99662 > 50 50 99.99831 > 51 51 100.0 > >plot(fre$no,fre$leiji) > > [[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 > __ 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
Re: [R] plot xy data with error bars
Hi Petr, I just needed to add an 'attach/detach' to get it going. A<-data.frame(x=1:10, y=1:10, erx=rnorm(10)^2, ery=rnorm(10)^2) attach(A) plot(x,y) arrows(x,y,x+erx/10,y, angle=90, length=.1) arrows(x,y,x-erx/10,y, angle=90, length=.1) arrows(x,y,x,y-ery/10, angle=90, length=.1) arrows(x,y,x,y+ery/10, angle=90, length=.1) detach(A) cheers and thanks! Sean On 25/05/06, Petr Pikal <[EMAIL PROTECTED]> wrote: > Hi > > > On 25 May 2006 at 1:08, Tibi Codilean wrote: > > Date sent: Thu, 25 May 2006 01:08:20 +0100 > From: "Tibi Codilean" <[EMAIL PROTECTED]> > To: r-help@stat.math.ethz.ch > Subject:[R] plot xy data with error bars > > > Dear All, > > > > I have x,y data with errors associated with both x and y. What would > > be the easiest way of creating plots with both x and y error bars? > > I know there is some function(s) in some package(s) for error bar > plotting but if you want to use your own, use arrows > > A<-data.frame(x=1:10, y=1:10, erx=rnorm(10)^2, ery=rnorm(10)^2) > plot(x,y) > arrows(x,y,x+erx/10,y, angle=90, length=.1) > arrows(x,y,x-erx/10,y, angle=90, length=.1) > arrows(x,y,x,y-ery/10, angle=90, length=.1) > arrows(x,y,x,y+ery/10, angle=90, length=.1) > > HTH > Petr > > > > > > > > > Thanks > > > > __ > > 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 > Petr Pikal > [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 > __ 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
Re: [R] win2k memory problem with merge()'ing repeatedly (long email)
Thank you very much indeed Bogdan!
> a2[duplicated(a2$mdate),]
value2 mdate
3180 2006-05-10
3220 2006-05-13
3240 2006-05-14
3260 2006-05-15
3280 2006-05-16
What a relief to know what is causing this problem... now to sort out
the root cause!
cheers and thanks again!
Sean
On 22/05/06, bogdan romocea <[EMAIL PROTECTED]> wrote:
> Repeated merge()-ing does not always increase the space requirements
> linearly. Keep in mind that a join between two tables where the same
> value appears M and N times will produce M*N rows for that particular
> value. My guess is that the number of rows in atot explodes because
> you have some duplicate values in your files (having the same
> duplicate date in each data frame would cause atot to contain 4, then
> 8, 16, 32, 64... rows for that date).
>
>
> > -Original Message-
> > From: [EMAIL PROTECTED]
> > [mailto:[EMAIL PROTECTED] On Behalf Of Sean O'Riordain
> > Sent: Monday, May 22, 2006 10:12 AM
> > To: r-help
> > Subject: [R] win2k memory problem with merge()'ing repeatedly
> > (long email)
> >
> > Good afternoon,
> >
> > I have a 63 small .csv files which I process daily, and until two
> > weeks ago they processed just fine and only took a matter of moments
> > and had non noticeable memory problem. Two weeks ago they have
> > reached 318 lines and my script "broke". There are some
> > missing-values in some of the files. I have tried hard many times
> > over the last two weeks to create a "small" repeatable example to give
> > you but I've failed - unless I use my data it works fine... :-(
> >
> > Am I missing something obvious? (again)
> >
> > A line in a typical file has lines which look like :
> > 01/06/2005,1372
> >
> > Though there are three files which have two values (files 3,32,33) and
> > these have lines which look like...
> > 01/06/2005,1766,
> > or
> > 15/05/2006,289,114
> >
> > a1 <- read.csv("file1.csv",header=F)
> > etc...
> > a63 <- read.csv("file63.csv",header=F)
> > names(a1) <- c("mdate","file1.column.description")
> >
> > atot <- merge(a1,a2,all=T)
> >
> > followed by repeatedly doing...
> > atot <- merge(atot, a3,all=T)
> > atot <- merge(atot, a4,all=T)
> > etc...
> >
> > I normally start R with --vanilla.
> >
> > What appears to happen is that atot doubles in size each iteration and
> > just falls over due to lack of memory at about i=17... even though the
> > total memory required for all of these individual a1...a63 is only
> > 1001384 bytes (doing an object.size() on a1..a63)
> > at this point I've been trying to pin down this problem for two weeks
> > and I just gave up...
> >
> > The following works fine as I'd expect with minimal memory usage...
> >
> > for (i in 3:67) {
> > datelist <- as.Date(start.date)+0:(count-1)
> > #remove a couple of elements...
> > datelist <- datelist[-(floor(runif(nacount)*count))]
> > a2 <- as.data.frame(datelist)
> > names(a2) <- "mdate"
> > vname <- paste("value", i, sep="")
> > a2[vname] <- runif(length(datelist))
> > #a2[floor(runif(nacount)*count), vname] <- NA
> >
> > # atot <- merge(atot,a2,all=T)
> > i <- 2
> > a.eval.text <- paste("merge(atot, a", i, ", all=T)", sep="")
> > cat("a.eval.text is: -", a.eval.text, "-\n", sep="")
> > atot <- eval(parse(text=a.eval.text))
> >
> > cat("i:", i, " ", gc(), "\n")
> > }
> >
> > this works fine... but on my files (as per attached 'lastsave.txt'
> > file) it just gobbles memory.
> > Am I doing something wrong? I (wrongly?) expected that repeatedly
> > merge(atot,aN) would only increase the memory requirement linearly
> > (with jumps perhaps as we go through a 2^n boundary)... which is what
> > happens when merging simulated data.frames as above... no problem at
> > all and its really fast...
> >
> > The attached text file shows a (slightly edited) session where the
> > memory required by the merge() operation just doubles with each use...
> > and I can only allow it to run until i=17!!!
> >
> > I've even run it with gctorture() set on... with similar,
[R] win2k memory problem with merge()'ing repeatedly (long email)
Good afternoon,
I have a 63 small .csv files which I process daily, and until two
weeks ago they processed just fine and only took a matter of moments
and had non noticeable memory problem. Two weeks ago they have
reached 318 lines and my script "broke". There are some
missing-values in some of the files. I have tried hard many times
over the last two weeks to create a "small" repeatable example to give
you but I've failed - unless I use my data it works fine... :-(
Am I missing something obvious? (again)
A line in a typical file has lines which look like :
01/06/2005,1372
Though there are three files which have two values (files 3,32,33) and
these have lines which look like...
01/06/2005,1766,
or
15/05/2006,289,114
a1 <- read.csv("file1.csv",header=F)
etc...
a63 <- read.csv("file63.csv",header=F)
names(a1) <- c("mdate","file1.column.description")
atot <- merge(a1,a2,all=T)
followed by repeatedly doing...
atot <- merge(atot, a3,all=T)
atot <- merge(atot, a4,all=T)
etc...
I normally start R with --vanilla.
What appears to happen is that atot doubles in size each iteration and
just falls over due to lack of memory at about i=17... even though the
total memory required for all of these individual a1...a63 is only
1001384 bytes (doing an object.size() on a1..a63)
at this point I've been trying to pin down this problem for two weeks
and I just gave up...
The following works fine as I'd expect with minimal memory usage...
for (i in 3:67) {
datelist <- as.Date(start.date)+0:(count-1)
#remove a couple of elements...
datelist <- datelist[-(floor(runif(nacount)*count))]
a2 <- as.data.frame(datelist)
names(a2) <- "mdate"
vname <- paste("value", i, sep="")
a2[vname] <- runif(length(datelist))
#a2[floor(runif(nacount)*count), vname] <- NA
# atot <- merge(atot,a2,all=T)
i <- 2
a.eval.text <- paste("merge(atot, a", i, ", all=T)", sep="")
cat("a.eval.text is: -", a.eval.text, "-\n", sep="")
atot <- eval(parse(text=a.eval.text))
cat("i:", i, " ", gc(), "\n")
}
this works fine... but on my files (as per attached 'lastsave.txt'
file) it just gobbles memory.
Am I doing something wrong? I (wrongly?) expected that repeatedly
merge(atot,aN) would only increase the memory requirement linearly
(with jumps perhaps as we go through a 2^n boundary)... which is what
happens when merging simulated data.frames as above... no problem at
all and its really fast...
The attached text file shows a (slightly edited) session where the
memory required by the merge() operation just doubles with each use...
and I can only allow it to run until i=17!!!
I've even run it with gctorture() set on... with similar, but
excruciatingly slow results...
Is there any relevant info that I'm missing? Unfortunately I am not
able to post the contents of the files to a public list like this...
As per a previous thread, I know that I can use a list to handle these
dataframes - but I had difficulty with the syntax of a list of
dataframes...
I'd like to know why the memory requirements for this merge just explode...
cheers, (and thanks in advance!)
Sean O'Riordain
==
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status Patched
major 2
minor 3.0
year 2006
month 05
day09
svn rev38014
language R
version.string Version 2.3.0 Patched (2006-05-09 r38014)
>
Running on Win2k with 1Gb ram.
I also tried it (with the same results) on 2.2.1 and 2.3.0.
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.0 Patched (2006-05-09 r38014)
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 178186 4.8 407500 10.9 35 9.4
Vcells 73112 0.6 786432 6.0 333585 2.6
> # take the information in the .csv files created from the emails
> setwd("C:/Documents and Settings/c_oriordain_s/My
> Documents/pas
Re: [R] Unreadable labels
Hi Maciej,
fyi - on winxp-pro 2.3.0-patched and up to date MASS - I can clearly
read the labels, except the start of the word 'black' is clipped, but
the font size is fine.
cheers,
Sean
On 21/05/06, Maciej Bliziński <[EMAIL PROTECTED]> wrote:
> Playing around with examples from MASS4, I found a font problem in the
> mosaicplot in R-2.3.0. It doesn't happen in other plots. Running this
> example from MASS4, page 326...
>
> library(MASS)
> caith1 <- as.matrix(caith)
> names(dimnames(caith1)) <- c("eyes", "hair")
> mosaicplot(caith1, color = TRUE)
>
> ...I get an image as attached. The column and row labels are unreadable.
> It is true for both x11() and png() devices.
>
> I can adjust the font sizes with the "cex.axis" argument and get a
> readable labels if the parameter is correct (0.8 works here), but the
> general problem it's not really the font sizes. There are small versions
> of the screen fonts that _are_ readable. I believe I should be able to
> get small, but readable labels. It's not possible to specify a font,
> because mosaicplot doesn't accept the "font.axis" parameter.
>
> Looking at the demo(graphics), I can also recognize some unreadable
> labels. Do you think it's only the matter of the X-Window system?
> Installed fonts? Any hints appreciated.
>
> Regards,
> Maciej
>
> --
> Maciej Bliziński <[EMAIL PROTECTED]>
> http://automatthias.wordpress.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
>
>
>
__
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
Re: [R] (Nothing to do with) merge problem... extra lines appear in the presence of NAs
Apologies all! Thank you Brian
Sean
On 20/05/06, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> I think you forgot to read over your own message before sending it: take a
> look at a1 which has FOUR rows with mdate == 2005-06-09. Those correspond
> to rows to 9:12 in the result, as you are merging on 'mdate'.
>
> You example is not reproducible, of course, since you used random values.
> Perhaps you intended
>
> a1[floor(runif(nacount)*count), "value"] <- NA
>
>
> On Sat, 20 May 2006, Sean O'Riordain wrote:
>
> > Good morning!
>
> [Or afternoon in Europe, ]
>
> > I've searched the docs etc... Am I doing something wrong or is this a bug?
> >
> > I'm doing a merge of two dataframes and getting extra rows in the
> > resulting dataframe - the dataframes being merged might have NAs...
> >
> > count <- 10
> > nacount <- 3
> > a1 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
> > names(a1) <- "mdate"
> > a1$value <- runif(count)
> > a1[floor(runif(nacount)*count),]$value <- NA
> >
> > a2 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
> > names(a2) <- "mdate"
> > a2$value2 <- runif(count)
> > #a2[floor(runif(nacount)*count),]$value2 <- NA
> >
> >> a1
> >mdate value
> > 1 2005-06-09NA
> > 2 2005-06-02 0.5287683
> > 3 2005-06-03 0.7563833
> > 4 2005-06-09NA
> > 5 2005-06-05 0.1027646
> > 6 2005-06-06 0.7775884
> > 7 2005-06-07 0.2993592
> > 8 2005-06-09NA
> > 9 2005-06-09 0.7434682
> > 10 2005-06-10 0.2096477
> >> a2
> >mdatevalue2
> > 1 2005-06-01 0.5347852
> > 2 2005-06-02 0.9322765
> > 3 2005-06-03 0.9106499
> > 4 2005-06-04 0.6810564
> > 5 2005-06-05 0.5871867
> > 6 2005-06-06 0.8123808
> > 7 2005-06-07 0.9675379
> > 8 2005-06-08 0.9470369
> > 9 2005-06-09 0.7493767
> > 10 2005-06-10 0.8864103
> >> atot <- merge(a1,a2,all=T)
> >
> > However, I find the following results to be quite un-intuitive - are
> > they correct? May I draw your attention to lines 9:12... Should
> > lines 9:11 be there?
> >
> >> atot
> >mdate valuevalue2
> > 1 2005-06-01NA 0.5347852
> > 2 2005-06-02 0.5287683 0.9322765
> > 3 2005-06-03 0.7563833 0.9106499
> > 4 2005-06-04NA 0.6810564
> > 5 2005-06-05 0.1027646 0.5871867
> > 6 2005-06-06 0.7775884 0.8123808
> > 7 2005-06-07 0.2993592 0.9675379
> > 8 2005-06-08NA 0.9470369
> > 9 2005-06-09NA 0.7493767
> > 10 2005-06-09NA 0.7493767
> > 11 2005-06-09NA 0.7493767
> > 12 2005-06-09 0.7434682 0.7493767
> > 13 2005-06-10 0.2096477 0.8864103
> >
> > Note with no NAs, it works perfectly and as expected...
> >> a1 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
> >> names(a1) <- "mdate"
> >> a1$value <- runif(count)
> >> #a1[floor(runif(nacount)*count),]$value <- NA
> >>
> >> atot <- merge(a1,a2,all=T)
> >>
> >> atot
> >mdate valuevalue2
> > 1 2005-06-01 0.35002519 0.5347852
> > 2 2005-06-02 0.76318940 0.9322765
> > 3 2005-06-03 0.32759570 0.9106499
> > 4 2005-06-04 0.47218729 0.6810564
> > 5 2005-06-05 0.74435374 0.5871867
> > 6 2005-06-06 0.81415290 0.8123808
> > 7 2005-06-07 0.04774783 0.9675379
> > 8 2005-06-08 0.21799101 0.9470369
> > 9 2005-06-09 0.99472758 0.7493767
> > 10 2005-06-10 0.41974293 0.8864103
> >
> > R started in each case with --vanilla
> > _
> > platform i386-pc-mingw32
> > arch i386
> > os mingw32
> > system i386, mingw32
> > status Patched
> > major 2
> > minor 3.0
> > year 2006
> > month 05
> > day11
> > svn rev38037
> > language R
> > version.string Version 2.3.0 Patched (2006-05-11 r38037)
> >
> > win-xp-pro sp2 - binary installs from CRAN
> >
> >
> > it works in a similar way if I say
> > atot <- merge(a1,a2,by.x="mdate",by.y="mdate",all=T)
> > or even
> > atot <- merge(a1,a2,by="mdate",all=T)
> >
> > also tested on versions 2.2.1, 2.3.0
> >
> > cheers,
> > Sean O'Riordain
> >
> > (ps. ctrl-v paste wouldn't work on 2.4.0-dev downloaded this morning -
> > didn't try very hard though)
> >
> > __
> > 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
> >
>
> --
> 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] merge problem... extra lines appear in the presence of NAs
Good morning!
I've searched the docs etc... Am I doing something wrong or is this a bug?
I'm doing a merge of two dataframes and getting extra rows in the
resulting dataframe - the dataframes being merged might have NAs...
count <- 10
nacount <- 3
a1 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
names(a1) <- "mdate"
a1$value <- runif(count)
a1[floor(runif(nacount)*count),]$value <- NA
a2 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
names(a2) <- "mdate"
a2$value2 <- runif(count)
#a2[floor(runif(nacount)*count),]$value2 <- NA
> a1
mdate value
1 2005-06-09NA
2 2005-06-02 0.5287683
3 2005-06-03 0.7563833
4 2005-06-09NA
5 2005-06-05 0.1027646
6 2005-06-06 0.7775884
7 2005-06-07 0.2993592
8 2005-06-09NA
9 2005-06-09 0.7434682
10 2005-06-10 0.2096477
> a2
mdatevalue2
1 2005-06-01 0.5347852
2 2005-06-02 0.9322765
3 2005-06-03 0.9106499
4 2005-06-04 0.6810564
5 2005-06-05 0.5871867
6 2005-06-06 0.8123808
7 2005-06-07 0.9675379
8 2005-06-08 0.9470369
9 2005-06-09 0.7493767
10 2005-06-10 0.8864103
> atot <- merge(a1,a2,all=T)
However, I find the following results to be quite un-intuitive - are
they correct? May I draw your attention to lines 9:12... Should
lines 9:11 be there?
> atot
mdate valuevalue2
1 2005-06-01NA 0.5347852
2 2005-06-02 0.5287683 0.9322765
3 2005-06-03 0.7563833 0.9106499
4 2005-06-04NA 0.6810564
5 2005-06-05 0.1027646 0.5871867
6 2005-06-06 0.7775884 0.8123808
7 2005-06-07 0.2993592 0.9675379
8 2005-06-08NA 0.9470369
9 2005-06-09NA 0.7493767
10 2005-06-09NA 0.7493767
11 2005-06-09NA 0.7493767
12 2005-06-09 0.7434682 0.7493767
13 2005-06-10 0.2096477 0.8864103
Note with no NAs, it works perfectly and as expected...
> a1 <- as.data.frame(as.Date("2005-06-01")+0:(count-1))
> names(a1) <- "mdate"
> a1$value <- runif(count)
> #a1[floor(runif(nacount)*count),]$value <- NA
>
> atot <- merge(a1,a2,all=T)
>
> atot
mdate valuevalue2
1 2005-06-01 0.35002519 0.5347852
2 2005-06-02 0.76318940 0.9322765
3 2005-06-03 0.32759570 0.9106499
4 2005-06-04 0.47218729 0.6810564
5 2005-06-05 0.74435374 0.5871867
6 2005-06-06 0.81415290 0.8123808
7 2005-06-07 0.04774783 0.9675379
8 2005-06-08 0.21799101 0.9470369
9 2005-06-09 0.99472758 0.7493767
10 2005-06-10 0.41974293 0.8864103
R started in each case with --vanilla
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status Patched
major 2
minor 3.0
year 2006
month 05
day11
svn rev38037
language R
version.string Version 2.3.0 Patched (2006-05-11 r38037)
win-xp-pro sp2 - binary installs from CRAN
it works in a similar way if I say
atot <- merge(a1,a2,by.x="mdate",by.y="mdate",all=T)
or even
atot <- merge(a1,a2,by="mdate",all=T)
also tested on versions 2.2.1, 2.3.0
cheers,
Sean O'Riordain
(ps. ctrl-v paste wouldn't work on 2.4.0-dev downloaded this morning -
didn't try very hard though)
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Re: [R] Precision in estimating log
Anthony, in the same way that we're not allowed to say if(x==0) if x is a real number, we can't say that 0.05=1-0.95... as 1-0.95 is not represented as a base 10 number on the computer, but in some base 2^i depending on your computer...and the representation is not necessarily exact... i.e. one-third (1/3) isn't representable exactly as a decimal number, but I'd guess that it is in some other base... I know it only answers part of your question... but perhaps that helps? cheers, Sean On 19/05/06, Gichangi, Anthony <[EMAIL PROTECTED]> wrote: > Hi R-users, > > I have the following code: > > f <-function(x,p)sqrt(-(x^2)-2*log(1-p)) > > r1 <-sqrt(-2*log(1-0.95)) > > r2 <-sqrt(-2*log(0.05)) > > on executing i get the following results > > > f(r1,0.95) > [1] 0 > > > > f(r2,0.95) > [1] NaN > Warning message: > NaNs produced in: sqrt(-(x^2) - 2 * log(1 - p)) > > I tried to track the problem and found that the answer to > log(0.05) is different from the answer to log(1-0.95) which > is ofcourse not true and hence it causes problems in the code > > print(log(0.05),digit=22) > > [1] -2.9957322735539909 > > print(log(1-0.95),digit=22) > > [1] -2.99573227355399 > > > Any possible explanation ? > > Regards > Anthony > > __ > 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 > __ 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
Re: [R] uniform and clumped point plots
Perhaps you're looking for something along the lines of Sobol
sequences - refer Section 7.7 of Numerical Recipes in C by Press et
al.
Sean
On 18/05/06, Ben Bolker <[EMAIL PROTECTED]> wrote:
> Beutel, Terry S dpi.qld.gov.au> writes:
>
> >
> > I am trying to generate two dimensional random coordinates.
> >
> > For randomly distributed data I have simply used
> >
> > >xy<-cbind(runif(100),runif(100))
> >
> > However I also want to generate coordinates that are more uniformly
> > distributed, and coordinates that are more contagiously distributed than
> > the above.
> >
> >
>
> here are some pictures I made for a talk recently, using
> the Poisson cluster process function from "splancs" and
> the Strauss process from "spatial" (I think)
>
> library(splancs)
> library(spatial)
> set.seed(1001)
> sq <- as.matrix(data.frame(x=c(0,1,1,0,0),y=c(0,0,1,1,0)))
> p.cl <- pcp.sim(rho=10,m=10,s2=0.001,region.poly=sq)
> plot(p.cl)
> n <- nrow(p.cl)
> p.ran <- matrix(runif(2*n),nrow=n,dimnames=list(NULL,c("x","y")))
> ppregion()
> p.reg <- Strauss(n,c=0.1,r=0.1)
> p.reg <- matrix(c(p.reg$x,p.reg$y),nrow=n,dimnames=list(NULL,c("x","y")))
> all <- data.frame(rbind(p.cl,p.ran,p.reg),
> tr=rep(c("clustered","random","regular"),each=n))
> library(lattice)
> lattice.options(default.theme = ltheme) ## set as default
> ltheme <- col.whitebg()
> ltheme$xyplot.background$col <- "transparent" ## change strip bg
>
> trellis.par.set(theme=col.whitebg())
> print(xyplot(y~x|tr,data=all,layout=c(3,1),aspect="iso",scales=list(draw=FALSE),
> bg="transparent",pch=16))
>
> Ben Bolker
>
> __
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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
>
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Re: [R] Newbie question about read.table
Hi David,
you might need to either:
a) attach(birthweight)
or
b) glm(low~age,binomial, data=birthweight)
refer ?attach / ?glm
cheers,
Sean
On 11/05/06, David Kaplan <[EMAIL PROTECTED]> wrote:
> Here is the code with the error
>
> birthweight <- read.table("c:/bw.dat", header = T)
> > summary(glm(low~age,binomial))
> Error in eval(expr, envir, enclos) : object "low" not found
> >
>
>
> The read.table function works fine and when look at the data it shows the
> variable names across the top. The data come from SPSS which I read out
> into a .dat file.
>
> Thanks
>
>
> - Original Message -
> From: "Sean O'Riordain" <[EMAIL PROTECTED]>
> To: "David Kaplan" <[EMAIL PROTECTED]>
> Sent: Thursday, May 11, 2006 1:46 PM
> Subject: Re: [R] Newbie question about read.table
>
>
> Hi David,
> Can you show us the code that you're trying to use?
> cheers,
> Sean
>
> On 11/05/06, David Kaplan <[EMAIL PROTECTED]> wrote:
> > Hi
> >
> > When I use the read.table function with header = T, I notice that it gives
> > me the variable names along the top as I expect. But, when I then attempt
> > an analysis, e.g. regression, it doesn't recognize the variable names. Am
> > I missing a step.
> >
> > Thank you
> >
> > David
> >
> >
> > [[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
> >
>
>
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Re: [R] data input strategy - lots of csv files
Thank you folks - most helpful as always!
Now I have a bit of studying to do :-) I've never really understood
before how to use lapply (or anyother apply) so this gives me a real
problem relating to my own to work with!
Thanks again,
Sean
On 11/05/06, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> Assuming:
>
> my.files <- c("file1.csv", "file2.csv", ..., "filen.csv")
>
> use read.zoo in the zoo package and merge.zoo (which
> can do a multiway merge):
>
> library(zoo)
> do.call("merge", lapply(my.files, read.zoo, ...any.other.read.zoo.args...))
>
> After loading zoo see:
> vignette("zoo")
> ?read.zoo
> ?merge.zoo
>
> On 5/11/06, Sean O'Riordain <[EMAIL PROTECTED]> wrote:
> > Good morning,
> > I have currently 63 .csv files most of which have lines which look like
> > 01/06/05,23445
> > Though some files have two numbers beside each date. There are
> > missing values, and currently the longest file has 318 rows.
> >
> > (merge() is losing the head and doing runaway memory allocation - but
> > thats another question - I'm still trying to pin that issue down and
> > make a small repeatable example)
> >
> > Currently I'm reading in these files with lines like
> > a1 <- read.csv("daft_file_name_1.csv",header=F)
> > ...
> > a63 <- read.csv("another_silly_filename_63.csv",header=F)
> >
> > and then i'm naming the columns in these like...
> > names(a1)[2] <- "silly column name"
> > ...
> > names(a63)[2] <- "daft column name"
> >
> > then trying to merge()...
> > atot <- merge(a1, a2, all=T)
> > and then using language manipulation to loop
> > atot <- merge(atot, a3, all=T)
> > ...
> > atot <- merge(atot, a63, all=T)
> > etc...
> >
> > followed by more language manipulation
> > for() {
> > rm(a1)
> > } etc...
> >
> > i.e.
> > for (i in 2:63) {
> >atot <- merge(atot, eval(parse(text=paste("a", i, sep=""))), all=T)
> ># eval(parse(text=paste("a",i,"[1] <- NULL",sep="")))
> >
> >cat("i is ", i, gc(), "\n")
> >
> ># now delete these 63 temporary objects...
> ># e.g. should look like rm(a33)
> >eval(parse(text=paste("rm(a",i,")", sep="")))
> > }
> >
> > eventually getting a dataframe with the first column being the date,
> > and the subsequent 63 columns being the data... with missing values
> > coded as NA...
> >
> > so my question is... is there a better strategy for reading in lots of
> > small files (only a few kbytes each) like that which are timeseries
> > with missing data... which doesn't go through the above awkwardness
> > (and language manipulation) but still ends up with a nice data.frame
> > with NA values correctly coded etc.
> >
> > Many thanks,
> > Sean O'Riordain
> >
> > __
> > 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
> >
>
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Re: [R] Boxplot and range of x-axis
Hi Rainer, boxplot(liste1,ylim=c(1,6)) boxplot(liste2,ylim=c(1,6)) or would you prefer boxplot(liste1,liste2) cheers, S/ On 11/05/06, Rainer Hahnekamp <[EMAIL PROTECTED]> wrote: > Hello there, > > could somebody help me with this: I have to create a lot of boxplots but > with same range concerning the x-axis. > For example I have following data: > liste1 <- c(3,4,5,3,3,4,4) > liste2 <- c(1,2,3,4,6) > png(file = "liste1.png") > boxplot(liste1) > png(file = "liste2.png") > boxplot(liste2) > q() > > Works perfectly, but what I need would be that both boxplots have their > x-axis from 1-6. > > Hopefully you could give me a hint.B > > Greetings, > -Rainer Hahnekamp > > __ > 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 > __ 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
Re: [R] Please help me to combine two datasets.
Hi Arun, so to clarify: you want to drop the first length(data.set.1)-length(data.set.2) rows... so you might say... new.ds1 <- data.set.1[(-(length(data.set.1)-length(data.set.2)),] and then add a new column... new.ds.combined <- cbind(new.ds1, data.set.2) cheers, Sean On 11/05/06, Arun Kumar Saha <[EMAIL PROTECTED]> wrote: > > Dear Sean, > > Thanks for this reply. But my problem is not solved. Actually I want to drop > first two rows from dataset-1 and then combine them. Can you give me any > idea? > > Thanks and regards, > Arun > > > > On 5/11/06, Sean O'Riordain <[EMAIL PROTECTED]> wrote: > > merge(data.set.1, data.set.2) > > > > but how do I know which rows to drop in ds1? > > > > if data.set.2 had dates, you could say > > > > merge(data.set.1, data.set.2, by.x=Date, by.y=Date, all=T) > > > > or do you just want to drop the first > > length(data.set.1)-length(data.set.2) from data.set.1? > > > > do you have NA values? > > > > cheers, > > Sean > > > > On 11/05/06, Arun Kumar Saha <[EMAIL PROTECTED]> wrote: > > > Dear r-users, > > > > > > Suppose I have two data sets > > > > > > data set-1 > > > > > > Date height > > > > > > 1/11/2005 10 > > > 2/11/2005 23 > > > 3/11/2005 54 > > > 4/11/2005 21 > > > 5/11/2005 22 > > > > > > data set-2 > > > > > > weight > > > > > > 32 > > > 45 > > > 11 > > > > > > > > > Now I want to combine this two data sets. i.e. i want to see: > > > > > > > > > Date height weight > > > --- > > > 3/11/2005 54 32 > > > 4/11/2005 21 45 > > > 5/11/2005 22 11 > > > > > > Can any one give me the required r-code to perform this? > > > > > > Thanks and regards, > > > Arun > > > > > > [[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 > > > > > > > > > -- > Arun Kumar Saha, M.Sc.[C.U.] > S T A T I S T I C I A N[Analyst] > RISK MANAGEMENT DIVISION > Transgraph Consulting [ www.transgraph.com] > Hyderabad, INDIA > Contact # Home: (91-033) 25558038 > Office: (91-040) 30685012 Ext. 17 > FAX: (91-040) 55755003 >Mobile: 919849957010 > E-Mail: [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
[R] data input strategy - lots of csv files
Good morning,
I have currently 63 .csv files most of which have lines which look like
01/06/05,23445
Though some files have two numbers beside each date. There are
missing values, and currently the longest file has 318 rows.
(merge() is losing the head and doing runaway memory allocation - but
thats another question - I'm still trying to pin that issue down and
make a small repeatable example)
Currently I'm reading in these files with lines like
a1 <- read.csv("daft_file_name_1.csv",header=F)
...
a63 <- read.csv("another_silly_filename_63.csv",header=F)
and then i'm naming the columns in these like...
names(a1)[2] <- "silly column name"
...
names(a63)[2] <- "daft column name"
then trying to merge()...
atot <- merge(a1, a2, all=T)
and then using language manipulation to loop
atot <- merge(atot, a3, all=T)
...
atot <- merge(atot, a63, all=T)
etc...
followed by more language manipulation
for() {
rm(a1)
} etc...
i.e.
for (i in 2:63) {
atot <- merge(atot, eval(parse(text=paste("a", i, sep=""))), all=T)
# eval(parse(text=paste("a",i,"[1] <- NULL",sep="")))
cat("i is ", i, gc(), "\n")
# now delete these 63 temporary objects...
# e.g. should look like rm(a33)
eval(parse(text=paste("rm(a",i,")", sep="")))
}
eventually getting a dataframe with the first column being the date,
and the subsequent 63 columns being the data... with missing values
coded as NA...
so my question is... is there a better strategy for reading in lots of
small files (only a few kbytes each) like that which are timeseries
with missing data... which doesn't go through the above awkwardness
(and language manipulation) but still ends up with a nice data.frame
with NA values correctly coded etc.
Many thanks,
Sean O'Riordain
__
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Re: [R] Please help me to combine two datasets.
merge(data.set.1, data.set.2) but how do I know which rows to drop in ds1? if data.set.2 had dates, you could say merge(data.set.1, data.set.2, by.x=Date, by.y=Date, all=T) or do you just want to drop the first length(data.set.1)-length(data.set.2) from data.set.1? do you have NA values? cheers, Sean On 11/05/06, Arun Kumar Saha <[EMAIL PROTECTED]> wrote: > Dear r-users, > > Suppose I have two data sets > > data set-1 > > Date height > > 1/11/2005 10 > 2/11/2005 23 > 3/11/2005 54 > 4/11/2005 21 > 5/11/2005 22 > > data set-2 > > weight > > 32 > 45 > 11 > > > Now I want to combine this two data sets. i.e. i want to see: > > > Date height weight > --- > 3/11/2005 54 32 > 4/11/2005 21 45 > 5/11/2005 22 11 > > Can any one give me the required r-code to perform this? > > Thanks and regards, > Arun > > [[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 > __ 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
Re: [R] The Perils of PowerPoint
I can't lay my hands n it at the moment - its around here somewhere, but in "Numerical Methods That Work" by Forman Acton, the author points out that "the result of computation should be insight, not numbers" ps. an excellent book if you haven't seen it. https://enterprise.maa.org/ecomtpro/Timssnet/products/TNT_products.cfm cheers, Sean On 02/09/05, Achim Zeileis <[EMAIL PROTECTED]> wrote: > On Fri, 2 Sep 2005 12:27:45 -0500 [EMAIL PROTECTED] wrote: > > > > > > -Original Message- > > > From: ... Robert Baer > > > Sent: Friday, September 02, 2005 11:30 AM > > > > > It is wrong to blame ANY tool for our own shortcomings! > > > > Surely a fortune! > > thx, added to the devel-version of fortunes. > > But allow me one remark: Although the above is certainly true, there are > computational tools that help us better to realize or avoid our own > shortcomings whereas others will make it harder to arrive at the right > conclusions. > I agree that PowerPoint cannot be blamed for the crash of the space > shuttle, but I also see the point that the way presentations are > generated in PowerPoint (or graphics in Excel) can easily tempt people > into producing presentations/graphics that conceal what is important. > This is certainly not an excuse, but I think some criticism (even > if phrased a bit provocatively) should be allowed. > > just my EUR 0.02. > Z > > > David L. Reiner > > > > __ > > 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 > > > > __ > 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 > __ 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
Re: [R] Reference manual is not available in the help menu of the rgui
Actually, I've started reading the reference manual... :-) I printed it out 2-to-a-page and I'm working my way through it, in order to learn about the full capabilities of the base system... I know I'm not going to remember everything, but when I bump into a particular problem, I'll know what type of solutions to use and what sort of keywords to search for... frequently the problem with help is knowing that vital keyword when I in my ignorant non-statistician way want to use another vocabularly... :-) cheers! Sean On 02/09/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > Alvarez Pedro wrote: > > Dear R list, > > > > I have installed R 2.1.1 for Windows. In the help menu > > of the Rgui I can load all manuals except the > > reference manual. I downloaded the reference manual > > from the cran-site separately and saved it into the > > same folder as the other manuals but still it is not > > available in the menu. How can I solve this problem? > > Re-install, and this time check the box to install that manual. But as > Peter says, it's not really very useful, it's just a collection of man > pages from the base packages. > > Duncan Murdoch > > __ > 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 > __ 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
Re: [R] R binaries, platform independent and Design of Experiments
On 02/09/05, Nam-Ky Nguyen <[EMAIL PROTECTED]> wrote: > > b) You do NOT want to do numerical computations on software available in > > Java byte code. > You do not want to do heavy numerical computations with R either. Most > statistical calculation using R requires a fraction of a second and I > cannot see a real difference between say 0.05 second and 0.07 second. NKN. It is my understanding that the problem with Java is that it wasn't written with serious numerical computation in mind - as far as I know only in the latest version have Sun started to be address this issue. The byte code for the java virtual machine has a flawed numerical model which is not fully compliant with the IEEE754 standard - this has nothing to do with speed of computation. Furthermore the integer model is very restrictive when you want to work on random numbers using bit-twiddling. cheers! Sean __ 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
Re: [R] memory
Ferran, What are you trying to do with such a large matrix? with 7e9 cells and a linear algorithm which is quite unlikely, your problem solution is likely to take a "very long time"(tm)... just quickly... at one micro-second per operation (very optimistic?) and 7e9 operations, thats > 7e9/1e6/60 [1] 116.6667 minutes... if we're doing something a little more complicated than linear, say O(n^2.5) on a square matrix of 7e9 cells, then we're talking > (7e9^.5)^2.5/1e6/60 [1] 33745.92 minutes... As Brian Ripley said, if you really want to to this then you must use another operating system which can handle more than 32-bit addressing, one such would be linux running and built for a 64-bit platform - of which there are a few. cheers! Sean On 30/08/05, Ferran Carrascosa <[EMAIL PROTECTED]> wrote: > Thanks Prof Brian for your answers, > I have read about 'ref' package to work with more efficient memory > work. Anybody know if this package could help me to work with a > 700.000 x 10.000 matrix? > > I will have problems with ref package on: > - Limit of 2 Gb in R for Windows. > -The maximum cells in one object 2*10^9 (aprox.) > > Thanks in advance, > -- > Ferran Carrascosa > > > 2005/8/30, Prof Brian Ripley <[EMAIL PROTECTED]>: > > On Mon, 29 Aug 2005, Ferran Carrascosa wrote: > > > > > Hi, > > > > > > I have a matrix with 700.000 x 10.000 cells with floating point data. > > > I would like to work with the entire table but I have a lot of memory > > > problems. I have read the ?memory > > > I work with Win 2000 with R2.1.0 > > > > > > The only solution that I have applied is: > > >> memory.limit(size=2048) > > > > > > But now my problems are: > > > - I need to work with more than 2 Gb. How I can exceed this limit? > > > > Re-read the rw-FAQ, or (preferably) get a more capable OS on a 64-bit CPU. > > > > > - When apply some algorithms, the maximum cells in one object 2*10^9 > > > (aprox.) is reached. > > > > You will never get that many cells (that is the address space in bytes, > > and they are several bytes each). Please do as the posting guide asks > > and report accurately what happened. > > > > > Please could you send me some advises/strategies about the work with > > > large amount of data in R? > > > > > > R have a way to work with less memory needs? > > > > Your matrix has 7e09 cells (assuming you are using . as a thousands > > separator) and needs 5.6e10 bytes to store. Your OS has a memory address > > limit of 3.2e09 bytes. Don't blame R for being limited by your OS. > > > > -- > > 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 > __ 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
Re: [R] [newbie] Want to perform some simple regressions.
Hi Thomas,
I'm not an expert - so I might use incorrect terminology, but
hopefully you'll get the picture!
Assuming that you've got your data in a .CSV file, you'd first read in
your data, where the first three lines might look like...
x,y
0,2.205954909440447
1,8.150580118785099
# load the info into a data.frame called mydata
mydata <- read.csv("mycsvfile.csv",header=TRUE)
# now "attach" to this data.frame, so that the internal
attach(mydata)
# now do the regression and store it in the object "myregr"
myregr <- lm(y~x)
# print out the info from myregr
myregr
# to get more info from myregr use the summary() method...
summary(myregr)
There is an enormous quantity of documentation available, though it
takes a little while to learn to use it properly and get the full
effectiveness from it...
I strongly recommend that you read the "Posting Guide"
http://www.R-project.org/posting-guide.html
which will help you.
For more information, have a look at the introduction to R; which is a
tad terse in places - so read it slowly :-)
Have a look also at the other documentation
http://www.r-project.org/other-docs.html
In particular I'd recommend John Maindonalds online book at
http://cran.r-project.org/other-docs.html
cheers!
Sean
On 28/08/05, Thomas Baruchel <[EMAIL PROTECTED]> wrote:
> On Sun, Aug 28, 2005 at 09:48:15AM +0200, Thomas Baruchel wrote:
> > Is R the right choice ? Please, could you step by step show me
> > how you would do on this example (data below) in order to let me
>
> I forgot my data :-(
>
> 0 2.205954909440447
> 1 8.150580118785099
> 2 15.851323727378597
> 3 22.442795956953574
> 4 29.358579800271354
> 5 36.46060528847214
> 6 43.7516923268591
> 7 51.223688311610026
> 8 58.86610205087116
> 9 66.66821956399055
> 10 74.61990268453171
> 11 82.71184423952718
> 12 90.93560520053082
> 13 99.28356700194489
> 14 107.74885489906521
> 15 116.3252559311549
> 16 125.00714110112291
> 17 133.78939523822717
> 18 142.6673553086964
> 19 151.63675679510055
> 20 160.69368733376777
> 21 169.834546691509
> 22 179.05601219606618
> 23 188.35500882314003
> 24 197.72868324657364
> 25 207.17438125936408
> 26 216.68962806440814
> 27 226.2721110130965
> 28 235.9196644372003
> 29 245.63025627606442
> 30 255.40197624835042
> 31 265.23302535689197
> 32 275.12170654792556
> 33 285.06641637317705
> 34 295.0656375259694
> 35 305.1179321414606
> 36 315.2219357669857
> 37 325.3763519217964
> 38 335.5799471767038
> 39 345.8315466936063
> 40 356.13003017290697
> 41 366.4743281636434
> 42 376.8634186969678
> 43 387.2963242085816
> 44 397.77210871999046
> 45 408.2898752521091
> 46 418.8487634479048
> 47 429.44794738349896
> 48 440.08663354951693
> 49 450.76405898653184
> 50 461.479489560246
> 51 472.2322183636179
> 52 483.02156423451737
> 53 493.84687037869463
> 54 504.707503088911
> 55 515.6028505520102
> 56 526.5323217365377
> 57 537.4953453542455
> 58 548.4913688894654
> 59 559.5198576909147
> 60 570.5802941210067
> 61 581.6721767581994
> 62 592.7950196483222
> 63 603.9483516011882
> 64 615.1317155291274
> 65 626.3446678243708
> 66 637.586724806
> 67 648.8576269992603
> 68 660.1568089487967
> 69 671.4839283904737
> 70 682.838600952985
> 71 694.2204526835204
> 72 705.6291196304554
> 73 717.0642474479981
> 74 728.5254910213728
> 75 740.0125141112243
> 76 751.5249890160294
> 77 763.062596251391
> 78 774.6250242451752
> 79 786.2119690475241
> 80 797.8231340548524
> 81 809.4582297469931
> 82 821.1169734367211
> 83 832.7990890309349
> 84 844.5043068028273
> 85 856.2323631744205
>
> Regards,
>
> --
> Thomas Baruchel
>
> __
> 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
>
__
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
Re: [R] writing to a fixed format (fortran) file
?sprintf more C than fortran, but you get the idea :-) cheers! Sean On 27/08/05, Duncan Golicher <[EMAIL PROTECTED]> wrote: > Could anyone help with what should be a simple task? I have data as a > fixed format (fortran) table. I have no trouble getting it into R using > read.table. Each column is separated by a space, including the first > column that begins with a space, and aligned. It reads into R as if > separated by tabs. However I want to manipulate two columns of data then > write the results out into exactly the same fortran format for use in > another program. It should be simple, but I've tried a variety of > experiments with print, cat and format, none of which have come close. > > Here is a sample of the data. > > 1 11 19.5 2.42 0.02 5.81 9.7 0.4 102. 4.8 320. 4.8 > 2 11 0.0 0.00 0.00 0.00 4.7 -4.0 178. 5.4 301. 0.2 > 3 11 8.2 1.64 0.08 6.93 6.9 -3.6 275. 2.7 84. -11.1 > 4 11 0.0 0.00 0.00 0.00 20.6 -4.8 221. 5.6 327. -10.4 > 5 11 0.0 0.00 0.00 0.00 11.6 8.2 168. 4.3 269. 6.8 > 6 11 0.0 0.00 0.00 0.00 18.7 16.9 155. 5.6 287. 8.2 > 7 11 0.0 0.00 0.00 0.00 7.0 2.1 195. 2.7 22. 0.1 > 8 11 0.0 0.00 0.00 0.00 17.6 6.5 281. 2.0 146. 1.5 > 9 11 41.2 1.54 0.82 6.96 12.2 7.8 268. 5.5 356. 4.5 > 10 11 0.0 0.00 0.00 0.00 14.6 -1.4 250. 3.6 344. 6.4 > 11 11 0.0 0.00 0.00 0.00 14.5 -3.7 300. 0.00. -16.9 > 12 11 0.0 0.00 0.00 0.00 8.8 -2.6 308. 0.00. 2.9 > 13 11 0.0 0.00 0.00 0.00 6.4 1.6 226. 3.3 335. 3.8 > > -- > > Dr Duncan Golicher > Ecologia y Sistematica Terrestre > Conservación de la Biodiversidad > El Colegio de la Frontera Sur > San Cristobal de Las Casas, > Chiapas, Mexico > > Email: [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 > __ 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
Re: [R] plotting GAM
Emil, I've no clue what gam() does nor how it works, but saying that is it possible to use lines(,lwd=???) in someway and plot on top of the original line? cheers, Sean On 24/08/05, Tkadlec Emil <[EMAIL PROTECTED]> wrote: > Sear Sean, > here is the more working example (I use the latest version of everything > on my PC): > > x1<-runif(100,-5,5) > x2<-runif(100,1,50) > e<-rnorm(100) > y<-.3*x1-0.5*x2+e > > mod<-gam(y~s(x1)+s(x2)) > par(mfrow=c(1,2)) > plot(mod,residuals=T,se=T) > > So you get two figs. My concern is to enlarge the regression line, not the > point or enything else. > Best, > Emil > > > > > Hi Emil, > > can you give us a working example of what you're trying to do? > > > > cheers! > > Sean > > > > ps. as per the posting-guide... :-) > > > > On 24/08/05, Tkadlec Emil <[EMAIL PROTECTED]> wrote: > > > Dear colleagues, > > > I would like to have GAM regression lines (package gam) thicker than > > > the default setting does. Is there any way to change the width of > > > regression line when plotting gam.objects from the package GAM with > > > more than one predictor? Changing lwd parameter in plot function > > > controls all line components, including points making them thicker > > > as well, which is not what I would like to have. Thanks for help. > > > Best, Emil > > > > > > ** > > > Emil Tkadlec > > > Palacky UniversityPrF UP > > > Faculty of Sciencekatedra ekologie > > > Department of Ecology tr. Svobody 26 > > > tr. Svobody 26771 46 OLOMOUC > > > 771 46 Olomouctel. 58 563 4561 > > > Czech Republic > > > email: [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 > > > > > > ** > Emil Tkadlec > Palacky UniversityPrF UP > Faculty of Sciencekatedra ekologie > Department of Ecology tr. Svobody 26 > tr. Svobody 26771 46 OLOMOUC > 771 46 Olomouctel. 58 563 4561 > Czech Republic > email: [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
Re: [R] plotting GAM
Hi Emil, can you give us a working example of what you're trying to do? cheers! Sean ps. as per the posting-guide... :-) On 24/08/05, Tkadlec Emil <[EMAIL PROTECTED]> wrote: > Dear colleagues, > I would like to have GAM regression lines (package gam) thicker than the > default > setting does. Is there any way to change the width of regression line when > plotting > gam.objects from the package GAM with more than one predictor? Changing lwd > parameter in plot function controls all line components, including points > making them > thicker as well, which is not what I would like to have. > Thanks for help. > Best, > Emil > > ** > Emil Tkadlec > Palacky UniversityPrF UP > Faculty of Sciencekatedra ekologie > Department of Ecology tr. Svobody 26 > tr. Svobody 26771 46 OLOMOUC > 771 46 Olomouctel. 58 563 4561 > Czech Republic > email: [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 > __ 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
Re: [R] read a table ignoring specific rows ?
Can you read in the entire file as a data.frame; and then construct a
new data.frame which excludes some rows?
perhaps something along the lines of...
> fred.file <- data.frame()
> fred.file <- edit(fred.file)
> fred.file
colA colB colC
1142
2233
3354
4433
552 25
> fred.new <- fred.file[fred.file$colC <= 3,]
> fred.new
colA colB colC
1142
2233
4433
s/
On 22/08/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Dear R users,
> First of all sorry for this question, surely quite naive.
> (I searched on the R site but was unable to find by myself).
>
> I have a table, called infile :
> 1 2 3
> 4 5 6
> 7 8 9
>
> I would like to read it and ignore the rows with 1st element > 3
> I do it now with a for loop, and it's ok,
> but I was expecting something simpler, like :
>
> intable = read.table(infile);
> newtable = intable[isgoodrow(intable)];
>
> where : isgoodrow = function(therow)
> {if (therow$V1 > 3) return(F) else return(T);};
>
> (... but this don't work).
>
> So, could somebody please tell me if there is a way to read
> a table ignoring specific rows, without using a for loop ?
> ... and if yes how ?
>
> Thanks
> Vincent
>
> __
> 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
>
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Console
Hi Daniela, Are you using the GUI (RGui.exe) or are you using R.exe inside the cmd.exe console? if the latter then you can right click on the blue bar at the top, select properties, and change "Screen Buffer Size" / Height to be something like 9000... then you can just use your mouse to slider back up to stuff you missed... On the number of questions per day... I think if you go through the "Posting Guide" http://www.r-project.org/posting-guide.html, the "Introduction to R", the FAQs (normal and Windows) http://cran.r-project.org/faqs.html and the other ancillary documentation, such asR-Tips http://www.ku.edu/~pauljohn/R/Rtips.html... all of which are mentioned in the Posting Guide... :-) The process of going through the posting guide each time, while a bit tedious is an incredible learning experience... many posts to the list just would never happen if the author went to the trouble of going through the posting guide... admittedly the introductory documentation is not as good as it could be and is a bit terse in places... However, that said, I am also a relative beginner at R, I try to read and understand every post, most of them just go straight over my head as my statistical skills are severely lacking and when people start talking about GLMs all I hear is a whooshing sound over my head :-) One way that I have found useful for learning is to pick on questions which are at my level and try and answer them... and in answering them, I learn with you. Of course sometimes I give sub-optimal answers, but there are plenty of experts around to nudge us in the right direction :-) cheers! Sean On 19/08/05, Daniela Salvini <[EMAIL PROTECTED]> wrote: > Hi Sean! > Thank you so much for replying so soon! Well, I am very bad at these things, > so I suppose my "platform" is Windows XP, is it what you need to know? I hope > so!... And how many questions are we allowed to pose to the mailing > list...per day? I suppose I will have quite a few ... : ) > Thank you so much! > Daniela > > PS Maybe I should read the Posting Guide, I did not notice there was one > > >>> [EMAIL PROTECTED] 08/19/05 8:29 am >>> > Hi Daniela, > > Which platform are you working on? If you're working within a console > on windows-98, then the answer is entirely different to working under > linux or RGui on windows. This is why the Posting Guide says to give > platform details :-) > > cheers! > Sean > > On 18/08/05, Daniela Salvini <[EMAIL PROTECTED]> wrote: > > I am at my first steps with R... and I already notice that the console has > > a quite limited number of lines. Can anyone tell me how to visualise all > > the information, which is actually present? I only see the last part of the > > output, which obviosly exceeds the maximum number of rows in the console. > > Thank you very much for your help! > > Daniela > > > > > > > > [[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 > > > > __ 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
Re: [R] Console
Hi Daniela, Which platform are you working on? If you're working within a console on windows-98, then the answer is entirely different to working under linux or RGui on windows. This is why the Posting Guide says to give platform details :-) cheers! Sean On 18/08/05, Daniela Salvini <[EMAIL PROTECTED]> wrote: > I am at my first steps with R... and I already notice that the console has a > quite limited number of lines. Can anyone tell me how to visualise all the > information, which is actually present? I only see the last part of the > output, which obviosly exceeds the maximum number of rows in the console. > Thank you very much for your help! > Daniela > > > > [[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 > __ 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
Re: [R] A. Mani : Avoiding loops
Hi, I'm not sure what you actually want from your email (following the posting guide is a good way of helping you explain things to the rest of us in a way we understand - it might even answer your question! I'm only a beginner at R so no doubt one of our expert colleagues will help me... > fred <- data.frame() > fred <- edit(fred) > fred A B C D E 1 1 2 X Y 1 2 2 3 G L 1 3 3 1 G L 5 > fred[,3] [1] X G G Levels: G X > fred[fred[,3]=="G",] A B C D E 2 2 3 G L 1 3 3 1 G L 5 so at this point I can create a new dataframe with column 3 (C) == "G"; either explicitly or implicitly... and if I want to calculate the sum() of column E, then I just say something like... > sum(fred[fred[,3]=="G",][,5]) [1] 6 > now naturally being a bit clueless at manipulating stuff in R, I didn't know how to do this before I started... and you guys only get to see the lines that I typed in and got a "successful" result... according to section 6 of the "Introduction to R" manual which comes with R, I could also have said > sum(fred[fred$C=="G",]$E) [1] 6 Hmmm I wonder would it be reasonable to put an example of this type into section 2.7 of the "Introduction to R"? cheers! Sean On 18/08/05, A. Mani <[EMAIL PROTECTED]> wrote: > Hello, > I want to avoid loops in the following situation. There is a 5-col > dataframe with col headers alone. two of the columns are non-numeric. The > problem is to calculate statistics(scores) for each element of one column. > The functions depend on matching in the other non-numeric column. > > A B C E F > 1 2 X Y 1 > 2 3 G L 1 > 3 1 G L 5 > and so on ...3+ entries. > > I need scores for col E entries which depend on conditional implications. > > > Thanks, > > A. Mani > Member, Cal. Math. Soc > > __ > 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 > __ 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
Re: [R] How to get a list work in RData file
you know about
?history
Sean
On 16/08/05, Liaw, Andy <[EMAIL PROTECTED]> wrote:
> If you want to keep track of the function call that produced an object,
> usually you need to do that inside the function that's being called, e.g.,
>
> > test.xy <- function(x,y) {
> + xy <- x+y
> + attr(xy, "Call") <- match.call()
> + xy
> + }
> > xyadd <- test.xy(x=2, y=3)
> > xyadd
> [1] 5
> attr(,"Call")
> test.xy(x = 2, y = 3)
> > str(xyadd)
> atomic [1:1] 5
> - attr(*, "Call")= language test.xy(x = 2, y = 3)
>
>
> Andy
>
> > From: Xiyan Lon
> >
> > Dear R-Helper,
> > I want to know how I get a list work which I saved in RData
> > file. For
> > example,
> >
> > > test.xy <- function(x,y) {
> > +xy <- x+y
> > +xy
> > + }
> > >
> > > xyadd <- test.xy(x=2, y=3)
> > > xyadd
> > [1] 5
> > > x1 <- c(2,43,60,8)
> > > y1 <- c(91,7,5,30)
> > >
> > > xyadd1 <- test.xy(x=x1, y=y1)
> > > xyadd1
> > [1] 93 50 65 38
> > > save(list = ls(all=TRUE), file = "testxy.RData")
> > > rm(list=ls(all=TRUE))
> > > load("C:/R/useR/testxy.RData")
> > > ls()
> > [1] "test.xy" "x1" "xyadd" "xyadd1" "y1"
> > >
> > > ls.str(pat="xyadd")
> > xyadd : num 5
> > xyadd1 : num [1:4] 93 50 65 38
> > >
> >
> > When I run, I know the result like above
> > > xyadd
> > [1] 5
> > > xyadd1
> > [1] 93 50 65 38
> > >
> > what I want to know, is there any function to make the result like:
> >
> > > xyadd
> >
> > test.xy(x=2, y=3)
> >
> > and
> >
> > > xyadd1
> >
> > test.xy(x=x1, y=y1)
> >
> > Best,
> > Xiyan Lon
> >
> > __
> > 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
> >
> >
> >
>
> __
> 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
>
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Re: [R] How to repeat code snippet for several variables in a data frame?
Sander,
consider writing a function to do your plotting, then pass in the
dataframe name so... something along the lines of...
# create a function which takes two arguments
# mydf - a dataframe of a particular format... eg. the abc column is number 4
# i the column we want to aggregate and plot this time around...
myplotfn <- function(mydf,i) {
# body of the function
# extract the relevant column - i
colval <- mydf[3+i]
tmp <- aggregate(colval, list(
mydf$bins, mydf$groups),
mean)
# grab the name of the column we're working on; eg. "abc"
colnam.r <- names(mydf)[3+i]
colnames(tmp) <- c("bins", "groups", colnam.r)
tmp
#pltName <- paste("line_datGrassChem_", colnam.r, ".eps", sep="")
#postscript(pltName)
labs <- c("-15/-9","-9/-6","-6/-3","-3/0")
sps <- trellis.par.get("superpose.symbol")
sps$pch <- 1:4
trellis.par.set("superpose.symbol", sps)
# create the proper formula for plotting something like "abc ~ bins"
myformula <- as.formula(paste(colnam.r, "~ bins"))
xyplot( myformula, data = tmp,
groups = groups, type = list("p", "l"),
scales = list(x = list(labels=labs)),
layout = c(1,1),
key = list(columns = 4,
text = list(paste(unique(tmp$groups))),
points = Rows(sps, 1:4)
)
)
#dev.off()
}
# then call it by
myplotfn(test,1)
myplotfn(test,2)
myplotfn(test,3)
obviously this can be put in a loop :-)
So how did I figure out how to do this? well in the introduction
manual it talks about functions... the tricky bit was the substitution
of abc into the relevant places...
I didn't know how to convert the string formula "abc ~ bins" into a
formula that I could plot, so first off, I looked at ?plot, in there
it mentioned ?plot.formula and in there it mentioned the class formula
so I said ?formula where it mentioned as.formula()... bingo... this
allowed me to say
myformula <- as.formula("abc ~ bins")
So I made this into a "learning experience" for me :-)
I'm relatively new to R... so giving myself little problems like this
is a good way of learning R... and hopefully helping somebody else!
:-)
I'm pretty sure that there is a better way of doing this in R - but
this works :-)
cheers
Sean
On 15/08/05, Sander Oom <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> I have a data frame containing the results of an experiment. Like this:
>
> a<-seq(1,4,by=1)
> b<-seq(1,2,by=1)
> test<-expand.grid(b,a,a)
> colnames(test)<-c("replicates","bins", "groups")
> test$abc <- rnorm(32)
> test$def <- rnorm(32)
> test$ghi <- rnorm(32)
> test
>
> The following code snippet aggregates the data for one variable and then
> draws a plot:
>
> tmp <- aggregate(test$abc, list(
>test$bins, test$groups),
>mean)
> colnames(tmp) <- c("bins", "groups", "abc")
> tmp
> #pltName <- paste("line_datGrassChem_", "abc", ".eps", sep="")
> #postscript(pltName)
>labs <- c("-15/-9","-9/-6","-6/-3","-3/0")
>sps <- trellis.par.get("superpose.symbol")
>sps$pch <- 1:4
>trellis.par.set("superpose.symbol", sps)
>xyplot( abc ~ bins, data = tmp,
> groups = groups, type = list("p", "l"),
> scales = list(x = list(labels=labs)),
> layout = c(1,1),
> key = list(columns = 4,
>text = list(paste(unique(tmp$groups))),
>points = Rows(sps, 1:4)
>)
>)
> #dev.off()
>
> How can I wrap R code around this code snippet, such that I can repeat
> the same code snippet for all other variables in the data frame (i.e.
> def, ghi, etc.).
>
> Thanks for your suggestions!
>
> Sander.
>
> --
>
> Dr Sander P. Oom
> Animal, Plant and Environmental Sciences,
> University of the Witwatersrand
> Private Bag 3, Wits 2050, South Africa
> Tel (work) +27 (0)11 717 64 04
> Tel (home) +27 (0)18 297 44 51
> Fax +27 (0)18 299 24 64
> Email [EMAIL PROTECTED]
> Web www.oomvanlieshout.net/sander
>
> __
> 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
>
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Re: [R] Problems runing R CMD check
hi! start - control panel - system - advanced - environmental variables probably better to be working in a directory with no spaces in the path... s/ On 13/08/05, Aleš Žiberna <[EMAIL PROTECTED]> wrote: > Hello! > > I have a problem checking the package. Firstly, I do not know how to specify > the package to check. I tied specify it by supplying the path and by runing > the R CMD check in the directory of the package. > > In addition to that, I get an error bellow. Any suggestions on how to set > TMPDIR would be greatly appriciated! > > C:\Ales\Statistika\Blocno modeliranje\dr\blockmodeling>R CMD check > * checking for working latex ...Error: environment variable TMPDIR not set > (or s > et to unusable value) and no default available. > at D:\PROGRA~1\R\rw2011\share\perl/R/Utils.pm line 72 > > Thank you in advance for any help! > Ales Ziberna > > P.S.: I am runing R 2.1.1 on Win XP, SP2. I installed rtools, mingw, perl as > suggested in the manuals.Here are some details about R: > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major2 > minor1.1 > year 2005 > month06 > day 20 > language 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 > __ 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
Re: [R] evaluating string variables
use paste() to construct the file name
e.g. fn <- paste(i,".mat",sep="")
Sean
On 12/08/05, Leonardo Sepulveda Durán <[EMAIL PROTECTED]> wrote:
> Hello!!!
>
> I have a folder (C:/R/) with matrix files, named by number, i.e.
> 0.mat, 1.mat,...,1250.mat. In this case, they are 5x5 simetric
> matrices. I would like to compute a property for each matrix and put
> calculated values into a data frame for posterior ploting and
> printing. Below there is an example for 7 matrices (0.mat..6.mat)
>
> #define data frame
> L <- data.frame(frame=numeric(7), L=numeric(7))
> f0<-1/(5*(5-1)) # first variable for computation
>
> #loop over matrices, Open it , calculate property and put into data frame
> for(i in 0:6){
> m<-matrix(scan('C:/R/i.mat', n=5*5),5,5, byrow=TRUE) # load matrix
> f1<-geodist(m)
> f2<-sum(colSums(f1$gdist))
> l <-f0*f2
># Calculate property
> L[i+1, ]<-c(i,l)
> # Fill data frame
> }
>
> but the matrix cannot be loaded, because it try to open a file named
> "i.mat". I don`t know how to loop with a counter named 'i', and use it
> to define the name of the file too. How can i do it? I have not found
> the way.
>
> Leonardo
>
> __
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>
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Re: [R] connexion problem getHdata (HMisc)
Hi Anne, does update.packages() work, or does it just hang? cheers! Sean On 11/08/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > Sorry about the missing info, I'm just trying to do too many things at the > same time! > I installed R on my Windows2000 computer (no choice there) . > > > version > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major2 > minor1.1 > year 2005 > month06 > day 20 > language R > > Hmisc version: 3.0-6 ; > > On my home computer (LINUX and Windows XT) with the same (latest) R and > Hmisc version installed, I had no problem with getHdata... > > Thanks > Anne > > > > > > > > Frank E Harrell Jr <[EMAIL PROTECTED]> > 09.08.2005 22:19 > > A > [EMAIL PROTECTED] > cc > r-help@stat.math.ethz.ch > Objet > Re: [R] connexion problem getHdata (HMisc) > > > > > > > [EMAIL PROTECTED] wrote: > > ** > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they > > are addressed. If you have received this email in error please notify > > the system manager. > > > > ** > > > > Hi > > > > Just installing R and some packages in my new job; trying to download > > dataset directly from > > biostatistics dptm of Vanderbilt University using getHdata from Hmisc I > > get the following: > > > > Error in file (file, "r") : connexion openinig not possible > > Furthermore : > > connexion to 'biostat.mc.vanderbilt.edu' impossible on port 80 > > > > Can one get around this problem? > > > > NOTE: I am not an administrator on the system > > > > > > Anne Piotet > > It is hard for me to help when you provided no code and no output from > typing > > version > > at the command prompt. You also did not include the version of Hmisc. > I tried a small test: > > library(Hmisc) > getHdata(titanic3) > > and it worked fine, using the most recent Hmisc. > > Frank > > > > > tél: 022 809 54 36 > > e-mail: [EMAIL PROTECTED] > > > > Office cantonal de l'assurance-invalidité (OCAI) > > rue de Lyon 97 > > 1203 Genève GE > > > >[[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 > > > -- > Frank E Harrell Jr Professor and Chair School of Medicine > Department of Biostatistics Vanderbilt 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 > > __ 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
Re: [R] connexion problem getHdata (HMisc)
Could this be a web-proxy problem? http://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-internet-download-functions-fail_002e Have you tried doing update.packages() ? does this work? I presume you're on some sort of Windows? Sean On 09/08/05, Frank E Harrell Jr <[EMAIL PROTECTED]> wrote: > [EMAIL PROTECTED] wrote: > > ** > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they > > are addressed. If you have received this email in error please notify > > the system manager. > > > > ** > > > > Hi > > > > Just installing R and some packages in my new job; trying to download > > dataset directly from > > biostatistics dptm of Vanderbilt University using getHdata from Hmisc I > > get the following: > > > > Error in file (file, "r") : connexion openinig not possible > > Furthermore : > > connexion to 'biostat.mc.vanderbilt.edu' impossible on port 80 > > > > Can one get around this problem? > > > > NOTE: I am not an administrator on the system > > > > > > Anne Piotet > > It is hard for me to help when you provided no code and no output from > typing > > version > > at the command prompt. You also did not include the version of Hmisc. > I tried a small test: > > library(Hmisc) > getHdata(titanic3) > > and it worked fine, using the most recent Hmisc. > > Frank > > > > > tél: 022 809 54 36 > > e-mail: [EMAIL PROTECTED] > > > > Office cantonal de l'assurance-invalidité (OCAI) > > rue de Lyon 97 > > 1203 Genève GE > > > > [[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 > > > -- > Frank E Harrell Jr Professor and Chair School of Medicine > Department of Biostatistics Vanderbilt University > > __ > 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 > __ 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
[R] solution: package install probs. win-xp. file move
Hi,
This is just an FYI documenting a conflict between R and
Google-Desktop. The solution was to click on the Google-Desktop icon
in the systray and click on "Pause Indexing". I also temporarily
suspended anti-virus scanning before successfully
install.packages("VR") many times without getting an error message.
I was getting an intermittant failure when I tried to install a
package or update a package under Win-XP-Pro-sp2.
There is 5gb of free space on the drive and I'm an admistrator on this
machine and most times (but not every time) I tried to
upgrade.packages() or install.packages() I got the following error
message "unable to move temporary installation" message.
It appears to be a file-locking issue with the Google-Desktop search -
ie. during the few seconds that install.packages() creates a file
directory tree, google-desktop starts reading these files and then
prevents this tree from being moved to its correct place under
\library
cheers,
Sean
==
Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0
I installed todays 2.2.0-pre and I get exactly the same thing. The
first time I did it, no problem; I exit out of R-2.2.0-pre (and 2.1.1)
and go back into 2.2.0-pre and type 'install.packages("VR")' and I get
the "unable to move temporary installation".
I've searched the archives and the web for the phrase "unable to move
temporary installation"; I've looked for similar bugs at r-bugs and I
found nothing.
Clearly something to do with file locking on windows - possibly anti-virus?
cheers,
Sean
==
e.g.
> install.packages("VR")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.uk.r-project.org/bin/windows/contrib/2.1/VR_7.2-17.zip'
Content type 'application/zip' length 1570833 bytes
opened URL
downloaded 1534Kb
bundle 'VR' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\soriorda\Local
Settings\Temp\Rtmp9355\downloaded_packages
updating HTML package descriptions
Warning message:
unable to move temporary installation 'C:\Program
Files\R\rw2011\library\file11565\MASS' to
'C:\PROGRA~1\R\rw2011\library\MASS'
=
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 Under development (unstable) (2005-08-04 r35153M)
> install.packages("VR")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.uk.r-project.org/bin/windows/contrib/2.2/VR_7.2-17.zip'
Content type 'application/zip' length 1570833 bytes
opened URL
downloaded 1534Kb
bundle 'VR' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\soriorda\Local
Settings\Temp\Rtmp10612\downloaded_packages
updating HTML package descriptions
Warning message:
unable to move temporary installation 'C:\Program
Files\R\R-2.2.0dev\library\file17748\MASS' to
'C:\PROGRA~1\R\R-22~1.0DE\library\MASS'
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Re: [R] help regarding functions & loops
Hi Rangesh,
Perhaps I mis-understand your question, but it could be as simple as...
p <- 1-exp(-exp(s))
In R, this is vectorized such that a new vector is calculated - one
value for each value of s, so p will have the same length as s.
In the "Introduction to R" read up on vectors and how to avoid loops.
cheers!
Sean
On 06/08/05, Rangesh Kunnavakkam <[EMAIL PROTECTED]> wrote:
> I am new to R,so excuse me if its too basic. I have a vector of scores
> S= {s1,s2,s3,sn}
> n could be very large.
> I want to find p-value for each score and I have the formula
> pvalue= 1-exp(-exp(S))
> so any ideas how to get this new vector P={p1,p2,p3,p4,p5pn}
> thankyou in advance
> Rangesh
>
> __
> 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
>
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Re: [R] nnet package for OS X
Hi Lisa, as far as I know, nnet is part of the VR bundle which is a recommended package... refer http://www.stats.bris.ac.uk/R/src/contrib/Descriptions/VR.html so just try library(nnet) and see what happens! cheers! Sean On 02/08/05, Lisa Schweitzer <[EMAIL PROTECTED]> wrote: > Hello every one-- > > My sincere apologies if I have missed something obvious, but I need > to construct some multinomial logit models. I remember using nnet > for this in the past, but I am having trouble locating a OS X version > of this (it's been a year or so since I had to use it). I found a > Windows version, but when I try to install across platforms, it > crashes R immediately--no error messages or anything helpful. Can > any one direct me to a repository, or alternatively, to another > package readily available Mac side that can do simple multinomial > logit models? This is basic survey data--nothing fancy needed. > > All best, > > Lisa > > __ > 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 > __ 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
Re: [R] R: graphics devices
actually X11() also works under windows!
X11()
plot(y~x)
X11()
plot(q~x)
On 29/07/05, Chuck Cleland <[EMAIL PROTECTED]> wrote:
>Is this on windows? If so, how about the following:
>
> > windows()
> > plot(y~x)
> > windows()
> > plot(q~x)
>
>For me, this creates two different plot _windows_ and you could tile
> them to see each side-by-side. But I'm not sure how that would be
> preferable to having the plots in the same window. What exactly do you
> mean by different screens?
>
> Clark Allan wrote:
> > one could use the par command to plot several plots on 1 graphics
> > device.
> >
> > i would like to do the following:
> >
> > say plot(y~x) on one screen and then
> >
> > plot(q~w) on another screen so that one can see both of them together
> > but not on the same graphics device.
> >
> > Sean O'Riordain wrote:
> >
> >>Alan,
> >>I'm not sure what you mean...
> >>
> >>perhaps
> >>
> >>plot(y~x) # to the screen
> >>pdf("myplot.pdf")
> >>plot(y~x) # write the plot to the file
> >>dev.off() # close the file
> >>dev.off() # close the graphics window
> >>
> >>s/
> >>
> >>On 29/07/05, Clark Allan <[EMAIL PROTECTED]> wrote:
> >>
> >>>a simple question
> >>>
> >>>how does one produce plots on two different graphics devices?
> >>>
> >>>/
> >>>allan
> >>>
> >>>__
> >>>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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>__
> >>>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
>
> --
> 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] R: graphics devices
Alan,
I'm not sure what you mean...
perhaps
plot(y~x) # to the screen
pdf("myplot.pdf")
plot(y~x) # write the plot to the file
dev.off() # close the file
dev.off() # close the graphics window
s/
On 29/07/05, Clark Allan <[EMAIL PROTECTED]> wrote:
> a simple question
>
> how does one produce plots on two different graphics devices?
>
> /
> allan
>
> __
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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
>
>
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Re: [R] How to save the object of linear regression in file and load it later
Hi Bahoo! I've found the R/Rpad Reference Card quite good at helping me find this sort of information... i.e. towards the bottom of the first column of the first page it says... save(file,...) saves the specified ojects (...) in the XDR platform independent binary format if I then say ?save it tells me that ?load is what you're looking for at another date... cheers! Sean On 25/07/05, Bahoo <[EMAIL PROTECTED]> wrote: > Hi, > > I am using locfit for regression. > After I do > out = locfit(...), > I want to save "out" in a file, and load it later for > prediction. > > How should I do it? Thanks! > > __ > 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 > __ 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
Re: [R] The steps of building library in R 2.1.1
Just a few thoughts... Good documentation helps everybody - the beginners and the experts (less beginner questions if there is thorough and accessible documentation. I fully appreciate that this is a volunteer effort - I'm just trying to pin down some places where we have documentation issues. Docs can be in a number of different forms - reference, examples, carefully and throughly explained. I personally find it difficult to understand reference type material until I have seen a worked example, and some of the reference material is a little light on the examples for me, and others like me who thrive on examples. The Linux-HOWTO collection are a good example of step-by-step documentation... If you're an expert, then you can read it fast and skip... otherwise you read every line. Since R comes as a computer "package" and a statistics "thingy"... the questions on this list come in three forms - those that are very 'package', e.g. "how do I reduce the space between two graphs" - to the statistics questions "how reliable is the coefficient of determination in the presence of outliers" (which shouldn't really be asked here), and then the how do I do 'statistic X' in R - "how do I calculate a confidence interval around the coefficent of determination in R?". The standard documentation got me so far in learning about R - I got a copy of MASS, S-Programming, "Introductory Statistics with R", and Michael Crawley's new book "Statistics : An Introduction using R" - along with every online book I could find on CRAN and elsewhere. Unfortunately for me, my experience leaves me in between the beginner books and the more advanced texts like MASS, David, Schervish etc... The learning curve is steep - but then like many people, I'd like to be able to do sophisticated modelling with deep understanding and no effort :-) I feel there is a bit of a hole in the middle of the documentation which could be attacked from both sides - the introduction element is starting to be covered - it's the next step up from that. And yes before you ask I would like to help - but my statistics knowledge is very poor! Should this conversation go to r-devel? Thanks for listening, Sean On 21/07/05, Uwe Ligges <[EMAIL PROTECTED]> wrote: > Duncan Murdoch wrote: > > > On 7/21/2005 10:29 AM, Uwe Ligges wrote: > > > >>Gabor Grothendieck wrote: > >> > >> > >>>I think you have been using R too long. Something like > >>>this is very much needed. There are two problems: > >>> > >>>1. the process itself is too complex (need to get rid of perl, > >>>integrate package development tools with package installation > >>> procedure [it should be as easy as downloading a package], > >>> remove necessity to set or modify any environment variables > >>>including the path variables). > >>> > >>>2. there is too much material to absorb just to create a package. > >>>The manuals are insufficient. > >>> > >>>A step-by-step simplification is very much needed. Its no > >>>coincidence that there are a number of such descriptions on > >>>the net (google for 'making creating R package') since I would > >>>guess that just about everyone has significant problems in creating > >>>their first package on Windows. > >> > >>OK, if people really think this is required, I will sit down on a clean > >>Windows XP machine, do the setup, and write it down for the next R Help > >>Desk in R News -- something like "Creating my first R package under > >>Windows"? > >> > >>If anybody else is willing to contribute and can write something up in a > >>manner that is *not* confusing or misleading (none of the other material > >>spread over the web satisfies this requirement, AFAICS), she/he is > >>invited to contribute, of course. > >> > >>BTW, everybody else is invited to submit proposals for R Help Desk!!! > > > > > > That sounds great. Could you also take notes as you go about specific > > problems in the writeup in the R-admin manual, so it can be improved for > > the next release? > > Of course. > > > > Another thing you could do which would be valuable: get a student or > > someone else who is reasonably computer literate, but unfamiliar with R > > details, to do this while you sit watching and recording their mistakes. > > Good idea. > > Uwe > > > > Duncan Murdoch > > __ > 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 > __ 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
Re: [R] convert to chron objects
are those dates in m/d/y or d/m/y ?
?chron and watch out for
format = c(dates = "d/m/y", times = "h:m:s")
On 13/07/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> [I had some emails problems so I am sending this again. Sorry
> if you get it twice.]
>
> On 7/13/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> >
> >
> > On 7/13/05, Young Cho <[EMAIL PROTECTED]> wrote:
> > > Hi,
> > >
> > > I have a column of a dataframe which has time stamps
> > > like:
> > >
> > > > eh$t[1]
> > > [1] 06/05/2005 01:15:25
> > >
> > > and was wondering how to convert it to chron variable.
> > > Thanks a lot.
> >
> >
> >
> >
> >
> Try this:
>
> # test data frame eh containing a factor variable t
> eh <- data.frame(t = c("06/05/2005 01:15:25", "06/07/2005 01:15:25"))
>
> # substring converts factor to character and extracts substring
> chron(dates = substring(eh$t, 1, 10), times = substring(eh$t, 12))
>
> See ?chron for more info. There is an article on dates in
> R News 4/1 and although it does not specifically answer this
> question it may be useful with chron and also provides a
> reference to more chron info elsewhere.
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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Re: [R] R: to the power
> (-8+0i)^(1/3) [1] 1+1.732051i ie complex... On 12/07/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > hi all > > why does R do this: > > (-8)^(1/3)=NaN > > the answer should be : -2 > > a silly question but i kept on getting errors in some of my code due to this > problem. > > i solve the problem as follows: > > say we want : (-a)^(1/3) > > then : sign(a)*(a^(1/3)) works > > but there has to be a simpler way of soing such a simple mathematical > operation. > > thanking you > / > allan > > __ > 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 > __ 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
Re: [R] Problem compiling R 2.1.* on SUSE 9.2
Hi! what point exactly in the command sequence does it fail? during make? or make install? You might try saving the output and the error from the build into a file? Something along the lines of ./configure 2>&1 >filename or even ./configure 2>&1 >filename | tee configure_output.txt etc. cheers! Sean On 7/8/05, J Dougherty <[EMAIL PROTECTED]> wrote: > I have been unable to compile either R 2.1.0 or 2.1.1 under SUSE 9.2. The > system simply hangs as far as I can tell. All key board and mouse > service dies. I have had no problem compiling earlier versions of R through > 2.0.1, aside from remembering to include readline in the configuration. > Configure runs without any warnings except that Info or html versions of the > R Manuals. The SUSE 9.2 install is generic with KDE 3.3 as the principal > GUI. Compiling also crashes under GNOME. Because of the system hang, I > can't provide any error codes. Perusing /var/log/messages doesn't seem to > yield any clues. The system is a KDE AMD XP 2100, there is 1 GB of system > ram, less than 10% of the harddisk space is in use, videocard is an nVidia > GeForce4 Ti 4400. The OS is SUSE 9.2 and it has current updates for > security. > > JWDougherty > > __ > 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 > __ 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
Re: [R] Tempfile error
Hi Harold, I know nothing about Sweave (though it certainly sounds like a great idea!). Does Sweave hold these files open simultaneously - many operating systems wouldn't be able to cope with 20,000 simultaneously open files. Could you be running out of disk space? or inodes - if you're on a unix type system? can the directory hold that many files? can the disk hold that many files? Many filesystems are formatted with an assumption about the average file size. Perhaps if you told us what type of operating system and type(s) of filesystem(s)? cheers! Sean On 7/6/05, Doran, Harold <[EMAIL PROTECTED]> wrote: > Dear List: > > I am encountering an error that I can't resolve. I'm looping through > rows of a dataframe to generate individual tex files using Sweave. At > random points along the way, I encounter the following error > > Error in file() : cannot find unused tempfile name > > At which point Sweave halts. There isn't a logical pattern that I can > identify in terms of why the program stops at certain points. It just > seems to be random as far as I can tell. I've searched the archives and > of course Sweave FAQs but haven't found much that sheds light on what > this error indicates and what I should do to resolve it. > > There are approximately 20,000 rows, meaning that about 20,000 tex files > are created. If I sample 5,000 or even 10,000 and run the program, I do > not encounter an error. It only occurs when I run the program on the > full dataframe and even then the error is not occuring at the same > point. That is, the row at which the program halts varies each time. > > Does anyone have any thoughts on this problem? > > -Harold > > > > > [[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 > __ 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
[R] finding out more about an object, e.g. lm
Hi! I'm trying to use lm(y~x) amongst others in an automated way; I've gone through the section on indexing in R-lang and I've looked MASS4. How do I find out more about the structure of the returned object? In perl I can look at object structure pretty-printed in the debugger - is there an R equivalent? I've used coef(lm(y~x))[[1]] and coef(lm(y~x))[[2]] to extract the intercept; but while summary(lm(y~x)) prints R-squared... it isn't entirely obvious how to extract this value as a scalar. ?lm doesn't give me the information by saying unlist(summary(lm(y~x))) it prints $r.squared [1] 0.267 so now I can say my.r.sq <- summary(lm(y~x))$r.squared but is there a better way? on my small lm model unlist(lm(y~x)) is a pretty long list! :-) Many thanks in advance, Sean O'Riordain __ 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
Re: [R] hellow
Hi, I suggest that you read the 'posting guide' - refer the bottom of all emails on the list. http://www.R-project.org/posting-guide.html (il ne faut que d'aller chez http://www.r-project.org/ vous meme). Sean karima alem wrote: can i ask you for logiciel R - Dialoguez en direct avec vos amis grâce à Yahoo! Messenger ! [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.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://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] access R remotely
This likely means that either R is not installed on that machine or the R binary is not in your PATH. : try asking your IT guy where R is installed... say Mr.IT.Guy says that R is installed in /usr/local/bin... then /usr/local/bin/R to start R... cheers, Sean. array chip wrote: Hi, not sure if this is kind of question that should be asked here, but here it is: I am trying to access R installed on a remote cluster (Linus), but I got the error message that R command not found when I simply typed "R" after the prompt after having successfully accessed the remote cluster using SSH. what could be the reason of the problem? is the problem on the cluster side or on my side? I am not a IT person at all, so I don't know much detail... Our IT guy on the cluster side is working on the problem, but seems not very efficiently targeting the problem. Thanks for any suggestion. __ [EMAIL PROTECTED] mailing list https://www.stat.math.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://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R commands
Hi Andy, I know it doesn't answer all of your questions but have you read the Posting guide (see the bottom of all posts) ? http://www.R-project.org/posting-guide.html and in particular, try reading "An Introduction to R", chapter 9? Note that in R, looping is relatively "slow" - if you can do things using a vector, this is much better. Try going to the R-project.org homepage and on the left hand side you'll see Search - does searching for "bootstrap monte carlo" answer your first question? cheers, Sean Chou Andy wrote: > I'm a R beginner. Recently I conduct a project about expected return > that involves using R for calculations. I encounter three questions as > follow: > > Q1. How to use R to demonstrate bootstrapping and Monte Carlo > simulation under 10,000 times of random selection? > Q2. How to do a loop in R? > Q3. How to use R to do binominal tree calculation under multiple periods? > > I'm perplexed by the R commands, so any hints or examples will be > highly appreciated. > > > Andy > > _ > 立即申請 MSN Mobile 服務：用手機和 MSN Messenger 網友隨時交談 > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.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://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R programming
Hi Henrick, if you checked the posting guide (refer the bottom of all emails) you'd have spotted a link # R Language Definition (aka `R Language Manual') describes the R language, data objects, etc. http://cran.r-project.org/doc/manuals/R-lang.pdf cheers, Sean ps. R is indeed a full and complete language Andersson, Henrik wrote: I have been using R for a few months to plot my data, and fit statistical models and so on. It is stated that R is not only a package for statistcs and graphics but also a programming language. Currently I am working with Fortran 90 to do numerical simulations (1D reactive -transport), and subsequently visualize it in some external software (spreadsheet). As I now started using R I will plot my results using R, but my question is: Could I use R as a replacement for the Fortran program, or is programming in R more restricted? E.g. is it possible to use subroutines in R? If you think programming in R is great and you have some documentation, please point me to it. Thanks, Henrik Andersson - Henrik Andersson Netherlands Institute of Ecology - Centre for Estuarine and Marine Ecology P.O. Box 140 4400 AC Yerseke Phone: +31 113 577473 mailto:[EMAIL PROTECTED] http://www.nioo.knaw.nl/ppages/handersson __ [EMAIL PROTECTED] mailing list https://www.stat.math.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://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] LCG with modulo 2^30
Hi Raheem,
Firstly - fair warning...I'm not an R expert at all! However it is my
understanding that the expression "for i in 1:m" creates a full vector
in memory of all the consecutive numbers 1 to m... (i presume these are
4-byte ints here otherwise it would have fallen over before 2^29), but
taking the minimal assumption of ints these take 4 bytes... 1:2^29
requires (2^29)*4 bytes of memory - running on a 32-bit platform you
have an absolute maximum of about 2^32 bytes of addressable memory (some
memory will be taken by the os...).
if you start R and say "gc()" it'll tell you about memory allocated...
then try k<-c(1:2^24); gc() and you might get a response something like...
> gc()
used (Mb) gc trigger (Mb)
Ncells 208431 5.6 407500 10.9
Vcells 73157 0.6 786432 6.0
> k <- c(1:2^24)
> gc()
used (Mb) gc trigger (Mb)
Ncells 208431 5.6 407500 10.9
Vcells 8428997 64.4 17108043 130.6
if you REALLY want to interate to 2^32 without allocating a huge memory
vector like that try using your own counter and a while loop instead
which won't allocate more memory than you have - but this will likely be
SLOW... something along the lines of
i <- 0
while (i < 2^32) {
# now we do stuff
i <- i+1
}
i'm quite sure that there are more 'R-ish' ways of doing things...
btw. what are you trying to achieve?
Sean
Enayetur Raheem wrote:
I can't run a function which generates random numbrers using linear
congruential generator. My multiplier is a=5+8^6, increment is b=1 and
modulo is m=2^30.
the code I have written works for modulo upto m=2^28.
For m= 2^29 , it says, can not allocate memory for the vector or
something like that.
For m= 2^31 or more, its says the argument "for i in 1:m " is too
large in magnitude.
I tried to increase the memory size but it did not work.
Any help will be appreciated.
Thanks.
Raheem
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Re: [R] R killed on Solaris
Hi Ott, could it be a per process "limit" or "ulimit"s set? i don't have a solaris box here so i can't remember what the appropriate commands are... cheers, Sean Ott Toomet wrote: Hello, I am running a preliminary data-processing job on solaris. Basically, the program reads a large number of ascii-lines (about 1M) by blocks (size 25000 lines), selects suitable observations (around 5000) and writes the results into a dataframe for latter processing. The problem is that when I run the job interactively (in emacs/ESS), everything works fine. If I try to run it from shell using R CMD BATCH, R will be killed after around 100 000 lines. Solaris says simply "killed" and thats it. The total memory consumption seems not to be a problem, around 200M on a 4G machine. Any suggestions? Has anyone else seen something similar? Best wishes Ott --- this is R 1.7.1, compiled as 32-bit appication, on 64bit sparc solaris 9 (sunos 5.9). __ [EMAIL PROTECTED] mailing list https://www.stat.math.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://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and RS232-Interface?
Hi, Personally, I would avoid Java for hardware handling - in my experience this is tricky and very hardware specific. Sascha, is this for a Unix type machine or under windows? If under Unix/Linux, it should not be particularly difficult to send characters and receive characters in C through a plain rs-232 port - though I don't have any code examples for you. Just open the relevant /dev/cua0 (or whatever it is called on your machine) in character mode and treat it like a file. cheers, Sean Henrik Bengtsson wrote: Hi, I recall I've seen a RS232-interface communication class in Java a few years ago. I can't remember for what platforms it were written for (I think it relied on some native code). If you find it, you then might be able to use the SJava package by Omegahat (http://www.omegahat.org/RSJava/). A long shot, but it might be better than nothing. Cheers Henrik Bengtsson -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Morach Sascha, moracsa1 Sent: den 14 november 2003 17:27 To: [EMAIL PROTECTED] Subject: [R] R and RS232-Interface? Hi there Does any one of you know something about R and an implemented RS232-Interface? Are there any packages? Or is it possible to write an extensions or something like that in C/C++ ? The problem is that i should handle the information from a measuring device via the RS232-Interface (probably you know LabVIEW, which provides this functionality). These informations should then directly be handled by R. Is this possible? (I hope I found the right words, I'm swiss, J ) thanks Sascha Morach, diplomastudent, ZHW __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailma> n/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Ignoring Errors in Simulations
?try Ken Kelley wrote: Hello all. I'm doing a simulation study and every so often I get an error that stops the simulation. I would like to ignore the errors *and* identify the particular iterations where they occurred. I have tried: options(error = expression(NULL)) which I thought would ignore the error, but the simulation is still stopped when an error occurs. I do not think try() is a good idea because of the significant computational time (that I think) it would add. Specifically I am using factanal() from the mva library and the error is: Error in factanal(Data, factors = 1, rotation = "none") : Unable to optimize from these starting value(s) -I am using R 1.7.1 on a Windows XP machine. Although increasing the number of starting values attempted would reduces the number or errors, I'm looking for a way that they are ignored and these (likely) untrustworthy results identified. Thanks for any thoughts, Ken __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Visualising Vectors
Hi Laura, you should find some useful information in the latest R news Volume 3/2, October 2003 http://cran.r-project.org/doc/Rnews/ refer page 8 where Paul's figure 2 shows some novel symbols showing "China Sea Wind Speed, Direction and Temperature"... plotted by lat.&long. s. Laura Quinn wrote: I sent a mail last week asking for some advise in relation to displaying wind vectors on a contour map of a region. Whilst I have had some useful feedback relating to the second part of this question (namely how to animate a time series of still frames), I haven't recieved any advise on how I might create the still images of the spatially distributed wind vector data at any given time point. Firstly, is there a way in which I can input orographical information (x,y,z co ords) into R to create a map, secondly, is there a way in which i can superimpose a visual wind vector (i.e. arrow of certain length and certain orientation) onto such a map? thanks in advance, Laura __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] generic algorithm (optimize)
help.search("optimize")
optim(base) General-purpose Optimization
optimize(base) One Dimensional Optimization
olvq1(class)Optimized Learning Vector Quantization 1
lmeScale(nlme) Scale for lme Optimization
zhu wang wrote:
Dear all,
Is there any generic algorithm code for optimization implemented in R? I
searched without success.
Thanks,
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Re: [R] r-ish ? how can i improve my code?
Hi Patrick, Spencer,
Thanks for that! Both your solutions are MUCH quicker!
afaik overwork_ratio = 4/pi # what a hard way to calculate this :-)
The real problem I'm actually working on is a little more complicated
:-) - 6 'random' variables, and 18 dependant variables (at last
count)... currently only 4 computed terms in the 'if() c<-c+1'
statement... I just created the x,y area problem as a simple example of
the style I was using.
In the past I've worked on other 'accident' related problems and one
difficulty was in getting enough final 'z' values to be statistically
significant as there was an enormous rejection ratio - but it was
running on a 486 written in compiled turbo pascal and it would take days
of work...
I'll have a go at recoding using your techniques.
Many Thanks,
Sean
Patrick Burns wrote:
For this particular problem you can probably use
polar coordinates.
But something similar to your code could be:
x <- runif(900)
y <- runif(900)
z <- sqrt(x^2 + y^2)
okay <- z < 1
while(any(!okay)) {
n.bad <- sum(!okay)
x[!okay] <- runif(n.bad)
y[!okay] <- runif(n.bad)
z <- sqrt(x^2 + y^2) # restricting to !okay may or may not be useful
okay <- z < 1
}
Patrick Burns
Burns Statistics
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and "A Guide for the Unwilling S User")
Sean O'Riordain wrote:
Hi Folks,
I'm trying to learn R. One of my intentions is to do some Monte-Carlo
type modelling of road "accidents".
Below, to simplify things, I've appended a little program which does a
'monte-carlo' type simulation. However, it is written in a way which
seems a bit un-natural in R. Could someone help me make this a bit
more R-ish please?
Or is there a completely different approach I should be taking?
Many thanks in advance,
Sean O'Riordain
seanpor AT acm.org
n <- 900; # number of valid items required...
x <- numeric(n);
y <- numeric(n);
z <- numeric(n);
c <- 1; # current 'array' pointer
tc <- 0; # total items actually looked at...
while (c <= n) {
x[c] = runif(1, 0, 1);
y[c] = runif(1, 0, 1);
z[c] = sqrt(x[c]^2 + y[c]^2);
if (z[c] < 1)
c <- c + 1;
tc <- tc + 1;
}
print("'overwork' ratio");
print(tc/(c-1));
plot(x,y);
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[R] r-ish ? how can i improve my code?
Hi Folks,
I'm trying to learn R. One of my intentions is to do some Monte-Carlo
type modelling of road "accidents".
Below, to simplify things, I've appended a little program which does a
'monte-carlo' type simulation. However, it is written in a way which
seems a bit un-natural in R. Could someone help me make this a bit more
R-ish please?
Or is there a completely different approach I should be taking?
Many thanks in advance,
Sean O'Riordain
seanpor AT acm.org
n <- 900; # number of valid items required...
x <- numeric(n);
y <- numeric(n);
z <- numeric(n);
c <- 1; # current 'array' pointer
tc <- 0; # total items actually looked at...
while (c <= n) {
x[c] = runif(1, 0, 1);
y[c] = runif(1, 0, 1);
z[c] = sqrt(x[c]^2 + y[c]^2);
if (z[c] < 1)
c <- c + 1;
tc <- tc + 1;
}
print("'overwork' ratio");
print(tc/(c-1));
plot(x,y);
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Re: [R] install error
Good morning Yuhong! I've just done a rebuild of R-1.6.2 on my machine here using the following commands (from my history)... 48 mkdir tmpR 49 cd tmpR 50 tar xzvf ../R-1.6.2.tgz 51 pwd 52 cd R-1.6.2/ 53 ./configure --prefix=/home/sean/software/R/tmpR 54 make 55 nice make check 56 nice make install it installed with no problem... creating the following directories... [sean@sean4 R-1.6.2]$ pwd /home/sean/software/R/tmpR/R-1.6.2 [sean@sean4 R-1.6.2]$ cd .. [sean@sean4 tmpR]$ ll total 16 drwxrwxr-x2 sean sean 4096 Feb 9 08:13 bin drwxrwxr-x3 sean sean 4096 Feb 9 08:13 lib drwxrwxr-x3 sean sean 4096 Feb 9 08:13 man drwxr-xr-x 15 sean sean 4096 Feb 9 07:56 R-1.6.2 where the last line is the build directory... note that I have full permissions from my home directory /home/sean downwards. could you be low on quota or disk space? cheers, Sean Yuhong Guo wrote: I just download R-1.6.2 source code for unix to install. I am intalling it under redhat linux. But after ./configure, when I try to make, there always error showed: /usr/bin/install: cannot change ownership of `../../bin/BATCH': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/LINK': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/Rcmd': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/Rdiff': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/Rd2dvi': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/Rd2txt': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/config': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/pager': Operation not permitted /usr/bin/install: cannot change ownership of `../../bin/texi2dvi': Operation not permitted Does anyone know what is the problem? (Oh, I install it as a common user to linux, not as root)? __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
