[R] how to replace some objects?
I want to replace some objects in one row or column.For example, One colume: a,b,a,c,b,b,a,a,c. I want to replace a with 1, b with 2, and c with 3. Like this: 1,2,1,3,2,2,1,1,3. How to do it? I donot know how to do it. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to replace some objects?
you can use as.numeric(factor( )); in your example: ex - sample(letters[1:3], 10, T) ex [1] b b c b a a b b a a as.numeric(factor(ex)) [1] 2 2 3 2 1 1 2 2 1 1 if the order is different, use levels: as.numeric(factor(ex, levels=letters[3:1])) [1] 2 2 1 2 3 3 2 2 3 3 --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr --- Zhang Jian a écrit : I want to replace some objects in one row or column.For example, One colume: a,b,a,c,b,b,a,a,c. I want to replace a with 1, b with 2, and c with 3. Like this: 1,2,1,3,2,2,1,1,3. How to do it? I donot know how to do it. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question about debug package
Hi all, I am using the debug package, and I would like some commands executed automatically as I quit by qqq( ), I tried the on.exit( ) , but it doesn't work in this case. Any suggestions on this? thanks a lot . tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to replace some objects?
The example is simply.But the other example: One column: acba,coma,acmo,acmo,acba,coma I want to replace acba with aaa, coma with bbb, and acmo with ddd. Like this: aaa,bbb,ddd,ddd,aaa,bbb How to do it? Thanks. On 12/19/06, Jacques VESLOT [EMAIL PROTECTED] wrote: you can use as.numeric(factor( )); in your example: ex - sample(letters[1:3], 10, T) ex [1] b b c b a a b b a a as.numeric(factor(ex)) [1] 2 2 3 2 1 1 2 2 1 1 if the order is different, use levels: as.numeric(factor(ex, levels=letters[3:1])) [1] 2 2 1 2 3 3 2 2 3 3 --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr --- Zhang Jian a écrit : I want to replace some objects in one row or column.For example, One colume: a,b,a,c,b,b,a,a,c. I want to replace a with 1, b with 2, and c with 3. Like this: 1,2,1,3,2,2,1,1,3. How to do it? I donot know how to do it. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to replace some objects?
similarly: as.character(factor(c(abca,coma),labels=c(aaa,bbb))) --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr --- Zhang Jian a écrit : The example is simply.But the other example: One column: acba,coma,acmo,acmo,acba,coma I want to replace acba with aaa, coma with bbb, and acmo with ddd. Like this: aaa,bbb,ddd,ddd,aaa,bbb How to do it? Thanks. On 12/19/06, *Jacques VESLOT* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: you can use as.numeric(factor( )); in your example: ex - sample(letters[1:3], 10, T) ex [1] b b c b a a b b a a as.numeric(factor(ex)) [1] 2 2 3 2 1 1 2 2 1 1 if the order is different, use levels: as.numeric(factor(ex, levels=letters[3:1])) [1] 2 2 1 2 3 3 2 2 3 3 --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr --- Zhang Jian a écrit : I want to replace some objects in one row or column.For example, One colume: a,b,a,c,b,b,a,a,c. I want to replace a with 1, b with 2, and c with 3. Like this: 1,2,1,3,2,2,1,1,3. How to do it? I donot know how to do it. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailto:R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] proc GLM with R
At 05:15 18/12/2006, Cressoni, Massimo \(NIH/NHLBI\) [F] wrote:
I want to migrate from SAS to R.
I used proc mixed to do comparison between multiple groups and to perform
multiple comparison between groups since, as far as I know, proc
mixed does not make assumptions about the data and so
it is better than a simple anova (data must only be normal).
Es. how can I translate a code like this (two way anova with a factor of
repetition) :
proc mixed;
class kind PEEP codice;
model PaO2_FiO2 = kind PEEP kind*PEEP;
repeated /type = un sub=codice;
lsmeans kind*PEEP /adjust=bon;
run;
codice is a unique identifier of patient
kind is a variable which subdivided the patient (i.e. red or brown hairs)
PEEP is positive end expiratory pressure. These are the steps of a clinical
trial. Patient did the trial at PEEP = 5 and PEEP = 10
You could investigate either nlme or lme4
The best documentation for nlme (which should be included in your system) is
@BOOK{pinheiro00,
author = {Pinheiro, J C and Bates, D M},
year = 2000,
title = {Mixed-effects models in {S} and {S-PLUS}},
publisher = {Springer-Verlag},
address = {New York},
keywords = {glm; mixed models}
}
lme4 is a more recent development by Bates which as yet has slightly
fewer helper functions and no book.
Since you are assuming normal error you can use nlme. I am afraid I
do not read SAS so I think it would be wrong of me to try to
translate your example (traddutore, traditore and all that)
Thank you
Massimo Cressoni
run;
Michael Dewey
http://www.aghmed.fsnet.co.uk
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Re: [R] how to replace some objects?
On Dec 19, 2006, at 3:05 AM, Zhang Jian wrote:
I want to replace some objects in one row or column.For example,
One colume: a,b,a,c,b,b,a,a,c.
I want to replace a with 1, b with 2, and c with 3.
Like this: 1,2,1,3,2,2,1,1,3.
let - c('a', 'b', 'a', 'c', 'b', 'b', 'a', 'a', 'c')
library(car)
num - recode(let, 'a' = 1; 'b' = 2; else = 3 )
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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[R] configure help
Hello, as I just spent a (too long) while searching for a way how to persistantly switch back the help display routines from chm to text, here a small documentation how to do that with the windows version of R. The windows installer asks which help type you want to use, I wanted to test the chm version -- which I didn't like. If you after installation want to switch back, you have to edit myRdirectory\etc\Rprofile.site and change the line options(chmhelp=TRUE) back to options(chmhelp=FALSE) It would be nice if -- in a future release -- this also could be changed in the GUI settings. Best, Fridolin -- Fridolin Wild, Institute for Information Systems and New Media, Vienna University of Economics and Business Administration (WUW), Augasse 2-6, A-1090 Wien, Austria fon +43-1-31336-4488, fax +43-1-31336-746 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure help
On Tue, 19 Dec 2006, Fridolin Wild wrote: Hello, as I just spent a (too long) while searching for a way how to persistantly switch back the help display routines from chm to text, here a small documentation how to do that with the windows version of R. The windows installer asks which help type you want to use, I wanted to test the chm version -- which I didn't like. If you after installation want to switch back, you have to edit myRdirectory\etc\Rprofile.site and change the line options(chmhelp=TRUE) back to options(chmhelp=FALSE) It would be nice if -- in a future release -- this also could be changed in the GUI settings. But it has nothing to do with the GUI preferences: it applies to the command-line version of R as well. What about ?help did you not understand? It says chmhelp = getOption(chmhelp), ... chmhelp: logical (or 'NULL'). Only relevant under Windows. If 'TRUE' the Compiled HTML version of the help on the topic will be shown in a help viewer. so you need to set options(chmhelp=FALSE): it is up to you where you set it. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 1-D Image as label?
I have a data set for visualisation that comprises several sets of 1-D points over a given time span (the time span of the experiment). These are basically just several variable-length arrays of values whose units are seconds. I have several sets of further data relating to the nature of the experiment; Each describes each second in the experiment with an RGB colour triplet; this amounts to a 1 dimensional bitmap image whose axis is the same time axis of the former data set. I envisage one possible visualisation with the X axis (time) being annotated with one set of the colours from the latter data set. The Y axis would be either a histogram of the points from the former dataset, or (better, since the points are somewhat imprecise) a probability density function over time, derived from the gathered times themselves but assuming each represents an event that happened somewhere close to it. I am looking into using a density estimation function for this, as described in http://en.wikipedia.org/wiki/Density_estimation This brings me to my question; What would be the easiest way of annotating an axis with an array of colour triplets? Thanks for any insights/information you can offer, Gav __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Random Effects Model
Hi Ryan
Your model code suggests that Type is a variable that you have in your FREE
data frame, but you don't mention it, that is probably part of your problem?
The second question is how are your data structured? Sex goes in the fixed part
of the model. Swimmer is almost certainly goes in the random component, as you
have identified. The question is what to do with Swim. This could either be the
key variable of interest or simply a label representing replicates. What is the
hypothesis you're trying to test? When swimmers 1..n undertake swim 1 is this
all at the same time? If this is the case, do you have reason to believe that
there could be some similarlites (not sure what, maybe temperature, wind
conditions, fatigue) between swimmers on the same swim?
Without information on the data structure then its difficult to suggest
anything further. As a first guess you could try comparing:
m1 - lme(Difference~Sex, random=~1|Swimmer, data=FREE)
m2 - lme(Difference~Sex, random=~1|Swimmer/Swim, data=FREE)
With Swim in the fixed component of the model you're suggesting a linear
relationship between Difference and Swim, are you sure this is what you want?
If you really think Swim should be in the fixed compoent then you might want to
compare:
m3 - lme(Difference~Sex*Swim, random=~1|Swimmer, data=FREE)
m4 - lme(Difference~Sex*Swim, random=~Swim|Swimmer, data=FREE)
The latter will fit an overall relationship between Difference and Swim, and
then estimate both intercept and slope random effects for Swim.
regards
Mike D
[EMAIL PROTECTED] 19/12/2006 03:18
Hello,
I am new to R, and I am trying to figure out how to use it for a
random effects model. I am using version 2.4.0, and I also have the
book Applied Linear Regression by Sanford Weisberg.
I have four variables: Swimmer, Sex, Swim, and Difference. Swimmer
identifies the number assigned to a particular person. Sex is
male/female. Swim identifies the number swim from 1 to 6. Difference
is my variable of interest (random).
The book says I should run something like this:
library(nlme)
data(FREE) #FREE is my dataset
xyplot(Difference~Swim|Type, group=Swimmer, data=FREE,
+ panel.groups=function(x,y,...){
+ panel.linejoin(x,y,horizontal=FALSE,...)}
+ )
m1 - lme(Difference~Swim+Type, data=FREE, random=~1+Type|Swimmer)
m2 - update(m1, random=~1|Swimmer)
I've pretty much decided that xyplot doesn't work. Instead, I think
plot will work much better. I keep getting errors about Type. Can
someone explain this to me? Does the code above look right?
Any kind of help will be appreciated...
Thanks in advance!
Ryan
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Re: [R] configure help
Hey Brian, But it has nothing to do with the GUI preferences: it applies to the command-line version of R as well. I was suspecting this argument ;) -- however, I think from a usability point of view it should be possible to re-set the default setting also somewhere *within* the GUI if the GUI installer allows to set it. Maybe in a different place? What about ?help did you not understand? It says That is where I found how to set it (for my current workspace). Finding where I can set it *permanently* was more difficult (especially when you never had the need to mingle with R-profiles before). That's why I decided to document it here in the mailinglist just in case others have troubles finding it, too. Best, Fridolin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem in Dates
Read R News 4/1 help desk article and the last line of every message to r-help. Also putting POSIXlt objects into data frames is asking for trouble. On 12/19/06, Shubha Karanth [EMAIL PROTECTED] wrote: Hi Experts, I have a problem in Dates. I have a zoo object called 'intra'. And the class of index(intra) is (Chron Dates Time). I need to put the index of this zoo object into a data frame. So I used, idat-data.frame(Datetime=as.POSIXlt(index(intra),GMT)) But I get the values of 'idat' to be: 01joulu2006 09:59:59 01joulu2006 10:09:59 01joulu2006 10:19:59 01joulu2006 10:30:00 01joulu2006 10:40:00 01joulu2006 10:50:00 But I need the 'idat' format to be: 2006-12-01 13:30:00 2006-12-01 13:40:00 2006-12-01 13:50:00 2006-12-01 14:00:00 2006-12-01 14:10:00 2006-12-01 14:19:59 2006-12-01 14:29:59 i.e., instead of joulu (The finnish version of December) I need to get in the number format. How do I do this? Do I need to change the OS date format? Because I read a documentation which says Unfortunately, the documentation of POSIXt objects is Operating system dependent and especially under MS Windows several problems appear in the management of time zones and day light saving times (Source: R Documentation, timeDate Class). Thought this may help you… Thank you, Shubha. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question on lmer() function
On 12/17/06, Guojing Yang [EMAIL PROTECTED] wrote: Dear R users, We have encountered a slight problem when using the lmer() function: 1. Data description: 11 locations; Nt: monthly mosquito population density from 1994-2005 in each location. 2. Question: to examine the degree of spatial heterogeneity in the system by testing model support for single versus multiple intercepts and slopes for the location effect. We applied the lmer() function and introduced location as spatial effect. Four different models were generated as following: a. 1 intercept 1 slope : lmer(r~log(N)+(1|location)), where r - log(Nt/Nt-1) and location is a random effect. b. Multi-intercept 1 slope: lmer(r~location+log(N)+(1|location)) c. 1 slope multi-intercept: ?? d. Multi-intercept multi-slope: lmer(r~location*log(N)+(1|location)) I'm not exactly sure what you want to do here but you definitely should not have location as a fixed-effects term and a random effects term of the form (1|location). Such terms would be confounded. I think the models you want to fit would all have an (implicit) intercept and a log(N) term in the fixed effects. They would differ in terms of whether you have a random effect for the intercept by location and/or a random effect for the slope with respect to log(N) by location. Four variants are # random effects for intercept only lmer(r ~ log(N) + (1|location)) # random effects for slope only lmer(r ~ log(N) + (0+log(N)|location)) # possibly correlated random effects for intercept and slope lmer(r ~ log(N) + (log(N)|location)) # independent random effects for intercept and slope lmer(r ~ log(N) + (1|location) + (0+log(N)|location)) As you can see, we have had trouble defining model c. Does anyone know how to code this using lmer? We really appreciate any response. Guojing [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nonparametric significance test for one sample
Hello, Gurus: I tried to test if the sample mean of a dataset is zero. The data has 1500 numbers with a lot of zeros and some small positive numbers. The data range on [0,1] but the distribution is unknown. It is zero inflated anyway. I tried to use the Wilcoxon Signed Ranks test. But I read from this website that it does assume the population pdf is symmetric. http://www.cas.lancs.ac.uk/glossary_v1.1/nonparam.html#wsrt The Wilcoxon Signed Ranks test does not require the assumption that the population is normally distributed. In many applications, this test is used in place of the one sample t-testhttp://www.cas.lancs.ac.uk/glossary_v1.1/hyptest.html#1samptwhen the normality assumption is questionable. It is a more powerful alternative to the sign test, but does assume that the population probability distribution is symmetric. I wonder if wilcox.test( ) in R also assumes the symmetric pdf? I checked the sign test too. But the sign *test* is not *testing equality*of population If wilcox.test() cannot work for my data, I wonder if you could suggest a kind of test? I already tried t-test (assume normality) but I want to find something else. Many thanks! S [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Neural Network with Multiple Outputs
Hi! I want to use an artificial neural network of type MLP (Multi Level Perception) as a kind of generalized regression. In this case there are several binary outputs. I have been using Matlab with good results. But has anybody found a good package in R. Ralf Finne SYH University of Applied Sciences, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing values
--- downunder [EMAIL PROTECTED] wrote: Hi all, I have to recode some values in a dataset. for example changing all zeros to . or 999 would be also ok. does anybody know how to do this? thanks in advance. lars Hi Lars. Marc has warned you about . 999 vs NA A couple of approachs: aa - c(2,3,5,7,7, 3) aa[aa==7] - 5 aa or library(car) ?recode __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] xaxt=n for image()
Hi, The argument xaxt=n for removing the x axis from a image plot does not work for me. I'm really using a function called plot.grassmeta() in library GRASS that is a wrapper for image(), but it seems to me that the problem is not in plot.grassmeta() but in image(). If I'm right could you tell me if there is a way to remove one axis from a call to image()? Thanks and wishes, Javier - -- Javier García-Pintado Institute of Earth Sciences Jaume Almera (CSIC) Lluis Sole Sabaris s/n, 08028 Barcelona Phone: +34 934095410 Fax: +34 934110012 e-mail:[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure help
Hi All, I ma running R under windows with xemacs and ESS. The Rprofile.site options, somehow gets overridden by xemacs and my options in Rprofile.site are not taken into account while they are when I use Rgui. How can I specify my options if I am using xemacs? and what configuration file xemacs+ess use for R. Thanks AA - Original Message From: Brian Ripley [EMAIL PROTECTED] To: Fridolin Wild [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, December 19, 2006 7:15:11 AM Subject: Re: [R] configure help On Tue, 19 Dec 2006, Fridolin Wild wrote: Hello, as I just spent a (too long) while searching for a way how to persistantly switch back the help display routines from chm to text, here a small documentation how to do that with the windows version of R. The windows installer asks which help type you want to use, I wanted to test the chm version -- which I didn't like. If you after installation want to switch back, you have to edit myRdirectory\etc\Rprofile.site and change the line options(chmhelp=TRUE) back to options(chmhelp=FALSE) It would be nice if -- in a future release -- this also could be changed in the GUI settings. But it has nothing to do with the GUI preferences: it applies to the command-line version of R as well. What about ?help did you not understand? It says chmhelp = getOption(chmhelp), ... chmhelp: logical (or 'NULL'). Only relevant under Windows. If 'TRUE' the Compiled HTML version of the help on the topic will be shown in a help viewer. so you need to set options(chmhelp=FALSE): it is up to you where you set it. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with glmmADMB
library(glmmADMB) #Example for glmm.admb data(epil2) glmm.admb(y~Base*trt+Age +Visit,random=~Visit,group=subject,data=epil2,family=nbinom) Gives: Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = subject, : The function maximizer failed ** R version 2.4.1 RC (2006-12-14 r40181) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] utils stats graphics grDevices datasets methods base other attached packages: glmmADMB JGRiplotsJavaGD rJava MASS lattice 0.3 1.4-14 1.0-5 0.3-5 0.4-12 7.2-30 0.14-16 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Summary Tables for t.test?
Hi there, kind of a newbie-question, but anyway: is there a way to aggregate a nice table with input and results of a t-Test? I'm looking for something like a summary of Mean, Median, SD (seperated for both distributions) and p-value, df, etc. for the t-Test. I'm asking because i need a dozen of them and want to avoid putting those together by hand (output as LaTeX would be a nice extra ;) Best Greetings, Robert __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R 2.4.1 changes for SuSE users
Hi UseRs! RPMs for SuSE Versions 9.3 to 10.2 and bleeding edge aka openSUSE_Factory are available at http://software.opensuse.org/download/home:/dsteuer/ as I shifted the creation of these packages onto the Opensuse Build Service compiler farm. You can use the directories therein as installation sources for the respective versions of SuSE Linux. My goal is to put R-base back onto (open)suse's installation DVD, as it was a long, long time ago. Well, may be before there were DVDs :-) As the opensuse developers will take into account the usage of their repository to determine what new packages to include, I recommend using opensuse.org to download the R packages. Besides R-base you'll find littler and emacs-ess rpms for download. R-patched and R-devel will be added soon . I will not, for the moment, maintain the CRAN directories as installation sources, only as a repository for downloading rpms for a manual install. (There were strange problems anyway ...) So CRAN will stay complete, but I´ll use the comfort of the build service by opensuse. If the build service will stop some day, I´ll once again start to put proper installation sources on CRAN. Happy R´ing! Detlef --- Detlef Steuer Helmut-Schmidt-Universität Hamburg FB WOW [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with glmmADMB
glmmADMB only runs under two operating systems: Windows and Linux. hans ___ Michael Kubovy wrote: library(glmmADMB) #Example for glmm.admb data(epil2) glmm.admb(y~Base*trt+Age +Visit,random=~Visit,group=subject,data=epil2,family=nbinom) Gives: Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = subject, : The function maximizer failed ** R version 2.4.1 RC (2006-12-14 r40181) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] utils stats graphics grDevices datasets methods base other attached packages: glmmADMB JGR iplots JavaGD rJava MASS lattice 0.3 1.4-14 1.0-5 0.3-5 0.4-12 7.2-30 0.14-16 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: *http://www.people.virginia.edu/~mk9y/*http://www.people.virginia.edu/~mk9y/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: nonparametric significance test for one sample
-- Forwarded message -- From: HelponR [EMAIL PROTECTED] Date: Dec 19, 2006 9:28 AM Subject: nonparametric significance test for one sample To: r-help r-help@stat.math.ethz.ch Hello, Gurus: I tried to test if the sample mean of a dataset is zero. The data has 1500 numbers with a lot of zeros and some small positive numbers. The data range on [0,1] but the distribution is unknown. It is zero inflated anyway. I tried to use the Wilcoxon Signed Ranks test. But I read from this website that it does assume the population pdf is symmetric. http://www.cas.lancs.ac.uk/glossary_v1.1/nonparam.html#wsrt The Wilcoxon Signed Ranks test does not require the assumption that the population is normally distributed. In many applications, this test is used in place of the one sample t-testhttp://www.cas.lancs.ac.uk/glossary_v1.1/hyptest.html#1samptwhen the normality assumption is questionable. It is a more powerful alternative to the sign test, but does assume that the population probability distribution is symmetric. I wonder if wilcox.test( ) in R also assumes the symmetric pdf? I checked the sign test too. But the sign *test* is not *testing equality*of population If wilcox.test() cannot work for my data, I wonder if you could suggest a kind of test? I already tried t-test (assume normality) but I want to find something else. Many thanks! S [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] effect plot
Dear R users, Is there a simple way to use the effect function (library(effects)) with a GEE estimated model? library(gee) library(MASS) library(effects) attach(epil) b = gee(y ~ lbase*trt + lage + V4, family=poisson, id=subject, corstr=exchangeable) plot(effect(lbase*trt, b)) # Errore in effect(lbase*trt, b) : nessun metodo applicabile per effect [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Course***Salt Lake City** R/Splus Fundamentals and Programming Techniques
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce our Salt Lake City R/S-plus Fundamentals and Programming Techniques : www.xlsolutions-corp.com/Rfund.htm *** Salt Lake City / February 15-16, 2007 Should we bring this course to your city? please let us know! Reserve your seat now at the early bird rates! Payment due AFTER the class Course Description: This two-day beginner to intermediate R/S-plus course focuses on a broad spectrum of topics, from reading raw data to a comparison of R and S. We will learn the essentials of data manipulation, graphical visualization and R/S-plus programming. We will explore statistical data analysis tools,including graphics with data sets. How to enhance your plots, build your own packages (librairies) and connect via ODBC,etc. We will perform some statistical modeling and fit linear regression models. Participants are encouraged to bring data for interactive sessions With the following outline: - An Overview of R and S - Data Manipulation and Graphics - Using Lattice Graphics - A Comparison of R and S-Plus - How can R Complement SAS? - Writing Functions - Avoiding Loops - Vectorization - Statistical Modeling - Project Management - Techniques for Effective use of R and S - Enhancing Plots - Using High-level Plotting Functions - Building and Distributing Packages (libraries) - Connecting; ODBC, Rweb, Orca via sockets and via Rjava Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/training.htm Please let us know if you and your colleagues are interested in this classto take advantage of group discount. Register now to secure your seat! Interested in R/Splus Advanced course? email us. Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nonparametric significance test for one sample
If you data is truly limited to be non-negative and you are testing a null hypothesis that the true distribution mean is 0, then the test is fairly straight forward. There exists only one distribution with mean 0 and all values required to be = 0 and that is a point mass of 1 at 0. So if all of your data values are 0 then that means a p-value of 1 and if any data values are greater than 0 (even if it is only 1 value and it is only slightly greater than 0) then the p-value is 0. If you want to then estimate what the true mean is for an unknown distribution, then you may want to look at using a bootstrap estimate. Hope this helps, -- 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 HelponR Sent: Tuesday, December 19, 2006 8:29 AM To: r-help Subject: [R] nonparametric significance test for one sample Hello, Gurus: I tried to test if the sample mean of a dataset is zero. The data has 1500 numbers with a lot of zeros and some small positive numbers. The data range on [0,1] but the distribution is unknown. It is zero inflated anyway. I tried to use the Wilcoxon Signed Ranks test. But I read from this website that it does assume the population pdf is symmetric. http://www.cas.lancs.ac.uk/glossary_v1.1/nonparam.html#wsrt The Wilcoxon Signed Ranks test does not require the assumption that the population is normally distributed. In many applications, this test is used in place of the one sample t-testhttp://www.cas.lancs.ac.uk/glossary_v1.1/hyptest.html#1samptwhen the normality assumption is questionable. It is a more powerful alternative to the sign test, but does assume that the population probability distribution is symmetric. I wonder if wilcox.test( ) in R also assumes the symmetric pdf? I checked the sign test too. But the sign *test* is not *testing equality*of population If wilcox.test() cannot work for my data, I wonder if you could suggest a kind of test? I already tried t-test (assume normality) but I want to find something else. Many thanks! S [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] BioC Advanced Course Jan 10th-12th (Space Still Available)
Hello all, There is still space available for the upcoming BioC Advanced Course being held in Seattle January 10th-12th. For details and registration, please visit: https://secure.bioconductor.org/biocadv/ Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fit sine?
Hello list, I am making scatterplots of data that vary sinusoidally over 24 hours. With a bit of previous help from this list, I now can get an x-axis with time tics from 00:00 on the left edge to 12:00 in the middle and 00:00 on the right edge, i.e., just 24 hours. Now I would like to fit a sin function to the plot. I've looked all over CRAN and the web in general, but have not found a method or package for this. Can anyone make a suggestion? Thanks, =Randy= Using R 2.4.0 on Solaris (unix). R. Zelick email: [EMAIL PROTECTED] Department of Biology voice: 503-725-3086 Portland State University fax: 503-725-3888 mailing: P.O. Box 751 Portland, OR 97207 shipping: 1719 SW 10th Ave, Room 246 Portland, OR 97201 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] attach and object masking
Hi R users! I am new to R. When I try to attach a simple dataset using the attach() command, I get the following message: attach(data1) The following object(s) are masked from package:base : write Can someone tell me what this means? (`write' is the name of a variable in the dataset). And, do I need to do do something about this. Thanks. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] attach and object masking
On Tue, 19 Dec 2006, DEEPANKAR BASU wrote: Hi R users! I am new to R. When I try to attach a simple dataset using the attach() command, I get the following message: attach(data1) The following object(s) are masked from package:base : write Can someone tell me what this means? (`write' is the name of a variable in the dataset). And, do I need to do do something about this. It means that 'write' is the name of a variable in the dataset. R is warning you that you have two things called 'write' -- your variable and a function in the base package. It also means that you have missed at least three upgrades of R (the fourth is just out) since in version 2.3.0 and more recent you don't get the warning when a variable and a function have the same name, only for two variables or two functions. There have been quite a lot of other changes since your version of R, so it would be worth upgrading. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] attach and object masking
On Tue, 19 Dec 2006, Thomas Lumley wrote: It also means that you have missed at least three upgrades of R (the fourth is just out) since in version 2.3.0 and more recent you don't get the warning when a variable and a function have the same name, only for two variables or two functions. There have been quite a lot of other changes since your version of R, so it would be worth upgrading. I just noticed I didn't say explicitly whether you need to do anything else about the warning. You don't. -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with glmmADMB
Hi Michael, this error should be reported to the package maintainer, whom I assume to be the package author, Dave Fournier. I saw on his website: Questions relating to the R-package should be posted to the ADMB user forum under the topic ADMB NBMM for R http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html Cheers Andrew On Tue, Dec 19, 2006 at 11:04:56AM -0500, Michael Kubovy wrote: library(glmmADMB) #Example for glmm.admb data(epil2) glmm.admb(y~Base*trt+Age +Visit,random=~Visit,group=subject,data=epil2,family=nbinom) Gives: Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = subject, : The function maximizer failed ** R version 2.4.1 RC (2006-12-14 r40181) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] utils stats graphics grDevices datasets methods base other attached packages: glmmADMB JGRiplotsJavaGD rJava MASS lattice 0.3 1.4-14 1.0-5 0.3-5 0.4-12 7.2-30 0.14-16 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fit sine?
Read up on the discrete Fourier transform: http://en.wikipedia.org/wiki/Discrete_Fourier_transform http://en.wikipedia.org/wiki/Frequency_spectrum#Spectrum_analysis -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Randy Zelick Sent: Tuesday, December 19, 2006 2:52 PM To: R list server posting Subject: [R] fit sine? Hello list, I am making scatterplots of data that vary sinusoidally over 24 hours. With a bit of previous help from this list, I now can get an x-axis with time tics from 00:00 on the left edge to 12:00 in the middle and 00:00 on the right edge, i.e., just 24 hours. Now I would like to fit a sin function to the plot. I've looked all over CRAN and the web in general, but have not found a method or package for this. Can anyone make a suggestion? Thanks, =Randy= Using R 2.4.0 on Solaris (unix). R. Zelick email: [EMAIL PROTECTED] Department of Biology voice: 503-725-3086 Portland State University fax: 503-725-3888 mailing: P.O. Box 751 Portland, OR 97207 shipping: 1719 SW 10th Ave, Room 246 Portland, OR 97201 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] effect plot
Dear Ambrogi, -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ambrogi Federico Sent: Tuesday, December 19, 2006 12:03 PM To: r-help@stat.math.ethz.ch Subject: [R] effect plot Dear R users, Is there a simple way to use the effect function (library(effects)) with a GEE estimated model? Not that I'm aware. Sorry, John library(gee) library(MASS) library(effects) attach(epil) b = gee(y ~ lbase*trt + lage + V4, family=poisson, id=subject, corstr=exchangeable) plot(effect(lbase*trt, b)) # Errore in effect(lbase*trt, b) : nessun metodo applicabile per effect [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure help
This is the wrong list for ESS questions, as both the FAQ and rw-FAQ point out. However, if you read ?Startup you will see that Rprofile.site is not necessarily read on startup (and this is why I gave a more careful answer to Fridolin, for his instructions are not generic). On Tue, 19 Dec 2006, ahmad ajakh wrote: Hi All, I ma running R under windows with xemacs and ESS. The Rprofile.site options, somehow gets overridden by xemacs and my options in Rprofile.site are not taken into account while they are when I use Rgui. How can I specify my options if I am using xemacs? and what configuration file xemacs+ess use for R. Thanks AA - Original Message From: Brian Ripley [EMAIL PROTECTED] To: Fridolin Wild [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, December 19, 2006 7:15:11 AM Subject: Re: [R] configure help On Tue, 19 Dec 2006, Fridolin Wild wrote: Hello, as I just spent a (too long) while searching for a way how to persistantly switch back the help display routines from chm to text, here a small documentation how to do that with the windows version of R. The windows installer asks which help type you want to use, I wanted to test the chm version -- which I didn't like. If you after installation want to switch back, you have to edit myRdirectory\etc\Rprofile.site and change the line options(chmhelp=TRUE) back to options(chmhelp=FALSE) It would be nice if -- in a future release -- this also could be changed in the GUI settings. But it has nothing to do with the GUI preferences: it applies to the command-line version of R as well. What about ?help did you not understand? It says chmhelp = getOption(chmhelp), ... chmhelp: logical (or 'NULL'). Only relevant under Windows. If 'TRUE' the Compiled HTML version of the help on the topic will be shown in a help viewer. so you need to set options(chmhelp=FALSE): it is up to you where you set it. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] xaxt=n for image()
As the footer says, PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. example(image) image(x, y, volcano, col = terrain.colors(100), xaxt=n) works as is should, and we have no way to reproduce what _you_ did. On Tue, 19 Dec 2006, javier garcia-pintado wrote: The argument xaxt=n for removing the x axis from a image plot does not work for me. I'm really using a function called plot.grassmeta() in library GRASS that is a wrapper for image(), but it seems to me that the problem is not in plot.grassmeta() but in image(). If I'm right could you tell me if there is a way to remove one axis from a call to image()? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] attach and object masking
DEEPANKAR BASU [EMAIL PROTECTED] wrote: Hi R users! I am new to R. When I try to attach a simple dataset using the attach() command, I get the following message: attach(data1) The following object(s) are masked from package:base : write Can someone tell me what this means? (`write' is the name of a variable in the dataset). And, do I need to do do something about this. Hi, I guess, you need not to do anything, unless you want to work with the variable 'write' from dataset you try to attach. But if you do want use it safely (?), one way is to rename the variable from your dataset, not to double the name from the package that is already attached (check out search() to know the pecking order ;) and use ?attach to interprete the help page for yourself). The package gdata make the renaming process easier for me. MJ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Upgrading
Hi! As per Thomas' advice, I upgraded R by using update.packages() and got the following warning messages: Warning messages: 1: installation of package 'lmtest' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 2: installation of package 'quadprog' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 3: installation of package 'cluster' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 4: installation of package 'tseries' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, Do I need to worry about these messages? Do I need to do something else to complete the upgrade process? Another question: what is the command for renaming an existing variable? Thanks. Deepankar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing values
Hi Marc, thanks a lot. Your hint wiht logical conditions helped me already. Problem is I am working with SAS beside of R. In SAS the import of data and data manipulation is not that easy, thats why I try to code the data in the right format. So Thanks a lot for your hints. greetings lars -- View this message in context: http://www.nabble.com/-R--Replacing-values-tf2841687.html#a7956809 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Upgrading
On Tue, 19 Dec 2006, DEEPANKAR BASU wrote: Hi! As per Thomas' advice, I upgraded R by using update.packages() and got the following warning messages: That was not my advice on how to upgrade. update.packages() updates the packages. You need to download a new version of R itself. You will then need to update or reinstall the packages. The warning messages are because you are updating to versions of the packages that do not run on your old version of R. -thomas Warning messages: 1: installation of package 'lmtest' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 2: installation of package 'quadprog' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 3: installation of package 'cluster' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, 4: installation of package 'tseries' had non-zero exit status in: install.packages(update[, Package], instlib, contriburl = contriburl, Do I need to worry about these messages? Do I need to do something else to complete the upgrade process? Another question: what is the command for renaming an existing variable? Thanks. Deepankar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing values
Hi John, your example works also fine. Thats what I am looking for. Thanks so far. Greetings lars -- View this message in context: http://www.nabble.com/-R--Replacing-values-tf2841687.html#a7967398 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure help
Thanks Prof. Ripley Your point about the ESS list is well taken. I did read the initialization at the start of an R session but could not figure out why some of the options are ignored in the Rprofile.site. But I found out that theses options are re-defined in init.el file in .xemacs directory which seems obvious now to me. Thanks again for your help. AA. - Original Message From: Prof Brian Ripley [EMAIL PROTECTED] To: ahmad ajakh [EMAIL PROTECTED] Cc: Fridolin Wild [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Sent: Tuesday, December 19, 2006 5:38:18 PM Subject: Re: [R] configure help This is the wrong list for ESS questions, as both the FAQ and rw-FAQ point out. However, if you read ?Startup you will see that Rprofile.site is not necessarily read on startup (and this is why I gave a more careful answer to Fridolin, for his instructions are not generic). On Tue, 19 Dec 2006, ahmad ajakh wrote: Hi All, I ma running R under windows with xemacs and ESS. The Rprofile.site options, somehow gets overridden by xemacs and my options in Rprofile.site are not taken into account while they are when I use Rgui. How can I specify my options if I am using xemacs? and what configuration file xemacs+ess use for R. Thanks AA - Original Message From: Brian Ripley [EMAIL PROTECTED] To: Fridolin Wild [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, December 19, 2006 7:15:11 AM Subject: Re: [R] configure help On Tue, 19 Dec 2006, Fridolin Wild wrote: Hello, as I just spent a (too long) while searching for a way how to persistantly switch back the help display routines from chm to text, here a small documentation how to do that with the windows version of R. The windows installer asks which help type you want to use, I wanted to test the chm version -- which I didn't like. If you after installation want to switch back, you have to edit myRdirectory\etc\Rprofile.site and change the line options(chmhelp=TRUE) back to options(chmhelp=FALSE) It would be nice if -- in a future release -- this also could be changed in the GUI settings. But it has nothing to do with the GUI preferences: it applies to the command-line version of R as well. What about ?help did you not understand? It says chmhelp = getOption(chmhelp), ... chmhelp: logical (or 'NULL'). Only relevant under Windows. If 'TRUE' the Compiled HTML version of the help on the topic will be shown in a help viewer. so you need to set options(chmhelp=FALSE): it is up to you where you set it. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Switching labels on a factor
Chris, Argh!!! I was writing a reply just now insisting that the output below makes no sense when it finally hit me: the first line of output from the unclass function is just the data and bears no relationship whatsoever with the order of the m and f below it. I had gotten the idea that it picked up on the first value and so displayed the label to match. I don't even want to think about how much time I spent working on a problem that was nonexistent! Thank you very much for your help! Bob unclass(mydata$gR) [1] 2 2 2 2 1 1 1 1 attr(,levels) [1] m f = Bob Muenchen (pronounced Min'-chen), Manager Statistical Consulting Center U of TN Office of Information Technology 200 Stokely Management Center, Knoxville, TN 37996-0520 Voice: (865) 974-5230 FAX: (865) 974-4810 Email: [EMAIL PROTECTED] Web: http://oit.utk.edu/scc, News: http://listserv.utk.edu/archives/statnews.html = -Original Message- From: Chris Andrews [mailto:[EMAIL PROTECTED] Sent: Monday, December 18, 2006 12:05 PM To: Muenchen, Robert A (Bob) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Switching labels on a factor Bob, This is I think exactly what one wants to have happen. The first four observations are still women. Both the labels and the underlying integers should change. (If you want to give all the people sex changes, try Relevel in the Epi package. mydata$afterthechange - Relevel(mydata$gender, list(m=f, f=m)) mydata workshop gender q1 q2 q3 q4 gR afterthechange 11 f 1 1 5 1 f m 22 f 2 1 4 1 f m 31 f 2 2 4 3 f m 42 f 3 1 NA 3 f m 51 m 4 5 2 4 m f 62 m 5 4 5 5 m f 71 m 5 3 4 4 m f 82 m 4 5 5 NA m f unclass(mydata$afterthechange) [1] 1 1 1 1 2 2 2 2 attr(,levels) [1] m f Chris Date: Fri, 15 Dec 2006 15:34:15 -0500 From: Muenchen, Robert A (Bob) [EMAIL PROTECTED] Subject: [R] Switching labels on a factor To: R-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=US-ASCII Hi All, I'm perplexed by the way the unclass function displays a factor whose labels have been swapped with the relevel function. I realize it won't affect any results and that the relevel did nothing useful in this particular case. I'm just doing it to learn ways to manipulate factors. The display of unclass leaves me feeling that the relevel had failed. I've checked three books searched R-help, but found no mention of this particular issue. The program below demonstrates the problem. Is this a bug, or is there a reason for it to work this way? Thanks, Bob mystring- (id,workshop,gender,q1,q2,q3,q4 1,1,f,1,1,5,1 2,2,f,2,1,4,1 3,1,f,2,2,4,3 4,2,f,3,1, ,3 5,1,m,4,5,2,4 6,2,m,5,4,5,5 7,1,m,5,3,4,4 8,2,m,4,5,5,9) mydata-read.table(textConnection(mystring), header=TRUE,sep=,,row.names=id,na.strings=9) mydata # Create a gender Releveled variable, gR. # Now 1=m, 2=f mydata$gR - relevel(mydata$gender, m) # Print the data to show that the labels of gR match those of gender. mydata # Show that the underlying codes have indeed reversed. as.numeric(mydata$gender) as.numeric(mydata$gR) # Unclass the two variables to see that print order # implies that both the codes and labels have # flipped, cancelling each other out. For gR, # m appears to be associated with 2, and f with 1 unclass(mydata$gender) unclass(mydata$gR) = Bob Muenchen (pronounced Min'-chen), Manager Statistical Consulting Center U of TN Office of Information Technology 200 Stokely Management Center, Knoxville, TN 37996-0520 Voice: (865) 974-5230 FAX: (865) 974-4810 Email: [EMAIL PROTECTED] Web: http://oit.utk.edu/scc, News: http://listserv.utk.edu/archives/statnews.html -- Christopher Andrews, PhD SUNY Buffalo, Department of Biostatistics 242 Farber Hall, [EMAIL PROTECTED], 716 829 2756 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to do muliple comparisons in linear mixed models
Hi all, i want to compare the several main effects in a linear model. i wonder how to do the multiple comparisons for less confident intervals. Thanks a lot! -- Sincerely yours, Liu, jcheng Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R.matlab question
Does anyone know how to solve this question about R.matlab? I am in windowsXP, my matlab is matlab 7.0.0 19920(R14) thanks, Aimin matlab - Matlab(host=localhost, port=9998) if (!open(matlab)) throw(Matlab server is not running: waited 30 seconds.) Error in list(throw(Matlab server is not running: waited 30 seconds.) = environment, : [2006-12-17 22:26:03] Exception: Matlab server is not running: waited 30 seconds. at throw(Exception(...)) at throw.default(Matlab server is not running: waited 30 seconds.) at throw(Matlab server is not running: waited 30 seconds.) In addition: There were 30 warnings (use warnings() to see them) warnings function (...) UseMethod(warnings) warnings() Warning messages: 1: localhost:9998 cannot be opened 2: localhost:9998 cannot be opened 3: localhost:9998 cannot be opened 4: localhost:9998 cannot be opened 5: localhost:9998 cannot be opened 6: localhost:9998 cannot be opened 7: localhost:9998 cannot be opened 8: localhost:9998 cannot be opened 9: localhost:9998 cannot be opened 10: localhost:9998 cannot be opened 11: localhost:9998 cannot be opened 12: localhost:9998 cannot be opened 13: localhost:9998 cannot be opened 14: localhost:9998 cannot be opened 15: localhost:9998 cannot be opened 16: localhost:9998 cannot be opened 17: localhost:9998 cannot be opened 18: localhost:9998 cannot be opened 19: localhost:9998 cannot be opened 20: localhost:9998 cannot be opened 21: localhost:9998 cannot be opened 22: localhost:9998 cannot be opened 23: localhost:9998 cannot be opened 24: localhost:9998 cannot be opened 25: localhost:9998 cannot be opened 26: localhost:9998 cannot be opened 27: localhost:9998 cannot be opened 28: localhost:9998 cannot be opened 29: localhost:9998 cannot be opened 30: localhost:9998 cannot be opened __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] biocondutor installation problem
Hi,
I am trying to install Bioconductor software on our server with Red Hat
Linux Enterprise (Server) edition version 4, 32GB Ram and automatic
proxy configuration (http://www.ntu.edu.sg/proxy.pac) setting.
from http://www.bioconductor.org http://www.bioconductor.org/ website
but couldn't install.
I encounter the following errors highlighted in RED when I try to
download from the website.
source(http://www.bioconductor.org/biocLite.R;)
Error in file(file, r, encoding = encoding) :
unable to open connection
In addition: Warning message:
unable to connect to 'www.bioconductor.org' on port 80.
I place the address http://www.bioconductor.org/getBioC.R; in my
browser (MOZILLA-LINUX SERVER) the output is below.
source(http://bioconductor.org/getBioC.R;)
biocLite - function(pkgs, groupName=lite, ...)
{
if (missing(pkgs))
getBioC(groupName=groupName, ...)
else
getBioC(pkgs=pkgs, groupName=groupName, ...)
}
How do I setup the browser setting on my LINUX RH4 server?
Please guide how we can get rid of these errors.
Thanks
K.Asaithambi
Laboratory Executive
Nanyang Technological University
BioInformatics Research Centre (BIRC)
50 Nanyang Drive, Research Techno Plaza
XFrontiers Block, 3rd Storey
Singapore 637553
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and provide commented, minimal, self-contained, reproducible code.
[R] call by reference
Can anyone help me about pass by reference of arguments in R functions? I have read about .Alias in base package however it is defunct and there is no replacement for it. Thanks in advance. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
