[R] if ( expr )
Hello,
I've searched the list but haven't found anything really applicable to my
question. Any advice would be super.
I'm working on a snippet of R code and I have a function with a prototype
like this:
foo - function( x, ... ){
if( is.na(x)[1] ) {etc...}
}
Where x is typically a vector of bools.
At times, however, x can be NA, and yet at other super rare times x can be
the result of this type of comparison:
c(4,5,13,2,3,4,5,7) == numeric(0)
which produces logical(0). When this is the case, if( is.na(x)[1] ) isn't
happy.
I'm trying to create a condition to my if statement inside foo that only
is true when x is NA but that doesn't die when its a logical(0).
Any suggestions on how best to approach this?
As always, thanks a bunch,
Greg
__
R-help@r-project.org 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] Odp: if ( expr )
Hi
[EMAIL PROTECTED] napsal dne 20.11.2007 10:03:53:
Hello,
I've searched the list but haven't found anything really applicable to
my
question. Any advice would be super.
I'm working on a snippet of R code and I have a function with a
prototype
like this:
foo - function( x, ... ){
if( is.na(x)[1] ) {etc...}
}
Where x is typically a vector of bools.
At times, however, x can be NA, and yet at other super rare times x can
be
the result of this type of comparison:
c(4,5,13,2,3,4,5,7) == numeric(0)
which produces logical(0). When this is the case, if( is.na(x)[1] )
isn't
happy.
Check the length. In case of numeric(0) or logical(0) the length is 0
which you can use for testing.
Regards
Petr
I'm trying to create a condition to my if statement inside foo that
only
is true when x is NA but that doesn't die when its a logical(0).
Any suggestions on how best to approach this?
As always, thanks a bunch,
Greg
__
R-help@r-project.org 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@r-project.org 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] How is the Gauss-Newton method compared to Levenberg-Marquardt for curve-fitting?
Almost every problem I have seen in the context of fitting mixtures of exponentials/Gaussians has near-equal performance under LM or GN in terms of iterations/evaluations to convergence and the SSE of the solution found. (However, very recently I have encountered a problem with a large number of nonlinear parameters (~100) for which LM finds a better optimum than GN; I am in the process of looking into why this is the case.) Regarding profiling: I have never looked for such literature; if you find it, realize that the results may not generalize to the SSE surface of the residual functions you will consider. Therefore you might be better off doing the profiling yourself for the residual functions that are typical in your problem domain (you can use the R package minpack.lm for LM). For general discussion of LM and GN, standard referencs are Bates and Watts, Nonlinear regression analysis and its applications, and Seber and Wild, Nonlinear regression. I believe that one of the main reasons that GN gets more use than LM by R users is that the former is in base R, and for many simple problems, writing the function to minimize using a formula is handy, which only nls, but not minpack.lm, allows. I don't think it's the case that LM is hardly competitive in general. On Tue, 20 Nov 2007, Ali - wrote: Hi, It seems to me that the most suitable method in R for curve-fitting is the use of nls, which uses a Gauss-Newton (GN) algorithm, while the use of the Levenberg-Marquardt (LM) algorithm does not seem to be very stressed in R. According to this [1] by Ripley, 'Levenberg-Marquardt is hardly competitive these days' which could imply the low emphasize on LM in R. The position of LM is, to some extend, confusing. Bonnans et al [2] introduce the trust-region-based method of LM like this: 'This chapter is mostly devoted to methods which, although less universal than the preceding, are useful in a good number of cases. The frst one (trust-region) is actually extremely important, and might supersede line-searches, sooner or later.' The above should demonstrate the contradiction. Since some R developers are indeed the pioneers in the optimisation theory, I would like to ask for references involving profiling of various methods, including more modern techniques, with an application in general model-fitting. [1] http://tolstoy.newcastle.edu.au/R/help/00b/2492.html [2] Numerical Optimization, 2nd ed _ 100?s of Music vouchers to be won with MSN Music __ R-help@r-project.org 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@r-project.org 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] Help with talking to R from Java (on Window)
Does anybody know any alternative ways to be able to call R from Java? JRI http://rosuda.org/JRI/ now contained in rJava http://www.rforge.net/rJava/ and new is this one which I think provides something on top of rJava maybe Rserve: http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt best wishes ido __ R-help@r-project.org 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] ASCII character set and hyphen
Am 19.11.2007 um 18:43 schrieb Prof Brian Ripley:
On Mon, 19 Nov 2007, Roland Kaiser wrote:
Hi all!
To add to my previous posting
I want to give some more deatils give a more precise
I want to print a hyphen to a pdf() or postscript() device.
As the documentaion of postscript says
ASCII Character 45(-) is mapped to a minus sign (ASCII Character
95) by default.
The advice given is to use \173 for a hyphen.
But, the following code produces a curly brace
instead of a hyphen.
Thanks for any advice?
Check your reading before posting? The advice actually is
There is an exception. Character 45 ('-') is always set as
minus (its value in Adobe ISOLatin1) even though it is hyphen in
the other encodings. Hyphen is available as character 173 (octal
0255) in all the Latin encodings, Cyrillic and Greek.
Sorry, I missed to honour the octal coding.
So try \255. And please don't post twice.
I tried that, bit it raised an error
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\255, side = 3)
dev.off()
Warning messages:
1: In mtext(\xad, side = 3) : ungültige Eingabe für mbcsToLatin1
Roland
library(rgr)
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\173, side = 3)
dev.off()
R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1
locale:
de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rgr_1.0.3 MASS_7.2-36 akima_0.5-1
__
R-help@r-project.org 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.
--
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@r-project.org 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] biplot
On Mon, 2007-11-19 at 13:51 -0500, Weiwei Shi wrote: Hi, I am wondering how to draw biplot with the same scales on both plots? For example, if the two plots have much different scales, generally the two x-y's are scaled so that the two plots are sitting in the center automatically. How to disable this? Thanks Hi WeiWei To solve your problem you must use the options xlim, ylim in your biplot par(mfrow=c(2,1)) biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...) biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...) -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org 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] ASCII character set and hyphen
On Tue, 20 Nov 2007, Roland Kaiser wrote:
Am 19.11.2007 um 18:43 schrieb Prof Brian Ripley:
On Mon, 19 Nov 2007, Roland Kaiser wrote:
Hi all!
To add to my previous posting
I want to give some more deatils give a more precise
I want to print a hyphen to a pdf() or postscript() device.
As the documentaion of postscript says
ASCII Character 45(-) is mapped to a minus sign (ASCII Character
95) by default.
The advice given is to use \173 for a hyphen.
But, the following code produces a curly brace
instead of a hyphen.
Thanks for any advice?
Check your reading before posting? The advice actually is
There is an exception. Character 45 ('-') is always set as
minus (its value in Adobe ISOLatin1) even though it is hyphen in
the other encodings. Hyphen is available as character 173 (octal
0255) in all the Latin encodings, Cyrillic and Greek.
Sorry, I missed to honour the octal coding.
So try \255. And please don't post twice.
I tried that, bit it raised an error
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\255, side = 3)
dev.off()
Warning messages:
1: In mtext(\xad, side = 3) : ungültige Eingabe für mbcsToLatin1
In UTF-8 you need \uad. Note that it is character 0255 in the 8-bit
encodings mentioned and in UTF-8, *but* \255 is not valid to produce
that character in UTF-8.
Roland
library(rgr)
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\173, side = 3)
dev.off()
R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1
locale:
de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rgr_1.0.3 MASS_7.2-36 akima_0.5-1
__
R-help@r-project.org 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.
--
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@r-project.org 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.
--
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@r-project.org 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] biplot
Also check the asp= parameter in plot.default and plot.window; this sets
the aspect ratio so that 1 unit in x is the same physicla length as 1
unit in y. I don;t know whether it is respeced by your particular
biplot, though.
Bernardo Rangel Tura [EMAIL PROTECTED] 20/11/2007 10:51:12
On Mon, 2007-11-19 at 13:51 -0500, Weiwei Shi wrote:
Hi,
I am wondering how to draw biplot with the same scales on both
plots?
For example, if the two plots have much different scales, generally
the two x-y's are scaled so that the two plots are sitting in the
center automatically. How to disable this?
Thanks
Hi WeiWei
To solve your problem you must use the options xlim, ylim in your
biplot
par(mfrow=c(2,1))
biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...)
biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...)
--
Bernardo Rangel Tura, M.D,MPH,Ph.D
National Institute of Cardiology
Brazil
__
R-help@r-project.org 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.
***
This email and any attachments are confidential. Any use...{{dropped:8}}
__
R-help@r-project.org 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] ASCII character set and hyphen
Am 20.11.2007 um 12:13 schrieb Prof Brian Ripley:
On Tue, 20 Nov 2007, Roland Kaiser wrote:
Am 19.11.2007 um 18:43 schrieb Prof Brian Ripley:
On Mon, 19 Nov 2007, Roland Kaiser wrote:
Hi all!
To add to my previous posting
I want to give some more deatils give a more precise
I want to print a hyphen to a pdf() or postscript() device.
As the documentaion of postscript says
ASCII Character 45(-) is mapped to a minus sign (ASCII Character
95) by default.
The advice given is to use \173 for a hyphen.
But, the following code produces a curly brace
instead of a hyphen.
Thanks for any advice?
Check your reading before posting? The advice actually is
There is an exception. Character 45 ('-') is always set as
minus (its value in Adobe ISOLatin1) even though it is
hyphen in
the other encodings. Hyphen is available as character 173
(octal
0255) in all the Latin encodings, Cyrillic and Greek.
Sorry, I missed to honour the octal coding.
So try \255. And please don't post twice.
I tried that, bit it raised an error
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\255, side = 3)
dev.off()
Warning messages:
1: In mtext(\xad, side = 3) : ungültige Eingabe für mbcsToLatin1
In UTF-8 you need \uad. Note that it is character 0255 in the 8-
bit encodings mentioned and in UTF-8, *but* \255 is not valid to
produce that character in UTF-8.
Great Thanks
for clarifying this point!
Roland
Roland
library(rgr)
pdf(foo.pdf, encoding = ISOLatin1)
display.ascii.d()
mtext(\173, side = 3)
dev.off()
R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1
locale:
de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] rgr_1.0.3 MASS_7.2-36 akima_0.5-1
__
R-help@r-project.org 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.
--
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@r-project.org 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.
--
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@r-project.org 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] significance levels for partial correlations?
I've seen that this question has been asked before, in the archives,
but I haven't been able to find a workable answer. This may be a
failure to understand the statistics!
The problem is that, while I can easily get partial correlation
values out of corpcor, how do I get significance values? Surely the
significance of a partial correlation between two variables isn't the
same as the simple bivariate correlation significance (cor.test)? As
I said, I may be misunderstanding the stats.
And just to round out the scenario, I should mention that I've
written a function that uses the corpcor library to perform partial
correlations on experimental variables while partialing out the
effect of control variables (as opposed to getting the partial
correlation of a single variable controlling for ALL other
variables). This is just a convenience function that allows me to
stick in a whole data frame and analyze only those variables I'm
interested in.
I won't paste in that function here, it's not relevant to the
problem, but if anyone wants a copy just let me know. Here is the
syntax:
pcor.n = function (df, cont, expi=) {
###
## Perform an n-order partial correlation, controlling for the
influence of
## control variables on experimental ones.
##
## df data frame containing all the variables.
## cont a list of control variable names (list of strings)
## expi a list of experimental variable names (list of strings).
## (defaults to all variables excluding controls)
##
## RETURN VALUES
## The function returns a matrix of partial correlation values,
excluding the
## effects of the control variables.
##
###
Thanks for any guidance,
-Ashish Ranpura.
-
Ashish Ranpura
Institute of Cognitive Neuroscience
University College London
17 Queen Square
London WC1N 3AR
tel: +44 (20) 7679 1126
web: http://www.icn.ucl.ac.uk
__
R-help@r-project.org 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] match.call idiom to call other function with same arguments
The R language definition (version 2.5.1, 2007-06-27, p37) outlines an
idiom (here perhaps abusively abbreviated)
m - match.call()
m[[1]] - as.name('plot')
eval(m, parent.frame() )
A posting (Subject: Re: [Rd] problems with plot.formula, Date: Wed 26
May 2004 - 05:44:34 EST, From: Prof Brian Ripley ([EMAIL PROTECTED]))
related to plot.formula reads
not a standard idiom for a generic with a formula method
Could someone kindly direct my attention to a tutorial/howto/intro or
other written material that provides insight on how this idiom (and
preferably other R-idioms) should be used and not used?
If the answer is that there is no such other material, so the solution is
go read the language definition again, go think again and go (hopefully)
figure that would be appreciated too.
Thanks, MJ
__
R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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] How to improve a function converting year, day of year, decimal hour into date ?
Hi,
I would like to build a date from a year, a day of the year and a decimal
hour.
Ex : reconst_date(2007,324,12.50) gives 2007-11-20 12:30:0
The following function is doing this job but I would like to know if there
is a function which directly converts the decimal hours into
hours:minutes:secondes ?
Thanks for your help,
Have a nice day,
Ptit Bleu.
reconst_date-function(annee, jour, heured) {
str_anneejour-paste(annee,jour,sep= )
str_anneemoisjour-strptime(str_anneejour, %Y %j)
heure-trunc(heured)
minute-trunc((heured-heure)*60)
seconde-((heured-heure)*60-minute)*60
seq_dateR-paste(str_anneemoisjour,
,heure,:,minute,:,round(seconde),sep=)
return(seq_dateR)
}
--
View this message in context:
http://www.nabble.com/How-to-improve-a-function-converting-year%2Cday-of-year%2Cdecimal-hour-into-date---tf4843032.html#a13855563
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
If you write an update.X method where X is the class of your graph objects then it will work on your graph objects and yet still work on lm, glm, etc. On Nov 20, 2007 7:01 AM, Søren Højsgaard [EMAIL PROTECTED] wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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] How to improve a function converting year, day of year, decimal hour into date ?
library(chron)
chron(paste(1/1/, year, sep = )) + julday + hour/24
That produces a chron, i.e. dates/times class datetime. If you want
it as a string use format(...above expression...)See the help desk
article in R News 4/1.
On Nov 20, 2007 6:53 AM, Ptit_Bleu [EMAIL PROTECTED] wrote:
Hi,
I would like to build a date from a year, a day of the year and a decimal
hour.
Ex : reconst_date(2007,324,12.50) gives 2007-11-20 12:30:0
The following function is doing this job but I would like to know if there
is a function which directly converts the decimal hours into
hours:minutes:secondes ?
Thanks for your help,
Have a nice day,
Ptit Bleu.
reconst_date-function(annee, jour, heured) {
str_anneejour-paste(annee,jour,sep= )
str_anneemoisjour-strptime(str_anneejour, %Y %j)
heure-trunc(heured)
minute-trunc((heured-heure)*60)
seconde-((heured-heure)*60-minute)*60
seq_dateR-paste(str_anneemoisjour,
,heure,:,minute,:,round(seconde),sep=)
return(seq_dateR)
}
--
View this message in context:
http://www.nabble.com/How-to-improve-a-function-converting-year%2Cday-of-year%2Cdecimal-hour-into-date---tf4843032.html#a13855563
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org 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@r-project.org 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] Problem with code for bootstrapping chi square test with count data
Hi, I'd like some advice on bootstrapping in R. I have a species x with 20 individuals and a factor containing 0 and 1's (in this case 5 zeros and 15 ones). I want to compare the frequency of the occurrence of 1 with a probability value. This code seems to work to do this in R. attach(test) p - c(0.5272, (1-0.5272)) sp1_1 - length(subset(x, x==1)) sp1_0 - length(subset(x, x==0)) obs1_1 - c(sp1_1, sp1_0) chisq.test(obs1_1, p=p) However, I'd like to bootstrap these 20 individuals to produce a whole population of samples and I'd like to do a chi-square test for each of the bootstrap sample to create a distribution of the chi-square statistic. I have bootstrapped the 0's and 1's of x 20 times using the following code: resamples - lapply(1:20, function(i) sample(x, replace=T)) What I can't get to work is how to calculate the observed values for 1's and 0's in each of the bootstrap samples, which I need to do a chi-square test for each sample. The methd I used above doesn't seem to work the results for resamples. Does anyone have an idea on how to get this to work? Or is there another easier way to do this? I hope it is clear what I am trying to do! I have tried looking on the internet and in the R archives, but I can't find what I am looking for. Thanks very much in advance for your help! Geertje Geertje van der Heijden PhD student Tropical Ecology School of Geography University of Leeds Leeds LS2 9JT Tel: (+44)(0)113 3433345 Email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
Gabor Grothendieck wrote: If you write an update.X method where X is the class of your graph objects then it will work on your graph objects and yet still work on lm, glm, etc. One example (for non-model objects) is e.g. the update method for survey design objects (update.survey.design) in the survey package by Thomas Lumley. HTH, Tobias On Nov 20, 2007 7:01 AM, Søren Højsgaard [EMAIL PROTECTED] wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren -- Tobias Verbeke - Consultant Business Decision Benelux Rue de la révolution 8 1000 Brussels - BELGIUM +32 499 36 33 15 [EMAIL PROTECTED] __ R-help@r-project.org 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] How to improve a function converting year, day of year, decimal hour into date ?
Thank you Gabor for your fast answer (received as I was reading R News 4/1) Ptit Bleu. library(chron) chron(paste(1/1/, year, sep = )) + julday + hour/24 That produces a chron, i.e. dates/times class datetime. If you want it as a string use format(...above expression...)See the help desk article in R News 4/1. -- View this message in context: http://www.nabble.com/How-to-improve-a-function-converting-year%2Cday-of-year%2Cdecimal-hour-into-date---tf4843032.html#a13856584 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- 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@r-project.org 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] How to map clusters to a correlation matrix
Dear All, I have several socio-economic and geographic variables for the 27 EU countries. I would to use these data to derive a correlation matrix between groups of countries (for a different application). I thought of using kmeans to cluster the groups, and then calibrate between group correlations using distances between the centroids, and within group correlations using distances in a cluster to the own centroid. To calibrate is to transform a distance to a (positive) correlation coefficient using some suitable function. Positive correlations reflect the strength of common tendencies among the countries. All the above seems crude to me, especially as you have to choice a transformation function for a distance to a correlation coefficient. Are there any better methods to do this? Thanks is advance, Serguei [[alternative HTML version deleted]] __ R-help@r-project.org 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] plotting confidence intervals of regression line
Hello, I am trying to generate a confidence interval (90 or 95%) of a regression line. This is primarily just for illustration on a scatter plot (i.e. I am trying to make this http://www.ast.cam.ac.uk/~rgm/scratch/statsbook/graphics/anima4.gif). I have been trying to use the predict.lm function, with interval set as confidence, but this still seems to be giving me a prediction interval (as below). It is giving the interval based on the x value of a given point, as opposed to the confidence interval of the regression line in general. Is predict.lm the correct function to be using, or is there something else more appropriate? predict.lm(test, interval = c(confidence), level = 0.90) fitlwr upr 1 4.170807 -0.2171226 8.558738 2 5.807453 2.1283100 9.486597 3 6.625776 3.2397994 10.011753 4 8.262422 5.2795295 11.245315 5 9.080745 6.1821741 11.979317 6 9.899068 6.9954692 12.802667 7 7.444099 4.2947040 10.593495 8 13.172360 9.4577068 16.887014 9 20.537267 13.0143098 28.060224 I have also tried using package 'ggplot' as follows: install.packages(ggplot) library(ggplot) qplot(wt, mpg, data=mtcars, type=c(point,smooth), method=lm) (following Hadley Wickham on this help list) This generates a plot that looks roughly like what I want, but there is some customizing of the plot that I would prefer to do in the standard 'plot' function of the 'graphics' package. Also, ggplot does not give me a vector of the values of the CI themselves, which would be useful to have. Any help would be very appreciated. Thanks, Tim [[alternative HTML version deleted]] __ R-help@r-project.org 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] p.adjust on matrix of P-values from correlations
Hi All, I'm stumped on something that must be trivial. I created a correlation matrix on 4 variables (6 correlations) using Hmisc's rcorr function. I wanted to correct the P-value matrix for the number of tests done, so I ran it through the p.adjust function. That function adjusted for the 12 p-values it saw, rather than 6. I added the argument n=6 to p.adjust but it requires that n be greater than the length of x. I guess its author assumed you would always be correcting for more tests than it could see. I changed the matrix into a long vector to see if that would matter. The help file says it requires vector, but the result was the same. If I were using the conservative Bonferroni correction, I could divide the corrected P-values by 2 to make n=6 after the fact. However, I'm using Holm's sequential method, so that's no good. Any ideas? Thanks, Bob P.S. I'm using R 2.6.0 Patched on Windows XP. = Bob Muenchen (pronounced Min'-chen), Manager, Statistical Consulting Center U of TN Office of Information Technology Stokely Management Center, Suite 200 916 Volunteer Blvd., Knoxville, TN 37996-0520 Voice: (865) 974-5230 FAX: (865) 974-4810 Email: [EMAIL PROTECTED] Web: http://oit.utk.edu/scc Map: http://www.utk.edu/maps News: http://listserv.utk.edu/archives/statnews.html = __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
On Tue, 20 Nov 2007, Prof Brian Ripley wrote: update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. Maybe. update is generic with a netral set of argument names; on the other hand, the _documentation_ of update is not generic -- it is specific to updating models. So there is opportunity for confusion from that direction. Best, luke On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu__ R-help@r-project.org 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] How to map clusters to a correlation matrix
To Walter, I am building a model of voting in the EU Council of Ministers. A voting scenario assumes the probabilities of yes votes, possible different for each country, and correlation coefficient between them. The country variables (data) reflect the background characteristics that are relevant for the likelihood of bloc formation in the Council. I would like to cluster the countries in what I call probabilistic voting blocs, and construct a correlation matrix between votes in different blocs and between votes in each bloc. I then use the probabilities and correlation coefficients to construct a joint probability distribution on the set of all conceivable voting outcomes and thus compute the probabilities of voting outcomes that are of interest, such as probability of a country casting a decisive vote, etc. Serguei Austrian Institute of Economic Research (WIFO) P.O.Box 91 Tel.: +43-1-7982601-231 1103 Vienna, AustriaFax: +43-1-7989386 Mail: [EMAIL PROTECTED] http://www.wifo.ac.at/Serguei.Kaniovski [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] adding an image to a plot
Hi, I'm writing code to generate a plot, in which I draw a series of rectangles. So my code is of the form plot.new() plot.window( ... ) draw rectangle draw rectangle ... Is there a way for me to insert a PNG or PDF graphic at a specific position in the plot (ideally in plot coordinates)? I realize that this might probably be better done in a separate image editor, but if it could be done programmatically that would be very handy Thanks, --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- So the Zen master asked the hot-dog vendor, Can you make me one with everything? - TauZero on Slashdot __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding an image to a plot
Check out this thread: http://tolstoy.newcastle.edu.au/R/e2/help/07/04/14273.html On Nov 20, 2007 9:26 AM, Rajarshi Guha [EMAIL PROTECTED] wrote: Hi, I'm writing code to generate a plot, in which I draw a series of rectangles. So my code is of the form plot.new() plot.window( ... ) draw rectangle draw rectangle ... Is there a way for me to insert a PNG or PDF graphic at a specific position in the plot (ideally in plot coordinates)? I realize that this might probably be better done in a separate image editor, but if it could be done programmatically that would be very handy Thanks, --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- So the Zen master asked the hot-dog vendor, Can you make me one with everything? - TauZero on Slashdot __ R-help@r-project.org 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@r-project.org 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] plotting coxph results using survfit() function
stephen,
Thanks for your help. I want to draw a plot which shows separate
survival curves for each category of X on the same plot(same set of
axes). Your code produces a separate curve for each combination of X
and Y but I don't want curves for combinations of X and Y since Y has
many levels and also the values of Y don't have any significance in my
case. Is there a way of doing what i want to do i.e. getting separate
survival curves for each level of X using the function survfit() on an
object mod.phm which is a coxph object such that:
mod.phm-coxph(formula=Surv(time,Flag_Death)~X+Y, data= datFrame)
Help
On Nov 14, 2007 9:08 AM, Stephen Weigand [EMAIL PROTECTED] wrote:
On Nov 13, 2007 5:53 AM, Shoaaib Mehmood [EMAIL PROTECTED] wrote:
i want to make survival plots for a coxph object using survfit
function. mod.phm is an object of coxph class which calculated results
using columns X and Y from the DataFrame. Both X and Y are
categorical. I want survival plots which shows a single line for each
of the categories of X i.e. '4' and 'C'. I am getting the following
error:
attach(DataFrame)
DataFrame.X-data.frame(X=c('4','C'),Y=rep(mean(Y),2))
detach()
As you have it, Y in DataFrame.X will be created as numeric
which isn't what you probably want (since you say Y is
categorical).
Also, you will run into problems if you create newdata and it
doesn't have all the levels of all the factors in your model. You
can do this:
newdat - expand.grid(X = c(4, C, plus all other levels),
Y = c(2, plus all other levels))
plot(survfit(cox.mod, newdata = subset(newdat, Y == 2)))
plot(survfit(mod.phm, newdata=DataFrame.X), lty=c(1,2),ylim=c(.6,1))
Error in `contrasts-`(`*tmp*`, value = contr.treatment) :
contrasts can be applied only to factors with 2 or more levels
any help will be appreciated.
--
Regards,
Rana Shoaaib Mehmood
__
R-help@r-project.org 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] reading graph metadata text from a file
I've tried tetxplot() but it fills the whole frame. I could either
use mfrow but it would devote unnecessarily large space to the text.
In fact I want it in a corner of my current plot, not occupied by the
curves. Here's what I ended up with -- it works, but I have to
manually move top text down as it's cut off by the upper boundary of
the graph. Any better/shorter/nicer ways?
First I fetch the dimensions of the current plot:
max.xy - function() {
p - par()
x.max - p$usr[2]
y.max - p$usr[4]
xy.coords(x=x.max, y=y.max)
}
Then, after plotting, I say
plot(...)
xy.max - max.xy()
# top-right -- need to move a bit down or letters are cut off on top:
text(xy.max$x,xy.max$y*0.99,story$text,adj=c(1,1),col=blue)
# bottom-right -- no cut-off, a small nice gap comes free:
# story.text is story$text with some more appended details
text(xy.max$x, 0, story.text,adj=c(1,0),col=blue)
As for the original question -- I ended up creating, in each data
directory, a file story.r, looking like this:
-
# R titles, labels, and story text for the plot
# when I assigned color=blue right in data.frame, it became an
integer level!
story - data.frame(title=,x=,y=,text=,color=)
story$title - graph title
story$x - x units
story$y - y units
story$text - story text -- this data has come long way. Once upon
a time there was R...
# we can separate colors of title, labels, and text like
# title.color, x.color, y.color, text.color
story$color - dark blue
-
First I create a data.frame and then assign to its components one by
one for readability. When I tried to assign color right in data.frame
(..., color=blue), it became integer levels! So I had to move it
out along with others. What's the logic here?
Cheers,
Alexy
On Nov 20, 2007, at 1:39 AM, Bert Gunter wrote:
... But is I understand correctly,this is certainly straightforward
without
textplot,too...
e.g.
mylegend - Some text...\n Some more text
mytitle - This is a title
plot(0:1,0:1, main = mytitle)
legend(.2,.2,leg=mylegend, bty=n)
Naturally, this could all be functionized and the various text
arguments
passed as arguments to the function (see ?plot.default or its
code); or they
could be components of a list, or ...
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On
Behalf Of Greg Snow
Sent: Monday, November 19, 2007 2:18 PM
To: Alexy Khrabrov; r-help@r-project.org
Subject: Re: [R] reading graph metadata text from a file
You may want to use the textplot function from the gplots package
rather
than the legend.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Alexy Khrabrov
Sent: Monday, November 19, 2007 1:17 PM
To: r-help@r-project.org
Subject: [R] reading graph metadata text from a file
I'd like to produce graphs with titles, axis labels, and
legend as parameters read from a separate text file.
Moreover, I'd like to use the legend for a short summary of
the data -- not necessarily for describing the line colors
per se. How do we do this?
Cheers,
Alexy
__
R-help@r-project.org 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@r-project.org 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@r-project.org 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] Friendly way to link R - MySQL and non-(R and Mysql) users ?
Thanks to your help, I managed to link R and a Mysql Database, send queries, plot the results and put everything in a pdf document (with Sweave). My co-workers find the job not bad but they would like to have a friendly interface to send queries and see the graphs (the pdf document is not necessary). Something like this coul be a good starting point : --- | Name of the X columns : ___ | | Name of the Y colums : ___ | | Send query Y/N : ___ | --- I read some posts about this topic but all need a server (if I read well). I'd just want to use it on a local machine. Is there a way to realize such an interface and to link it directly to an R-script (which will send the query to MySQL and will plot the result of the query) ? Thanks for your help, Ptit Bleu. -- View this message in context: http://www.nabble.com/Friendly-way-to--link-R---MySQL-and-non-%28R-and-Mysql%29-users---tf4844081.html#a13858847 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] biplot
On Tue, 20 Nov 2007, S Ellison wrote: Also check the asp= parameter in plot.default and plot.window; this sets the aspect ratio so that 1 unit in x is the same physicla length as 1 unit in y. I don;t know whether it is respeced by your particular biplot, though. That's not how biplot.default() does it: rather it always plots a square plot within the device window with axes it manages itself and which do ensure that the scales are the same in both directions. I don't understand the request: the two quantities plotted on a conventional biplot are dimensionally different, so why would one want them to have the same scale? Bernardo Rangel Tura [EMAIL PROTECTED] 20/11/2007 10:51:12 On Mon, 2007-11-19 at 13:51 -0500, Weiwei Shi wrote: Hi, I am wondering how to draw biplot with the same scales on both plots? For example, if the two plots have much different scales, generally the two x-y's are scaled so that the two plots are sitting in the center automatically. How to disable this? Thanks Hi WeiWei To solve your problem you must use the options xlim, ylim in your biplot par(mfrow=c(2,1)) biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...) biplot(...,xlim=c(minimun,maximun),ylim=c(minimun,maximun),...) Hmm: that is two biplots, each two superimposed plots. -- 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@r-project.org 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] Move R to a clean Linux install from an old install
Hi everybody! I just joined, I started using R a few weeks ago and it seems to be a really versatile system. Last weekend I half-accidentally installed all R packages to my computer. Independent of this (at least I hope), I managed to break my Kubuntu's KDE and so far haven't been able to repair it even with the Kubuntu Forums' help (I can start KDE as root but apparently this has broken my install even further :( However, I found several links that may allow me to save my GBs of downloaded Linux programs so that at least I would't have to download everything again (which is nice, since I don't have internet at home, only at work) when I do a clean reinstall of my Kubuntu, like http://aptoncd.sourceforge.net/. So this solves the problem of software repositories. But what about R? What is the best way to transfer my R packages (I guess the R itself goes with the Ubuntu downloaded files and I thought R's packages are separate, if I'm wrong the problem does not even exist!) to the new install? Although the installation of the packages actually took longer than downloading them, I still prefer not to download them again, if that's possible (due to the lack of internet at home). I apologize if this subject has been dealt with, I tried to search internet and the mail list archives, but the closest thing I found dealt with new R version install (although the solution to my problem must be similar). BR, Pekka Horttanainen __ R-help@r-project.org 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] as.character(seq(-.35,.95,.1))
see FAQ 7.31 On Nov 20, 2007 10:50 AM, Ken Fullish [EMAIL PROTECTED] wrote: as.character(seq(-.25,.95,.1)) [1] -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95 as.character(seq(-.35,.95,.1)) [1] -0.35 -0.25 -0.15 -0.0499 0.05 [6] 0.150.25 0.350.450.55 [11] 0.650.75 0.850.95 Not a big deal, just curiosity: Why do I obtain this ugly -0.0499 instead of the expected -0.05 ? Regards K. __ R-help@r-project.org 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org 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] as.character(seq(-.35,.95,.1))
On 11/20/2007 10:50 AM, Ken Fullish wrote: as.character(seq(-.25,.95,.1)) [1] -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95 as.character(seq(-.35,.95,.1)) [1] -0.35 -0.25 -0.15 -0.0499 0.05 [6] 0.150.25 0.350.450.55 [11] 0.650.75 0.850.95 Not a big deal, just curiosity: Why do I obtain this ugly -0.0499 instead of the expected -0.05 ? Because as.character() tries to do an accurate conversion, and the number in your vector is closer to -0.0499 than to -0.05. You could get the -0.05 by something like round( seq(...), 2). The reason seq() doesn't give you exactly -0.05 is that the starting values and step size you've chosen are not exactly representable in R's floating point format. It can only store fractions exactly when the denominator is a power of 2. Duncan Murdoch __ R-help@r-project.org 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] xy.coords and log10
On 11/20/2007 10:41 AM, Alexy Khrabrov wrote: Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? xy.coords doesn't do any transformation other than setting non-positive values to NA. So your question doesn't make sense; could you elaborate on what you're seeing that you don't want to see? Duncan Murdoch __ R-help@r-project.org 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] as.character(seq(-.35,.95,.1))
as.character(seq(-.25,.95,.1)) [1] -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95 as.character(seq(-.35,.95,.1)) [1] -0.35 -0.25 -0.15 -0.0499 0.05 [6] 0.150.25 0.350.450.55 [11] 0.650.75 0.850.95 Not a big deal, just curiosity: Why do I obtain this ugly -0.0499 instead of the expected -0.05 ? Regards K. __ R-help@r-project.org 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] xy.coords and log10
Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? Cheers, Alexy __ R-help@r-project.org 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] intercept in multiple regression
Hi all! Is it possible to model a multiple regression in which the response becomes zero when one of the two covariates is zero? lm(y~ x1+x2) and y=0 if x1=0. However, when x1=0, y=x2+1(intercept). Does this mean I cannot have a second covariate and intercept or should I eliminate only the intercept? thank you! __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
Thanks, Luke Tierney - the documentation of update was exactly what prompted my question. Yet, I conclude that writing an update.myobject method is OK. Regards Søren Fra: Luke Tierney [mailto:[EMAIL PROTECTED] Sendt: ti 20-11-2007 14:54 Til: Prof Brian Ripley Cc: Søren Højsgaard; [EMAIL PROTECTED] Emne: Re: [R] Use and misuse of update function for non-models. Any views/recommendations?? On Tue, 20 Nov 2007, Prof Brian Ripley wrote: update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. Maybe. update is generic with a netral set of argument names; on the other hand, the _documentation_ of update is not generic -- it is specific to updating models. So there is opportunity for confusion from that direction. Best, luke On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu http://www.stat.uiowa.edu/ __ R-help@r-project.org 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] Friendly way to link R - MySQL and non-(R and Mysql) users ?
Simplest would be to use the select.list() R command: xnames - select.list(colnames(iris)) For a prettier and more functional approach the gWidgets package provides a layer over a number of lower level packages for creating GUI front ends in R. http://wiener.math.csi.cuny.edu/pmg/gWidgets Other R GUI projects are listed here: http://www.sciviews.org/_rgui/ On Nov 20, 2007 10:12 AM, Ptit_Bleu [EMAIL PROTECTED] wrote: Thanks to your help, I managed to link R and a Mysql Database, send queries, plot the results and put everything in a pdf document (with Sweave). My co-workers find the job not bad but they would like to have a friendly interface to send queries and see the graphs (the pdf document is not necessary). Something like this coul be a good starting point : --- | Name of the X columns : ___ | | Name of the Y colums : ___ | | Send query Y/N : ___ | --- I read some posts about this topic but all need a server (if I read well). I'd just want to use it on a local machine. Is there a way to realize such an interface and to link it directly to an R-script (which will send the query to MySQL and will plot the result of the query) ? Thanks for your help, Ptit Bleu. -- View this message in context: http://www.nabble.com/Friendly-way-to--link-R---MySQL-and-non-%28R-and-Mysql%29-users---tf4844081.html#a13858847 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] Trying to get around R
Good morning and thank you
One correction please
I was not the poster
I am [EMAIL PROTECTED]
Poster was Epselon [EMAIL PROTECTED]
What you say is most certainly true. But then the newbie corrections might
have the style displayed by Mr. Bolker to both educate and further promote
participation.
Loren Engrav
Univ Wash
Seattle
From: ecatchpole [EMAIL PROTECTED]
Date: Tue, 20 Nov 2007 17:07:23 +1100
To: Loren Engrav [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] Trying to get around R
Loren,
There's a good reason for replying to the list, rather than just to you
personally: to let other readers of the list see the response, so that
they don't duplicate it. Your original posting certainly looked like
homework questions to me. This impression was reinforced by the fact
that the posting was anonymous: this is surely a breach of general
netiquette, rather than an R newbie error?
Students do attempt to get people on this list to do their homework for
them. It is important, for the integrity of their degrees, that we
minimise the occurrence of this. Regular contributors to this list (and
I am not one) perform a huge public service. we should all be grateful
for this.
Ted Catchpole.
Visiting Fellow
Univ of New South Wales at ADFA, Canberra, Australia
_ and University of Kent, Canterbury, England
'v' - www.pems.adfa.edu.au/~ecatchpole
/ \ - fax: +61 2 6268 8786
m m- ph: +61 2 6268 8895
Loren Engrav wrote on 11/20/2007 04:43 PM:
I am a newbie to R and Bio emails and
It is clear that newbies make mistakes, I made several which were pointed
out and I am trying to fix them, and as I fix one I make another, in time
perhaps I will know it all, but if it is like surgery, I will make
mistakes until I retire
But the response of the old-timers to these mistakes seems arrogant and
cruel and off putting and does NOT encourage more participation. In fact
it takes real stuff to continue after this putdown and that putdown.
There are 3,783 links to posting guidelines, which took 1.5 hours to find
and read and understand.
Why not a link on how the mistakes of the newbies will be dealt with?
Or a kindly response from the moderator personal to the newbie rather than
to the entire world?
Or a kindly general response as from Ben Bolker to my last infraction which
was You might have better luck with this on the Bioconductor mailing list
...
Rather than to the universe...
Using the wrong list: this is for R-sig-mac, and the topic occcurred
there recently.
All in an effort to encourage promote useful and increasing exchange
participation
Or not
Loren Engrav, MD
Univ Washington
From: Julian Burgos [EMAIL PROTECTED]
Date: Mon, 19 Nov 2007 10:44:49 -0800
To: Epselon [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] Trying to get around R
Hello Epselon (if that is your name),
This sounds like homework questions.
From the R-help posting guide:
Basic statistics and classroom homework:
R-help is not intended for
these.
If you have a specific question on R
coding, do ask it (and provide
reproducible code). But you should not expect
for people on the list to
do your homework for you. That is a big
no-no.
Cheers,
Julian
Epselon wrote:
I have three problems I am trying to
simulate, that I am having difficulty
getting around with.
Problem 1.
I want to determine the 85 percentile (the x value for which the sum of
probabilities becomes 0.85) of the following distributions (two binomials
and a Poisson with rate Lmbda= np of the two binomials): X ~B(10, 0.3),
Y~P(3) ,
Z~B(30, 0.1). I want to show that that Y is a good approximation
for Z but
not for X...(by examining these distributions for few
different
percentiles)
Problem 2:
For a binomial distribution X ~ B(20, 0.4), I
want to use R to calculate
P{|X - μ| 2} and verify that it is near or
larger than 0.95. (Hint from
the text book: Since μ = 8 and 2.3 then
you
may want to read the
weights, or probabilities, of the values 6:10, into a
vector v and then use
the command sum(v) to
calculate the sum.) Repeat
this for another set of parameters of your
choice.
Problem 3:
Draw a
sample of size 10, from a Poisson with Lambda= 5, and calculate the
mean
and
the standard deviation of this sample, Repeat this calculation with
size 20
and 30 and demonstrate
that ¯X gets closer to μ as the sample size
increases.
Thanks.
I would appreciate it if someone accompanied the
codes with a brief
explanation so I can be able to replicate it
myself.
Re: [R] Canonical Correlation Analysis
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Animesh Acharjee Sent: Tuesday, November 20, 2007 7:47 AM To: [EMAIL PROTECTED] Subject: [R] Canonical Correlation Analysis Dear Sir/Madam, This is Animesh working on Canonical Correlation Analysis ( CCA ) and I am using CCA package in R. I have a doubt and it may be very basic question. Hope someone will get back to me with answer. I am trying to follow the documentation of CCA but could not make out some of the stuffs. 1) I simulated some of the data sets and got the result. I want to ask you why there are two circles in the plots? and what does it mean? And also how it decidces the center of the Circle. 2) X and Y axis values in between 1 and -1 . Is it due to max and min values of correlation . 3) what is the dimensions means in X and Y axis? It will be very useful if someone help me out with probable solution. Thanks for your time Animesh Animesh, In order to get useful help, you should post the code you used to simulate your data, run the CCA, and create the plot, so we can see what you are seeing (as the posting guide suggests). Dan Daniel J. Nordlund Research and Data Analysis Washington State Department of Social and Health Services Olympia, WA 98504-5204 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding an image to a plot
Selon Rajarshi Guha [EMAIL PROTECTED]: Hi, I'm writing code to generate a plot, in which I draw a series of rectangles. So my code is of the form plot.new() plot.window( ... ) draw rectangle draw rectangle ... Is there a way for me to insert a PNG or PDF graphic at a specific position in the plot (ideally in plot coordinates)? I realize that this might probably be better done in a separate image editor, but if it could be done programmatically that would be very handy Thanks, Hi, you can insert pixmaps at specified coordinates using s.logo in the ade4 package. Regards, Thibaut. __ R-help@r-project.org 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] Canonical Correlation Analysis
Dear Sir/Madam, This is Animesh working on Canonical Correlation Analysis ( CCA ) and I am using CCA package in R. I have a doubt and it may be very basic question. Hope someone will get back to me with answer. I am trying to follow the documentation of CCA but could not make out some of the stuffs. 1) I simulated some of the data sets and got the result. I want to ask you why there are two circles in the plots? and what does it mean? And also how it decidces the center of the Circle. 2) X and Y axis values in between 1 and -1 . Is it due to max and min values of correlation . 3) what is the dimensions means in X and Y axis? It will be very useful if someone help me out with probable solution. Thanks for your time Animesh [[alternative HTML version deleted]] __ R-help@r-project.org 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] print character
R-help, Sorry if this question has been discussed/posted before but I can't just find it myself. How can I print the comment character () ? Thanks in advance __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
update already has formula and packageStatus methods so its being extended beyond models already even within core packages. On Nov 20, 2007 8:54 AM, Luke Tierney [EMAIL PROTECTED] wrote: On Tue, 20 Nov 2007, Prof Brian Ripley wrote: update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. Maybe. update is generic with a netral set of argument names; on the other hand, the _documentation_ of update is not generic -- it is specific to updating models. So there is opportunity for confusion from that direction. Best, luke On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-help@r-project.org 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@r-project.org 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] xy.coords and log10
xy.coords can have a log=xy parameter which then plot interprets to use log scale. I wonder whether plot can be instructed in a similar way to use log10 scale instead of natural logs. Cheers, Alexy On Nov 20, 2007, at 7:01 PM, Duncan Murdoch wrote: On 11/20/2007 10:41 AM, Alexy Khrabrov wrote: Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? xy.coords doesn't do any transformation other than setting non- positive values to NA. So your question doesn't make sense; could you elaborate on what you're seeing that you don't want to see? __ R-help@r-project.org 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] print character
LRC == Luis Ridao Cruz [EMAIL PROTECTED]
on Tue, 20 Nov 2007 15:57:07 + writes:
LRC R-help,
LRC Sorry if this question has been discussed/posted before
LRC but I can't just find it myself.
LRC How can I print the comment character () ?
Note that ' ' is *not* the comment character (but '#' is)
What does 'print' mean ? Maybe
cat('My name is Luis, what\'s your name? \n')
My name is Luis, what's your name?
or equivalently
cat(My name is \Luis\, what's your name? \n)
My name is Luis, what's your name?
Pay close attention to both single and double quotes
used above and to the use of '\' as escape character.
Note that 'character' (a vector of strings) is the basic type
R uses here. Also see
?character
?Quotes
and the 'see also's inside them.
Martin Maechler, ETH Zurich
__
R-help@r-project.org 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] as.character(seq(-.35,.95,.1))
On Tue, 2007-11-20 at 11:07 -0500, Duncan Murdoch wrote: On 11/20/2007 10:50 AM, Ken Fullish wrote: as.character(seq(-.25,.95,.1)) [1] -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 0.45 0.55 0.65 0.75 0.85 0.95 as.character(seq(-.35,.95,.1)) [1] -0.35 -0.25 -0.15 -0.0499 0.05 [6] 0.150.25 0.350.450.55 [11] 0.650.75 0.850.95 Not a big deal, just curiosity: Why do I obtain this ugly -0.0499 instead of the expected -0.05 ? Because as.character() tries to do an accurate conversion, and the number in your vector is closer to -0.0499 than to -0.05. You could get the -0.05 by something like round( seq(...), 2). The reason seq() doesn't give you exactly -0.05 is that the starting values and step size you've chosen are not exactly representable in R's floating point format. It can only store fractions exactly when the denominator is a power of 2. In addition, if you want to take numeric values and format them for output with a known number of fixed decimal places, use either ?formatC or ?sprintf, the latter being generally preferred: sprintf(%.2f, seq(-.25,.95,.1)) [1] -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 0.45 [9] 0.55 0.65 0.75 0.85 0.95 sprintf(%.2f, seq(-.35,.95,.1)) [1] -0.35 -0.25 -0.15 -0.05 0.05 0.15 0.25 0.35 [9] 0.45 0.55 0.65 0.75 0.85 0.95 HTH, Marc Schwartz __ R-help@r-project.org 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] Problems with fonts on linux using GDD
Hi
Apologies for this question.
I have read the help for GDD and font mapping, and it tells me that the
config file, /usr/lib/R/library/GDD/fonts/basefont.mapping is
responsible for mapping fonts to the GDD library.
However:
.GDD.font()
[1] /usr/X11R6/lib/X11/fonts/Type1/l048013t.afm
[2] /usr/X11R6/lib/X11/fonts/Type1/l048016t.afm
[3] /usr/X11R6/lib/X11/fonts/Type1/l048033t.afm
[4] /usr/X11R6/lib/X11/fonts/Type1/l048036t.afm
[5] NA
Those fonts aren't even mentioned in the basefont.mapping file, so how
exactly does the basefont.mapping file intervene?
I have this in basefont.mapping:
base.norm:/usr/share/fonts/default/TrueType/FreeSans.ttf
base.ital:/usr/share/fonts/default/TrueType/FreeSerifItalic.ttf
base.bold:/usr/share/fonts/default/TrueType/FreeSansBold.ttf
base.bita:/usr/share/fonts/default/TrueType/FreeSerifBoldItalic.ttf
I have the well rehearsed problem that my GDD plots do not display any
fonts.
My questions:
1) why are the defaults fonts, eg
/usr/X11R6/lib/X11/fonts/Type1/l048013t.afm, not in my basefont.mapping
file?
2) why do I not get a font displayed, despite the default font files
being present?
3) why when I edit basefont.mapping to point to some TrueType files does
this not affect anything?
4) how do I get my GDD images to display fonts?
Many thanks in advance for your help
Mick
The information contained in this message may be confide...{{dropped:14}}
__
R-help@r-project.org 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] barplot problem
Hello, I'm trying to find out how I can move the y axis label of a horizontal barplot further away from the axis, in order to avoid overlap between the names (which I have rotated using las=1) and the label. I have been fiddling with the graphical parameters but nothing seems to work. Maybe a graphical representation of the graphical parameters would be helpful (cf the CSS box model). Thanks! Pieter -- This message was sent on behalf of [EMAIL PROTECTED] at openSubscriber.com http://www.opensubscriber.com/messages/[EMAIL PROTECTED]/topic.html __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
On Tue, 2007-11-20 at 16:32 +0100, Søren Højsgaard wrote: Thanks, Luke Tierney - the documentation of update was exactly what prompted my question. Yet, I conclude that writing an update.myobject method is OK. I think Luke's point was that whilst it would be OK if you wrote your own method in as much as you wouldn't be breaking anything, you may confuse people by having a method do one thing for one class of object and something totally different for another class of object - this is what I believe you are planning. Some may view this as not being OK. Perhaps it would be better to choose a slightly different name, say Update(), but that might be just as confusing! Or perhaps choose another word that has the same meaning as update and one such candidate would be amend(). Just a thought, G Regards Søren Fra: Luke Tierney [mailto:[EMAIL PROTECTED] Sendt: ti 20-11-2007 14:54 Til: Prof Brian Ripley Cc: Søren Højsgaard; [EMAIL PROTECTED] Emne: Re: [R] Use and misuse of update function for non-models. Any views/recommendations?? On Tue, 20 Nov 2007, Prof Brian Ripley wrote: update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. Maybe. update is generic with a netral set of argument names; on the other hand, the _documentation_ of update is not generic -- it is specific to updating models. So there is opportunity for confusion from that direction. Best, luke On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu http://www.stat.uiowa.edu/ __ R-help@r-project.org 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org 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] xy.coords and log10
Have a look at scale_x_log10() and scale_y_log10() from the ggplot2 package. The helpfile with some examples is at http://had.co.nz/ggplot2/scale_continuous.html HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Alexy Khrabrov Verzonden: dinsdag 20 november 2007 17:23 Aan: Duncan Murdoch CC: r-help@r-project.org Onderwerp: Re: [R] xy.coords and log10 xy.coords can have a log=xy parameter which then plot interprets to use log scale. I wonder whether plot can be instructed in a similar way to use log10 scale instead of natural logs. Cheers, Alexy On Nov 20, 2007, at 7:01 PM, Duncan Murdoch wrote: On 11/20/2007 10:41 AM, Alexy Khrabrov wrote: Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? xy.coords doesn't do any transformation other than setting non- positive values to NA. So your question doesn't make sense; could you elaborate on what you're seeing that you don't want to see? __ R-help@r-project.org 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@r-project.org 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] try FlexMix RE: mulitmodal distributions
Hi, Marion, I believe the package FlexMix provides a more generalized version of finite mixture modeling than is found in mclust/mclust02. Please see: http://cran.r-project.org/doc/vignettes/flexmix/flexmix-intro.pdf Karen --- Karen M. Green, Ph.D. [EMAIL PROTECTED] Research Investigator Drug Design Group Sanofi Aventis Pharmaceuticals -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marion Wittmann Sent: Monday, November 19, 2007 2:57 PM To: r-help@r-project.org Subject: [R] mulitmodal distributions Hello, I see that mclust is a pacakge that handles fitting mixtures of normals. Are there any other packages out that that can handle mixtures of gammas or other exponentials? Additionally, are there any packages out there that can fit bimodal distributions without mixtures? i.e., Cobb et al. 1983 using moment recursion relations? Thank you! mw Marion Wittmann, Ph.D. candidate Environmental Science Management University of California Santa Barbara, CA 93106-5131 Lab: (805) 893 5890 Mobile: (805) 448 8259 Email: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] Web: http://www.bren.ucsb.edu/~mwittmann www.bren.ucsb.edu/~mwittmann [[alternative HTML version deleted]] __ R-help@r-project.org 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] barplot problem
Here's an example of my problem: modelledprofile - c(7.072289e-01, 2.625354e-01, 2.932886e-02, 8.986474e-04, 8.155270e-06, 2.537943e-08, 3.137954e-11, 1.729522e-14, 4.579875e-18, 6.069698e-22, 4.100828e-26, 1.423359e-30, 1.272139e-35, 5.449925e-46, 1.431925e-57, 1.629660e-70) depthnames - c(0-0.5,0.5-1,1-1.5,1.5-2,2-2.5,2.5-3,3-3.5,3.5-4,4-4.5,4.5-5,5-5.5,5.5-6,6-7,7-8,8-9,9-10) par(omi=c(0,0.5,0,0)) barplot(rev(modelledprofile),horiz=TRUE,xlim=c(0,1),col=cornflowerblue,names.arg=rev(depthnames),las=1,ylab=depth) Thanks -- This message was sent on behalf of [EMAIL PROTECTED] at openSubscriber.com http://www.opensubscriber.com/message/r-help@r-project.org/8030546.html __ R-help@r-project.org 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] Use and misuse of update function for non-models. Any views/recommendations??
On Nov 20, 2007 10:29 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: update already has formula and packageStatus methods so its being extended beyond models already even within core packages. Also, update methods are extensively used for the other kind of graphs in the lattice package. Deepayan encourages users to think of storing and updating lattice objects. On Nov 20, 2007 8:54 AM, Luke Tierney [EMAIL PROTECTED] wrote: On Tue, 20 Nov 2007, Prof Brian Ripley wrote: update() is generic, so the recommended approach would be to write a method for your objects. Creating your own function update() in a package would probably not break too much, as namespaces would protect most functions using the generic in stats. But it could be very confusing to users. Maybe. update is generic with a netral set of argument names; on the other hand, the _documentation_ of update is not generic -- it is specific to updating models. So there is opportunity for confusion from that direction. Best, luke On Tue, 20 Nov 2007, Søren Højsgaard wrote: Dear all, I wonder if it is bad style (or something worse) to create an update function which does not work on model objects of the lm, glm etc. type. Specifically, I have some graph objects (graphs as mathematical objects, not as displays) which I want to alter and for that purpose I thought of writing an update function. Would doing so violate a deeper philosophy in the R system or have other unfortunate consequences. If so, I'm happy to hear other suggestions... Regards Søren __ R-help@r-project.org 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. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-help@r-project.org 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@r-project.org 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@r-project.org 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] Trying to get around R
Hi Loren,
It wasn't my intention to sound arrogant, cruel or off putting.
English is not my first language, and perhaps my message had a tone I
did not intended. The person posting the message I responded was
literally asking for somebody on the list to do his/hers homework (there
are even references to hints from the textbook). This is not only
academically non-kosher, is also not the purpose of the R-help list. I
pointed this to this person and invited him/her to come back with
specific questions on R coding.
The posting guidelines are easily accessible. The first line in the
Mailing Lists section of the R website
(http://www.r-project.org/mail.html) states Please read the
instructions below and the posting guide before sending anything to any
mailing list!, and displays a link to the guide. There also a link to
the guide at the bottom of every message send through this list. The
posting guide is not hard to find, and (in my opinion) it isn't long or
difficult to understand (in particular for anyone taking college level
statistics).
Julian
Loren Engrav wrote:
I am a newbie to R and Bio emails and
It is clear that newbies make mistakes, I made several which were pointed
out and I am trying to fix them, and as I fix one I make another, in time
perhaps I will know it all, but if it is like surgery, I will make
mistakes until I retire
But the response of the old-timers to these mistakes seems arrogant and
cruel and off putting and does NOT encourage more participation. In fact
it takes real stuff to continue after this putdown and that putdown.
There are 3,783 links to posting guidelines, which took 1.5 hours to find
and read and understand.
Why not a link on how the mistakes of the newbies will be dealt with?
Or a kindly response from the moderator personal to the newbie rather than
to the entire world?
Or a kindly general response as from Ben Bolker to my last infraction which
was You might have better luck with this on the Bioconductor mailing list
...
Rather than to the universe...
Using the wrong list: this is for R-sig-mac, and the topic occcurred
there recently.
All in an effort to encourage promote useful and increasing exchange
participation
Or not
Loren Engrav, MD
Univ Washington
From: Julian Burgos [EMAIL PROTECTED]
Date: Mon, 19 Nov 2007 10:44:49 -0800
To: Epselon [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] Trying to get around R
Hello Epselon (if that is your name),
This sounds like homework questions.
From the R-help posting guide:
Basic statistics and classroom homework:
R-help is not intended for
these.
If you have a specific question on R
coding, do ask it (and provide
reproducible code). But you should not expect
for people on the list to
do your homework for you. That is a big
no-no.
Cheers,
Julian
Epselon wrote:
I have three problems I am trying to
simulate, that I am having difficulty
getting around with.
Problem 1.
I want to determine the 85 percentile (the x value for which the sum of
probabilities becomes 0.85) of the following distributions (two binomials
and a Poisson with rate Lmbda= np of the two binomials): X ~B(10, 0.3),
Y~P(3) ,
Z~B(30, 0.1). I want to show that that Y is a good approximation
for Z but
not for X...(by examining these distributions for few
different
percentiles)
Problem 2:
For a binomial distribution X ~ B(20, 0.4), I
want to use R to calculate
P{|X - μ| 2} and verify that it is near or
larger than 0.95. (Hint from
the text book: Since μ = 8 and 2.3 then
you
may want to read the
weights, or probabilities, of the values 6:10, into a
vector v and then use
the command sum(v) to
calculate the sum.) Repeat
this for another set of parameters of your
choice.
Problem 3:
Draw a
sample of size 10, from a Poisson with Lambda= 5, and calculate the
mean
and
the standard deviation of this sample, Repeat this calculation with
size 20
and 30 and demonstrate
that ¯X gets closer to μ as the sample size
increases.
Thanks.
I would appreciate it if someone accompanied the
codes with a brief
explanation so I can be able to replicate it
myself.
__
R-help@r-project.org
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@r-project.org 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@r-project.org 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,
Re: [R] R and reading matlab compressed files
According to the Octave manual (page 146 of Edition 3 for Octave
version 2.9.16) Octave can read Matlab version 7 files. It can also
output with similar options to Matlab. As there are no issues or
licencing problems when running Octave and R on the one machine. Note
that there is a new native Windows version of Octave now available
that does not require cygwin.
Best Reards
John
On 17/11/2007, Prof Leslie Smith [EMAIL PROTECTED] wrote:
Is there any way to read these files (standard .mat files, created by
matlab version 7 onwards are compressed)? I know that R.matlab doesn't
read them (it even says in the file MatlabServer.m Matlab v7 saves
compressed files, which is not recognized by R.matlab's readMat() (lines
47-8)).
I know I should be able to make R call Matlab and transfer data (not that
I managed to make it work yet!), but I'd rather not run Matlab R
together: I'd like to use R to read matlab files on machines not licensed
for matlab!
Are there any ways to make this work?
--Leslie Smith
--
Prof Leslie Smith
Computing Science and Maths
University of Stirling FK9 4LA
Scotland
Tel (44) 1786 467435
--
The University of Stirling is a university established i...{{dropped:11}}
__
R-help@r-project.org 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.
--
John C Frain
Trinity College Dublin
Dublin 2
Ireland
www.tcd.ie/Economics/staff/frainj/home.html
mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
__
R-help@r-project.org 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] Process multiple columns of data.frame
It really depends on what you want to set the values that contain NAs to for the various type of the columns. Do you always want numerics =0, characters =, and factors =whatever? Do you want to do this for all the columns in a dataframe? If you want to it for all the columns in a matrix, it is easy, since all are the same type, and you are setting them to zero (e.g., yourMatrix[is.na(yourMatrix)] - 0). You can always write a function that can take in the names of the columns and then depending on their types set the corresponding values. So it depends on what you mean by concisely and how often you want to do it. On Nov 20, 2007 12:27 PM, Thompson, David (MNR) [EMAIL PROTECTED] wrote: Hello, How do I do the following more concisely? Bout[is.na(Bout$bd.n), 'bd.n'] - 0 Bout[is.na(Bout$ht.n), 'ht.n'] - 0 Bout[is.na(Bout$dbh.n), 'dbh.n'] - 0 Would the form of such a command be different between numeric, character and factor columns? . . . between data.frames and matrices? Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On Nov 20, 2007 11:14 AM, David Afshartous [EMAIL PROTECTED]
wrote:
All,
I'm trying to make a basic plot: data points superimposed upon the a line
connecting the points w/ a different color. Example below doesn't work
as the first xyplot call doesn't remain. Suggestions?
xyplot(y ~ Hour, type = 'b', lwd = 2, pch= 16, col.symbol = red, cex=3)
or for finer control
xyplot(y ~ Hour,
panel = function(x, y, ...) {
panel.lines(x, y, lwd = 2)
panel.points(x, y, pch = 16, cex = 3, col = red)
})
-Deepayan
Deepayan,
is there any way to do something similar, but when the data used to plot the
lines and the points come from different dataframes and a grouping variable
is used?
thanks,
Dylan
David
Hour = c(NA,1,2,3,4)
y = c(2,2,3,2,1.5)
xyplot(y ~ Hour, xlab = list(Hour, font=2, cex=2), ylab= list(U_x *
V, font=2, cex=2), type = 'l', scales = list( x= list(tick.number=5,
cex=2, limits=c(0,4.5)), y=list(cex=0)), lines=TRUE, lwd = 2 , add=TRUE
)
xyplot(y ~ Hour, xlab= , ylab=, pch= 16, col= red, cex=3 , xlim =
c(0, 4.5), add=TRUE)
__
R-help@r-project.org 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.
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On Nov 20, 2007 11:14 AM, David Afshartous [EMAIL PROTECTED] wrote:
All,
I'm trying to make a basic plot: data points superimposed upon the a line
connecting the points w/ a different color. Example below doesn't work as
the first xyplot call doesn't remain. Suggestions?
xyplot(y ~ Hour, type = 'b', lwd = 2, pch= 16, col.symbol = red, cex=3)
or for finer control
xyplot(y ~ Hour,
panel = function(x, y, ...) {
panel.lines(x, y, lwd = 2)
panel.points(x, y, pch = 16, cex = 3, col = red)
})
-Deepayan
David
Hour = c(NA,1,2,3,4)
y = c(2,2,3,2,1.5)
xyplot(y ~ Hour, xlab = list(Hour, font=2, cex=2), ylab= list(U_x * V,
font=2, cex=2), type = 'l', scales = list( x= list(tick.number=5, cex=2,
limits=c(0,4.5)), y=list(cex=0)), lines=TRUE, lwd = 2 , add=TRUE)
xyplot(y ~ Hour, xlab= , ylab=, pch= 16, col= red, cex=3 , xlim =
c(0, 4.5), add=TRUE)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On Nov 20, 2007 11:14 AM, David Afshartous [EMAIL PROTECTED]
wrote:
All,
I'm trying to make a basic plot: data points superimposed upon the a line
connecting the points w/ a different color. Example below doesn't work
as the first xyplot call doesn't remain. Suggestions?
xyplot(y ~ Hour, type = 'b', lwd = 2, pch= 16, col.symbol = red, cex=3)
or for finer control
xyplot(y ~ Hour,
panel = function(x, y, ...) {
panel.lines(x, y, lwd = 2)
panel.points(x, y, pch = 16, cex = 3, col = red)
})
-Deepayan
Deepayan,
is there any way to do something similar, but when the data used to plot the
lines and the points come from different dataframes and a grouping variable
is used?
There's a way to do almost everything, but we need a reproducible
example (preferably minimal) and a clear statement of what you want to
do to help.
-Deepayan
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On 21/11/2007, at 8:40 AM, Deepayan Sarkar wrote:
There's a way to do almost everything, but we need a reproducible
example (preferably minimal) and a clear statement of what you want to
do to help.
Is this a candidate for fortune() ?
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
R-help@r-project.org 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] asymptote
I have a graph which looks like hyperbole. I'd like to fit a straight line to the lower segment going to infinity, approaching the X axis -- I'm interested in the angle. If I'd do it manually, I'd cut off a certain initial part of the range, [0..x_min], and then do an lm with the rest. Yet I wonder whether those curve fitting packages mentioned earlier do something similar automatically? Cheers, Alexy __ R-help@r-project.org 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] Loc function in R??
Does anyone know which function (if any) will return the index of the true locations in a Boolean vector? For instance: A=c(1,3,5,7,4); B=c(2,4,77,3,3); X=AB; So X is: X [1] TRUE TRUE TRUE FALSE FALSE I'd like to know if there is a function that will tell me the locations of where the TRUE values are? for instance a vector that will list that the locations are at 1, 2, 3. This function is sometimes called loc() in other languages. Thanks, Jennifer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On Nov 20, 2007 11:14 AM, David Afshartous [EMAIL PROTECTED]
wrote:
All,
I'm trying to make a basic plot: data points superimposed upon the a
line connecting the points w/ a different color. Example below
doesn't work as the first xyplot call doesn't remain. Suggestions?
xyplot(y ~ Hour, type = 'b', lwd = 2, pch= 16, col.symbol = red,
cex=3)
or for finer control
xyplot(y ~ Hour,
panel = function(x, y, ...) {
panel.lines(x, y, lwd = 2)
panel.points(x, y, pch = 16, cex = 3, col = red)
})
-Deepayan
Deepayan,
is there any way to do something similar, but when the data used to plot
the lines and the points come from different dataframes and a grouping
variable is used?
There's a way to do almost everything, but we need a reproducible
example (preferably minimal) and a clear statement of what you want to
do to help.
-Deepayan
Of course! Sorry about that.
Example:
library(lattice)
# generate some data:
resp - rnorm(100)
pred - resp*1.5 + rnorm(100)
d - data.frame(resp=resp, pred=pred)
# add a grouping factor:
d$grp - gl(4, 25, labels=letters[1:4])
# plot: looks ok!
main.plot - xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{panel.xyplot(x, y, ...) ; panel.lmline(x,y, ...) })
# however, we have some other information which needs to go in each panel
# note that the dimensions (i.e. no of obs) are not the same as the original
# data, and the values are different, but on the same scale
resp.other - rnorm(20)
pred.other - resp.other*1.5 + rnorm(20)
d.other - data.frame(resp=resp.other, pred=pred.other)
d.other$grp - gl(4, 5, labels=letters[1:4])
The big question:
Now that we have the main plot (main.plot) looking ok, how can we add the data
from d.other to the frames of main.plot without using subset() for each level
of our grouping variable?
# after some messing around, how about this:
xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
# now the other data:
panel.superpose(d.other$pred, d.other$resp, groups=d.other$grp,
col=c('red', 'blue', 'green', 'orange')[as.numeric(d.other$grp)], pch=16,
subscripts=TRUE)
}
)
#... hmm it doesn't look like the information from 'd.other' is being
stratified into the panels setup in panel.xyplot() ...
The main point to this rather contrived example is this :
1. i have a data frame with continuous predictions, the response, and the
grouping variable -- which plot nicely with the default use of xyplot()
2. I would like to embellish each panel with the original response and
predictor values to illustrate the relationship between the original data and
the smooth, fitted curve.
ideas?
thanks!
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
R-help@r-project.org 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] Loc function in R??
?which which(X) [1] 1 2 3 Max -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Barb, Jennifer (NIH/CIT) [E] Sent: Tuesday, November 20, 2007 3:07 PM To: [EMAIL PROTECTED] Subject: [R] Loc function in R?? Does anyone know which function (if any) will return the index of the true locations in a Boolean vector? For instance: A=c(1,3,5,7,4); B=c(2,4,77,3,3); X=AB; So X is: X [1] TRUE TRUE TRUE FALSE FALSE I'd like to know if there is a function that will tell me the locations of where the TRUE values are? for instance a vector that will list that the locations are at 1, 2, 3. This function is sometimes called loc() in other languages. Thanks, Jennifer [[alternative HTML version deleted]] __ R-help@r-project.org 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@r-project.org 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] Loc function in R??
?which
On 21/11/2007, at 9:06 AM, Barb, Jennifer (NIH/CIT) [E] wrote:
Does anyone know which function (if any) will return the index of the
true locations in a Boolean vector?
For instance:
A=c(1,3,5,7,4);
B=c(2,4,77,3,3);
X=AB;
So X is:
X
[1] TRUE TRUE TRUE FALSE FALSE
I'd like to know if there is a function that will tell me the
locations
of where the TRUE values are? for instance a vector that will list
that
the locations are at 1, 2, 3. This function is sometimes called loc()
in other languages.
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
R-help@r-project.org 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] Loc function in R??
which(A B) On Nov 20, 2007, at 3:06 PM, Barb, Jennifer (NIH/CIT) [E] wrote: Does anyone know which function (if any) will return the index of the true locations in a Boolean vector? For instance: A=c(1,3,5,7,4); B=c(2,4,77,3,3); X=AB; So X is: X [1] TRUE TRUE TRUE FALSE FALSE I'd like to know if there is a function that will tell me the locations of where the TRUE values are? for instance a vector that will list that the locations are at 1, 2, 3. This function is sometimes called loc() in other languages. Thanks, Jennifer [[alternative HTML version deleted]] __ R-help@r-project.org 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@r-project.org 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] Loc function in R??
try: which(X) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm Quoting Barb, Jennifer (NIH/CIT) [E] [EMAIL PROTECTED]: Does anyone know which function (if any) will return the index of the true locations in a Boolean vector? For instance: A=c(1,3,5,7,4); B=c(2,4,77,3,3); X=AB; So X is: X [1] TRUE TRUE TRUE FALSE FALSE I'd like to know if there is a function that will tell me the locations of where the TRUE values are? for instance a vector that will list that the locations are at 1, 2, 3. This function is sometimes called loc() in other languages. Thanks, Jennifer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@r-project.org 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] Loc function in R??
?which On Tue, 20 Nov 2007, Barb, Jennifer (NIH/CIT) [E] wrote: Does anyone know which function (if any) will return the index of the true locations in a Boolean vector? For instance: A=c(1,3,5,7,4); B=c(2,4,77,3,3); X=AB; So X is: X [1] TRUE TRUE TRUE FALSE FALSE I'd like to know if there is a function that will tell me the locations of where the TRUE values are? for instance a vector that will list that the locations are at 1, 2, 3. This function is sometimes called loc() in other languages. Thanks, Jennifer [[alternative HTML version deleted]] __ R-help@r-project.org 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. _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics Director of Consulting, Department of Statistics __ R-help@r-project.org 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] Problem with code for bootstrapping chi square test with count data
On Tue, 20 Nov 2007, Geertje Van der Heijden wrote:
Hi,
I'd like some advice on bootstrapping in R.
I have a species x with 20 individuals and a factor containing 0 and 1's
(in this case 5 zeros and 15 ones). I want to compare the frequency of
the occurrence of 1 with a probability value. This code seems to work to
do this in R.
attach(test)
p - c(0.5272, (1-0.5272))
sp1_1 - length(subset(x, x==1))
sp1_0 - length(subset(x, x==0))
obs1_1 - c(sp1_1, sp1_0)
chisq.test(obs1_1, p=p)
However, I'd like to bootstrap these 20 individuals to produce a whole
population of samples and I'd like to do a chi-square test for each of
the bootstrap sample to create a distribution of the chi-square
statistic.
And what do you want to do with that distribution? It is 'a
distribution', but it is not obviously connected with the test you say you
want to do. It seems to me that the real issue here is understanding the
applicability of the bootstrap.
We can make your example reproducible by
x - c(rep(0,5), rep(1, 15))
N - sum(x) # 15
p - c(0.5272, (1-0.5272))
chisq.test(c(N, 20-N), p=p)
I have bootstrapped the 0's and 1's of x 20 times using the following
code:
resamples - lapply(1:20, function(i) sample(x, replace=T))
What I can't get to work is how to calculate the observed values for 1's
and 0's in each of the bootstrap samples, which I need to do a
chi-square test for each sample. The methd I used above doesn't seem to
work the results for resamples. Does anyone have an idea on how to get
this to work? Or is there another easier way to do this? I hope it is
clear what I am trying to do!
You can make this easier by noticing that the number of ones will be
binomial(20, 15/20). So e.g.
res - replicate(1000, {N - rbinom(1, 20, 15/20);
chisq.test(c(N, 20-N), p=p)$statistic})
Now what are you going to do with this?
It is not simulation under the null hypothesis, which would be
res - replicate(1000, {N - rbinom(1, 20, 0.5272);
chisq.test(c(N, 20-N), p=p)$statistic})
mean(res 3.983)
and shows good agreement with the theoretical approximating distribution.
Also, why do you want a chisq test to do this? We can use
binom.test(15, 20, 0.5272), which is exact. (The only assumption it makes
iid trials, which the bootstrap methods are also making.)
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
[...]
Example:
library(lattice)
# generate some data:
resp - rnorm(100)
pred - resp*1.5 + rnorm(100)
d - data.frame(resp=resp, pred=pred)
# add a grouping factor:
d$grp - gl(4, 25, labels=letters[1:4])
# plot: looks ok!
main.plot - xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{panel.xyplot(x, y, ...) ; panel.lmline(x,y, ...) })
# however, we have some other information which needs to go in each panel
# note that the dimensions (i.e. no of obs) are not the same as the
original # data, and the values are different, but on the same scale
resp.other - rnorm(20)
pred.other - resp.other*1.5 + rnorm(20)
d.other - data.frame(resp=resp.other, pred=pred.other)
d.other$grp - gl(4, 5, labels=letters[1:4])
The big question:
Now that we have the main plot (main.plot) looking ok, how can we add the
data from d.other to the frames of main.plot without using subset() for
each level of our grouping variable?
Hi,
I would say you are asking the wrong question. The right question is:
how do I manipulate my data so that it becomes easy to work with. Try
combined - make.groups(d, d.other)
excellent! this makes complete sense...
xyplot(resp ~ pred | grp, data=combined, groups = which,
panel = panel.superpose,
panel.groups = function(x,y, ...) {
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
})
Is that close to what you want? Does it extend to your real example?
-Deepayan
This is close for the contrived example, but not quite what I need. I would
like to plot the first 'group' of data as lines, and the second as points. I
have tried specifying type=c('l', 'p') but this does not appear to work.
If I plot everything as point, the data plot correctly, but not in the symbols
that I would like.
Cheers,
Dylan
# after some messing around, how about this:
xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
# now the other data:
panel.superpose(d.other$pred, d.other$resp, groups=d.other$grp,
col=c('red', 'blue', 'green', 'orange')[as.numeric(d.other$grp)], pch=16,
subscripts=TRUE)
}
)
#... hmm it doesn't look like the information from 'd.other' is being
stratified into the panels setup in panel.xyplot() ...
The main point to this rather contrived example is this :
1. i have a data frame with continuous predictions, the response, and the
grouping variable -- which plot nicely with the default use of xyplot()
2. I would like to embellish each panel with the original response and
predictor values to illustrate the relationship between the original data
and the smooth, fitted curve.
ideas?
thanks!
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
[...]
Example:
library(lattice)
# generate some data:
resp - rnorm(100)
pred - resp*1.5 + rnorm(100)
d - data.frame(resp=resp, pred=pred)
# add a grouping factor:
d$grp - gl(4, 25, labels=letters[1:4])
# plot: looks ok!
main.plot - xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{panel.xyplot(x, y, ...) ; panel.lmline(x,y, ...) })
# however, we have some other information which needs to go in each panel
# note that the dimensions (i.e. no of obs) are not the same as the
original # data, and the values are different, but on the same scale
resp.other - rnorm(20)
pred.other - resp.other*1.5 + rnorm(20)
d.other - data.frame(resp=resp.other, pred=pred.other)
d.other$grp - gl(4, 5, labels=letters[1:4])
The big question:
Now that we have the main plot (main.plot) looking ok, how can we add the
data from d.other to the frames of main.plot without using subset() for
each level of our grouping variable?
Hi,
I would say you are asking the wrong question. The right question is:
how do I manipulate my data so that it becomes easy to work with. Try
combined - make.groups(d, d.other)
excellent! this makes complete sense...
xyplot(resp ~ pred | grp, data=combined, groups = which,
panel = panel.superpose,
panel.groups = function(x,y, ...) {
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
})
Is that close to what you want? Does it extend to your real example?
-Deepayan
This is close for the contrived example, but not quite what I need. I would
like to plot the first 'group' of data as lines, and the second as points. I
have tried specifying type=c('l', 'p') but this does not appear to work.
Try adding 'distribute.type = TRUE' (see ?panel.superpose). My UseR!
2007 talk had some relevant examples, so you might find those slides
useful:
http://www.user2007.org/program/presentations/sarkar.pdf
-Deepayan
If I plot everything as point, the data plot correctly, but not in the symbols
that I would like.
Cheers,
Dylan
# after some messing around, how about this:
xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
# now the other data:
panel.superpose(d.other$pred, d.other$resp, groups=d.other$grp,
col=c('red', 'blue', 'green', 'orange')[as.numeric(d.other$grp)], pch=16,
subscripts=TRUE)
}
)
#... hmm it doesn't look like the information from 'd.other' is being
stratified into the panels setup in panel.xyplot() ...
The main point to this rather contrived example is this :
1. i have a data frame with continuous predictions, the response, and the
grouping variable -- which plot nicely with the default use of xyplot()
2. I would like to embellish each panel with the original response and
predictor values to illustrate the relationship between the original data
and the smooth, fitted curve.
ideas?
thanks!
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
R-help@r-project.org 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] Process multiple columns of data.frame
I did specify only the three columns of interest
c('bd.n','ht.n','dbh.n')
as the second (column) index, and I did superficially check the results
which turned out as I had hoped. Only the three columns listed were
changed and existing values _in_ those columns were retained.
So, I appear to be on my way again.
Thanx again, DaveT.
*
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: November 20, 2007 04:21 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] Process multiple columns of data.frame
The problem with that solution is that if any of the columns in a row
has an NA in it, then all the columns of that row will be set to zero.
Is the what you want, or do you only want the specific entries set to
0?
On Nov 20, 2007 4:07 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Jim,
What I'm getting at is my lack of understanding when manipulating
data frame indices. I have tried something like your matrix example
with variants of: Bout[
is.na(Bout[,c('bd.n','ht.n','dbh.n')]), ] - 0
only to receive the following error message:
Error in `[-.data.frame`(`*tmp*`, is.na(Bout[, c(bd.n, ht.n,
dbh.n)]), :
non-existent rows not allowed
My questions were not focussed on the assignment value but,
on the selection of multiple columns (of a single type) to process.
Which is what I meant by concisely.
And, lo and behold, in my attempts to reframe my questions I
(finally)
came upon a solution:
Bout[is.na(Bout$bd.n) | is.na(Bout$ht.n) | is.na(Bout$dbh.n),
c('bd.n','ht.n','dbh.n')] - 0
Thank you for your time, DaveT.
*
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: November 20, 2007 02:25 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] Process multiple columns of data.frame
It really depends on what you want to set the values that
contain NAs
to for the various type of the columns. Do you always want numerics
=0, characters =, and factors =whatever? Do you want to
do this for
all the columns in a dataframe? If you want to it for all
the columns
in a matrix, it is easy, since all are the same type, and you are
setting them to zero (e.g., yourMatrix[is.na(yourMatrix)] - 0).
You can always write a function that can take in the names of the
columns and then depending on their types set the corresponding
values. So it depends on what you mean by concisely and how often
you want to do it.
On Nov 20, 2007 12:27 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
How do I do the following more concisely?
Bout[is.na(Bout$bd.n), 'bd.n'] - 0
Bout[is.na(Bout$ht.n), 'ht.n'] - 0
Bout[is.na(Bout$dbh.n), 'dbh.n'] - 0
Would the form of such a command be different
between numeric, character and factor columns?
. . . between data.frames and matrices?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
__
R-help@r-project.org 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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@r-project.org 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] Problems with NA's
Thomas L Jones, PhD wrote:
Difficulty handling NA's:
Assume that I have a numeric vector y. For simplicity, assume that it has 10
elements. Assume that the third element has the value NA. I give it the
following:
NA_test - function (){
y - numeric (10)
y [3] - NA
if (y [3] != NA){(print (no)}
print (Leaving NA_test)
return ()
}# End of function
-
Unfortunately, things become confused involving the NA element.
Here is the output, starting with the loading process:
--
NA_test - function (){
+ y - numeric (10)
+ y [3] - NA
+ if (y [3] != NA){(print (no)}
Error: syntax error in:
y [3] - NA
if (y [3] != NA){(print (no)}
print (Leaving NA_test)
[1] Leaving NA_test
return ()
Error: no function to return from, jumping to top level
}# End of function
Error: syntax error in }
-
I have enclosed the print operation in braces to avoid possible problems
with it.
Your advice?
Tom Jones
What Messrs. Schwartz and Olshansky told you is valid, but will not cure
syntax errors. My advice is to check the matching of parentheses in the
line
if (y [3] != NA){(print (no)}
J. R. M. Hosking
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding points on top of lines in xyplot [solved]
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
On Tuesday 20 November 2007, Deepayan Sarkar wrote:
On 11/20/07, Dylan Beaudette [EMAIL PROTECTED] wrote:
[...]
Example:
library(lattice)
# generate some data:
resp - rnorm(100)
pred - resp*1.5 + rnorm(100)
d - data.frame(resp=resp, pred=pred)
# add a grouping factor:
d$grp - gl(4, 25, labels=letters[1:4])
# plot: looks ok!
main.plot - xyplot(resp ~ pred | grp, data=d, panel=function(x,y,
...) {panel.xyplot(x, y, ...) ; panel.lmline(x,y, ...) })
# however, we have some other information which needs to go in each
panel # note that the dimensions (i.e. no of obs) are not the same as
the original # data, and the values are different, but on the same
scale resp.other - rnorm(20)
pred.other - resp.other*1.5 + rnorm(20)
d.other - data.frame(resp=resp.other, pred=pred.other)
d.other$grp - gl(4, 5, labels=letters[1:4])
The big question:
Now that we have the main plot (main.plot) looking ok, how can we add
the data from d.other to the frames of main.plot without using
subset() for each level of our grouping variable?
Hi,
I would say you are asking the wrong question. The right question is:
how do I manipulate my data so that it becomes easy to work with. Try
combined - make.groups(d, d.other)
excellent! this makes complete sense...
xyplot(resp ~ pred | grp, data=combined, groups = which,
panel = panel.superpose,
panel.groups = function(x,y, ...) {
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
})
Is that close to what you want? Does it extend to your real example?
-Deepayan
This is close for the contrived example, but not quite what I need. I
would like to plot the first 'group' of data as lines, and the second as
points. I have tried specifying type=c('l', 'p') but this does not appear
to work.
That was the trick! Here was the general concept:
xyplot(a + b + c ~ d, panel=panel.superpose, distribute.type = TRUE,
type=c('l', 'l', 'p'))
I will work up an example and post it on the lab website so Google will catch
similar calls for help.
Thanks again Deepayan, I am only starting to grasp the time-saving potential
of lattice graphics... but like the output!
Dylan
Try adding 'distribute.type = TRUE' (see ?panel.superpose). My UseR!
2007 talk had some relevant examples, so you might find those slides
useful:
http://www.user2007.org/program/presentations/sarkar.pdf
-Deepayan
If I plot everything as point, the data plot correctly, but not in the
symbols that I would like.
Cheers,
Dylan
# after some messing around, how about this:
xyplot(resp ~ pred | grp, data=d, panel=function(x,y, ...)
{
panel.xyplot(x, y, ...)
panel.lmline(x,y, ...)
# now the other data:
panel.superpose(d.other$pred, d.other$resp, groups=d.other$grp,
col=c('red', 'blue', 'green', 'orange')[as.numeric(d.other$grp)],
pch=16, subscripts=TRUE)
}
)
#... hmm it doesn't look like the information from 'd.other' is being
stratified into the panels setup in panel.xyplot() ...
The main point to this rather contrived example is this :
1. i have a data frame with continuous predictions, the response, and
the grouping variable -- which plot nicely with the default use of
xyplot()
2. I would like to embellish each panel with the original response
and predictor values to illustrate the relationship between the
original data and the smooth, fitted curve.
ideas?
thanks!
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
__
R-help@r-project.org 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] Trying to get around R
Hi and thank you
Discussion is surely tough via the web
And I have trouble with tone also, and English
My only point was that Epselon [EMAIL PROTECTED] received education
but not much encouragement IMO and
With the method of Bolker, it might be possible to achieve both for newbies,
ie both education and encouragement
But some might say and why is that your problem? which has some validity
And some might say can't stand the heat? Then perhaps try leaving the
kitchen, which has some truth also
Probably best now return to makeGOGraph and postscript output as at this
point I either have a decorum point or I don't
Thank you for discussing/listening
Loren Engrav
Univ Wash
Seattle
From: Julian Burgos [EMAIL PROTECTED]
Date: Tue, 20 Nov 2007 11:12:45 -0800
To: Loren Engrav [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] Trying to get around R
Hi Loren,
It wasn't my intention to sound arrogant, cruel or off putting.
English is not my first language, and perhaps my message had a tone I
did not intended. The person posting the message I responded was
literally asking for somebody on the list to do his/hers homework (there
are even references to hints from the textbook). This is not only
academically non-kosher, is also not the purpose of the R-help list. I
pointed this to this person and invited him/her to come back with
specific questions on R coding.
The posting guidelines are easily accessible. The first line in the
Mailing Lists section of the R website
(http://www.r-project.org/mail.html) states Please read the
instructions below and the posting guide before sending anything to any
mailing list!, and displays a link to the guide. There also a link to
the guide at the bottom of every message send through this list. The
posting guide is not hard to find, and (in my opinion) it isn't long or
difficult to understand (in particular for anyone taking college level
statistics).
Julian
Loren Engrav wrote:
I am a newbie to R and Bio emails and
It is clear that newbies make mistakes, I made several which were pointed
out and I am trying to fix them, and as I fix one I make another, in time
perhaps I will know it all, but if it is like surgery, I will make
mistakes until I retire
But the response of the old-timers to these mistakes seems arrogant and
cruel and off putting and does NOT encourage more participation. In fact
it takes real stuff to continue after this putdown and that putdown.
There are 3,783 links to posting guidelines, which took 1.5 hours to find
and read and understand.
Why not a link on how the mistakes of the newbies will be dealt with?
Or a kindly response from the moderator personal to the newbie rather than
to the entire world?
Or a kindly general response as from Ben Bolker to my last infraction which
was You might have better luck with this on the Bioconductor mailing list
...
Rather than to the universe...
Using the wrong list: this is for R-sig-mac, and the topic occcurred
there recently.
All in an effort to encourage promote useful and increasing exchange
participation
Or not
Loren Engrav, MD
Univ Washington
From: Julian Burgos [EMAIL PROTECTED]
Date: Mon, 19 Nov 2007 10:44:49 -0800
To: Epselon [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] Trying to get around R
Hello Epselon (if that is your name),
This sounds like homework questions.
From the R-help posting guide:
Basic statistics and classroom homework:
R-help is not intended for
these.
If you have a specific question on R
coding, do ask it (and provide
reproducible code). But you should not expect
for people on the list to
do your homework for you. That is a big
no-no.
Cheers,
Julian
Epselon wrote:
I have three problems I am trying to
simulate, that I am having difficulty
getting around with.
Problem 1.
I want to determine the 85 percentile (the x value for which the sum of
probabilities becomes 0.85) of the following distributions (two binomials
and a Poisson with rate Lmbda= np of the two binomials): X ~B(10, 0.3),
Y~P(3) ,
Z~B(30, 0.1). I want to show that that Y is a good approximation
for Z but
not for X...(by examining these distributions for few
different
percentiles)
Problem 2:
For a binomial distribution X ~ B(20, 0.4), I
want to use R to calculate
P{|X - μ| 2} and verify that it is near or
larger than 0.95. (Hint from
the text book: Since μ = 8 and 2.3 then
you
may want to read the
weights, or probabilities, of the values 6:10, into a
vector v and then use
the command sum(v) to
calculate the sum.) Repeat
this for another set of parameters of your
choice.
Problem 3:
Draw a
sample of size 10, from a Poisson with Lambda= 5, and calculate the
mean
and
the standard deviation of this sample, Repeat this calculation with
size 20
and 30 and demonstrate
that ~X gets closer to μ as the sample size
increases.
Thanks.
I would
Re: [R] display basename
z=read.table(chosen - file.choose(),dec=.,header=TRUE) will assign the return value of file.choose (the path names of the file as a character string) to chosen. This sort of code is seductive, but I find it quite difficult to read. I have also gotten myself into trouble from time to time doing it sloppily. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mysimbaa Sent: Tuesday, November 20, 2007 2:30 PM To: r-help@r-project.org Subject: [R] display basename Hello everybody, I'm sorry for asking a dumb question, but I don't find how to loos it. I need to display the name of the choosing file using this command : z=read.table(file.choose(),dec=.,header=TRUE) Thanks for any help. -- View this message in context: http://www.nabble.com/display-basename-tf4846650.html#a13866718 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] skewness: generating distribution and estimating M3.
Dear all, How can I generate values which distrituions have left or rigth skewness. After that, which function compute the skewness of each distributions? Kind regards. miltinho para armazenamento! [[alternative HTML version deleted]] __ R-help@r-project.org 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] barplot problem
Thanks guys, that's exactly what I was looking for! Pieter -- This message was sent on behalf of [EMAIL PROTECTED] at openSubscriber.com http://www.opensubscriber.com/message/r-help@r-project.org/8030546.html __ R-help@r-project.org 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] Vectorization/Speed Problem
Hi,
I cannot find a 'vectorized' solution to this 'for loop' kind of problem.
Do you see a vectorized, fast-running solution?
Objective:
Take the value of X at each timepoint and calculate the corresponding value
of Y. Leading 0's and all 1's for X are assigned to Y; otherwise Y is
incremented by the number of 0's adjacent to the last 1. The frequency and
distribution of X vary widely and may have ~100 repeated 0's or 1's in a
vector of 10k timepoints.
Example:
time 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
X0 1 0 1 0 1 0 0 1 1 1 0 0 0 . .
Y0 1 2 1 2 1 2 3 1 1 1 2 3 4 . .
What I have done:
My for() and apply()-related standard solutions are too slow. They are 6
times slower than my prototype, vectorized code which uses cumsum().
However(!)... my results are inaccurate and I can't correct them without
introducing a for()! Here is my shot at a vectorized solution, as far as I
can take it.
Preliminary Vectorized Code:
X - matrix(sample(c(1,0,0,0,0), 500, replace = TRUE), 25, 20, byrow=TRUE)
colnames(X) - c(paste(a, 1:20, sep=))
noX - X; noX[X!=0] - 0; cumX - noX; cumNoX - noX; Y1 - noX; Y2 - X; Y3
- X
for (e in 1:ncol(X)) {
cumX[,e] - cumsum(X[,e])
noX[X[,e] 1 cumsum(X[,e]) 0 ,e] - 1
cumNoX[,e] - cumsum(noX[,e])
}
Y1[cumNoX 0] - cumNoX[cumNoX 0] + 1
Y2[X == 0 noX 0] - Y1[X == 0 noX 0]
Y3 - Y2
Y3[cumX 1 noX 0] - Y2[cumX 1 noX 0] - cumX[cumX 1 noX 0]
X; Y3
Your help would be greatly appreciated! I'm stuck.
Thank you,
Tom
Johnson
__
R-help@r-project.org 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] display basename
Of course. I was just putting it inline to be as minimalist as possible... I'm in a minimal mood today... -- Bert Bert Gunter Nonclinical Statistics 7-7374 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Henrik Bengtsson Sent: Tuesday, November 20, 2007 3:25 PM To: Bert Gunter Cc: mysimbaa; r-help@r-project.org Subject: Re: [R] display basename So why not suggest pathname - file.choose() z - read.table(pathname, dec=., header=TRUE) instead. /Henrik On Nov 20, 2007 2:58 PM, Bert Gunter [EMAIL PROTECTED] wrote: z=read.table(chosen - file.choose(),dec=.,header=TRUE) will assign the return value of file.choose (the path names of the file as a character string) to chosen. This sort of code is seductive, but I find it quite difficult to read. I have also gotten myself into trouble from time to time doing it sloppily. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mysimbaa Sent: Tuesday, November 20, 2007 2:30 PM To: r-help@r-project.org Subject: [R] display basename Hello everybody, I'm sorry for asking a dumb question, but I don't find how to loos it. I need to display the name of the choosing file using this command : z=read.table(file.choose(),dec=.,header=TRUE) Thanks for any help. -- View this message in context: http://www.nabble.com/display-basename-tf4846650.html#a13866718 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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@r-project.org 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] Logarithmic axis
Hey John, You can do simply plot(reizstaerke, kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),log=x) but if you want to fine tune where the tick marks are, you can do it by hand. kennlinie1 - c(8.0746909, 3.9916973, 9.9789444, 19.962869); kennlinie2 - c(6.0994206, 8.9661081, 19.924883, 31.879496); reizstaerke - c(76, 92, 108, 124); plot(log10(reizstaerke), kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),axes=F) box() axis(1,at=log10(seq(75,125,by=5)),label=seq(75,125,by=5)) axis(2) The obvious reason that you are getting a plot with a single 100 and nothing else is that the range of the values in the reizstaerke vector is away from 10 and from 1000. If you really want to have the log scale in the way you described, you could do something like this: plot(log10(reizstaerke), kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),axes=F,xlim=log10(c(1,1000))) box() axis(1,at=log10(c(1,10,100,1000)),label=c(1,10,100,1000)) axis(2) Julian John Wiedenhoeft wrote: Hi there, I guess this must be a standard issue, but I'm starting to go crazy with it. I simply want a plot with the x axis being logarithmic, having labels 1, 10, 100..., and ten unlabelled ticks between each of them - just as they introduce logarithmic axis at school. I've played around a bit with log=x, xlog=T (where exactly is the difference here?), xaxp, and xaxt (unfortunately xaxt=l isn't implemented). The best I get is a plot with an axis having a single 100 and nothing else... here is what I've tried: pdf(file=kennlinien.pdf); par(log=x, xlog=TRUE); kennlinie1 - c(8.0746909, 3.9916973, 9.9789444, 19.962869); kennlinie2 - c(6.0994206, 8.9661081, 19.924883, 31.879496); reizstaerke - c(76, 92, 108, 124); #plot(reizstaerke, kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)), xlim=c(0, max(reizstaerke)), log=x, xlog=TRUE, xaxp=c(1, 2, 1), type=b); #plot(reizstaerke, kennlinie1, type=b, log=x, xlog=TRUE, xaxp=c(1, 2, 3)); plot(reizstaerke, kennlinie1, type=b,usr=c(min(reizstaerke), max(reizstaerke), min(kennlinie1, kennlinie2), max(kennlinie1, kennlinie2)), log=x, xlog=TRUE, xaxp=c(1, 2, 3)); #points(reizstaerke, kennlinie2, xlog=TRUE, xaxp=c(1, 3, 3), type=b); dev.off(); Certainly I've missed something, but I can't figure it out. Any help appreciated, Cheers, John platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) __ R-help@r-project.org 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@r-project.org 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] Logarithmic axis
Like always, there is much to be learned from the R-help list! Another message had a much simpler approach. plot(xy.coords(reizstaerke, kennlinie1, log=x), log=x) Julian Julian Burgos wrote: Hey John, You can do simply plot(reizstaerke, kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),log=x) but if you want to fine tune where the tick marks are, you can do it by hand. kennlinie1 - c(8.0746909, 3.9916973, 9.9789444, 19.962869); kennlinie2 - c(6.0994206, 8.9661081, 19.924883, 31.879496); reizstaerke - c(76, 92, 108, 124); plot(log10(reizstaerke), kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),axes=F) box() axis(1,at=log10(seq(75,125,by=5)),label=seq(75,125,by=5)) axis(2) The obvious reason that you are getting a plot with a single 100 and nothing else is that the range of the values in the reizstaerke vector is away from 10 and from 1000. If you really want to have the log scale in the way you described, you could do something like this: plot(log10(reizstaerke), kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)),axes=F,xlim=log10(c(1,1000))) box() axis(1,at=log10(c(1,10,100,1000)),label=c(1,10,100,1000)) axis(2) Julian John Wiedenhoeft wrote: Hi there, I guess this must be a standard issue, but I'm starting to go crazy with it. I simply want a plot with the x axis being logarithmic, having labels 1, 10, 100..., and ten unlabelled ticks between each of them - just as they introduce logarithmic axis at school. I've played around a bit with log=x, xlog=T (where exactly is the difference here?), xaxp, and xaxt (unfortunately xaxt=l isn't implemented). The best I get is a plot with an axis having a single 100 and nothing else... here is what I've tried: pdf(file=kennlinien.pdf); par(log=x, xlog=TRUE); kennlinie1 - c(8.0746909, 3.9916973, 9.9789444, 19.962869); kennlinie2 - c(6.0994206, 8.9661081, 19.924883, 31.879496); reizstaerke - c(76, 92, 108, 124); #plot(reizstaerke, kennlinie1, ylim=c(0, max(kennlinie1, kennlinie2)), xlim=c(0, max(reizstaerke)), log=x, xlog=TRUE, xaxp=c(1, 2, 1), type=b); #plot(reizstaerke, kennlinie1, type=b, log=x, xlog=TRUE, xaxp=c(1, 2, 3)); plot(reizstaerke, kennlinie1, type=b,usr=c(min(reizstaerke), max(reizstaerke), min(kennlinie1, kennlinie2), max(kennlinie1, kennlinie2)), log=x, xlog=TRUE, xaxp=c(1, 2, 3)); #points(reizstaerke, kennlinie2, xlog=TRUE, xaxp=c(1, 3, 3), type=b); dev.off(); Certainly I've missed something, but I can't figure it out. Any help appreciated, Cheers, John platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) __ R-help@r-project.org 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@r-project.org 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] Vectorization/Speed Problem
Let x be the input vector and cx be the cumulative running sum of it.
Then seq_along(cx) - match(cx, cx) gives increasing sequences
starting at 0 and for those after the leading zeros we start them
at 1 by adding cummax(x).
x - c(0, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0) # input
cx - cumsum(x)
seq_along(cx) - match(cx, cx) + cummax(x)
On Nov 20, 2007 6:42 PM, Tom Johnson [EMAIL PROTECTED] wrote:
Hi,
I cannot find a 'vectorized' solution to this 'for loop' kind of problem.
Do you see a vectorized, fast-running solution?
Objective:
Take the value of X at each timepoint and calculate the corresponding value
of Y. Leading 0's and all 1's for X are assigned to Y; otherwise Y is
incremented by the number of 0's adjacent to the last 1. The frequency and
distribution of X vary widely and may have ~100 repeated 0's or 1's in a
vector of 10k timepoints.
Example:
time 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
X0 1 0 1 0 1 0 0 1 1 1 0 0 0 . .
Y0 1 2 1 2 1 2 3 1 1 1 2 3 4 . .
What I have done:
My for() and apply()-related standard solutions are too slow. They are 6
times slower than my prototype, vectorized code which uses cumsum().
However(!)... my results are inaccurate and I can't correct them without
introducing a for()! Here is my shot at a vectorized solution, as far as I
can take it.
Preliminary Vectorized Code:
X - matrix(sample(c(1,0,0,0,0), 500, replace = TRUE), 25, 20,
byrow=TRUE)
colnames(X) - c(paste(a, 1:20, sep=))
noX - X; noX[X!=0] - 0; cumX - noX; cumNoX - noX; Y1 - noX; Y2 - X; Y3
- X
for (e in 1:ncol(X)) {
cumX[,e] - cumsum(X[,e])
noX[X[,e] 1 cumsum(X[,e]) 0 ,e] - 1
cumNoX[,e] - cumsum(noX[,e])
}
Y1[cumNoX 0] - cumNoX[cumNoX 0] + 1
Y2[X == 0 noX 0] - Y1[X == 0 noX 0]
Y3 - Y2
Y3[cumX 1 noX 0] - Y2[cumX 1 noX 0] - cumX[cumX 1 noX 0]
X; Y3
Your help would be greatly appreciated! I'm stuck.
Thank you,
Tom
Johnson
__
R-help@r-project.org 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] Is there a simpler way to do this?
Dear Friends,
My objective is to do element wise multiplication of two vectors. For example
suppose I have
a - (1,1,1)
b - (2,4)
My output should be (2,4,2,4,2,4). I managed to write it down with loops as
follows
r - c(1,1,1)
l - c(2,4)
x - 1
for (j in 1:3)
{
for (i in 1:2)
{
new[x,] - r[j]*l[i]
x - x+1
}
}
Is there a simpler solution to this without using the loops?
Thanks and Regards
Anup
-
Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.
[[alternative HTML version deleted]]
__
R-help@r-project.org 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] Is there a simpler way to do this?
On Tue, 2007-11-20 at 17:13 -0800, Anup Nandialath wrote:
Dear Friends,
My objective is to do element wise multiplication of two vectors. For example
suppose I have
a - (1,1,1)
b - (2,4)
My output should be (2,4,2,4,2,4). I managed to write it down with loops as
follows
r - c(1,1,1)
l - c(2,4)
x - 1
for (j in 1:3)
{
for (i in 1:2)
{
new[x,] - r[j]*l[i]
x - x+1
}
}
Is there a simpler solution to this without using the loops?
Thanks and Regards
Anup
Try this:
as.vector(t(a %o% b))
[1] 2 4 2 4 2 4
See ?outer for more information.
HTH,
Marc Schwartz
__
R-help@r-project.org 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] rowSums() and is.integer()
I wrote the original rowSums (in S-PLUS). There, rowSums() does not coerce integer to double. However, one advantage of coercion is to avoid integer overflow. Tim Hesterberg ... So, why does rowSums() coerce to double (behaviour that is undesirable for me)? __ R-help@r-project.org 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] How to select rows with identical index from two matrix?
Dear list, I have two martix like these, each rows with name in the matrix. I try to select rows with identical name from two matrix and calculate their correlation. Matrix1: 2-Sep9 5.51 7.18 10.08 139.45 2-Sep7 4.915 8.22 61.68 9 123.62 4-Sep 5-Sep AAMP A2M A2M . . . Matrix2: 2-Sep 4 71 6.8 128 19.4 2-Sep 2815 2.2 6.8 12 13.2 4-Sep AAMP AAMP ABCA5 A2M A2M I try to select rows with identical name from two matrix and calculate their correlation. However, I got trouble when loading these two matrix into R as header=TRUE. So I use header=FLASE and these name become character in the first column. How do I extract the first column of matrix 1 and compare to the first column of matrix 2? And if they are identical I compute their correlation? SIncerely yours, Chiahsin Liu [[alternative HTML version deleted]] __ R-help@r-project.org 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] Manipulating x axis in stripchart
Hi all,
I I need to manipulate the x axis in a stripchart.
I will use one of the data sets included in R to
explain what I need to do.
attach(ToothGrowth)
stripchart(len[supp=='VC']~dose[supp=='VC'],
vertical=TRUE, group.names=c('A','A','A'))
stripchart(len[supp=='OJ']~dose[supp=='OJ'], add=TRUE,
vertical=TRUE, at=c(1:3)+.1,
group.names=c('B','B','B'))
As you can read from the code above, I wanted to add
the 'B' to the x axis to diffrenciate each pair of
strips from each other. But only the 'A's appear.
I tried something like this too, but now '.5','1' and
'2' along with the 'A' and 'B'.
attach(ToothGrowth)
stripchart(len[supp=='VC']~dose[supp=='VC'],
vertical=TRUE)
axis(side=1,labels=c('A','B','A','B','A','B'),
at=c(.4,.5,.9,1.1,1.9,2.1))
stripchart(len[supp=='OJ']~dose[supp=='OJ'], add=TRUE,
vertical=TRUE, at=c(1:3)+.1)
And finally I tried setting par(xaxt='n') before
stripchart, but then I can't add anything to the x
axis.
Is there a way to manipulate the x axis in a
stripchart like this?
Thank you very much in advance for your help,
Judith
__
R-help@r-project.org 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] Manipulating x axis in stripchart
If its ok to use lattice try this:
library(lattice)
# no attach needed
# we want VC to be first level, not OJ
ToothGrowth$supp - relevel(ToothGrowth$supp, VC)
# rename levels
levels(ToothGrowth$supp) - c(A, B)
# plot
dotplot(len ~ supp | dose, ToothGrowth, layout = c(3, 1))
On Nov 20, 2007 10:04 PM, Judith Flores [EMAIL PROTECTED] wrote:
Hi all,
I I need to manipulate the x axis in a stripchart.
I will use one of the data sets included in R to
explain what I need to do.
attach(ToothGrowth)
stripchart(len[supp=='VC']~dose[supp=='VC'],
vertical=TRUE, group.names=c('A','A','A'))
stripchart(len[supp=='OJ']~dose[supp=='OJ'], add=TRUE,
vertical=TRUE, at=c(1:3)+.1,
group.names=c('B','B','B'))
As you can read from the code above, I wanted to add
the 'B' to the x axis to diffrenciate each pair of
strips from each other. But only the 'A's appear.
I tried something like this too, but now '.5','1' and
'2' along with the 'A' and 'B'.
attach(ToothGrowth)
stripchart(len[supp=='VC']~dose[supp=='VC'],
vertical=TRUE)
axis(side=1,labels=c('A','B','A','B','A','B'),
at=c(.4,.5,.9,1.1,1.9,2.1))
stripchart(len[supp=='OJ']~dose[supp=='OJ'], add=TRUE,
vertical=TRUE, at=c(1:3)+.1)
And finally I tried setting par(xaxt='n') before
stripchart, but then I can't add anything to the x
axis.
Is there a way to manipulate the x axis in a
stripchart like this?
Thank you very much in advance for your help,
Judith
__
R-help@r-project.org 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@r-project.org 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] skewness: generating distribution and estimating M3.
Dear Milton, package distrEx has methods to compute skewness. library(distrEx) ?skewness To generate new distributions you could use package distr. hth, Matthias Milton Cezar Ribeiro wrote: Dear all, How can I generate values which distrituions have left or rigth skewness. After that, which function compute the skewness of each distributions? Kind regards. miltinho para armazenamento! [[alternative HTML version deleted]] __ R-help@r-project.org 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@r-project.org 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] problem modeling time series
Good afternoon! I'm trying to model a ts but unfortunately i'.m very new to this kind of modeling so i 'll be very grateful if you have an advice. This was my syntax: t-c(16115,17391,19011,20256,19034,18851,20016,18088,19166,21163,18463,19397,15800,16113,18879,20598,17252,19753,19110,19605,20836,18868,20204,24384,15817,18223,19884,21059,18545,19853,20027,20061,21679,20210,20351,21322,16891,17111,20166,18735,16821,17891,17058,19250) plot.ts(t) acf(t) pacf(t) arima(t,order=c(13,2,0), seasonal=list(order=c(1,1,1)))-fit predict(fit, n.ahead=1) Now, choosing my order, was a trial and error process where i used the acf, pcf and AIC (which is minimized by taking those specific values) but as you can imagine this is something made by ear. I want to know if there is some test which can give me the proper values for the order? (i haven't found some full examples which describe the process fully from head to toe) Second, if this is the best fitting model for that specific ts, now don't you think that those standard errors are huge! Say, if the novice client eliminates that great rise/damp in the series and wants to predict solely based on his impressions from the time series he would probably give me the same interval, as the arima gave me, and i can't give him some new piece of info. Is there something wrong with my ts, or with my arima model, and how could i make that confidence interval smaller ? Thank you and have a great day! - [[alternative HTML version deleted]] __ R-help@r-project.org 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] Problems with NA's
somewhere I read that !is.na(your_vector) is better than your_vector!=NA
.
Thomas L Jones, PhD wrote:
Difficulty handling NA's:
Assume that I have a numeric vector y. For simplicity, assume that it has
10
elements. Assume that the third element has the value NA. I give it the
following:
NA_test - function (){
y - numeric (10)
y [3] - NA
if (y [3] != NA){(print (no)}
print (Leaving NA_test)
return ()
}# End of function
-
Unfortunately, things become confused involving the NA element.
Here is the output, starting with the loading process:
--
NA_test - function (){
+ y - numeric (10)
+ y [3] - NA
+ if (y [3] != NA){(print (no)}
Error: syntax error in:
y [3] - NA
if (y [3] != NA){(print (no)}
print (Leaving NA_test)
[1] Leaving NA_test
return ()
Error: no function to return from, jumping to top level
}# End of function
Error: syntax error in }
-
I have enclosed the print operation in braces to avoid possible problems
with it.
Your advice?
Tom Jones
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://www.nabble.com/Problems-with-NA%27s-tf4840964.html#a13872489
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org 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.
