Re: [R] text command - how to get a white background to cover grid lines
On 02/06/2012 08:23 AM, Henry wrote: New to R - rookie question. I'm a mechanical engineer and enjoying using R to make high quality graphs. I've searched. I want to put text notation on graph plot areas and have the text background box white to cover over the grid lines. my command so far text(15,5200,Air Flow,cex=.8,col=blue, background=white) # this doesn't work... I've tried bg=white, background color=white and a number of other attempts. The text is getting placed on the chart where I want it. Hi Henry, have a look at the boxed.labels function in the plotrix package. Jim __ 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] R-RApache to develop Knowledge Base
Hi, I am not sure about your data structure, but if you do not alter those often from third-party programs, then storing the information in R's native file formats (like RData) might give you some performance boost against always querying MySQL. Of course this depends on data structure and volume. Also, checking out some NoSQL techniques (like CouchDB or redis) might be a good idea for a web service - if your data is not profiting from relational database structure. Well, you need some benchmarks here. About plots: I would not say that the base graphics library (or even lattice) would be slow, although ggplot2 has some issues. So IMHO it depends on what type of plots would you generate, but I would say there would be no serious performance issues. After all: I think going the direct R way is great option :) Best, Gergely On Mon, Feb 6, 2012 at 07:36, MLSC mlscm...@gmail.com wrote: Hi all, I need your opinion about using R-Rapache to build a knowlegde base to bioinformatics field. I have copious amount of genotype information (some few million records) and would like to store it in MySQL database. Then, using RMySQL connector I would like to use it for further analysis using R over a web interface. The web interface which I am thnking off, just does not serve the purose of statistical analysis, it should also serve as displaying data in grids and interactive maps etc on web interface. I had thought of doing the same using python-MySQLdb to store data and then R-rpy for further statistical analysis. But as R is now directly made to work on web I am very much excited about RApache project. Very recently I was introducing Rapache project and concept of building knowledge base using Rapache-R-MySQL combination to our team memebrs, Unfortunately few memebers were not that happy with using R directly in middle tier. There were serious comments about R that it is slow and generating plots on the fly wont be too fast. there was also discussion about maturity of RMySQL database connector, i mean fastness of querying MySQL will vary significantly with RMySQL when campared to MySQLdb connector? It would be nice if you give me a detailed opinion on this. Thanking you all in anticipation. Regards, mlsc -- You received this message because you are subscribed to the Google Groups rapache group. To post to this group, send email to rapa...@googlegroups.com. To unsubscribe from this group, send email to rapache+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/rapache?hl=en. [[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] Problem with Snowball RWeka
Le jeudi 12 janvier 2012 à 15:18 -0800, plecto a écrit : Thanks! I read your shoer term solution and thanks to it was able to make stemming working in R for Mac OS X. I actually used Sys.setenv(NOAWT=TRUE) instead of Sys.setenv(NOAWT, true), as the latter produces the following error message: Error in Sys.setenv(NOAWT, true) : all arguments must be named. For people that might bump on this thread later while searching for help: if this solution did not work for you, make sure you run Sys.setenv(NOAWT= true) *before* loading Snowball/RWeka/rJava via library(). Else it won't have any effect. Hope this will save you some time ;-) __ 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] Makefile to compile .so in src
On 05.02.2012 23:17, Matyas Sustik wrote: Hi Uwe, 1. I don't believe you really need all the flags from above. If so, within a package, use a Makevars file. 2. R CMD SHLIB QUIC.cpp shoudl do the trick already, perhaps some linker flags are required for blas that can be specified in the same line, see R CMD SHLIB --help Thanks, I think I understand now better. I was not familiar with Makevars files (I only dealt with Makefiles before). I ended up simply using in the Makevars file: PKG_LIBS = $(LAPACK_LIBS) $(FLIBS) $(BLAS_LIBS) PKG_CXXFLAGS = -D_LANG_R which seems to do the job. I am just slightly uncertain about the $() notation; in some docs I saw @BLAS_LIBS@ to appear. So is $() ok? Is it the right syntax? The @BLAS_LIBS@ should typically appear in an .in file only rather than the Makevars file itself. Uwe Ligges Thanks again! -Matyas __ 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] Simple lm/regression question
On Mon, 6 Feb 2012, James Annan wrote: I am trying to use lm for a simple linear fit with weights. The results I get from IDL (which I am more familiar with) seem correct and intuitive, but the lm function in R gives outputs that seem strange to me. Unweighted case: x-1:4 y-(1:4)^2 summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: 1 2 3 4 1 -1 -1 1 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -5. 1.7321 -2.887 0.1020 x 5. 0.6325 7.906 0.0156 * So far, so good - IDL does much the same: IDL vec=linfit(x,y,sigma=sig) IDL print,vec,sig -5.0 5.0 1.73205 0.632456 Now, if the dependent variable has known (measurement) uncertainties (10, say) then it is appropriate to use weights defined as the inverse of the variances, right? If you think that in y = x'b + e the error has E(e^2) = sigma^2 * w then you should use weights = 1/w in R because that is how the weights enter the objective function sum 1/w (y - x'b)^2 summary(lm(y~x,weights=c(.01,.01,.01,.01))) Call: lm(formula = y ~ x, weights = c(0.01, 0.01, 0.01, 0.01)) Residuals: 1234 0.1 -0.1 -0.1 0.1 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -5. 1.7321 -2.887 0.1020 x 5. 0.6325 7.906 0.0156 * But here the *residuals* have changed and are no longer the actual response minus fitted values. (They seem to be scaled by the sqrt of the weights). The summary() shows under Residuals the contributions to the objective function, i.e. sqrt(1/w) (y - x'b) in the notation above. However, by using the residuals extractor function you can get the unweighted residuals: residuals(lm(y~x,weights=c(.01,.01,.01,.01))) The uncertainties on the parameter estimates, however, have *not* changed, which seems very odd to me. lm() interprets the weights as precision weights, not as case weights. Thus, the scaling in the variances is done by the number of (non-zero) weights, not by the sum of weights. The behaviour of IDL is rather different and intuitive to me: IDL vec=linfit(x,y,sigma=sig,measure_errors=[1,1,1,1]) IDL print,vec,sig -5.0 5.0 1.22474 0.447214 IDL vec=linfit(x,y,sigma=sig,measure_errors=[10,10,10,10]) IDL print,vec,sig -5.0 5.0 12.2474 4.47214 This appears to use sandwich standard errors. If you load the sandwich and lmtest package you can do coeftest(m, vcov = sandwich) where 'm' is the fitted lm object. Hope that helps, Z Note that the uncertainties are 10* larger when the errors are 10* larger. My question is really how to replicate these results in R. I suspect there is some terminology or convention that I'm confused by. But in the lm help page documentation, even the straightforward definition of residual seems incompatible with what the code actually returns: residuals: the residuals, that is response minus fitted values. But, in the weighted case, this is not actually true... James -- James D Annan jdan...@jamstec.go.jp Tel: +81-45-778-5618 (Fax 5707) Senior Scientist, Research Institute for Global Change, JAMSTEC Yokohama Institute for Earth Sciences, 3173-25 Showamachi, Kanazawa-ku, Yokohama City, Kanagawa, 236-0001 Japan http://www.jamstec.go.jp/frcgc/research/d5/jdannan/ __ 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] R's memory capabilities
Dear all, I have tried to create a diagonal matrix of size diag(65536) I am getting the message that the array function can not create so big array as the value I ask is larger than the environment: namespace:base .Machine$integer [1] 2147483647 as you will see my .Machine$integer is the one above. What that variable means? I am using R in a system that has 500 GB of ram available. Would it be something wrong in the installation? Regards Alex [[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] Simple lm/regression question
On Feb 6, 2012, at 10:57 , Achim Zeileis wrote: On Mon, 6 Feb 2012, James Annan wrote: The summary() shows under Residuals the contributions to the objective function, i.e. sqrt(1/w) (y - x'b) in the notation above. However, by using the residuals extractor function you can get the unweighted residuals: residuals(lm(y~x,weights=c(.01,.01,.01,.01))) The uncertainties on the parameter estimates, however, have *not* changed, which seems very odd to me. lm() interprets the weights as precision weights, not as case weights. Thus, the scaling in the variances is done by the number of (non-zero) weights, not by the sum of weights. The behaviour of IDL is rather different and intuitive to me: IDL vec=linfit(x,y,sigma=sig,measure_errors=[1,1,1,1]) IDL print,vec,sig -5.0 5.0 1.22474 0.447214 IDL vec=linfit(x,y,sigma=sig,measure_errors=[10,10,10,10]) IDL print,vec,sig -5.0 5.0 12.2474 4.47214 This appears to use sandwich standard errors. Actually, I think the issue is slightly different: IDL assumes that the errors _are_ something (notice that setting measure_errors to 1 is not equvalent to omitting them), R assumes that they are _proportional_ to the inverse weights, and proportionality to c(.01,.01,.01,.01) is not different from proportionality to c(1,1,1,1)... There are a couple of ways to avoid the use of the estimated multiplicative dispersion parameter in R, one is to extract cov.unscaled from the summary, another is to use summary.glm with dispersion=1, but I'm not quite sure how they interact with weights (and I don't have the time to check just now.) -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] R's memory capabilities
On Feb 6, 2012, at 11:15 , Alaios wrote: Dear all, I have tried to create a diagonal matrix of size diag(65536) I am getting the message that the array function can not create so big array as the value I ask is larger than the environment: namespace:base .Machine$integer [1] 2147483647 as you will see my .Machine$integer is the one above. What that variable means? I am using R in a system that has 500 GB of ram available. Would it be something wrong in the installation? Well, it means what it says. Indexing is limited by the size of a 32-bit integer and (2^16)^2 is too big for that. So you are limited to roughly 16 GB for any single object in R. This issue has been foreseeable for some time. It can only be fixed by internal changes in the R engine, but switching to long integers has various issues, so it is not a straightforward modification. Meanwhile, you might want to consider whether you really do need a diagonal matrix of that size stored in full. It's an awful lot of zeroes to carry around Regards Alex [[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. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] creating more vectors out of one
Dear R-helpers, I have got a vector which looks like the following: apkz - c(1,2,3,4,5,6,1,1,2,1,2,3,4) now I am trying to find a way to automatically create several vectors, each starting with the number 1, namely: First vector 1 2 3 4 5 6 Second vector 1 Thrid vector 1 2 Fourth vector 1 2 3 4 Does anyone know how to do that? Thank you very much for your help in advance! Marion [[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] creating more vectors out of one
Hi, This piece of R code does the trick: do.call(c, sapply(c(6,1,2,4), seq, from = 1)) regards, Paul On 02/06/2012 11:15 AM, Marion Wenty wrote: Dear R-helpers, I have got a vector which looks like the following: apkz - c(1,2,3,4,5,6,1,1,2,1,2,3,4) now I am trying to find a way to automatically create several vectors, each starting with the number 1, namely: First vector 1 2 3 4 5 6 Second vector 1 Thrid vector 1 2 Fourth vector 1 2 3 4 Does anyone know how to do that? Thank you very much for your help in advance! Marion [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 __ 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] creating more vectors out of one
Hi Dear R-helpers, I have got a vector which looks like the following: apkz - c(1,2,3,4,5,6,1,1,2,1,2,3,4) now I am trying to find a way to automatically create several vectors, each starting with the number 1, namely: First vector 1 2 3 4 5 6 Second vector 1 Thrid vector 1 2 Fourth vector 1 2 3 4 Does anyone know how to do that? This came to my mind as first, but I believe there are other options. split(apkz, cumsum(apkz==1)) Regards Petr Thank you very much for your help in advance! Marion [[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] fractional cointegration
Some typo in my question below: I am *attempting* to...not stempting... Regards Mamush -- Forwarded message -- From: mamush bukana mamushbuk...@gmail.com Date: Sun, Feb 5, 2012 at 12:13 AM Subject: fractional cointegration To: r-help@r-project.org Dear folk, I am stempting to estimate a vector error correction model using a seemingly fractionally integrated multivariate time series. The *fracdiff *package provides tools to estimate degree of fractional integration. But *fracdiff *can't help me to: 1. test equality of two degrees of fractional integration, say d1=d2? 2. estimate a multivariate cointegrating error correction model, like* ca.jo *function in* urca* does for standard cointegration. Can anyone suggest me if there is a way to do these in R please? Thanks in advance Mamush. [[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] R-Censoring
Hi there, can somebody give me a guide as to how to generate data from weibull distribution with censoring for example, the code below generates only failure data, what do i add to get the censored data, either right or interval censoring q-rweibull(100,2,10). Thank you Grace Kam student, University of Ghana [[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] R enterprise for linux
Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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] glht (multicomparisons) with a binomial response variable
Making sure you have the most recent version of rms, try require(rms) dd - datadist(catroj, month); options(datadist='dd') f - lrm(catroj ~ month) contrast(f, list(month=2:12), list(month=1), conf.type='simultaneous') The actual coding will depend on how month is defined. The contrast above contrasts January with all other months, with simultaneous confidence intervals provided by glht. Frank gaiarrido wrote Hi, I,ve a run a model like this mcrm-glm(catroj~month,binomial) being catroj a binary response variable with two levels (infected and non infected) anova(mcrm3,test=Chisq) Df Deviance Resid. Df Resid. Dev P(|Chi|) NULL 520 149.81 mes 316.86 517 132.94 0.0007551 *** When I´m trying to do a post comparisons between factors i tried with glht of multcomp package by Torsten Hothorn I use Tukey contrast, but dídn't get diferencies summary(glht(mcrm3,linfct=mcp(month=Tukey))) Estimate Std. Error z value Pr(|z|) may - april == 0 -18.2470 1555.0564 -0.012 1. june - april == 0 -1.9436 0.8307 -2.340 0.0671 . july - april == 0 -0.6253 0.5477 -1.142 0.6133 june - may == 016.3034 1555.0565 0.010 1. july - may == 017.6216 1555.0563 0.011 1. july - june == 01.3182 0.7899 1.669 0.2870 I'm afraid Tukey it is not the correct contrast, but, What should i use for a binary response variable? Any advice, please? - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/glht-multicomparisons-with-a-binomial-response-variable-tp4360898p4361171.html 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] coxme with frailty--variance of random effect?
In answer to the several questions: 1. Variance of the random effect: Your example is not reproducable since you didn't give the random number seed. Instead I'll use one of the data sets that comes with the survival package. library(coxme) fit - coxme(Surv(tstart, tstop, status) ~ treat + (1|center), cgd) VarCorr(fit)$center Intercept 0.1643779 var(ranef(fit)$center) Intercept [1] 0.06261608 Yes, it is true that for a random effects model, the estimated variance of the random effect is not equal to var(estimated per center effects). Exactly the same is true of a linear mixed effects model: try the same with lmer library(lme4) lfit(status ~ treat + (1|center), cgd) VarCorr(lfit)$center var(ranef(lfit)$center) Why? It's a statistical insight that took me a while, so I don't think I can explain it over email. Find someone familiar with mixed efffects models and have a chat. 2. coxph( +frailty(center)) and coxme give different results. Read the documentation. One of them is fitting a gamma distribution for the random effect, the other a Gaussian. Terry Therneau __ 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] 'deparse(substitute'))' then 'assign' in a S4 methods
Thanks Bill,
In France, there is a famous joke about politician: Tell me what you need,
I will explain you how to do without... But in my specific case, I can not
use the classical - and [, it is why I ask my question.
More precisely, my fonction fooBis can be very long to end. So I want to
update the value of my variable from time to time.
'assign' + break will work, whereas `fooBis-` - function(x, value) { x -
4 ; for(i in 1:1000){};x } + break will not work.
Christophe
--
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] R enterprise for linux
Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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] R's memory capabilities
peter dalgaard pdalgd at gmail.com writes: On Feb 6, 2012, at 11:15 , Alaios wrote: Dear all, I have tried to create a diagonal matrix of size diag(65536) [snip ...] Well, it means what it says. Indexing is limited by the size of a 32-bit integer and (2^16)^2 is too big for that. So you are limited to roughly 16 GB for any single object in R. This issue has been foreseeable for some time. It can only be fixed by internal changes in the R engine, but switching to long integers has various issues, so it is not a straightforward modification. Meanwhile, you might want to consider whether you really do need a diagonal matrix of that size stored in full. It's an awful lot of zeroes to carry around What Peter is hinting at (I think) is that you depending on your application you may be able to get away with using sparse matrices, which only store the positions and values of non-zero elements rather than the values of all elements. For example: library(Matrix) d - Diagonal(2^16) str(d) Formal class 'ddiMatrix' [package Matrix] with 4 slots ..@ diag: chr U ..@ Dim : int [1:2] 65536 65536 ..@ Dimnames:List of 2 .. ..$ : NULL .. ..$ : NULL ..@ x : num(0) object.size(d) 652 bytes vignette(Intro2Matrix) __ 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] GAM (mgcv) warning: matrix not positive definite
Thanks for the explanation !
Happy to know there is no problem with my models.
Have a good day,
Arnaud
2012/2/3 Simon Wood s.w...@bath.ac.uk
It is completely safe to ignore this. Here is what is going on...
mgcv routine 'mroot' is calling R routine 'chol' to find the *pivoted*
Choleski factor of a positive semi definite matrix. This is deliberate, and
completely ok to do, but 'chol' issues a warning when a matrix is only
positive semi-definite (as opposed to strictly +ve def), even if pivoting
has been requested. 'mroot' therefore suppresses the warning.
best,
Simon
On 03/02/12 20:38, Arnaud Mosnier wrote:
Dear list,
I fitted the same GAM model using directly the function gam(mgcv) ...
then as a parameter of another function that capture the warnings
messages (see below).
In the first case, there is no warning message printed, but in the last
one, the function find two warning messages stating matrix not positive
definite
So my question is: Do I have to worry about those warnings and then why
are they not printed in the simple use of the gam function.
##**###
Here is some further description:
## Simple use of gam
gam(USE ~ X1 + s(X2) + s(X3), family = binomial, data = data,
method=REML) # print no warning message.
## Using a function that capture warnings
Model_n_Warnings - function(expr) {
localWarnings - list()
outModel - withCallingHandlers(expr,
warning = function(w) {
localWarnings[[length(**localWarnings)+1]] - w$message #
store warning message
invokeRestart(muffleWarning) # avoid printing warning
message to console
})
list(outModel=outModel, warnings=localWarnings)
}
out - Model_n_Warnings (gam(USE ~ X1 + s(X2) + s(X3), family =
binomial, data = data, method=REML))
out$warnings
[[1]]
[1] matrix not positive definite
[[2]]
[1] matrix not positive definite
Thanks,
Arnaud
--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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Re: [R] Covariate model in nlme
SHAILLY MEHROTRA shaillymehrotra at gmail.com writes: I am using nlme to fit a pharmacokinetic model. The base model is parameterized in terms of CL, V1, V2 and Q. basemodel-nlme(Conc ~TwoCompModel(CL,Q,V1,V2,Time,ID), data = data2, fixed=list(CL+Q+V1+V2~1), random = pdDiag(CL+V1+V2~1), start=c(CL=log(20),Q=log(252),V1=log(24.9),V2=log(120)), control=list(returnObject=TRUE,msVerbose=TRUE, msMaxIter=20,pnlsMaxIter=20,pnlsTol=1), verbose=TRUE). Now, I want to include covariates (age and weight) in the base model. The relationships between CL and covariate is linear and given as the following equation. CL=TVCL+a*wt-b*age, where TVCL is mean clearance, a and b are coefficients of weight and age, respectively. I believe you want something like fixed=list(Q+V1+V2~1,CL~wt+age) Questions about mixed models may in general have better success on the r-sig-mixed-models at r-project.org mailing list. Ben Bolker __ 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] R enterprise for linux
Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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] R enterprise for linux
Are you sure? I just ran N - 128 system.time(matrix(rnorm(N^2),N) %*% matrix(rnorm(N^2),N)) and it took less than 0.044s on my (old-ish) laptop while doing other things (and that includes the expensive rng calls). There might be some other issues in play here. Even N - 1280 takes 5 seconds with the rng call. Michael On Mon, Feb 6, 2012 at 9:29 AM, Alaios ala...@yahoo.com wrote: Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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] R enterprise for linux
On Mon, 6 Feb 2012, Alaios wrote: Actually, I would like to speed up matrix multiplication which is really too slow. I believe that R supports openmp during configuration. This is the multi-processor library that allows threads to run on different cores or processors. In addition to Red Hat packages you can build Slackware packages using the scripts at www.slackbuilds.org. Rich __ 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] Logistic Regression
I am looking for R packages that can make a Logistic Regression model with parameter estimation by Maximum Likelihood Estimation. Many thanks for helping out. __ 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] R enterprise for linux
6-02-2012, 06:29 (-0800); Alaios escriu: Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. It doesn't seem normal to me... in my computer such a multiplication takes a fraction of a second: system.time(array(rnorm(128*128), c(128,128)) %*% array(rnorm(128*128), c(128,128))) user system elapsed 0.008 0.000 0.006 Am I missing something? Cheers, Ernest __ 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] R enterprise for linux
My bad.. these are the real matrices G-DiagonalGaussian( NumberOfImagePixels,sd=Gsd) str(G) num [1:16384, 1:16384] 1400 0 0 0 0 ... S-PointSamplingMatrix(EffectiveSensors,NumberOfImagePixels) str(S) num [1:10650, 1:16384] 0 0 0 0 0 0 0 0 0 0 ... A-S %*% G From: R. Michael Weylandt michael.weyla...@gmail.com Cc: Paul Hiemstra paul.hiems...@knmi.nl; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 3:39 PM Subject: Re: [R] R enterprise for linux Are you sure? I just ran N - 128 system.time(matrix(rnorm(N^2),N) %*% matrix(rnorm(N^2),N)) and it took less than 0.044s on my (old-ish) laptop while doing other things (and that includes the expensive rng calls). There might be some other issues in play here. Even N - 1280 takes 5 seconds with the rng call. Michael Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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. [[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] Logistic Regression
Hi, On Mon, Feb 6, 2012 at 10:08 AM, Ana rrast...@gmail.com wrote: I am looking for R packages that can make a Logistic Regression model with parameter estimation by Maximum Likelihood Estimation. How are you looking? Did you perhaps try Google https://www.google.com/#q=r-help+Logistic+Regression+Maximum+Likelihood+Estimation or rseek.org http://www.rseek.org/?cx=010923144343702598753%3Aboaz1reyxd4newwindow=1q=Logistic+Regression+Maximum+Likelihood+Estimationsa=Search+functions%2C+lists%2C+and+morecof=FORID%3A11siteurl=rseek.org%2F or one of the other R-centric search functions out there, like the ones built right into R? How did what you found not meet your needs? Sarah Many thanks for helping out. -- Sarah Goslee http://www.functionaldiversity.org __ 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] Writing to a file
Dear All!!
I am also new in R
and trying to write my results into a file I post here..hopefully is the
proper place
To be more secific I have this loop
counter = 0
for (i in 1:nrow(y))
{
for (j in 1:ncol(y))
{
if (y[i,j]==Func_0005634) {
counter = counter + 1 }
if(y[i,j]==Func_0005737){
counter = counter + 1 }
if(y[i,j]==Func_0005515){
counter = counter + 1 }
}
if(counter == 2) {
k-structure(list(print(y[i,1])), class = data.frame)
}
if(counter == 3 ){
l-structure(list(print(y[i,1])), class = data.frame)
}
counter = 0
}
for counter==2 or counter ==3
I want to get print(y[i,1])
where in column 1 exists the name of the protein
whereas in the rest columns exist somewhere randomly the strings im looking
for
I want to get the names of the proteins in a file and those that have either
2 or 3 functions be named as cancer.
the specific part of code gives me as a result in the command line this (is
a sample cause im working on 8500lines)
[1] Prot_10035
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
[1] Prot_10041
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
[1] Prot_10045
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
which is fine i can see the names of the proteins but i cant use them so to
label them
When I try to write it in a file ..then is kept only the last result because
unfortunatelly
he overwrites himself :(
How can I use those data? How can I write them in a file and add as an extra
column the word cancel
for those containing the specific functions?
Any hint you may give me it would be more than helpful for me!
Thank you a lot in advance!
Looking forward to your reply :)
--
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[R] glht (multicomparisons) with a binomial response variable
Hi, I,ve a run a model like this mcrm-glm(catroj~month,binomial) being catroj a binary response variable with two levels (infected and non infected) anova(mcrm3,test=Chisq) Df Deviance Resid. Df Resid. Dev P(|Chi|) NULL 520 149.81 mes 316.86 517 132.94 0.0007551 *** When I´m trying to do a post comparisons between factors i tried with glht of multcomp package by Torsten Hothorn I use Tukey contrast, but dídn't get diferencies summary(glht(mcrm3,linfct=mcp(month=Tukey))) Estimate Std. Error z value Pr(|z|) may - april == 0 -18.2470 1555.0564 -0.012 1. june - april == 0 -1.9436 0.8307 -2.340 0.0671 . july - april == 0 -0.6253 0.5477 -1.142 0.6133 june - may == 016.3034 1555.0565 0.010 1. july - may == 017.6216 1555.0563 0.011 1. july - june == 01.3182 0.7899 1.669 0.2870 I'm afraid Tukey it is not the correct contrast, but, What should i use for a binary response variable? Any advice, please? - Mario Garrido Escudero PhD student Dpto. de Biología Animal, Ecología, Parasitología, Edafología y Qca. Agrícola Universidad de Salamanca -- View this message in context: http://r.789695.n4.nabble.com/glht-multicomparisons-with-a-binomial-response-variable-tp4360898p4360898.html 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] AIC for piecewise and cuadratic comparison
Hi everybody, I would like to compare using the Akaike Information Criteria (AIC) a quadratic model and a piecewise fitted model. Is it correct to use AIC to compare this models with such a different structure? Thanks in advance Angel # A simple example a-1 b-2 xx-seq(-15,15,length=50) # Generate sequence of xs yy- 2 + 1.2*xx -0.2*xx^2 + runif(50, 0,8) #add some noise ## FIT models lmXX-lm(yy~xx) # Fit linear model cuad-lm(yy~xx+I(xx^2)) # Fit quadratic model require(quantreg) segXX-segmented(lmXX,seg.Z=~xx,psi=list(xx=5)) # Fit piecewise model ## Visualize results plot(xx,yy) plot.segmented(segXX,add=T) lines(xx,coef(cuad)[1]+coef(cuad)[2]*xx + coef(cuad)[3]*xx^2,col=blue) c(AIC_cuadratic=AIC(cuad),AIC_segmented=AIC(segXX)) # Obviously AIC for the cuadratic model is lower than piecewise, so I would chose this model over a piecewise fit in this case. But is the use of AIC correct? [[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] appending variable's values in table like fashion
i have two variable pyar [1] M 12 34 13 gita [1] U 22 33 44 want to append gita object below pyar object as want to take in anther variable M 12 34 13 U 22 33 44 write it in table fashion inside file -- View this message in context: http://r.789695.n4.nabble.com/appending-variable-s-values-in-table-like-fashion-tp4360966p4360966.html 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] how to access values from functions
Hi All
I would like to know how to access the values of the variable
lambda.mu and and see what abs(lambdas[1])
does since lambdas is not a keyword.
Snippet of the code:
scoreFunction - function(lambdas)
{
lambda.mu - abs(lambdas[1])
sme.em(yi,tmei,Xi,Ni,G,lambda.mu,lambda.v)$AICc
}
Thanks in advance.
Regards
Ap
--
Aparna Sampath
Master of Science (Bioinformatics)
Nanyang Technological University
Mob no : +65 91601854
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[R] using file in hdfs for data mining algorithms in r
hi all, i am new to r , i am trying to run data mining algorithms using map reduce framework.. * *i have few basic doubts* *1. can i give file in hdfs to kmeans( ) ? ?I tried as file1 = hdfs.file(testdata/synthetic_control.data) isf = hdfs.read(lsf,5242880,0) l = kmeans(isf,2,10) its not working.. please help 2. How to access the file in hdfs and give as input to algorithms ? please reply.. Regards, ./T.karthik* * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multiple comparisons in nested design
Dear professors and collegues I need to perform a analysis of dates from a nested experimental design. From Bioestatical Analysis of Zar Bimetry of Sokal Rohlf Design and Analysis of Experiments of Montgomery I have: Sum (mean(x)_i - mean(x)_T)2 / (a-1) - var(epsilon) + n sigma2_B + n b (sum alfa_i)2 / (a-1) Sum (mean(x)_ij - mean(x)_i)2 / (ba-a) - var(epsilon) + n sigma2_B Sum (x_ijl - mean(x)_ij)2 / (abn-ab) - var(epsilon) Dates for the execution of a example: # Mesures - as.data.frame(matrix(rnorm(45*1, mean=10, sd=1), ncol=1)) # colnames(Mesures) - VR # Mesures$trat - as.factor(rep(1:5,rep(9,5))) # Mesures$patient - as.factor(rep(1:15,rep(3,15))) The Analysis of Variance could be: # AnovaModel.1 -aov(VR ~ trat + trat/patient, data=Mesures) # summary(AnovaModel.1) Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.751 0.565 trat:patient 10 4.811 0.4811 0.915 0.533 Residuals30 15.778 0.5259 But this methods causes pseudoreplication because the F is the ratio of MS of trat and MS of res. However the variability of trat is at least as big as the variability of patient. The correct analysis suggested by ?aov is: # AnovaModel.2 - aov(VR ~ trat + Error(patient),data=Mesures) # summary(AnovaModel.2) Error: patient Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.821 0.541 Residuals 10 4.811 0.4811 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 30 15.78 0.5259 Althougth the Anova Model object it isn't a object of class aov but a object of classaovlist: # attr(AnovaModel.2,class) [1] aovlist listof This class isn't suitable for the glht function neither TukeyHSD function. I can extract a object of class aov through: # ls.str(pat=AnovaModel.2) AnovaModel.2 : List of 3 $ (Intercept):List of 9 $ patient:List of 9 $ Within :List of 6 # AnovaModel.3-AnovaModel.2$patient # attr(AnovaModel.3,class) [1] aov lm This model is suitable for confidence intervals: # confint(AnovaModel.3) 2.5 %97.5 % trat2 -0.9107959 0.5462655 trat3 -0.9848351 0.4722263 trat4 -1.2997235 0.1573379 trat5 -1.0623118 0.3947496 But it is useless for multiple comparisons: # Pairs - glht(AnovaModel.3, linfct = mcp(Tratamiento = Tukey)) Error in model.matrix.default(model, data = structure(list(method = lm), .Names = method), : model structure is invalid Error in factor_contrasts(model) : no 'model.matrix' method for 'model' found! # TukeyHSD(AnovaModel.3, Tratamiento) Error in model.tables.aov(x, means) : this fit does not inherit from lm Another way of analysis is through lme4 package: # AnovaModel.3 - lmer(VR ~ trat+(1|trat/patient), data=Mesures) But the anova test isn't the correct ratio above shown: # anova(AnovaModel.3) Analysis of Variance Table Df Sum Sq Mean Sq F value trat 4 0.43112 0.10778 0.2094 Other options for lmer: # anova(AnovaModel.4) Analysis of Variance Table Df Sum Sq Mean Sq F value trat 4 1.5801 0.39501 0.7675 Neither is the F ratio searched and above shown: # summary(AnovaModel.2) Error: patient Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.821 0.541 Residuals 10 4.811 0.4811 I can also take the mean of treatment, but if a measures of some patient fails, and the design becomes unbalanced, the results would be very difficult. Can anyone give me the right model and multiple comparisons? Thanks very much for the help and please excuse for my bad english. -- _---^---_ Univ. de Extremadura Dept. Matemáticas. Despacho B29 Tf: + 34 924 289 300 Ext. 86823 [[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] Orthogonal contrasts in mixed-effect models
Hello all, I am wiriting here to look for help!!! I am running a mixed-model effect lmer() relating the total species richnees observed in one place with some landscape indicators depending on three positions at field scale (Boundary, edge, centre) nested to the location where the survey was conducted. The model follow the next instruction lmer(a~position*%naturalvegetation + position*P/A+ (1|location) However, running the model in this way it is not possible to compare position between them and I have to run orthogonal contrast for this porpouse. my data matrix has the following structure Richness Location%NVP/A Location 3 1 34.3 0,43 B 5 2 45.2 0.33 B 12 3 21.2 0.21 E 64 11.2 0.21 E 8 135 76.3 0.29 C How can I run the orthogonal contrast. Somebody now how tu run it and the necessary code. Excuse me because I am not an stadistic people. I am botanic Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Orthogonal-contrasts-in-mixed-effect-models-tp4361007p4361007.html 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] multiple comparisons in nested design (error correction)
The last model is: AnovaModel.4 - lmer(VR ~ trat+(1|patient:trat), data=Mesures) Sorry. El 06/02/12 13:43, José Trujillo Carmona escribió: Dear professors and collegues I need to perform a analysis of dates from a nested experimental design. From Bioestatical Analysis of Zar Bimetry of Sokal Rohlf Design and Analysis of Experiments of Montgomery I have: Sum (mean(x)_i - mean(x)_T)2 / (a-1) - var(epsilon) + n sigma2_B + n b (sum alfa_i)2 / (a-1) Sum (mean(x)_ij - mean(x)_i)2 / (ba-a) - var(epsilon) + n sigma2_B Sum (x_ijl - mean(x)_ij)2 / (abn-ab) - var(epsilon) Dates for the execution of a example: # Mesures - as.data.frame(matrix(rnorm(45*1, mean=10, sd=1), ncol=1)) # colnames(Mesures) - VR # Mesures$trat - as.factor(rep(1:5,rep(9,5))) # Mesures$patient - as.factor(rep(1:15,rep(3,15))) The Analysis of Variance could be: # AnovaModel.1 -aov(VR ~ trat + trat/patient, data=Mesures) # summary(AnovaModel.1) Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.751 0.565 trat:patient 10 4.811 0.4811 0.915 0.533 Residuals30 15.778 0.5259 But this methods causes pseudoreplication because the F is the ratio of MS of trat and MS of res. However the variability of trat is at least as big as the variability of patient. The correct analysis suggested by ?aov is: # AnovaModel.2 - aov(VR ~ trat + Error(patient),data=Mesures) # summary(AnovaModel.2) Error: patient Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.821 0.541 Residuals 10 4.811 0.4811 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 30 15.78 0.5259 Althougth the Anova Model object it isn't a object of class aov but a object of classaovlist: # attr(AnovaModel.2,class) [1] aovlist listof This class isn't suitable for the glht function neither TukeyHSD function. I can extract a object of class aov through: # ls.str(pat=AnovaModel.2) AnovaModel.2 : List of 3 $ (Intercept):List of 9 $ patient:List of 9 $ Within :List of 6 # AnovaModel.3-AnovaModel.2$patient # attr(AnovaModel.3,class) [1] aov lm This model is suitable for confidence intervals: # confint(AnovaModel.3) 2.5 %97.5 % trat2 -0.9107959 0.5462655 trat3 -0.9848351 0.4722263 trat4 -1.2997235 0.1573379 trat5 -1.0623118 0.3947496 But it is useless for multiple comparisons: # Pairs - glht(AnovaModel.3, linfct = mcp(Tratamiento = Tukey)) Error in model.matrix.default(model, data = structure(list(method = lm), .Names = method), : model structure is invalid Error in factor_contrasts(model) : no 'model.matrix' method for 'model' found! # TukeyHSD(AnovaModel.3, Tratamiento) Error in model.tables.aov(x, means) : this fit does not inherit from lm Another way of analysis is through lme4 package: # AnovaModel.3 - lmer(VR ~ trat+(1|trat/patient), data=Mesures) But the anova test isn't the correct ratio above shown: # anova(AnovaModel.3) Analysis of Variance Table Df Sum Sq Mean Sq F value trat 4 0.43112 0.10778 0.2094 Other options for lmer: # anova(AnovaModel.4) Analysis of Variance Table Df Sum Sq Mean Sq F value trat 4 1.5801 0.39501 0.7675 Neither is the F ratio searched and above shown: # summary(AnovaModel.2) Error: patient Df Sum Sq Mean Sq F value Pr(F) trat 4 1.580 0.3950 0.821 0.541 Residuals 10 4.811 0.4811 I can also take the mean of treatment, but if a measures of some patient fails, and the design becomes unbalanced, the results would be very difficult. Can anyone give me the right model and multiple comparisons? Thanks very much for the help and please excuse for my bad english. -- _---^---_ Univ. de Extremadura Dept. Matemáticas. Despacho B29 Tf: + 34 924 289 300 Ext. 86823 -- _---^---_ Univ. de Extremadura Dept. Matemáticas. Despacho B29 Tf: + 34 924 289 300 Ext. 86823 [[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] MLEs using optim
I am trying to use the optim command to get the MLEs for a number of parameters based on some data. Is it possible to write a program that maximizes the likelihood and stores the parameters (many times)? I need to do this a lot of times, each time the data will be updated with more entries (rows). I need to see how the new data is affecting the previous parameter estimates of the model. What is the best way to do it? Thanks. -- View this message in context: http://r.789695.n4.nabble.com/MLEs-using-optim-tp4361361p4361361.html 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] Multi-page PDF using dev.copy2pdf(filename, onefile=TRUE)?
Hi all. I want to generate a sequence of n plots and save them into a single
PDF file, one plot per page. From the R docs and other sources I gather the
basic way to do this is save plot 1 into a file then append the 2:n plots to
the same file.
This code shows my basic approach, but for some reason only the last plot is
saved into the pdf. I've tried different variations (e.g. using onefile only in
the second call, or only in the first), to no avail. The comments show what I
see if I step through the code one line at a time:
scratch-function() {
graphics.off()
plot(1:7, 1:7) # Opens a graphics window and displays a 7-point plot in it, as
expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # I see the 7-point plot in Adobe
reader, as expected
plot(1:5, 1:5) # Overwrites in the graphics window the 7-point plot with a
5-point, as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # Overwrites test.pdf so that it
contains only the 7-point plot
}
A couple things:
(1) The reason I don't just use something like pdf(filename) plot(...)
plot(...) dev.off() is that I also want to see the plots before they're saved
(I pause after each plot() command). But according to the docs for
dev.copy2pdf(), that function accepts the same args as pdf() does, including
onefile.
(2) I wrap my code in a function to be able to use it in the StatEt debugger in
Eclipse.
If you know what I'm doing wrong, or know of a different/better way, advise
away! Thanks, Doug
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[R] Colors vector based on group
Hi everyone. I have a vector like this: x = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2) I would like to associate a colour to each of these entry. For example, I could use /topo.colors(3)/ (since I have 3 groups). I know it is easy to do this with /if/else/ statements, but I would like to find a proper way to do this. Thanks in advance, Phil -- View this message in context: http://r.789695.n4.nabble.com/Colors-vector-based-on-group-tp4361425p4361425.html 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] lmer with spatial and temporal random factors, not nested
Hi, I am new to this list. I have a question regarding including both spatial and temporal random factors in lmer. These two are not nested, and an example of model I try to fit is model1-lmer(Richness~Y+Canopy+Veg_cm+Treatment+(1|Site/Block/Plot)+(1|Year), family=poisson, REML=FALSE), where richness = integer Y Treatment = factor Canopy Veg_cm = numerical, continous Site/Block/Plot= factor Year = integer I get the following warning message: Warning messages: 1: In mer_finalize(ans) : Cholmod warning 'not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 2: In mer_finalize(ans) : singular convergence (7) Is this due to the nature of my fixed/random factors or the way I put up the random factors? In lme I could include a component for autocorrelation, ex:cor=corAR1(form=~Year|Site/Block/ID). Does the equivalent exist for lmer? I will be very happy if someone can help me! -- Thanks a lot Marte __ 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] R enterprise for linux
On Feb 6, 2012, at 10:17 AM, Alaios wrote: My bad.. these are the real matrices G-DiagonalGaussian( NumberOfImagePixels,sd=Gsd) str(G) num [1:16384, 1:16384] 1400 0 0 0 0 ... S-PointSamplingMatrix(EffectiveSensors,NumberOfImagePixels) str(S) num [1:10650, 1:16384] 0 0 0 0 0 0 0 0 0 0 ... A-S %*% G You seems confused about the size of your objects. You earlier said they were [128,128] which we took to mean 128 x 128 matrices, they are far larger than that. I'm guessing that you are consuming all of your RAM and paging out to disk. But that is just a guess since you provided none of the system information that the Posting Guide suggests. -- David. ___ From: R. Michael Weylandt michael.weyla...@gmail.com Cc: Paul Hiemstra paul.hiems...@knmi.nl; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 3:39 PM Subject: Re: [R] R enterprise for linux Are you sure? I just ran N - 128 system.time(matrix(rnorm(N^2),N) %*% matrix(rnorm(N^2),N)) and it took less than 0.044s on my (old-ish) laptop while doing other things (and that includes the expensive rng calls). There might be some other issues in play here. Even N - 1280 takes 5 seconds with the rng call. Michael Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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. [[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 Winsemius, MD West Hartford, CT __ 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] R enterprise for linux
That was my bad. (doing two things at same time) I am not out of memory by no means it is just that it only runs at one core. IF somehow R was able to see the many cores in my system. Regards Alex From: David Winsemius dwinsem...@comcast.net Cc: R. Michael Weylandt michael.weyla...@gmail.com; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 4:31 PM Subject: Re: [R] R enterprise for linux On Feb 6, 2012, at 10:17 AM, Alaios wrote: My bad.. these are the real matrices G-DiagonalGaussian( NumberOfImagePixels,sd=Gsd) str(G) num [1:16384, 1:16384] 1400 0 0 0 0 ... S-PointSamplingMatrix(EffectiveSensors,NumberOfImagePixels) str(S) num [1:10650, 1:16384] 0 0 0 0 0 0 0 0 0 0 ... A-S %*% G You seems confused about the size of your objects. You earlier said they were [128,128] which we took to mean 128 x 128 matrices, they are far larger than that. I'm guessing that you are consuming all of your RAM and paging out to disk. But that is just a guess since you provided none of the system information that the Posting Guide suggests. --David. ___ From: R. Michael Weylandt michael.weyla...@gmail.com Cc: Paul Hiemstra paul.hiems...@knmi.nl; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 3:39 PM Subject: Re: [R] R enterprise for linux Are you sure? I just ran N - 128 system.time(matrix(rnorm(N^2),N) %*% matrix(rnorm(N^2),N)) and it took less than 0.044s on my (old-ish) laptop while doing other things (and that includes the expensive rng calls). There might be some other issues in play here. Even N - 1280 takes 5 seconds with the rng call. Michael Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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. [[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 Winsemius, MD West Hartford, CT [[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] Colors vector based on group
On Feb 6, 2012, at 9:40 AM, Filoche wrote: Hi everyone. I have a vector like this: x = c (1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2 ) I would like to associate a colour to each of these entry. For example, I could use /topo.colors(3)/ (since I have 3 groups). I know it is easy to do this with /if/else/ statements, but I would like to find a proper way to do this. topo.colors(3)[c(1,2,3,1,2,3)] [1] #4C00 #00FF4DFF #00FF #4C00 #00FF4DFF #00FF -- David Winsemius, MD West Hartford, CT __ 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] appending variable's values in table like fashion
On Feb 6, 2012, at 6:29 AM, sagarnikam123 wrote: i have two variable pyar [1] M 12 34 13 gita [1] U 22 33 44 want to append gita object below pyar object as want to take in anther variable You could make a character matrix: cmat - matrix(c(pyar,gita), nrow=2, byrow=T) M 12 34 13 U 22 33 44 write it in table fashion inside file write.table(cmat, row.names=F, col.names=F) M 12 34 13 U 22 33 44 -- David Winsemius, MD West Hartford, CT __ 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] Colors vector based on group
On Mon, 6 Feb 2012, Filoche wrote: Hi everyone. I have a vector like this: x = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2) I would like to associate a colour to each of these entry. For example, I could use /topo.colors(3)/ (since I have 3 groups). I know it is easy to do this with /if/else/ statements, but I would like to find a proper way to do this. Simply use 'x' for subsetting, i.e., with your example topo.colors(3)[x]. See also the packages 'colorspace' or 'RColorBrewer' (amongst others) for different color palettes. hth, Z Thanks in advance, Phil -- View this message in context: http://r.789695.n4.nabble.com/Colors-vector-based-on-group-tp4361425p4361425.html 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] R's memory capabilities
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Alaios Sent: Monday, February 06, 2012 3:11 AM To: peter dalgaard Cc: R-help@r-project.org Subject: Re: [R] R's memory capabilities Thanks a lot for your answer :) actually I am converting a 256*256 image to a vector so to apply some 1-d transformations. Is it possible to create in R a sparse matrix instead of carrying all those zeros? So that means that I want to have a diagonal sparse matrix.. Thanks a lot Alex maybe look at ?as.vector. But it is really hard to know without knowing what you expect your vector to look like or what transforms you will be doing. Hope this is helpful, Dan Daniel Nordlund Bothell, WA USA __ 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] R-RApache to develop Knowledge Base
Have you tried Bioconductor (www.bioconductor.org http://www.bioconductor.org/)? Spencer On 2/5/2012 10:36 PM, MLSC wrote: Hi all, I need your opinion about using R-Rapache to build a knowlegde base to bioinformatics field. I have copious amount of genotype information (some few million records) and would like to store it in MySQL database. Then, using RMySQL connector I would like to use it for further analysis using R over a web interface. The web interface which I am thnking off, just does not serve the purose of statistical analysis, it should also serve as displaying data in grids and interactive maps etc on web interface. I had thought of doing the same using python-MySQLdb to store data and then R-rpy for further statistical analysis. But as R is now directly made to work on web I am very much excited about RApache project. Very recently I was introducing Rapache project and concept of building knowledge base using Rapache-R-MySQL combination to our team memebrs, Unfortunately few memebers were not that happy with using R directly in middle tier. There were serious comments about R that it is slow and generating plots on the fly wont be too fast. there was also discussion about maturity of RMySQL database connector, i mean fastness of querying MySQL will vary significantly with RMySQL when campared to MySQLdb connector? It would be nice if you give me a detailed opinion on this. Thanking you all in anticipation. Regards, mlsc [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web:www.structuremonitoring.com -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.com [[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] 'deparse(substitute'))' then 'assign' in a S4 methods
The interrupt issue is somewhat orthogonal to the SV4/scoping issue
you asked about. Trying to put things in the callers frame is
very tricky. E.g., SV4 methods can insert new frames between
your code and the caller. Perhaps you could try the following
sort of construct, in which your desired function is inside a
wrapper, whose only job is to collect results from the inner function.
Then make the outer function your SV4 method.
f - function (n) {
retval - NULL # just a placeholder so - from f_inner lands here
f_inner - function(n) {
on.exit({
retval - retval_inner # or could use assign(env=parent.env(), ...)
message(stashed retval_inner as retval)
})
retval_inner - 100
tryCatch(
expr = for (i in seq_len(n)) {
Sys.sleep(1)
retval_inner - retval_inner + 1
},
interrupt = function(...) message(interrupted in iteration , i))
}
f_inner(n)
retval
}
E.g.,
r - f(5)
stashed retval_inner as retval
r
[1] 105
rm(r)
r - f(50) # hit interrupt key after a few seconds
interrupted in iteration 4
stashed retval_inner as retval
r
[1] 103
sapply( 5:1, f) # hit interrupt key sporadically
stashed retval_inner as retval
interrupted in iteration 2
stashed retval_inner as retval
interrupted in iteration 3
stashed retval_inner as retval
interrupted in iteration 2
stashed retval_inner as retval
stashed retval_inner as retval
[1] 105 101 102 101 101
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of cgenolin
Sent: Monday, February 06, 2012 5:13 AM
To: r-help@r-project.org
Subject: Re: [R] 'deparse(substitute'))' then 'assign' in a S4 methods
Thanks Bill,
In France, there is a famous joke about politician: Tell me what you need,
I will explain you how to do without... But in my specific case, I can not
use the classical - and [, it is why I ask my question.
More precisely, my fonction fooBis can be very long to end. So I want to
update the value of my variable from time to time.
'assign' + break will work, whereas `fooBis-` - function(x, value) { x -
4 ; for(i in 1:1000){};x } + break will not work.
Christophe
--
View this message in context:
http://r.789695.n4.nabble.com/deparse-substitute-then-assign-in-a-S4-
methods-tp4356748p4361210.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] an unusual use for R
I love it. I hope you are planning a talk at the UseR!2012 in Nashville. Do remember the history that one of the origins of punchcards is the Jaquard loom. Rich On Thu, Feb 2, 2012 at 5:54 PM, Sarah Goslee sarah.gos...@gmail.com wrote: I thought some of you might be amused by this. In my non-work time, I'm an avid weaver and teacher of weaving. I'm working on a project involving creating many detailed weaving patterns, so I wrote R code to automate it. Details here: http://stringpage.com/blog/?p=822 If the overlap between R users and avid tablet weavers turns out to be 1, I'll polish it up and turn it into a package. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] histogram
Thanks. How do you suggest I use the reference population? Sorry, I'm new to R and just don't see it. If i can get a plot that is counts or density relative to my reference data it would be ideal. On Mon, Feb 6, 2012 at 1:12 AM, David Winsemius dwinsem...@comcast.netwrote: On Feb 5, 2012, at 8:31 PM, Francis Keyes wrote: With R and the hist function, is there a way to make a histogram in which the y axis denotes propotion with respect to a separate sample dataset of the same range instead of frequency? hist() returns an object with both counts and density. If you had a reference population it should be a fairly simple matter to use one or the other of those. -- David Winsemius, MD West Hartford, CT [[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] Multi-page PDF using dev.copy2pdf(filename, onefile=TRUE)?
Doug,
dev.copy2pdf closes the connection after it's done, so onefile is
meaningless. To look at each plot before copy to a single pdf, you
could open a pdf(...) but revert between it and your graphic device:
graphics.off()
plot(1:7, 1:7)
x11c- dev.cur() # your current graphics device
pdf(file=test.pdf)
dev.set(which=x11c) # back from pdf
dev.copy() # copy
dev.set(which=x11c)# back to graphic
plot(1:5, 1:5,col=2,pch=2)
dev.copy()
dev.set(which=x11c)
# ... etc. however many more plots
# don't forget to close the pdf device at the end:
dev.off(which=x11c+1)
# Both plots are in 'test.pdf'
Depending on your application you might be able to simplify things
with dev.next/dev.prev, or wrap this sequence into a little helper
function to be used in a loop.
Enjoy,
Elai
On Mon, Feb 6, 2012 at 6:44 AM, Doug Hill logic...@yahoo.com wrote:
Hi all. I want to generate a sequence of n plots and save them into a single
PDF file, one plot per page. From the R docs and other sources I gather the
basic way to do this is save plot 1 into a file then append the 2:n plots to
the same file.
This code shows my basic approach, but for some reason only the last plot is
saved into the pdf. I've tried different variations (e.g. using onefile only
in the second call, or only in the first), to no avail. The comments show
what I see if I step through the code one line at a time:
scratch-function() {
graphics.off()
plot(1:7, 1:7) # Opens a graphics window and displays a 7-point plot in it,
as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # I see the 7-point plot in Adobe
reader, as expected
plot(1:5, 1:5) # Overwrites in the graphics window the 7-point plot with a
5-point, as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # Overwrites test.pdf so that it
contains only the 7-point plot
}
A couple things:
(1) The reason I don't just use something like pdf(filename) plot(...)
plot(...) dev.off() is that I also want to see the plots before they're saved
(I pause after each plot() command). But according to the docs for
dev.copy2pdf(), that function accepts the same args as pdf() does, including
onefile.
(2) I wrap my code in a function to be able to use it in the StatEt debugger
in Eclipse.
If you know what I'm doing wrong, or know of a different/better way, advise
away! Thanks, Doug
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Re: [R] Logistic Regression
On 02/06/2012 03:08 PM, Ana wrote: I am looking for R packages that can make a Logistic Regression model with parameter estimation by Maximum Likelihood Estimation. Many thanks for helping out. __ 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. Hi Ana, I worked out some maximum likelihood estimates for logistic regression in R on my website: http://www.netstorm.be/home/lrm Best regards Thomas __ 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] histogram
On Feb 6, 2012, at 12:23 PM, Francis Keyes wrote: Thanks. How do you suggest I use the reference population? Sorry, I'm new to R and just don't see it. If i can get a plot that is counts or density relative to my reference data it would be ideal. It is difficult to specify how when we have no what. The what is your responsibility, not ours. My thought was to use the ratio of the results of hist() on the two populations which would then be offered back to hist or barplot. which (of course) requires that the 'breaks' be the same. Provide an example of your R representations of the reference population and tested population and all will become clear. (And learn to post in plain text, please.) -- David Winsemius, MD West Hartford, CT On Mon, Feb 6, 2012 at 1:12 AM, David Winsemius dwinsem...@comcast.net wrote: On Feb 5, 2012, at 8:31 PM, Francis Keyes wrote: With R and the hist function, is there a way to make a histogram in which the y axis denotes propotion with respect to a separate sample dataset of the same range instead of frequency? hist() returns an object with both counts and density. If you had a reference population it should be a fairly simple matter to use one or the other of those. __ 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 access values from functions
You can modify the function and add either a print() statement or a
browser() call as make sense for your purposes.
Type the name of the function to get the source: copy and edit it as
desired, and then run something like
funcName - newSource
Now when you run funcName it will run your new version rather than
whatever package you are using.
Michael
On Mon, Feb 6, 2012 at 6:52 AM, Aparna Sampath
aparna.sampat...@gmail.com wrote:
Hi All
I would like to know how to access the values of the variable
lambda.mu and and see what abs(lambdas[1])
does since lambdas is not a keyword.
Snippet of the code:
scoreFunction - function(lambdas)
{
lambda.mu - abs(lambdas[1])
sme.em(yi,tmei,Xi,Ni,G,lambda.mu,lambda.v)$AICc
}
Thanks in advance.
Regards
Ap
--
Aparna Sampath
Master of Science (Bioinformatics)
Nanyang Technological University
Mob no : +65 91601854
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Re: [R] R's memory capabilities
Use the Matrix package which provides easy access to sparse matrices. I think (unchecked) there's even easy provision for a diagonal sparse matrix. That said, if you are always working with diagonal matrices, couldn't you just keep the diagonals as vectors since the formulas for matrix multiplication reduce nicely in that case? Michael On Mon, Feb 6, 2012 at 6:10 AM, Alaios ala...@yahoo.com wrote: Thanks a lot for your answer :) actually I am converting a 256*256 image to a vector so to apply some 1-d transformations. Is it possible to create in R a sparse matrix instead of carrying all those zeros? So that means that I want to have a diagonal sparse matrix.. Thanks a lot Alex From: peter dalgaard pda...@gmail.com Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 11:54 AM Subject: Re: [R] R's memory capabilities On Feb 6, 2012, at 11:15 , Alaios wrote: Dear all, I have tried to create a diagonal matrix of size diag(65536) I am getting the message that the array function can not create so big array as the value I ask is larger than the environment: namespace:base .Machine$integer [1] 2147483647 as you will see my .Machine$integer is the one above. What that variable means? I am using R in a system that has 500 GB of ram available. Would it be something wrong in the installation? Well, it means what it says. Indexing is limited by the size of a 32-bit integer and (2^16)^2 is too big for that. So you are limited to roughly 16 GB for any single object in R. This issue has been foreseeable for some time. It can only be fixed by internal changes in the R engine, but switching to long integers has various issues, so it is not a straightforward modification. Meanwhile, you might want to consider whether you really do need a diagonal matrix of that size stored in full. It's an awful lot of zeroes to carry around Regards Alex [[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. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com [[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] na.action in stats::factanal() must be using formula interface and dataframe input to specify na.action?
hi, Does factanal() force the user to use the formula interface if they wish to specify an na.action? v1 - c(1,1,1,1,1,1,1,1,NA,1,3,3,3,3,3,4,5,6) v2 - c(1,2,1,1,1,1,2,1,2,1,3,NA,3,3,3,4,6,5) v3 - c(3,3,3,3,3,1,1,1,1,1,1,1,1,1,1,5,4,6) v4 - c(3,3,4,NA,3,1,1,2,1,1,1,1,2,NA,1,5,6,4) v5 - c(1,1,1,1,1,3,3,3,3,3,1,1,1,1,1,6,4,5) v6 - c(1,1,1,2,1,3,3,3,4,3,1,1,1,2,1,6,5,4) m1 - data.frame(cbind(v1,v2,v3,v4,v5,v6)) factOut = factanal(m1, factors = 1,scores = Bartlett, na.action=na.exclude) factOut = factanal(~v1+v2+v3+v4+v5+v6, data=m1, factors = 1,scores = Bartlett, na.action=na.exclude) __ 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] R enterprise for linux
I think there is some support for multi-processor matrix multiplication (google around for it) but in your case, it might suffice to use an optimized BLAS and R's builtin parallel facilities. As I said in your other thread -- if you are working with diagonal/sparse matrices, it's also possible to use special cases for efficient manipulations. Michael On Mon, Feb 6, 2012 at 10:47 AM, Alaios ala...@yahoo.com wrote: That was my bad. (doing two things at same time) I am not out of memory by no means it is just that it only runs at one core. IF somehow R was able to see the many cores in my system. Regards Alex From: David Winsemius dwinsem...@comcast.net To: Alaios ala...@yahoo.com Cc: R. Michael Weylandt michael.weyla...@gmail.com; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 4:31 PM Subject: Re: [R] R enterprise for linux On Feb 6, 2012, at 10:17 AM, Alaios wrote: My bad.. these are the real matrices G-DiagonalGaussian( NumberOfImagePixels,sd=Gsd) str(G) num [1:16384, 1:16384] 1400 0 0 0 0 ... S-PointSamplingMatrix(EffectiveSensors,NumberOfImagePixels) str(S) num [1:10650, 1:16384] 0 0 0 0 0 0 0 0 0 0 ... A-S %*% G You seems confused about the size of your objects. You earlier said they were [128,128] which we took to mean 128 x 128 matrices, they are far larger than that. I'm guessing that you are consuming all of your RAM and paging out to disk. But that is just a guess since you provided none of the system information that the Posting Guide suggests. --David. ___ From: R. Michael Weylandt michael.weyla...@gmail.com Cc: Paul Hiemstra paul.hiems...@knmi.nl; R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 3:39 PM Subject: Re: [R] R enterprise for linux Are you sure? I just ran N - 128 system.time(matrix(rnorm(N^2),N) %*% matrix(rnorm(N^2),N)) and it took less than 0.044s on my (old-ish) laptop while doing other things (and that includes the expensive rng calls). There might be some other issues in play here. Even N - 1280 takes 5 seconds with the rng call. Michael Actually, I would like to speed up matrix multiplication which is really too slow. MatrixA %*% MatrixB (each one is a [128,128] table) is running four hours now... and just imagine that I want to calculate many of those. Which other alternative do I have? Regards Alex From: Paul Hiemstra paul.hiems...@knmi.nl Cc: R-help@r-project.org R-help@r-project.org Sent: Monday, February 6, 2012 2:30 PM Subject: Re: [R] R enterprise for linux Dear Alex, By Enterprise R, do you mean Revolution R? I can also only find red hat packages. You could send them an e-mail to ask for sources. They probably want to help you, especially when you pay. But why do you need RevoR and not standard R. Paul On 02/06/2012 12:55 PM, Alaios wrote: Dear all, I would like to ask you if it would be possible to install R enterprise in opensuse. Actually it seems that there are only Red Hat packages and I was wondering if their source code is available so one to try and compile it. I would like to thank you in advance for your reply Regards Alex [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 [[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. [[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 Winsemius, MD West Hartford, CT __ 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] Writing to a file
You don't say how you are writing to a file, but some methods have an
append = TRUE option that might be helpful.
Your code looks really inefficient as well: I don't have time to look
at it fully now, but it seems to me that you can vectorize the inner
loops quite directly:
for(j in ncol(y)){
if(y[i,j]==Func_0005515){
counter = counter + 1 }
}
}
could become
counter = counter + sum(y[i, ] == Func_0005515)
Michael
On Mon, Feb 6, 2012 at 5:50 AM, Felicity felicity...@hotmail.com wrote:
Dear All!!
I am also new in R
and trying to write my results into a file I post here..hopefully is the
proper place
To be more secific I have this loop
counter = 0
for (i in 1:nrow(y))
{
for (j in 1:ncol(y))
{
if (y[i,j]==Func_0005634) {
counter = counter + 1 }
if(y[i,j]==Func_0005737){
counter = counter + 1 }
if(y[i,j]==Func_0005515){
counter = counter + 1 }
}
if(counter == 2) {
k-structure(list(print(y[i,1])), class = data.frame)
}
if(counter == 3 ){
l-structure(list(print(y[i,1])), class = data.frame)
}
counter = 0
}
for counter==2 or counter ==3
I want to get print(y[i,1])
where in column 1 exists the name of the protein
whereas in the rest columns exist somewhere randomly the strings im looking
for
I want to get the names of the proteins in a file and those that have either
2 or 3 functions be named as cancer.
the specific part of code gives me as a result in the command line this (is
a sample cause im working on 8500lines)
[1] Prot_10035
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
[1] Prot_10041
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
[1] Prot_10045
8527 Levels: Prot_0 Prot_1 Prot_10 Prot_100 Prot_1000 Prot_1 ...
Prot_9996
which is fine i can see the names of the proteins but i cant use them so to
label them
When I try to write it in a file ..then is kept only the last result because
unfortunatelly
he overwrites himself :(
How can I use those data? How can I write them in a file and add as an extra
column the word cancel
for those containing the specific functions?
Any hint you may give me it would be more than helpful for me!
Thank you a lot in advance!
Looking forward to your reply :)
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Re: [R] [newbie] storage/use of user's own functions?
At 04:06 06/02/2012, Joshua Wiley wrote: Hi Tom, I don't believe there is a standard location. You can set variables or have functions run (say to source other functions in) in your .Rprofile file. That way, you always have them. Once you get more than a handful of functions, it is probably time to consider putting them into your own package. This allows you to document them etc. then accessing them is as easy as loading your package. Also makes checking and distributing to others easier of that ever comes up. May I endorse Josh's suggestion to consider writing your own package to include them. I put off doing this for too long. There is a bit of learning to do first but the investment will repay itself. You need the extensions manual, at least the early chapters. Hope this helps, Josh On Feb 5, 2012, at 19:48, Tom Roche tom_ro...@pobox.com wrote: I'm new but am already starting to accumulate utility functions for the fairly specialized kinds of data files with which I work. I'd like to keep those functions in a single folder, or filetree rooted at a specific folder under my $HOME (I'm running linux), for ease of * source()-ing * git commit to bitbucket * scp to clusters I'm wondering, 1 is there a canonical location for personal functions, notably on linuxen? 2 how can one make that location most easily available? or must one always provide either a relative path from one's R cwd, or an FQ path to, the personal-functions folder? Apologies if this is a FAQ, but I didn't see anything about it @ http://cran.r-project.org/doc/FAQ/R-FAQ.html http://cran.r-project.org/doc/manuals/R-admin.html or in casual rseek-ing. TIA, Tom Roche tom_ro...@pobox.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. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.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] ggplot2 geom_polygon fill
Hi everyone,
i've been trying to make a special plot with ggplot2, but I can't get it to
fill the polygon I'd like to see filled so very very much.
I want to display the difference or change in the distribution of the
modified Rankin Scale between two groups. mRS is a scale for disability or
daily activities competence.
It looks like this.
http://r.789695.n4.nabble.com/file/n4361919/rankinplot.png
I just wish the polygons in between the bars would fill in the same colors
as the bar segments do.
Interestingly, in the example provided by the geom_polygon help page, there
is a fill, which leads me to suspect that something with my data frame might
be wrong.
If I supply a colour argument, I get borders, but not always in the color
I defined. The attached image has such borders, to make clear what polygons
I am talking about. In the final plot I don't desire such borders, only the
as of yet unattainable fill.
Here's my code:
library(ggplot2)
library(plyr)
# define good looks
no_margins - opts(
axis.line = theme_blank(),
axis.text.x = theme_blank(),
axis.ticks =theme_blank(),
axis.title.x = theme_text(size = 12, vjust = 0.15),
axis.title.y = theme_text(angle = 90, size = 12, vjust = 0.2),
axis.ticks.length = unit(0, cm),
axis.ticks.margin = unit(0, cm),
panel.background = theme_blank(),
panel.grid.major = theme_blank(),
panel.grid.minor = theme_blank(),
plot.background = theme_blank(),
plot.title =theme_blank(),
plot.margin = unit(c(1, 1, 1, 1.5), lines)
)
sfm = scale_fill_manual(mRS, c(0=darkgreen,
1=forestgreen,
2=mediumseagreen,
3=coral,
4=red,
5=darkred,
6=black))
barwidth = 0.6
# good looks defined
smalldummy = data.frame(
mRS = as.factor(rep(0:6,2)),
rsfreq = sample(0:6,14,replace=T),
treatment = factor(rep(c(one,two),each=7))
)
smalldummy = ddply(smalldummy, .(treatment), transform,
textpos = cumsum(rsfreq/sum(rsfreq)) -
rsfreq/sum(rsfreq)/2, # center within segment
lineposx = cumsum(rsfreq/sum(rsfreq)))
# segment borders without 0
# make the xs of the polygon
polylo = 1 + barwidth/2
polyhi = 2 - barwidth/2
xs = rep(c(polylo,polyhi,polyhi,polylo), 7)
# make the ys of the polygon
tmp1 = c(0, smalldummy$lineposx[1:7])
tmp2 = c(0, smalldummy$lineposx[8:14])
ys = c()
for(i in 1:7) {
nu = c(tmp1[i], tmp2[i], tmp2[i+1], tmp1[i+1])
ys = c(ys, nu)
}
m = as.factor(rep(0:6, each=4))
tmpdf = data.frame(xs, ys, mRS = m)
bigdummy = merge(smalldummy, tmpdf, by = mRS)
ggplot(data = bigdummy, aes(x = treatment, y = rsfreq, fill = mRS)) +
geom_bar(aes(width = barwidth),stat=identity,position=fill) +
geom_text(aes(label=as.character(mRS),
y = ifelse(rsfreq != 0, textpos, NA)),
size = 8, colour = white) +
geom_polygon(aes(x = xs, y = ys, group = mRS, fill = mRS)) +
ylab(Modified Rankin Scale) + xlab(Treatment) +
coord_flip() + theme_bw() + opts(legend.position = none) + no_margins +
sfm
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Colors vector based on group
Hello, I have a vector like this: x = c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,2,2,2,2,2,2,2,2) I would like to associate a colour to each of these entry. For example, I could use topo.colors(3) (since I have 3 groups). I know it is easy to do this with if/else statements, but I would like to find a proper way to do this. Easy, after knowing how many colors are there, just use 'x' as an index vector: ncolrs - length(unique(x)) colrs - topo.colors(ncolrs) xcolrs - colrs[x] Or, in one instruction, xcolrs2 - topo.colors(length(unique(x)))[x] all.equal(xcolrs, xcolrs2) Hope this helps, Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/Colors-vector-based-on-group-tp4361425p4361662.html 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] UTF8
trying to change the locale like this * Sys.setlocale(Macintosh HD)* failed with the following error: *Error in Sys.setlocale(Macintosh HD) : invalid 'category' argument* -- View this message in context: http://r.789695.n4.nabble.com/UTF8-tp873280p4361803.html 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] Colors vector based on group
Hi there. I should have thought about that myself (/shame). Thank you very much for your time. Phil -- View this message in context: http://r.789695.n4.nabble.com/Colors-vector-based-on-group-tp4361425p4361686.html 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] UTF8
As far as I can see it, those are two problems. The default locale and the language problem. I have exactly the same, I am using Mac OSX 10.6.8. I have also tried installation of packages. When installing a package I get a related error message: *tar: Failed to set default locale* if I enter * Sys.getlocale()* the results is *[1]=C* so, I guess I have to tell R that the default system disk it shall work with is Macintosh HD ... but how do I do that? Additionally I have this language/ASCII problem, and the help suggested by the R Cran Project (to enter *defaults write org.R-project.R force.LANG 'en_US'.UTF-8*) does not work. I get the message *Error: unexpected symbol in defaults write* I am new to R and just installed it onto my computer, after a basic training course ... maybe someone could help us? Thank you, Norma -- View this message in context: http://r.789695.n4.nabble.com/UTF8-tp873280p4361777.html 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] Heckman selection Model with HLM structure
Hello, I am trying to estimate a 2-stage selection Model where the first probit stage is whether the customer bought (0/1) and the second stage is given that the customer bought, how much did they spend (revenue). However, in my data, customers are nested within customer service agents and customer service agents are nested within countries, thereby requiring an mixed model or HLM format. Do you know of code that would accommodate this? I found code for a Heckit model and one more HLM models but not one that combines both. Any help would be greatly appreciated. Thanks in advance. Nita [[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] an unusual use for R
On Mon, Feb 6, 2012 at 5:14 PM, Richard M. Heiberger r...@temple.edu wrote: I love it. I hope you are planning a talk at the UseR!2012 in Nashville. Maybe we'll have hand-woven R-logo lanyards for our conference badges? Get weaving Sarah! Barry __ 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] Disable contrasts in lme
Dear all, I am trying to disable the contrast statement in the lme function of the package nlme. Is there a way to do this? This is needed as I have only one group. Thank you so much in advance, Saskia Freytag -- Saskia Freytag Department of Genetic Epidemiology Georg-August University Göttingen Humboltallee 32 37073 Göttingen Germany Office Phone: +49 551 39 14234 __ 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] UTF8
On Feb 6, 2012, at 11:26 AM, Norma wrote: trying to change the locale like this * Sys.setlocale(Macintosh HD)* failed with the following error: *Error in Sys.setlocale(Macintosh HD) : invalid 'category' argument* You are confused about what the locale setting is used for. They are for your geographic location (to have reasonable defaults for language and character sets), not for manipulating your hardware settings. ?locales You should also post Mac-specific questipn to the Mac-SIG list and even more important describe what you are trying to do. -- David Winsemius, MD West Hartford, CT __ 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] Suggestion for drop the loser design and analysis in R?
Hello all, I would like to plan and analyse a study with k treatments (one of which is a control), with some binary outcome, in order to find the best treatment (e.g: the one with a high number of successes). If this was done with a fixed sample size, the analysis is well known. However, I would rather be able to drop treatment(s), if at any (or some specific) point in the analysis, I find it (or them) inferior to the control. *What correction/analysis might I use in order to find the best treatment, while dropping bad treatments during the experiment?* After searching through google scholar, the most relevant article I found was Drop-the-losers design: Binomial case by Michael W. Sill , Allan R. Sampson - yet I was not able to find an implementation for their ideas. Thanks up front for any lead/idea on this topic. (p.s: this question was also cross-posted to http://stats.stackexchange.com/questions/22355/suggestion-for-drop-the-loser-design-and-analysis-in-r ) With regards, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[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] UTF8
On Feb 6, 2012, at 11:18 AM, Norma wrote: As far as I can see it, those are two problems. The default locale and the language problem. I have exactly the same, I am using Mac OSX 10.6.8. I have also tried installation of packages. When installing a package I get a related error message: *tar: Failed to set default locale* You should include details about the name of the package , the repository where you got it and the R console commands you issued. The error message makes me wonder if you are trying to install a source package without the correct settings and software, but that is very much a wild guess in the absence of those missing elements. if I enter * Sys.getlocale()* the results is *[1]=C* It would be much better if you abandoned the convention of sticking asterisks at the ends of output. People cannot tell whether those are actually there. (I suspect not on the basis of my experience.) so, I guess I have to tell R that the default system disk it shall work with is Macintosh HD ... but how do I do that? Additionally I have this language/ASCII problem, and the help suggested by the R Cran Project (to enter *defaults write org.R-project.R force.LANG 'en_US'.UTF-8*) My settings do not have the single quotes around: en_US.UTF-8 does not work. I get the message *Error: unexpected symbol in defaults write* Tjat looks like an R message. It appears you are entering that string at the R console. It is only going to work if you use it in a Terminal session ( _without_ the asterisks and probably _without_ the unnecessary single quotes.) I am new to R and just installed it onto my computer, after a basic training course ... maybe someone could help us? You appear to also need to spend time studying the Mac OS, since you are conflating OS commands with R commands. I suggest you first read through the Mac R FAQ before doing anything more to alter your system settings. Thank you, Norma -- View this message in context: http://r.789695.n4.nabble.com/UTF8-tp873280p4361777.html 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. David Winsemius, MD West Hartford, CT __ 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] Genetic based classification tree induction
Hi , everybody Does R has some package is able genetic based search for optimal decision tree model Thanks, Nissim [[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] I bet apply has a solution
Hi all For the data below, I would like to return a logical value indicating differences in the data. #Create data Data..-data.frame(a=rep(1,10),b=c(rep(1,9),2),c=c(rep(1,8),2,2)) a b c 1 1 1 1 2 1 1 1 3 1 1 1 4 1 1 1 5 1 1 1 6 1 1 1 7 1 1 1 8 1 1 1 9 1 1 2 10 1 2 2 So what I want is to return logical value telling me if all the values are the same. So the result would be a b c DidChange 1 1 1 1 FALSE 2 1 1 1 FALSE 3 1 1 1 FALSE 4 1 1 1 FALSE 5 1 1 1 FALSE 6 1 1 1 FALSE 7 1 1 1 FALSE 8 1 1 1 FALSE 9 1 1 2 TRUE 10 1 2 2 TRUE I bet apply could handle this elegantly but that family of functions is still not 100% intuitive to me. Thoughts. Thanks everyone Cheers, Josh -- View this message in context: http://r.789695.n4.nabble.com/I-bet-apply-has-a-solution-tp4362294p4362294.html 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] Writing to a file
maybe I could keep each line (having the strings) in a file or somewhere and then call a print function that prints them all together from where I saved them? Please let me know as soon as Possible!! thank you! -- View this message in context: http://r.789695.n4.nabble.com/Writing-to-a-file-tp3070617p4362340.html 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] Reordering levels of a factor when the factor is part of a data frame
Hello R-users, I have a data frame whose names of columns I don't know a priori, but the user of my code will know them. The user is supposed to save the name of the column that will need some reordering of the levels of the factor later on. The name of the column will be saved in an object called: variab the data frame is called df. If I try to the do following: df[variab]-factor(df[variab], levels=c(A2B,B31,C33)) it won't work because df[variab] is a data frame. The reason for reordering the levels of the factor is because once that variable is plotted, the levels of the factor need to appear in certain order. How can I re-order the levels of a factor whose name I don't know? Thank you, Judith [[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] I bet apply has a solution
How bout: apply(Data..,1, function(vec) !all(vec==vec[1])) [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE On Mon, Feb 6, 2012 at 10:34 AM, LCOG1 jr...@lcog.org wrote: Hi all For the data below, I would like to return a logical value indicating differences in the data. #Create data Data..-data.frame(a=rep(1,10),b=c(rep(1,9),2),c=c(rep(1,8),2,2)) a b c 1 1 1 1 2 1 1 1 3 1 1 1 4 1 1 1 5 1 1 1 6 1 1 1 7 1 1 1 8 1 1 1 9 1 1 2 10 1 2 2 So what I want is to return logical value telling me if all the values are the same. So the result would be a b c DidChange 1 1 1 1 FALSE 2 1 1 1 FALSE 3 1 1 1 FALSE 4 1 1 1 FALSE 5 1 1 1 FALSE 6 1 1 1 FALSE 7 1 1 1 FALSE 8 1 1 1 FALSE 9 1 1 2 TRUE 10 1 2 2 TRUE I bet apply could handle this elegantly but that family of functions is still not 100% intuitive to me. Thoughts. Thanks everyone Cheers, Josh -- View this message in context: http://r.789695.n4.nabble.com/I-bet-apply-has-a-solution-tp4362294p4362294.html 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. [[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] I bet apply has a solution
Hi Josh, How about apply(Data, 1, function(row) sd(row) == 0) ? Best, Ista On Mon, Feb 6, 2012 at 1:34 PM, LCOG1 jr...@lcog.org wrote: Hi all For the data below, I would like to return a logical value indicating differences in the data. #Create data Data..-data.frame(a=rep(1,10),b=c(rep(1,9),2),c=c(rep(1,8),2,2)) a b c 1 1 1 1 2 1 1 1 3 1 1 1 4 1 1 1 5 1 1 1 6 1 1 1 7 1 1 1 8 1 1 1 9 1 1 2 10 1 2 2 So what I want is to return logical value telling me if all the values are the same. So the result would be a b c DidChange 1 1 1 1 FALSE 2 1 1 1 FALSE 3 1 1 1 FALSE 4 1 1 1 FALSE 5 1 1 1 FALSE 6 1 1 1 FALSE 7 1 1 1 FALSE 8 1 1 1 FALSE 9 1 1 2 TRUE 10 1 2 2 TRUE I bet apply could handle this elegantly but that family of functions is still not 100% intuitive to me. Thoughts. Thanks everyone Cheers, Josh -- View this message in context: http://r.789695.n4.nabble.com/I-bet-apply-has-a-solution-tp4362294p4362294.html 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] Reordering levels of a factor when the factor is part of a data frame
Hi Judith, You should use double brackets, like this: df[[variab]]-factor(df[[variab]], levels=c(A2B,B31,C33)) see ?[ for details, noting that the help page assumes that you know data.frames are list-like objects. Best, Ista On Mon, Feb 6, 2012 at 2:03 PM, Judith Flores jur...@yahoo.com wrote: Hello R-users, I have a data frame whose names of columns I don't know a priori, but the user of my code will know them. The user is supposed to save the name of the column that will need some reordering of the levels of the factor later on. The name of the column will be saved in an object called: variab the data frame is called df. If I try to the do following: df[variab]-factor(df[variab], levels=c(A2B,B31,C33)) it won't work because df[variab] is a data frame. The reason for reordering the levels of the factor is because once that variable is plotted, the levels of the factor need to appear in certain order. How can I re-order the levels of a factor whose name I don't know? Thank you, Judith [[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] dividing values of each column in a dataframe
Hey Guys I want to divide(numerically) all the columns of a data frame by different numbers. Here is what I am doing but getting a weird error. The values in each column are not getting divided by the corresponding value in the denominator vector instead by the alternative values. I am sure I am messing up something. Appreciate your help -Abhi head(counts) WT_CON WT_RB MU_CON MU_RB row1 839 180477 187 head(counts/c(2,3,4,5)) WT_CONWT_RBMU_CONMU_RB row1 419.5 45. 238.5000 46.7500 __ 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] I bet apply has a solution
duplicated(Data..) On Mon, Feb 6, 2012 at 11:34 AM, LCOG1 jr...@lcog.org wrote: Hi all For the data below, I would like to return a logical value indicating differences in the data. #Create data Data..-data.frame(a=rep(1,10),b=c(rep(1,9),2),c=c(rep(1,8),2,2)) a b c 1 1 1 1 2 1 1 1 3 1 1 1 4 1 1 1 5 1 1 1 6 1 1 1 7 1 1 1 8 1 1 1 9 1 1 2 10 1 2 2 So what I want is to return logical value telling me if all the values are the same. So the result would be a b c DidChange 1 1 1 1 FALSE 2 1 1 1 FALSE 3 1 1 1 FALSE 4 1 1 1 FALSE 5 1 1 1 FALSE 6 1 1 1 FALSE 7 1 1 1 FALSE 8 1 1 1 FALSE 9 1 1 2 TRUE 10 1 2 2 TRUE I bet apply could handle this elegantly but that family of functions is still not 100% intuitive to me. Thoughts. Thanks everyone Cheers, Josh -- View this message in context: http://r.789695.n4.nabble.com/I-bet-apply-has-a-solution-tp4362294p4362294.html 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] dividing values of each column in a dataframe
On Feb 6, 2012, at 2:22 PM, Abhishek Pratap wrote: Hey Guys I want to divide(numerically) all the columns of a data frame by different numbers. Here is what I am doing but getting a weird error. The values in each column are not getting divided by the corresponding value in the denominator vector instead by the alternative values. I am sure I am messing up something. Appreciate your help -Abhi head(counts) WT_CON WT_RB MU_CON MU_RB row1 839 180477 187 head(counts/c(2,3,4,5)) WT_CONWT_RBMU_CONMU_RB row1 419.5 45. 238.5000 46.7500 The argument recycling is going to be done on a column basis. You apaear to expect it to be done on a row basis. For that you need apply Probably: t( apply(counts, 1, /, c(2,3,4,5)) ) But untested in absence of example. --- David Winsemius, MD West Hartford, CT __ 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] Multi-page PDF using dev.copy2pdf(filename, onefile=TRUE)?
Thanks Elai, that did it! I never considered using any X11 options, as I'm on
Windows, and in the docs I read it sounded like X11 options only pertained to
the OSX/Linux/.. world. Thanks for your help, Doug
--- On Mon, 2/6/12, ilai ke...@math.montana.edu wrote:
From: ilai ke...@math.montana.edu
Subject: Re: [R] Multi-page PDF using dev.copy2pdf(filename, onefile=TRUE)?
To: Doug Hill logic...@yahoo.com
Cc: r-help@r-project.org
Date: Monday, February 6, 2012, 12:24 PM
Doug,
dev.copy2pdf closes the connection after it's done, so onefile is
meaningless. To look at each plot before copy to a single pdf, you
could open a pdf(...) but revert between it and your graphic device:
graphics.off()
plot(1:7, 1:7)
x11c- dev.cur() # your current graphics device
pdf(file=test.pdf)
dev.set(which=x11c) # back from pdf
dev.copy() # copy
dev.set(which=x11c) # back to graphic
plot(1:5, 1:5,col=2,pch=2)
dev.copy()
dev.set(which=x11c)
# ... etc. however many more plots
# don't forget to close the pdf device at the end:
dev.off(which=x11c+1)
# Both plots are in 'test.pdf'
Depending on your application you might be able to simplify things
with dev.next/dev.prev, or wrap this sequence into a little helper
function to be used in a loop.
Enjoy,
Elai
On Mon, Feb 6, 2012 at 6:44 AM, Doug Hill logic...@yahoo.com wrote:
Hi all. I want to generate a sequence of n plots and save them into a single
PDF file, one plot per page. From the R docs and other sources I gather the
basic way to do this is save plot 1 into a file then append the 2:n plots to
the same file.
This code shows my basic approach, but for some reason only the last plot is
saved into the pdf. I've tried different variations (e.g. using onefile only
in the second call, or only in the first), to no avail. The comments show
what I see if I step through the code one line at a time:
scratch-function() {
graphics.off()
plot(1:7, 1:7) # Opens a graphics window and displays a 7-point plot in it,
as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # I see the 7-point plot in Adobe
reader, as expected
plot(1:5, 1:5) # Overwrites in the graphics window the 7-point plot with a
5-point, as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # Overwrites test.pdf so that it
contains only the 7-point plot
}
A couple things:
(1) The reason I don't just use something like pdf(filename) plot(...)
plot(...) dev.off() is that I also want to see the plots before they're saved
(I pause after each plot() command). But according to the docs for
dev.copy2pdf(), that function accepts the same args as pdf() does, including
onefile.
(2) I wrap my code in a function to be able to use it in the StatEt debugger
in Eclipse.
If you know what I'm doing wrong, or know of a different/better way, advise
away! Thanks, Doug
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] dividing values of each column in a dataframe
On 06-02-2012, at 20:22, Abhishek Pratap wrote: Hey Guys I want to divide(numerically) all the columns of a data frame by different numbers. Here is what I am doing but getting a weird error. I don't think you are getting an error. You are getting an unexpected result (you think). The values in each column are not getting divided by the corresponding value in the denominator vector instead by the alternative values. I am sure I am messing up something. Appreciate your help -Abhi head(counts) WT_CON WT_RB MU_CON MU_RB row1 839 180477 187 head(counts/c(2,3,4,5)) WT_CONWT_RBMU_CONMU_RB row1 419.5 45. 238.5000 46.7500 I tried this df - data.frame(a=runif(10),b=runif(10),c=runif(10)) scal - c(2,3,4) df a b c 1 0.47661685 0.73457617 0.90045279 2 0.06916502 0.76374600 0.07630196 3 0.17029174 0.29450289 0.07416969 4 0.03126839 0.09864740 0.08230353 5 0.23713816 0.06342224 0.91241698 6 0.21970595 0.86890690 0.47316101 7 0.46380324 0.26142304 0.87823277 8 0.81256517 0.76097474 0.98956553 9 0.74425369 0.29228545 0.27496707 10 0.65425285 0.40166967 0.12231213 df/scal a b c 1 0.23830843 0.24485872 0.22511320 2 0.02305501 0.19093650 0.03815098 3 0.04257293 0.14725144 0.02472323 4 0.01563419 0.03288247 0.02057588 5 0.07904605 0.01585556 0.45620849 6 0.05492649 0.43445345 0.15772034 7 0.23190162 0.08714101 0.21955819 8 0.27085506 0.19024369 0.49478276 9 0.18606342 0.14614273 0.09165569 10 0.32712642 0.13388989 0.03057803 Checking: df[4,]/scal a b c 4 0.01563419 0.03288247 0.02057588 This is what you want guessing from your description. You haven't given us an example with desired output. Berend __ 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] Any R course in New York or Washington DC in March?
Hey Folks, I am looking for a R course in New York or Washington DC, please email me any course announcement you know of for these dates. Best - Eugene [[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] I bet apply has a solution
Ah. That's the one. Thank you. -Original Message- From: Ista Zahn [mailto:istaz...@gmail.com] Sent: Monday, February 06, 2012 11:12 AM To: ROLL Josh F Cc: r-help@r-project.org Subject: Re: [R] I bet apply has a solution Hi Josh, How about apply(Data, 1, function(row) sd(row) == 0) ? Best, Ista On Mon, Feb 6, 2012 at 1:34 PM, LCOG1 jr...@lcog.org wrote: Hi all For the data below, I would like to return a logical value indicating differences in the data. #Create data Data..-data.frame(a=rep(1,10),b=c(rep(1,9),2),c=c(rep(1,8),2,2)) a b c 1 1 1 1 2 1 1 1 3 1 1 1 4 1 1 1 5 1 1 1 6 1 1 1 7 1 1 1 8 1 1 1 9 1 1 2 10 1 2 2 So what I want is to return logical value telling me if all the values are the same. So the result would be a b c DidChange 1 1 1 1 FALSE 2 1 1 1 FALSE 3 1 1 1 FALSE 4 1 1 1 FALSE 5 1 1 1 FALSE 6 1 1 1 FALSE 7 1 1 1 FALSE 8 1 1 1 FALSE 9 1 1 2 TRUE 10 1 2 2 TRUE I bet apply could handle this elegantly but that family of functions is still not 100% intuitive to me. Thoughts. Thanks everyone Cheers, Josh -- View this message in context: http://r.789695.n4.nabble.com/I-bet-apply-has-a-solution-tp4362294p436 2294.html 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] sqsSave() test using Test.R script returning error suggesting no values upon insert
Hi.
I attempted to use RODBC and decided to execute all the tests provided in
Test.r under the unpacked package RODBC folder.
Beginning with the following:
library(RODBC)
library(MASS)
USArrests[1,2] - NA
hills - hills[1:15,]
row.names(hills)[12] - Dollar ('$')
set.seed(1)
# MySQL
## testdb3 is ODBC/Connector 3.51.x, testdb5 is 5.1.x
channel - odbcConnect(MysqlODBC) #my database
odbcGetInfo(channel)
sqlTypeInfo(channel)
sqlTables(channel)
sqlDrop(channel, test.USArrests,errors = FALSE) #explicit database AND table
call as MySQL doesn't allow general table creation
Everything works as advertised.
---
#Then we get here. I have the USArrests data and checked it but tried to save
as it produced an error.
sqlSave(channel, USArrests,test.USArrests,rownames = state, addPK = TRUE)
Error in odbcUpdate(channel, query, mydata, coldata[m, ], test = test, :
no parameters, so nothing to update
The database table exists and upon edit of the table fields, all table info
created correctly.
Attempted again adding verbose=TRUE:
sqlSave(channel, USArrests,test.USArrests,rownames = state, addPK = TRUE,
verbose=TRUE)
Query: CREATE TABLE test.usarrests (`state` varchar(255) NOT NULL PRIMARY KEY,
`murder` double, `assault` integer, `urbanpop` integer, `rape` double)
Query: INSERT INTO test.usarrests ( `` ) VALUES ( ?,?,?,?,? )
Error in odbcUpdate(channel, query, mydata, coldata[m, ], test = test, :
no parameters, so nothing to update
Does anyone know what is happening? For whatever reason it is not seeing or
ingesting the data (BOLDED Query:...
I've seen one other post that did not receive an answer (probably due to its
lack of brevity).
I'm using Window's Vista, R 2.11.1
Here's is my MySQL info:
odbcGetInfo(channel)
DBMS_Name DBMS_Ver Driver_ODBC_Ver
Data_Source_Name Driver_Name Driver_Ver
MySQL 5.1.33-community 03.51
MysqlODBC myodbc5.dll 05.01.0007
ODBC_Ver Server_Name
03.52. localhost via TCP/IP
Thank you for your time.
Mark LoPresti
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[R] Random draws from an ANOVA-like design with given population effect sizes
Hi all, Let's say that you have a 3-group categorical predictor x that has the orthogonal contrasts c1 and c2. I am trying to create a function that, given x, c1, and c2, creates a normally-distributed y such that c1 and c2 have effect sizes r1 and r2 specified by the user. For example, let's say that x, c1, c2, r1, and r2 were created like the following: x - factor(rep(c(1, 2, 3), 100)) (contrasts(x) - matrix(c(0, -.5, .5, -2/3, 1/3, 1/3), nrow = 3, ncol = 2, dimnames = list(c(1, 2, 3), c(c1, c2 r1 - .09 r2 - 0 I'd like to create a function create.y(x, r1, r2) that returns a vector y of identical length to x such that the effect size (delta R^2) of c1 = r1 = .09 and the effect size (delta R^2) of c2 = r2 = 0. Does anybody on the list have any advice about how to do this? I know that I should be using the rnorm function, but I'm stuck on which population means / sds rnorm should use when it does its sampling. Thanks in advance for your help, -- Patrick S Forscher PhD Candidate University of Wisconsin-Madison __ 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] Getting the list of lines evaluated in a function call
Hello useRs
I am looking for a function that can give the list of lines that were evaluated
or used to generatethe last output from any function, whether an error message
was generated or not. For example, let's say I have a function like this:
foo - function( x ){ if( x10 ){
ans - x+100
}else{ ans - x-100 } ans
}
and I type:
foo(4)[1] -96
I would like a function that returns something like this
list.lines(foo)[1] 1 3 4 5 6
or:
foo(hello)Error in x + 100 : non-numeric argument to binary operator
list.lines(foo)[1] 1 2
Is there already a function in R doing something similar or anybody has any
hints for functions that I could use to create such a function?
Sincerely,Francois Rousseu
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Re: [R] Reordering levels of a factor when the factor is part of a data frame
6-02-2012, 11:03 (-0800); Judith Flores escriu: The name of the column will be saved in an object called: variab the data frame is called df. If I try to the do following: df[variab]-factor(df[variab], levels=c(A2B,B31,C33)) it won't work because df[variab] is a data frame. I think you need to use df[[variab]] instead. Cheers, Ernest __ 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] Duplicate rows when I combine two data.frames with merge!
Hello all, First I have done extensive searches on this forum and others and nothing seems to work. So I decided to post thinking someone could point me to the write post or give me some help. I have drawn a 100 samples from a fictitious population (N=1000), and then randomly selected 25% of the 100 samples. I would like to now merge the data.frame from the 100 samples with the data.frame for the 25 individuals from the sample. When I do this with the following code I get duplicate rows, when I should have at most is 100. x-mapply(rnorm,1000,c(54,78,89),c(3.5,5.5,5.9)) #sets up 1000 random numbers for age 3,4,5 x.3-sample(x[,1],60) #randomly selects 60 lengths from age 3 x.4-sample(x[,2],740) x.5-sample(x[,3],200) length-c(x.3,x.4,x.5) length-round(length,digits=0) #rounds lengths to whole number age3-rep(3,60) age4-rep(4,740) age5-rep(5,200) age-c(age3,age4,age5) #combines ages into one vector unique-1:1000 #gives each fish a unique id pop-data.frame(unique,length,age) pop-pop[sample(1:1000,size=1000,replace=FALSE),] #randomized the order of pop c.one-pop[sample(1:1000,size=100,replace=TRUE),] a.one.qtr-c.one[sample(1:100,size=25,replace=TRUE),] merge-merge(c.one,a.one.qtr,by=unique,all=TRUE) What I would ultimately like to have is one row for all 100 in the sample and three columns (unique, length, age). And then some way to identify the 25 individual selected rows. Thank you upfront for any help. I have been stuck for days. Ryan -- View this message in context: http://r.789695.n4.nabble.com/Duplicate-rows-when-I-combine-two-data-frames-with-merge-tp4362685p4362685.html 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] Multi-page PDF using dev.copy2pdf(filename, onefile=TRUE)?
On Feb 6, 2012, at 2:51 PM, Doug Hill wrote:
Thanks Elai, that did it! I never considered using any X11 options,
as I'm on Windows, and in the docs I read it sounded like X11
options only pertained to the OSX/Linux/.. world. Thanks for your
help, Doug
You are confused about the difference of a named variable and its
contents. There is no X11 device in that solution, just a name for
the current device which in your case is probably not an X11 device.
If you looked at the value of `x11c`, you would see it's just a number.
Elai is just switching back and forth between the screen device and
the file device.
--
David.
--- On Mon, 2/6/12, ilai ke...@math.montana.edu wrote:
From: ilai ke...@math.montana.edu
Subject: Re: [R] Multi-page PDF using dev.copy2pdf(filename,
onefile=TRUE)?
To: Doug Hill logic...@yahoo.com
Cc: r-help@r-project.org
Date: Monday, February 6, 2012, 12:24 PM
Doug,
dev.copy2pdf closes the connection after it's done, so onefile is
meaningless. To look at each plot before copy to a single pdf, you
could open a pdf(...) but revert between it and your graphic device:
graphics.off()
plot(1:7, 1:7)
x11c- dev.cur() # your current graphics device
pdf(file=test.pdf)
dev.set(which=x11c) # back from pdf
dev.copy() # copy
dev.set(which=x11c)# back to graphic
plot(1:5, 1:5,col=2,pch=2)
dev.copy()
dev.set(which=x11c)
# ... etc. however many more plots
# don't forget to close the pdf device at the end:
dev.off(which=x11c+1)
# Both plots are in 'test.pdf'
Depending on your application you might be able to simplify things
with dev.next/dev.prev, or wrap this sequence into a little helper
function to be used in a loop.
Enjoy,
Elai
On Mon, Feb 6, 2012 at 6:44 AM, Doug Hill logic...@yahoo.com wrote:
Hi all. I want to generate a sequence of n plots and save them into
a single PDF file, one plot per page. From the R docs and other
sources I gather the basic way to do this is save plot 1 into a
file then append the 2:n plots to the same file.
This code shows my basic approach, but for some reason only the
last plot is saved into the pdf. I've tried different variations
(e.g. using onefile only in the second call, or only in the first),
to no avail. The comments show what I see if I step through the
code one line at a time:
scratch-function() {
graphics.off()
plot(1:7, 1:7) # Opens a graphics window and displays a 7-point
plot in it, as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # I see the 7-point
plot in Adobe reader, as expected
plot(1:5, 1:5) # Overwrites in the graphics window the 7-point plot
with a 5-point, as expected
dev.copy2pdf(file=test.pdf, onefile=TRUE) # Overwrites test.pdf
so that it contains only the 7-point plot
}
A couple things:
(1) The reason I don't just use something like pdf(filename)
plot(...) plot(...) dev.off() is that I also want to see the plots
before they're saved (I pause after each plot() command). But
according to the docs for dev.copy2pdf(), that function accepts the
same args as pdf() does, including onefile.
(2) I wrap my code in a function to be able to use it in the StatEt
debugger in Eclipse.
If you know what I'm doing wrong, or know of a different/better
way, advise away! Thanks, Doug
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David Winsemius, MD
West Hartford, CT
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Re: [R] nice report generator?
2. It's more flexible to construct the language object as a language object, rather than pasting something together and parsing it. For one thing, that allows non-syntactic variable names; I think it's also easier to read. So your code txt- paste(tabular(value*v*, LEFT , ~ ,RIGHT ,, data = m_xx, suppressLabels = 2,...), sep = ) eval(parse(text = txt )) could be rewritten as formula- substitute( value*v*LEFT ~ RIGHT, list(LEFT=LEFT, RIGHT=RIGHT)) tabular(formula, data = m_xx, suppressLabels = 2, ...) To be strictly correct, shouldn't that be: formula- eval(substitute( value*v*LEFT ~ RIGHT, list(LEFT=LEFT, RIGHT=RIGHT))) ? It might make sense to put something like this into the tables package, but I don't want to have a dependency on reshape. Would you consider making tabular generic? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ 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 do I get the CEM (coarsened exact matching) package to run?
Hi,
I am running a MacBook Pro with OS X 10.6.8. When I try to load library(cem)
and run any function, R crashes. Any suggestions as to why this is? Thanks in
advance. I think the problem is that I don't have all the infrastructure I
need to run CEM, but I have no clue what to do either...
#Do I have tcltk (I have no clue what that is)
capabilities(tcltk)
tcltk
TRUE
#Installing cem
trying URL 'http://r.iq.harvard.edu/src/contrib/cem_1.0.218.tar.gz'
Content type 'application/x-gzip' length 886578 bytes (865 Kb)
opened URL
==
downloaded 865 Kb
* installing *source* package ‘cem’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
Can't find a usable tk.tcl in the following directories:
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5/Resources/Scripts
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5/Resources/Scripts
./lib/tk8.5 ./lib/tk8.5/Resources/Scripts ~/Library/Tcl/tk8.5
~/Library/Tcl/tk8.5/Resources/Scripts /Library/Tcl/tk8.5
/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/tk8.5
/System/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/8.5/tk8.5
/System/Library/Tcl/8.5/tk8.5/Resources/Scripts ~/Library/Frameworks/tk8.5
~/Library/Frameworks/tk8.5/Resources/Scripts /Library/Frameworks/tk8.5
/Library/Frameworks/tk8.5/Resources/Scripts /System/Library/Frameworks/tk8.5
/System/Library/Frameworks/tk8.5/Resources/Scripts ./library
This probably means that tk wasn't installed properly.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘cem.Rnw’
** testing if installed package can be loaded
How to use CEM? Type vignette(cem)
Warning message:
In fun(libname, pkgname) :
Can't find a usable tk.tcl in the following directories:
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5/Resources/Scripts
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5
/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5/Resources/Scripts
./lib/tk8.5 ./lib/tk8.5/Resources/Scripts ~/Library/Tcl/tk8.5
~/Library/Tcl/tk8.5/Resources/Scripts /Library/Tcl/tk8.5
/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/tk8.5
/System/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/8.5/tk8.5
/System/Library/Tcl/8.5/tk8.5/Resources/Scripts ~/Library/Frameworks/tk8.5
~/Library/Frameworks/tk8.5/Resources/Scripts /Library/Frameworks/tk8.5
/Library/Frameworks/tk8.5/Resources/Scripts /System/Library/Frameworks/tk8.5
/System/Library/Frameworks/tk8.5/Resources/Scripts ./library
This probably means that tk wasn't installed properly.
* DONE (cem)
The downloaded packages are in
‘/private/var/folders/q5/q5YCJSnWH7arB5jzTZBIfTI/-Tmp-/RtmptU5v1f/downloaded_packages’
#Session info
sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
#Loading CEM and trying to execute a function
library(cem) #Version 1.0.218
Loading required package: nlme
Loading required package: lattice
Loading required package: randomForest
randomForest 4.6-6
Type rfNews() to see new features/changes/bug fixes.
Loading required package: tcltk
Loading Tcl/Tk interface ...
#If I try to execute any function a crash occurs
#Error code that I
Resulting error message:
*** caught segfault ***
address 0x1180, cause 'memory not mapped'
Traceback:
1: sys.parent()
2: sys.function(sys.parent())
3: formals(sys.function(sys.parent()))
4: match.arg(type)
5: sink()
6: args(cem)
7: print(args(cem))
8: eval(expr, envir, enclos)
9: eval(expr, pf)
10: withVisible(eval(expr, pf))
11: evalVis(expr)
12: capture.output(print(args(cem)))
13: paste(capture.output(print(args(cem))), collapse = )
14: gsub(\\s+, , paste(capture.output(print(args(cem))), collapse = ))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(expr, error = function(e) {call - conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]], quote(doTryCatch)))
call - sys.call(-4L)dcall - deparse(call)[1L]prefix -
paste(Error in, dcall, : )LONG - 75Lmsg -
conditionMessage(e)sm - strsplit(msg, \n)[[1L]]w - 14L +
nchar(dcall, type = w) + nchar(sm[1L], type = w)if (is.na(w))
w - 14L + nchar(dcall,
Re: [R] Duplicate rows when I combine two data.frames with merge!
On Mon, Feb 06, 2012 at 12:29:53PM -0800, RKinzer wrote: Hello all, First I have done extensive searches on this forum and others and nothing seems to work. So I decided to post thinking someone could point me to the write post or give me some help. I have drawn a 100 samples from a fictitious population (N=1000), and then randomly selected 25% of the 100 samples. I would like to now merge the data.frame from the 100 samples with the data.frame for the 25 individuals from the sample. When I do this with the following code I get duplicate rows, when I should have at most is 100. x-mapply(rnorm,1000,c(54,78,89),c(3.5,5.5,5.9)) #sets up 1000 random numbers for age 3,4,5 x.3-sample(x[,1],60) #randomly selects 60 lengths from age 3 x.4-sample(x[,2],740) x.5-sample(x[,3],200) length-c(x.3,x.4,x.5) length-round(length,digits=0) #rounds lengths to whole number age3-rep(3,60) age4-rep(4,740) age5-rep(5,200) age-c(age3,age4,age5) #combines ages into one vector unique-1:1000 #gives each fish a unique id pop-data.frame(unique,length,age) pop-pop[sample(1:1000,size=1000,replace=FALSE),] #randomized the order of pop c.one-pop[sample(1:1000,size=100,replace=TRUE),] a.one.qtr-c.one[sample(1:100,size=25,replace=TRUE),] merge-merge(c.one,a.one.qtr,by=unique,all=TRUE) What I would ultimately like to have is one row for all 100 in the sample and three columns (unique, length, age). And then some way to identify the 25 individual selected rows. The function merge() here includes additional columns, which contain in the rows from a.one.qtr copies of the columns length and age. So, the same values appear twice in the row. I am not sure, whether this is intended. Another representation of the subsample a.one.qtr may be done by adding a column to c.one, which specifies, how many times was the row selected to a.one.qtr. For example as follows. a.one.qtr2 - sample(1:100,size=25,replace=TRUE) c.one2 - cbind(c.one, selected=tabulate(a.one.qtr2, nbins=100)) # a random result may look like c.one2 unique length age selected 657 657 81 40 488 488 78 41 886 886 85 50 448 448 82 40 292 292 80 40 431 431 78 40 683 683 82 40 3232 56 32 740 740 80 40 519 519 81 41 986 986 88 50 437 437 84 40 247 247 88 40 122 122 73 40 ... The sum of the column selected is 25. Hope this helps. Petr Savicky. __ 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] Colors vector based on group
Thank for your answer. Problem solved. Regards, Phil -- View this message in context: http://r.789695.n4.nabble.com/Colors-vector-based-on-group-tp4361425p4362746.html 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] Duplicate rows when I combine two data.frames with merge!
Hi, Why do you need to merge them? c.one contains what I think you want, and then you want to randomly select 25 rows from that without replacement: c.one - cbind(c.one, a.qtr = sample(c(rep(TRUE, 25), rep(FALSE, 75 head(c.one) unique length age a.qtr 649649 71 4 TRUE 200200 79 4 FALSE 410410 82 4 TRUE 620620 73 4 FALSE 723723 81 4 FALSE 855855 96 5 FALSE If what you mean by the subject line is that there are duplicate rows in the merged data frame, of course there are, because there are duplicated rows in c.one, because you selected sampling with replacement when selecting rows from pop to make c.one. Something to be VERY careful of: length, merge and unique are all base functions, and shouldn't be used as variable names. After you named something merge, what happens when you try to use merge()? If I'm misunderstanding the question, then please try to explain more clearly what you are looking for. Sarah On Mon, Feb 6, 2012 at 3:29 PM, RKinzer ry...@nezperce.org wrote: Hello all, First I have done extensive searches on this forum and others and nothing seems to work. So I decided to post thinking someone could point me to the write post or give me some help. I have drawn a 100 samples from a fictitious population (N=1000), and then randomly selected 25% of the 100 samples. I would like to now merge the data.frame from the 100 samples with the data.frame for the 25 individuals from the sample. When I do this with the following code I get duplicate rows, when I should have at most is 100. x-mapply(rnorm,1000,c(54,78,89),c(3.5,5.5,5.9)) #sets up 1000 random numbers for age 3,4,5 x.3-sample(x[,1],60) #randomly selects 60 lengths from age 3 x.4-sample(x[,2],740) x.5-sample(x[,3],200) length-c(x.3,x.4,x.5) length-round(length,digits=0) #rounds lengths to whole number age3-rep(3,60) age4-rep(4,740) age5-rep(5,200) age-c(age3,age4,age5) #combines ages into one vector unique-1:1000 #gives each fish a unique id pop-data.frame(unique,length,age) pop-pop[sample(1:1000,size=1000,replace=FALSE),] #randomized the order of pop c.one-pop[sample(1:1000,size=100,replace=TRUE),] a.one.qtr-c.one[sample(1:100,size=25,replace=TRUE),] merge-merge(c.one,a.one.qtr,by=unique,all=TRUE) What I would ultimately like to have is one row for all 100 in the sample and three columns (unique, length, age). And then some way to identify the 25 individual selected rows. Thank you upfront for any help. I have been stuck for days. Ryan -- View this message in context: http://r.789695.n4.nabble.com/Duplicate-rows-when-I-combine-two-data-frames-with-merge-tp4362685p4362685.html 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. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org __ 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] Creating time series (ts) object
Hi everyone. I have have a dataset with daily measurement from January 1st of 1966 up to December 31th of 2011. Here's the first part of the data: DateSLEV 1/1/19661.086 1/2/19661.079 1/3/19661.133 1/4/19661.261 1/5/19661.391 1/6/19661.571 1/7/19661.728 1/8/19661.823 1/9/19661.97 1/10/1966 1.804 1/11/1966 2.02 1/12/1966 2.017 1/13/1966 1.86 1/14/1966 1.96 1/15/1966 1.813 1/16/1966 1.773 1/17/1966 1.647 1/18/1966 1.634 1/19/1966 1.815 1/20/1966 1.928 1/21/1966 1.937 1/22/1966 2.187 1/23/1966 2.133 1/24/1966 2.162 1/25/1966 2.026 1/26/1966 2.055 1/27/1966 2.051 1/28/1966 1.998 1/29/1966 2.178 1/30/1966 1.709 1/31/1966 1.79 ... 12/31/2011 0.599 I would like to perform some sort of time series analysis. To do so, I'm trying to create a ts() object with my data. However, I'm not sure how ti create it and what frequency to use. In the help file, they say to use /*frequency = 7*/ for daily observation, but the result don't seems coherent: */Series: Start = c(1966, 1) End = c(4337, 5) Frequency = 7/ * Anyone can help me? Thank is advance, Phil -- View this message in context: http://r.789695.n4.nabble.com/Creating-time-series-ts-object-tp4362762p4362762.html 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] Creating time series (ts) object
The documentation doesn't say what you think it says: The value of argument ‘frequency’ is used when the series is sampled an integral number of times in each unit time interval. For example, one could use a value of ‘7’ for ‘frequency’ when the data are sampled daily, and the natural time period is a week, If your natural time period is a year, then there are 365 samples per time period and that's your frequency. Of course, this might have problems with leap days: good luck with that. Michael On Mon, Feb 6, 2012 at 3:53 PM, Filoche pmassico...@hotmail.com wrote: Hi everyone. I have have a dataset with daily measurement from January 1st of 1966 up to December 31th of 2011. Here's the first part of the data: Date SLEV 1/1/1966 1.086 1/2/1966 1.079 1/3/1966 1.133 1/4/1966 1.261 1/5/1966 1.391 1/6/1966 1.571 1/7/1966 1.728 1/8/1966 1.823 1/9/1966 1.97 1/10/1966 1.804 1/11/1966 2.02 1/12/1966 2.017 1/13/1966 1.86 1/14/1966 1.96 1/15/1966 1.813 1/16/1966 1.773 1/17/1966 1.647 1/18/1966 1.634 1/19/1966 1.815 1/20/1966 1.928 1/21/1966 1.937 1/22/1966 2.187 1/23/1966 2.133 1/24/1966 2.162 1/25/1966 2.026 1/26/1966 2.055 1/27/1966 2.051 1/28/1966 1.998 1/29/1966 2.178 1/30/1966 1.709 1/31/1966 1.79 ... 12/31/2011 0.599 I would like to perform some sort of time series analysis. To do so, I'm trying to create a ts() object with my data. However, I'm not sure how ti create it and what frequency to use. In the help file, they say to use /*frequency = 7*/ for daily observation, but the result don't seems coherent: */Series: Start = c(1966, 1) End = c(4337, 5) Frequency = 7/ * Anyone can help me? Thank is advance, Phil -- View this message in context: http://r.789695.n4.nabble.com/Creating-time-series-ts-object-tp4362762p4362762.html 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] histogram
Hi David, I have 2 tables, each with several columns and rows of data. I am only interested in the data from column 6, which contains values in the range -PI to PI. I want to plot the data from tableD with the y axis denoting percentage with respect to tableR. So if data points in the break 2 - 3 appear half as often in tableD as in tableR, the y axis should show 50 percent. Does that make sense? I've been plotting the data like this to date: hist(tableD[,6],ylab=frequency, xlab=angle) Thanks a lot for your help On Mon, Feb 6, 2012 at 1:31 PM, David Winsemius dwinsem...@comcast.net wrote: On Feb 6, 2012, at 12:23 PM, Francis Keyes wrote: Thanks. How do you suggest I use the reference population? Sorry, I'm new to R and just don't see it. If i can get a plot that is counts or density relative to my reference data it would be ideal. It is difficult to specify how when we have no what. The what is your responsibility, not ours. My thought was to use the ratio of the results of hist() on the two populations which would then be offered back to hist or barplot. which (of course) requires that the 'breaks' be the same. Provide an example of your R representations of the reference population and tested population and all will become clear. (And learn to post in plain text, please.) -- David Winsemius, MD West Hartford, CT On Mon, Feb 6, 2012 at 1:12 AM, David Winsemius dwinsem...@comcast.net wrote: On Feb 5, 2012, at 8:31 PM, Francis Keyes wrote: With R and the hist function, is there a way to make a histogram in which the y axis denotes propotion with respect to a separate sample dataset of the same range instead of frequency? hist() returns an object with both counts and density. If you had a reference population it should be a fairly simple matter to use one or the other of those. __ 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] Disable contrasts in lme
Saskia Freytag saskia.freytag at med.uni-goettingen.de writes: I am trying to disable the contrast statement in the lme function of the package nlme. Is there a way to do this? This is needed as I have only one group. Can you be more specific please? My first interpretation of this question is if you only have one group why do you need to fit a mixed- effects model?, but with further explanation you might get some useful advice. Also, it would be best to follow up to r-sig-mixed-mod...@r-project.org where you can get more specialized help with (n)lme. __ 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.
