Re: [R] Testing memory limits in R??
Duncan Murdoch wrote: On 06/07/2009 4:16 PM, Peter Dalgaard wrote: Scott Zentz wrote: Hello Everyone, We have recently purchased a server which has 64GB of memory running a 64bit OS and I have compiled R from source with the following config ./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib --enable-BLAS-shlib --enable-shared --with-readline --with-iconv --with-x --with-tcktk --with-aqua --with-libpng --with-jpeglib and I would like to verify that I can use 55GB-60GB of the 64GB of memory within R. Does anyone know how this is possible? Will R be able to access that amount of memory from a single process? I am not an R user myself but I just wanted to test this before I turned the server over to the researchers.. Hmm, it's slightly tricky because R often duplicates objects, so you may hit the limit only transiently. Also, R has an internal 2GB limit on single vectors. But something like this Is it a 2 GB limit in size, or in the number of elements? I'm still spending almost all my time in 32 bit land, so it's hard to check. It's in length. I was getting a couple of wires crossed there. -p Duncan Murdoch Y - replicate(30, rnorm(2^28-1)) should create an object of about 30*2GB. Then lapply(Y, mean) should generate 30 very good and very expensive approximations to 0. (For obvious reasons, I haven't tested this on a 1GB ThinkPad X40) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] bigglm() results different from glm()+Another question
Trust me, it is the same total data I am using, even the chunksizes are all equal. I also crosschecked by manually creating the chunks and updating as in example given on biglm help page. ?biglm Regards Utkarsh Greg Snow wrote: Are you sure that you are fitting all the models on the same total data? A first glance looks like you may be including more data in some of the chunk sizes, or be producing an error that update does not know how to deal with. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 *From:* utkarshsinghal [mailto:utkarsh.sing...@global-analytics.com] *Sent:* Monday, July 06, 2009 8:58 AM *To:* Thomas Lumley; Greg Snow *Cc:* r help *Subject:* Re: [R] bigglm() results different from glm()+Another question The AIC of the biglm models is highly dependent on the size of chunks selected (example provided below). This I can somehow expect because the model error will increase with the number of chunks. It will be helpful if you can provide your opinion for comparing different models in such cases: * can I compare two models fitted with different chunksizes, or should I always use the same chunk size. * although I am not going to use AIC at all in my model selection, but I think any other model parameters will also vary in the same way. Am I right? * what would be the ideal chunksize? should it be the maximum possible size R and my system's RAM is able to handle? Any comments will be helpful. *Example of AIC variation with chunksize:* I ran the following code on my data which has 1 observations and 3 independent variables chunksize = 500 fit = biglm(y~x1+x2+x3, data=xx[1:chunksize,]) for(i in seq(chunksize,1,chunksize)) fit=update(fit, data=xx[(i+1):(i+chunksize),]) AIC(fit) [1] 30647.79 Here are the AIC for other chunksizes: chunksizeAIC 500 30647.79 100029647.79 200027647.79 250026647.79 500021647.79 1 11647.79 Regards Utkarsh utkarshsinghal wrote: Thank you Mr. Lumley and Mr. Greg. That was helpful. Regards Utkarsh Thomas Lumley wrote: On Fri, 3 Jul 2009, utkarshsinghal wrote: Hi Sir, Thanks for making package available to us. I am facing few problems if you can give some hints: Problem-1: The model summary and residual deviance matched (in the mail below) but I didn't understand why AIC is still different. AIC(m1) [1] 532965 AIC(m1big_longer) [1] 101442.9 That's because AIC.default uses the unnormalized loglikelihood and AIC.biglm uses the deviance. Only differences in AIC between models are meaningful, not individual values. Problem-2: chunksize argument is there in bigglm but not in biglm, consequently, udate.biglm is there, but not update.bigglm Is my observation correct? If yes, why is this difference? Because update.bigglm is impossible. Fitting a glm requires iteration, which means that it requires multiple passes through the data. Fitting a linear model requires only a single pass. update.biglm can take a fitted or partially fitted biglm and add more data. To do the same thing for a bigglm you would need to start over again from the beginning of the data set. To fit a glm, you need to specify a data source that bigglm() can iterate over. You do this with a function that can be called repeatedly to return the next chunk of data. -thomas Thomas LumleyAssoc. Professor, Biostatistics tlum...@u.washington.edu mailto:tlum...@u.washington.edu University of Washington, Seattle I don't know why the AIC is different, but remember that there are multiple definitions for AIC (generally differing in the constant added) and it may just be a difference in the constant, or it could be that you have not fit the whole dataset (based on your other question). For an lm model biglm only needs to make a single pass through the data. This was the first function written for the package and the update mechanism was an easy way to write the function (and still works well). The bigglm function came later and the models other than Gaussian require multiple passes through the data so instead of the update mechanism that biglm uses, bigglm requires the data argument to be a function that returns the next chunk of data and can restart to the beginning of the dataset. Also note that the bigglm function usually only does a few passes through the data, usually this is good enough, but in some cases you may need to increase the number of passes. Hope this helps, [[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
Re: [R] Solving quadratic equations with covariance term
Hi, more precisely I consider a matrix with three column vectors a_i (i=1,2,3), i.e. A=(a_1,a_2,a_3). On the other hand x should take vectors as values, i.e. x=v_j, while j goes also from 1 till 3. Now I just want to calculate the equation Cov(a_i,x_j) = 0, where Cov(a_i,x_j) is the covariance matrix. A is a given value and x is the variable I am looking for. In my opinion this is an quadratic equation and makes sense. Best wishes, Luba -Urspr?ngliche Nachricht- Von: Rolf Turner [mailto:r.tur...@auckland.ac.nz] Gesendet: Montag, 6. Juli 2009 23:16 An: Stein, Luba (AIM SE) Cc: R-help@r-project.org Betreff: Re: [R] Solving quadratic equations with covariance term On 7/07/2009, at 2:15 AM, Stein, Luba (AIM SE) wrote: Hi, I would like to solve the following equation with R: Cov(A,x)=0. A is a given matrix, x is the an unknown vector. Is there any nice solution for this? What on earth do you mean by ``Cov(A,x)''? This makes no sense at all. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.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] OK - I got the data - now what? :-)
Hi r-help-boun...@r-project.org napsal dne 06.07.2009 01:58:38: On Sun, Jul 5, 2009 at 1:44 PM, hadley wickhamh.wick...@gmail.com wrote: I think the root cause of a number of my coding problems in R right now is my lack of skills in reading and grabbing portions of the data out of arrays. I'm new at this. (And not a programmer) I need to find some good examples to read and test on that subject. If I could locate which column was called C1, then read row 3 from C1 up to the last value before a 0, I'd have proper data to plot for one line. Repeat as necessary through the array and I get all the lines. Doing the lines one at a time should allow me the opportunity to apply color or not plot based on values in the first few columns. Thanks, Mark test - data.frame(A=1:10, B=100, C1=runif(10), C2=runif(10), C3=runif(10), C4=runif(10), C5=runif(10), C6=runif(10)) test-round(test,2) #Make array ragged test$C3[2]-0;test$C4[2]-0;test$C5[2]-0;test$C6[2]-0 test$C4[3]-0;test$C5[3]-0;test$C6[3]-0 test$C6[7]-0 test$C4[8]-0;test$C5[8]-0;test$C6[8]-0 #Print array test Are the zeros always going to be arranged like this? i.e. for experiment there is a point at which all later values are zero? If so, the following is a much simpler way of getting to the core of your data, without fussing with overly complicated matrix indexing: library(reshape) testm - melt(test, id = c(A, B)) subset(testm, value 0) I suspect you will also find this form easier to plot and analyse. Hadley -- http://had.co.nz/ Hi Hadley, I wanted to look at reshape. Yes, there exists a point in each row (unless I get to the end with all numbers) where I get to a zero and everything to the right is zero. I'm looking at ReShape. It's interesting but I clearly don't understand it yet so I'm reading your ReShaping data with the reshap package form 11/07. Interesting. I know so little about R that I'm sort of drowning at this point that it's hard for me to understand why this would make plotting easier. Analysis possibly. Just the way it goes when you get started with something new. E.g. to give different colour according to C1-C6 and/or different shape for each A value. test. - subset(testm, value 0) plot(test.$value, col=as.numeric(test.$variable), pch=test.$A) And even fancier plots with ggplot2 package. Regards Petr In ReShape lingo I think I have ID's. They cover things like time, date, success/failure and a few other things of interest. Once the data starts on a row it is all data from there on to the end of the row. My initial goal is to make a line plot of the data on a single row. All the data points should connect together. There is no real interaction planned with data on other rows, at least at this time. Thanks for the pointers and the code stub. I'll be looking at this. Cheers, Mark __ 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] How to separate the string?
Hi everyone, Hi want to separate the string(column1) for example column1 column2 column3 column4 column5 column6 bear b e a r cat c a t tigert i g e r I know how to do this in excel where using MID function. Now I want to solve it using R. The list of strings is in text file. I looked up the help but did not find it. Can someone help me here? Thank you very much. Regards, Hema [[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] How to separate the string?
hi hema may be strsplit can help on the job. bests. milton On Tue, Jul 7, 2009 at 3:54 AM, Hemavathi Ramulu hema.ram...@gmail.comwrote: Hi everyone, Hi want to separate the string(column1) for example column1 column2 column3 column4 column5 column6 bear b e a r cat c a t tigert i g e r I know how to do this in excel where using MID function. Now I want to solve it using R. The list of strings is in text file. I looked up the help but did not find it. Can someone help me here?H Thank you very much. Regards, Hema [[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.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.
[R] Multiplication of data frame with vector
Dear group: sorry for my beginners question, but I'm rather new to R and was searching high and low without success: I have a data frame (df) with variables in the rows and observations in the columns like (the actual data frame has 15 columns and 1789 rows): early1 early2 early3 early4 early5 M386T1000 57056 55372 58012 55546 57309 M336T9011063 10312 10674 10840 11208 M427T9112064 11956 12692 12340 11924 M429T91 4594 3890 4096 4019 4204 M447T9026553 27647 26889 26751 26929 Now I'm trying to transform each value column-wise to make columns to all have the same mean with: df * mean(mean(df)) / mean(df). I just can't get my head around this: mean(df) gives me the correct column means vector, and mean(mean(df)) gives me the correct total mean. The above operation works correctly for individual rows, i.e. if I do df[1,]*mean(mean(df))/mean(df) Can someone tell me what I am doing wrong?? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: How to separate the string?
Hi r-help-boun...@r-project.org napsal dne 07.07.2009 09:54:30: Hi everyone, Hi want to separate the string(column1) for example Well, how did you get the data in R? Are they in separated columns of data.frame? What do you mean by separate? column1 column2 column3 column4 column5 column6 bear b e a r cat c a t tigert i g e r I know how to do this in excel where using MID function. As Microsoft is more user friendly and uses translated functions in language specific versions of Excel I do not have function MID. I suspect it takes values from middle of string set by some identifiers. If it is the case see ?substr However I would start with ?read.table and related read.* functions to get the data into R in appropriate shape. Regards Petr Now I want to solve it using R. The list of strings is in text file. I looked up the help but did not find it. Can someone help me here? Thank you very much. Regards, Hema [[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] output too large to display all
Dear All Thanks for the suggestions. Mark's suggestion to specify corr=FALSE did the job and removed the reams of correlations that were being outputted from the model and using up all the output space. Thanks Christine --On 06 July 2009 12:44 -0600 Lyman, Mark mark.ly...@atk.com wrote: Take a look at the print method for the mer class, class?mer. I believe setting the correlation argument to FALSE will give you what you want. See the examples. Mark Lyman, Statistician Engineering Systems Integration, ATK Hi R Users, Hopefully a very simple solution, but I am stumped nevertheless. I am running glmer in which the output is too large so that not all the correlations are displayed. I expanded the max.print as recommended on this website. However, this still does not allow me to see the relevant information regarding the model fit (AIC etc), random and fixed effects. I have not been able to find any similar posts. I would be very grateful if someone could specify what I need to state in order to view all the results generated from the model. Many thanks in advance, Christine __ R-help at 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] Odp: Multiplication of data frame with vector
Hi r-help-boun...@r-project.org napsal dne 07.07.2009 10:05:09: Dear group: sorry for my beginners question, but I'm rather new to R and was searching high and low without success: I have a data frame (df) with variables in the rows and observations in the columns like (the actual data frame has 15 columns and 1789 rows): early1 early2 early3 early4 early5 M386T1000 57056 55372 58012 55546 57309 M336T9011063 10312 10674 10840 11208 M427T9112064 11956 12692 12340 11924 M429T91 4594 3890 4096 4019 4204 M447T9026553 27647 26889 26751 26929 Now I'm trying to transform each value column-wise to make columns to all have the same mean with: df * mean(mean(df)) / mean(df). I just can't get my head around this: mean(df) gives me the correct column means vector, and mean(mean(df)) gives me the correct total mean. The above operation works correctly for individual rows, i.e. if I do df[1,]*mean(mean(df))/mean(df) a little bit awkward t(t(as.matrix(df))*mean(mean(df))/mean(df)) or with apply ttt-mean(mean(df))/mean(df) t(apply(df, 1, function(x) x*ttt)) There could be some sapply version of it but at present time I can not find it. Regards Petr Can someone tell me what I am doing wrong?? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to separate the string?
Hi Petr, The data in text file and not csv format. The word separate which I mean in this content is like split/separate the string to each alphabet where each alphabet will be in different column. thanks alot. regards, Hema. On Tue, Jul 7, 2009 at 4:12 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 07.07.2009 09:54:30: Hi everyone, Hi want to separate the string(column1) for example Well, how did you get the data in R? Are they in separated columns of data.frame? What do you mean by separate? column1 column2 column3 column4 column5 column6 bear b e a r cat c a t tigert i g e r I know how to do this in excel where using MID function. As Microsoft is more user friendly and uses translated functions in language specific versions of Excel I do not have function MID. I suspect it takes values from middle of string set by some identifiers. If it is the case see ?substr However I would start with ?read.table and related read.* functions to get the data into R in appropriate shape. Regards Petr Now I want to solve it using R. The list of strings is in text file. I looked up the help but did not find it. Can someone help me here? Thank you very much. Regards, Hema [[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.
[R] help me about data format.
Hi I am used to handle bio information such as NMR data or IR data . I want to perform pls regression, so I search the help page of plsr. and I use the example of plsr. But I have a problem to make appropriate data format to do plsr. these example data type like this : A data frame with components NIR Numeric matrix of NIR measurements density Numeric vector of densities train Logical vector with TRUE for the training samples and FALSE for the test samples I want to make a matrix and vector in same data frame. how can I do ? [[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] How to separate the string?
Hi If you have data frame like this test=data.frame(x=c(abcd, abc, abcde)) than strsplit(as.matrix(test), ) makes a list with splitted character vectors. If you want them in data frame you would need to combine vectors of unequal length. However I would try reading your text file with read.fwf(file, 1) Regards Petr Hemavathi Ramulu hema.ram...@gmail.com napsal dne 07.07.2009 10:36:40: Hi Petr, The data in text file and not csv format. The word separate which I mean in this content is like split/separate the string to each alphabet where each alphabet will be in different column. thanks alot. regards, Hema. On Tue, Jul 7, 2009 at 4:12 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 07.07.2009 09:54:30: Hi everyone, Hi want to separate the string(column1) for example Well, how did you get the data in R? Are they in separated columns of data.frame? What do you mean by separate? column1 column2 column3 column4 column5 column6 bear b e a r cat c a t tigert i g e r I know how to do this in excel where using MID function. As Microsoft is more user friendly and uses translated functions in language specific versions of Excel I do not have function MID. I suspect it takes values from middle of string set by some identifiers. If it is the case see ?substr However I would start with ?read.table and related read.* functions to get the data into R in appropriate shape. Regards Petr Now I want to solve it using R. The list of strings is in text file. I looked up the help but did not find it. Can someone help me here? Thank you very much. Regards, Hema [[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] curve from a formula with ggplot2
Hi all, I'm smoothly transferring my lattice graphs to ggplot2 graphs, but I'm stuck on representing a curve from a formula. I'm looking for the equivalent of curve() in ggplot2, Hadley Wickham mentions geom_curve, but as far as I've seen in the help it doesn't exist. My need is to plot a regular scatter plot of experimental data (easy to do actually) and then add the fitting model according to a specific formula like y = a*(b*x^n)/(1+b*x^p) where a,b,n and p are known parameters. I guess it's possible and easy to add this layer with ggplot, somehow I didn't find the right function. Any help would be warmly appreciated. Regards/Cordialement - Benoit Boulinguiez Ph.D student Ecole de Chimie de Rennes (ENSCR) Bureau 1.20 Equipe CIP UMR CNRS 6226 Sciences Chimiques de Rennes Avenue du Général Leclerc CS 50837 35708 Rennes CEDEX 7 Tel 33 (0)2 23 23 80 83 Fax 33 (0)2 23 23 81 20 http://www.ensc-rennes.fr/ http://www.ensc-rennes.fr/ [[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] Large Stata file Import in R
Thomas Lumley vas escriure el dia dt, 30 jun 2009: On Tue, 30 Jun 2009, Xavier wrote: saurav pathak vas escriure el dia dl, 29 jun 2009: Hi I am using Stata 10 and I need to import a data set in stata 10 to R, I have saved the dataset in lower versions of Stata as well by using saveold command in Stata. My RAM is 4gb and the stata file is 600MB, I am getting an error message which says : Error: cannot allocate vector of size 3.4 Mb In addition: There were 50 or more warnings (use warnings() to see the first 50) Thus far I have already tried the following Maybe it does not adress the R problem that you are asking for, but you can try to compress the stata file prior to save it. And maybe the size of the file will decrease. This can't possibly help. The problem is that *R* is running out of memory, and storing the data elements in less space *on disk* won't help with the space used in memory. Stata's -compress- option just chooses smaller data types, eg, byte instead of integer. I have done a small test and it seems that it can help. I have a big dataset in stata (big) to which I apply the compress command (in Stata), getting a small file. Those are the sizes in stata: -8--- # original data size in stata Contains data from G:\tmp\example-big.dta obs:52,547 Written by R. vars:54 size:21,807,005 (96.4% of memory free) # data size once compress has been used Contains data from example-small.dta obs:52,547 Written by R. vars:54 3 Jul 2009 15:27 size:17,918,527 (97.1% of memory free) -8--- And when loaded into R: -8--- library(foreign) big - read.dta(example-big.dta) small - read.dta(example-small.dta) object.size(big) 20819600 bytes object.size(small) 19558520 bytes -8--- Maybe the difference once objects are stored in memory is not as big as it is when stored in disk, but it seems a good idea to compress data in stata prior to load it into R, if memory is a problem. -- - Xavier - __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help me about data format.
I want to make a matrix and vector in same data frame. You need to protect your matrix by I () Btw: I'm actually writing a package for handling spectra that I plan to release in some weeks. It contains a vignette showing how pls calibration can be done. If you want to give it a try, let me know. Claudia Beleites -- Claudia Beleites DMRN, Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste __ 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] Error in object$coefficients : $ operator not defined for this S4 class
Hallo, I received this error message while calculating the coefficents coef(fit, matrix=TRUE) Error in object$coefficients : $ operator not defined for this S4 class what is this? How can I solve it? Ale -- View this message in context: http://www.nabble.com/Error-in-object%24coefficients-%3A-%24-operator-not-defined-for-this-S4-class-tp24371231p24371231.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] rle
Hallo, I have an other problem, I have this vector signData with an alternation of 1 and -1 that corrispond to the duration of two different percepts. I extracted the durations like this: signData- scan(dataTR10.txt) dur-rle(signData)$length Now I would like to extract only the positive duration, e.g. signData - c(1,1,1,1,-1,-1,-1,1,1,-1,-1) posduration - c(4,2) I think I should use rle in a nested way, this is what I tried but it doesn't work: posduration- rle(signData[=1])$length Could you please help me? Thanks a lot, this forum is extremely useful. Ale -- View this message in context: http://www.nabble.com/rle-tp24371336p24371336.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] Error in object$coefficients : $ operator not defined for this S4 class
What is fit in your example? Ronggui 2009/7/7 aledanda danda.ga...@gmail.com: Hallo, I received this error message while calculating the coefficents coef(fit, matrix=TRUE) Error in object$coefficients : $ operator not defined for this S4 class what is this? How can I solve it? Ale -- View this message in context: http://www.nabble.com/Error-in-object%24coefficients-%3A-%24-operator-not-defined-for-this-S4-class-tp24371231p24371231.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. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rle
Try this: rle(signData)$lengths[rle(signData)$values == 1] On Tue, Jul 7, 2009 at 8:11 AM, aledanda danda.ga...@gmail.com wrote: Hallo, I have an other problem, I have this vector signData with an alternation of 1 and -1 that corrispond to the duration of two different percepts. I extracted the durations like this: signData- scan(dataTR10.txt) dur-rle(signData)$length Now I would like to extract only the positive duration, e.g. signData - c(1,1,1,1,-1,-1,-1,1,1,-1,-1) posduration - c(4,2) I think I should use rle in a nested way, this is what I tried but it doesn't work: posduration- rle(signData[=1])$length Could you please help me? Thanks a lot, this forum is extremely useful. Ale -- View this message in context: http://www.nabble.com/rle-tp24371336p24371336.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] rle
Or: with(rle(signData), lengths[values == 1]) On Tue, Jul 7, 2009 at 8:26 AM, Henrique Dallazuanna www...@gmail.comwrote: Try this: rle(signData)$lengths[rle(signData)$values == 1] On Tue, Jul 7, 2009 at 8:11 AM, aledanda danda.ga...@gmail.com wrote: Hallo, I have an other problem, I have this vector signData with an alternation of 1 and -1 that corrispond to the duration of two different percepts. I extracted the durations like this: signData- scan(dataTR10.txt) dur-rle(signData)$length Now I would like to extract only the positive duration, e.g. signData - c(1,1,1,1,-1,-1,-1,1,1,-1,-1) posduration - c(4,2) I think I should use rle in a nested way, this is what I tried but it doesn't work: posduration- rle(signData[=1])$length Could you please help me? Thanks a lot, this forum is extremely useful. Ale -- View this message in context: http://www.nabble.com/rle-tp24371336p24371336.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] rle
I have an other problem, I have this vector signData with an alternation
of
1 and -1 that corrispond to the duration of two different percepts. I
extracted the durations like this:
signData- scan(dataTR10.txt)
dur-rle(signData)$length
I think that last line should be
dur-rle(signData)$lengths
Now I would like to extract only the positive duration, e.g.
signData - c(1,1,1,1,-1,-1,-1,1,1,-1,-1)
posduration - c(4,2)
If you know that the first element of signData will always be 1, then you
can simply extract the first, third, fifth etc values from signdata, like
so:
posduration - dur[c(TRUE, FALSE)]
Otherwise you need to test to see if you are extracting odd or even
elements.
if(signData[1]==1)
{
index - c(TRUE, FALSE)
} else
{
index - c(FALSE, TRUE)
}
posduration - dur[index]
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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Re: [R] Remove all spaces from a string so it can be used by assign() -- A Fortune?
Thank you for all the advice and I shall listen with regards to assign() and think of another way of writing what I want. Cheers! From: gunter.ber...@gene.com To: greg.s...@imail.org; kurt.sm...@hotmail.co.uk; r-help@r-project.org Subject: RE: [R] Remove all spaces from a string so it can be used by assign() -- A Fortune? Date: Mon, 6 Jul 2009 08:35:30 -0700 The below seems like a Fortunes candidate to me. -- Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Greg Snow Sent: Friday, July 03, 2009 7:00 PM To: Kurt Smith; r-help@r-project.org Subject: Re: [R] Remove all spaces from a string so it can be used by assign() The only people who should use the assign function are those who fully understand why you should never use the assign function. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 _ [[elided Hotmail spam]] [[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] Odp: Multiplication of data frame with vector
maybe with sweep: sweep(df, 2, mean(mean(df))/mean(df), *) On Tue, Jul 7, 2009 at 5:36 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 07.07.2009 10:05:09: Dear group: sorry for my beginners question, but I'm rather new to R and was searching high and low without success: I have a data frame (df) with variables in the rows and observations in the columns like (the actual data frame has 15 columns and 1789 rows): early1 early2 early3 early4 early5 M386T1000 57056 55372 58012 55546 57309 M336T9011063 10312 10674 10840 11208 M427T9112064 11956 12692 12340 11924 M429T91 4594 3890 4096 4019 4204 M447T9026553 27647 26889 26751 26929 Now I'm trying to transform each value column-wise to make columns to all have the same mean with: df * mean(mean(df)) / mean(df). I just can't get my head around this: mean(df) gives me the correct column means vector, and mean(mean(df)) gives me the correct total mean. The above operation works correctly for individual rows, i.e. if I do df[1,]*mean(mean(df))/mean(df) a little bit awkward t(t(as.matrix(df))*mean(mean(df))/mean(df)) or with apply ttt-mean(mean(df))/mean(df) t(apply(df, 1, function(x) x*ttt)) There could be some sapply version of it but at present time I can not find it. Regards Petr Can someone tell me what I am doing wrong?? Thanks! __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Mathematical annotation axis in lattice
Dear list, making mathematical expressions in plots is not difficult: expression(phi[1]) for example. At this moment I am stuck in creating a vector of expressions: pos - 1:10 lab - letters[pos] Now, I would like to create a vector of expressions which I could use for labeling the x-axis of a lattice plot. ll - as.expression(paste(pos, phi[,lab,],sep = ) xyplot(1:10~11:10,scales = list(x = list(labels = ll,at = 1:10))) does not work. I read about the function substitute, but that did not solve it. Could you recommend me how I should do this? Thanks in advance, Albart Coster Wageningen Universiteit Netherlands __ 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] Error in object$coefficients : $ operator not defined for this S4 class
I can not reproduce your problem with the latest version of VGAM. Besides, if you want to get the coef and std. error etc. you can use summary(fit)@coef3 Value Std. Error t value (Intercept):1 -1.020388 0.03215889 -31.72957 (Intercept):2 1.335657 0.04206706 31.75067 2009/7/7 Alessandra Galli danda.ga...@gmail.com: Sure, sorry, I am fitting with beta distribution: y= rbeta(n - 1000, shape1=exp(0), shape2=exp(1)) fit = vglm (y ~ 1, betaff, trace =TRUE) Thanks 2009/7/7 Ronggui Huang ronggui.hu...@gmail.com What is fit in your example? Ronggui 2009/7/7 aledanda danda.ga...@gmail.com: Hallo, I received this error message while calculating the coefficents coef(fit, matrix=TRUE) Error in object$coefficients : $ operator not defined for this S4 class what is this? How can I solve it? Ale -- View this message in context: http://www.nabble.com/Error-in-object%24coefficients-%3A-%24-operator-not-defined-for-this-S4-class-tp24371231p24371231.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. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html -- Alessandra Galli Mechelsestraat 155 /6 3000 Leuven Belgium T: +32 473 588179 -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.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] logic question
Setting: 200 input variables, 1 binary target variable. Run a principle component analysis on the data then use the output of the principle component analysis (the generated factors) as input into a neural network -but first having partitioned the pca data into training and testing sets so that a neural network model can be trained on the first partition and tested on the second. I was told that it was not logically sound to include the target variable as an input into the principle component algorithm. Normally that sounds correct. You never want to include the target variable as an input variable in your model. However, I argued that it is ok here because I am only using the target variable to build the principle components the model. So each record now has a value for each of the principle components. Then take the training partition only to build the neural network. Then test the neural network on the testing partition. Is this wrong? (sorry to post this twice, the first time I was not properly logged in and I don't think it registered correctly, won't happen again as I have registered and logged in correctly now) -- View this message in context: http://www.nabble.com/logic-question-tp24372208p24372208.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] logic question
Setting: 200 input variables, 1 binary target variable. Run a principle component analysis on the data then use the output of the principle component analysis (the generated factors) as input into a neural network -but first having partitioned the pca data into training and testing sets so that a neural network model can be trained on the first partition and tested on the second. I was told that it was not logically sound to include the target variable as an input into the principle component algorithm. Normally that sounds correct. You never want to include the target variable as an input variable in your model. However, I argued that it is ok here because I am only using the target variable to build the principle components the model. So each record now has a value for each of the principle components. Then take the training partition only to build the neural network. Then test the neural network on the testing partition. Is this wrong? -- View this message in context: http://www.nabble.com/logic-question-tp24369772p24369772.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] subscripted assignment of grid units
Hi, I want to do subscripted assignment of grid units, but I cannot find a straightforward way of doing it (and I have searched all forums and places I could think about, including Paul Murrell,s page). The usual subscripted assignment operator does replace the numeric part, but does not update the attributes. Before I write my own function, manipulating attributes etc I would like to know if such a function already exists (I am sure it does). What I want to do can be reflected as in the code below: testUnit - unit(1, lines) testUnit [1] 1lines testUnits - rep(testUnit, 5) testUnits [1] 1lines 1lines 1lines 1lines 1lines testUnit2 - unit(0.5, grobwidth, textGrob(Testing)) testUnits[3] - testUnit2 testUnits [1] 1lines 1lines 0.5lines 1lines 1lines I would like to obtain [1] 1lines 1lines 0.5grobwidth 1lines 1lines Any tips? Thanks, Pedro -- View this message in context: http://www.nabble.com/subscripted-assignment-of-grid-units-tp24371172p24371172.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] Testing memory limits in R??
Hello Everyone! Thanks for all your replies! This was very helpful! I found that there seems to be a limitation to only 32GB of memory which I think will be fine. I was able to consume the 32GB of memory with the following: Start R with the following command: R --max-vsize 55000M then within R run x=rep(0.1,2.141e9) and watch the process with top and R will consume about 32GB of memory... Hopefully this will be enough for the researchers ;) Thanks! -scz Scott Zentz wrote: Hello Everyone, We have recently purchased a server which has 64GB of memory running a 64bit OS and I have compiled R from source with the following config ./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib --enable-BLAS-shlib --enable-shared --with-readline --with-iconv --with-x --with-tcktk --with-aqua --with-libpng --with-jpeglib and I would like to verify that I can use 55GB-60GB of the 64GB of memory within R. Does anyone know how this is possible? Will R be able to access that amount of memory from a single process? I am not an R user myself but I just wanted to test this before I turned the server over to the researchers.. Thanks! -scz __ 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] Multiplication of data frame with vector
Would the scale function work for this? Something like new=scale(df, center=T) HTH, david freedman cir p wrote: Dear group: sorry for my beginners question, but I'm rather new to R and was searching high and low without success: I have a data frame (df) with variables in the rows and observations in the columns like (the actual data frame has 15 columns and 1789 rows): early1 early2 early3 early4 early5 M386T1000 57056 55372 58012 55546 57309 M336T9011063 10312 10674 10840 11208 M427T9112064 11956 12692 12340 11924 M429T91 4594 3890 4096 4019 4204 M447T9026553 27647 26889 26751 26929 Now I'm trying to transform each value column-wise to make columns to all have the same mean with: df * mean(mean(df)) / mean(df). I just can't get my head around this: mean(df) gives me the correct column means vector, and mean(mean(df)) gives me the correct total mean. The above operation works correctly for individual rows, i.e. if I do df[1,]*mean(mean(df))/mean(df) Can someone tell me what I am doing wrong?? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Multiplication-of-data-frame-with-vector-tp24368878p24372764.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] Testing memory limits in R??
Seems strange. I can go all the way up to 50GB on our machine which
has 64GB as well. It starts swapping after that, so I killed the
process.
try this:
ans - list()
for(i in 1:100) {
ans[[ i ]] - numeric(2^30/2)
cat(iteration: ,i,\n)
print(gc())
}
source(scripts/test.memory.r)
iteration: 1
used (Mb) gc trigger (Mb) max used (Mb)
Ncells1091715.9 35 18.735 18.7
Vcells 536990895 4097.0 592369806 4519.5 536992095 4097.0
iteration: 2
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1092765.9 35 18.7 35 18.7
Vcells 1073861851 8193.0 1184270079 9035.3 1073861858 8193.0
...
...
...
iteration: 13
used(Mb) gc trigger(Mb) max used(Mb)
Ncells 109287 5.9 3518.7 3518.7
Vcells 6979441897 53249.0 7458515495 56904.0 6979442076 53249.0
you might want to check your kernel.shmmax setting, although I'm not
sure if it will help R.
-Whit
On Tue, Jul 7, 2009 at 8:39 AM, Scott Zentzze...@email.unc.edu wrote:
Hello Everyone!
Thanks for all your replies! This was very helpful! I found that there
seems to be a limitation to only 32GB of memory which I think will be fine.
I was able to consume the 32GB of memory with the following:
Start R with the following command: R --max-vsize 55000M
then within R run
x=rep(0.1,2.141e9)
and watch the process with top and R will consume about 32GB of memory...
Hopefully this will be enough for the researchers ;)
Thanks!
-scz
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory running a
64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
--enable-BLAS-shlib --enable-shared --with-readline --with-iconv --with-x
--with-tcktk --with-aqua --with-libpng --with-jpeglib
and I would like to verify that I can use 55GB-60GB of the 64GB of memory
within R. Does anyone know how this is possible? Will R be able to access
that amount of memory from a single process? I am not an R user myself but I
just wanted to test this before I turned the server over to the
researchers..
Thanks!
-scz
__
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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Uncorrelated random vectors
Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba [[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] how to get R to print only one column per line when outputting a matrix?
Hi, I'm trying to make it easier for my survey evaluators to read the results of my survey analysis. To that end, I'd like to suppress R's habit of filling every line up to width columns. How do I do that? For instance, using 'print()', R outputs something like: [,1] [,2] var2 someshortname someothershortname r0.33417550.3275274 N136 136 [,3] var2 somereallyreallyreallyreallyreallylongname r0.323306 N136 [,4] var2 someotherreallyreallyreallyreallyreallylongname r0.3121291 N101 How can I get it to place every column on a new line to avoid confusing the reader? I read the help for print, print.default, format, cat, and options(width) and wasn't able to find an answer. Thanks! - Godmar __ 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] Testing memory limits in R??
Hey Whit,
That worked! I was able to consume all the memory on the server!
Thanks!
-scz
Whit Armstrong wrote:
Seems strange. I can go all the way up to 50GB on our machine which
has 64GB as well. It starts swapping after that, so I killed the
process.
try this:
ans - list()
for(i in 1:100) {
ans[[ i ]] - numeric(2^30/2)
cat(iteration: ,i,\n)
print(gc())
}
source(scripts/test.memory.r)
iteration: 1
used (Mb) gc trigger (Mb) max used (Mb)
Ncells1091715.9 35 18.735 18.7
Vcells 536990895 4097.0 592369806 4519.5 536992095 4097.0
iteration: 2
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1092765.9 35 18.7 35 18.7
Vcells 1073861851 8193.0 1184270079 9035.3 1073861858 8193.0
...
...
...
iteration: 13
used(Mb) gc trigger(Mb) max used(Mb)
Ncells 109287 5.9 3518.7 3518.7
Vcells 6979441897 53249.0 7458515495 56904.0 6979442076 53249.0
you might want to check your kernel.shmmax setting, although I'm not
sure if it will help R.
-Whit
On Tue, Jul 7, 2009 at 8:39 AM, Scott Zentzze...@email.unc.edu wrote:
Hello Everyone!
Thanks for all your replies! This was very helpful! I found that there
seems to be a limitation to only 32GB of memory which I think will be fine.
I was able to consume the 32GB of memory with the following:
Start R with the following command: R --max-vsize 55000M
then within R run
x=rep(0.1,2.141e9)
and watch the process with top and R will consume about 32GB of memory...
Hopefully this will be enough for the researchers ;)
Thanks!
-scz
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory running a
64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
--enable-BLAS-shlib --enable-shared --with-readline --with-iconv --with-x
--with-tcktk --with-aqua --with-libpng --with-jpeglib
and I would like to verify that I can use 55GB-60GB of the 64GB of memory
within R. Does anyone know how this is possible? Will R be able to access
that amount of memory from a single process? I am not an R user myself but I
just wanted to test this before I turned the server over to the
researchers..
Thanks!
-scz
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Re: [R] Multiplication of data frame with vector
Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von David Freedman Gesendet: Dienstag, 7. Juli 2009 14:53 An: r-help@r-project.org Betreff: Re: [R] Multiplication of data frame with vector Would the scale function work for this? Something like new=scale(df, center=T) HTH, david freedman cir p wrote: Dear group: sorry for my beginners question, but I'm rather new to R and was searching high and low without success: I have a data frame (df) with variables in the rows and observations in the columns like (the actual data frame has 15 columns and 1789 rows): early1 early2 early3 early4 early5 M386T1000 57056 55372 58012 55546 57309 M336T9011063 10312 10674 10840 11208 M427T9112064 11956 12692 12340 11924 M429T91 4594 3890 4096 4019 4204 M447T9026553 27647 26889 26751 26929 Now I'm trying to transform each value column-wise to make columns to all have the same mean with: df * mean(mean(df)) / mean(df). I just can't get my head around this: mean(df) gives me the correct column means vector, and mean(mean(df)) gives me the correct total mean. The above operation works correctly for individual rows, i.e. if I do df[1,]*mean(mean(df))/mean(df) Can someone tell me what I am doing wrong?? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Multiplication-of-data-frame-with-vector-tp24368878p24372764.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] Uncorrelated random vectors
Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Gesendet: Dienstag, 7. Juli 2009 15:51 An: Stein, Luba (AIM SE); r-help@r-project.org Betreff: RE: [R] Uncorrelated random vectors cor.test(rnorm(1), rnorm(1)) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Stein, Luba (AIM SE) Verzonden: dinsdag 7 juli 2009 15:46 Aan: r-help@r-project.org Onderwerp: [R] Uncorrelated random vectors Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba [[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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] cor vs cor.test
Hi,
I am trying to use R for some survey analysis, and need to compute the
significance of some correlations. I read the man pages for cor and
cor.test, but I am confused about
- whether these functions are intended to work the same way
- about how these functions handle NA values
- whether cor.test supports 'use = complete.obs'.
Some example output may explain why I am confused:
---
WORKS:
cor(q[[9]], q[[10]])
perceivedlearningcurve
overallimpression 0.7440637
---
DOES NOT WORK:
cor.test(q[[9]], q[[10]])
Error in `[.data.frame`(x, OK) : undefined columns selected
---
(I assume that's because of R's generous type coercions does R
have a typeof operator to learn what the type of q[[9]] is?)
---
WORKS:
cor.test(q[[9]][,1], q[[10]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[10]][, 1]
t = 12.9877, df = 136, p-value 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.6588821 0.8104055
sample estimates:
cor
0.7440637
---
WORKS, but propagates NAs:
cor(q[[9]], q[[51]])
usefulnessautodetectionbox_ord
overallimpression NA
---
WORKS, and uses complete observations only
cor(q[[9]], q[[51]], use=complete.obs)
usefulnessautodetectionbox_ord
overallimpression 0.2859895
---
WORKS, apparently, but does not require 'use=complete.obs' (!?)
cor.test(q[[9]][,1], q[[51]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[51]][, 1]
t = 3.1016, df = 108, p-value = 0.002456
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.1043351 0.4491779
sample estimates:
cor
0.2859895
---
The help page for cor.test states that 'getOption('na.action')'
describes the action taken on NAs:
getOption(na.option)
NULL
---
No action is taken, yet cor.test appears to only use complete observations (!?)
Others believe that cor.test accepts 'use=complete.obs':
http://markmail.org/message/nuzqeouqhbb7f6ok
--
Needless to say, this makes writing robust code very hard.
I'm wondering what the rationale for the inconsistencies between cor
and cor.test is.
Thanks!
- Godmar
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Re: [R] Uncorrelated random vectors
You could use the mvtnorm package to generate correlated vectors of random normal deviates where the nominal correlation is 0. library(mvtnorm) rho - 0.0 Cor - array(c(1, rho, rho, 1), dim=c(2,2)) Y - rmvnorm(1000, sigma=Cor) plot(Y) cor(Y) cor.test(Y[,1],Y[,2]) Any given random set will have some small amount of random correlation. You can then transform the distribution of the normal random deviates to another distribution using pnorm, qnorm and their equivalents for the other dist. Andy. andydol...@gmail.com 2009/7/7 Stein, Luba (AIM SE) luba.st...@allianz.com Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Gesendet: Dienstag, 7. Juli 2009 15:51 An: Stein, Luba (AIM SE); r-help@r-project.org Betreff: RE: [R] Uncorrelated random vectors cor.test(rnorm(1), rnorm(1)) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Stein, Luba (AIM SE) Verzonden: dinsdag 7 juli 2009 15:46 Aan: r-help@r-project.org Onderwerp: [R] Uncorrelated random vectors Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba [[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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] bigglm() results different from glm()+Another question
How many rows does xx have? Let's look at your example for chunksize 1, you initially fit the first 1 observations, then the seq results in just the value 1 which means that you do the update based on vaues 10001 through 2, if xx only has 1 rows, then this should give at least one error. If xx has 2 or more rows, then only chunksize 1 will ever see the 2th value, the other chunksizes will use less of the data. Also looking at the help for update.biglm, the 2nd argument is moredata not data, so if the code below is the code that you actually ran, then the new data chunks are going into the ... argument (and being ignored as that is there for future expansion and does nothing yet) and the moredata argument is left empty, which should also be giving an error. For the code below, the model is only being fit to the initial chunk and never updated, so with different chunk sizes, there is different amounts of data per model. You can check this by doing summary(fit) and looking at the sample size in the 2nd line. It is easier for us to help you if you provide code that can be run by copying and pasting (we don't have xx, so we can't just run the code below, you could include a line to randomly generate an xx, or a link to where a copy of xx can be downloaded from). It also helps if you mention any errors or warnings that you receive in the process of running your code. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 From: utkarshsinghal [mailto:utkarsh.sing...@global-analytics.com] Sent: Tuesday, July 07, 2009 12:10 AM To: Greg Snow Cc: Thomas Lumley; r help Subject: Re: [R] bigglm() results different from glm()+Another question Trust me, it is the same total data I am using, even the chunksizes are all equal. I also crosschecked by manually creating the chunks and updating as in example given on biglm help page. ?biglm Regards Utkarsh Greg Snow wrote: Are you sure that you are fitting all the models on the same total data? A first glance looks like you may be including more data in some of the chunk sizes, or be producing an error that update does not know how to deal with. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.orgmailto:greg.s...@imail.org 801.408.8111 From: utkarshsinghal [mailto:utkarsh.sing...@global-analytics.com] Sent: Monday, July 06, 2009 8:58 AM To: Thomas Lumley; Greg Snow Cc: r help Subject: Re: [R] bigglm() results different from glm()+Another question The AIC of the biglm models is highly dependent on the size of chunks selected (example provided below). This I can somehow expect because the model error will increase with the number of chunks. It will be helpful if you can provide your opinion for comparing different models in such cases: * can I compare two models fitted with different chunksizes, or should I always use the same chunk size. * although I am not going to use AIC at all in my model selection, but I think any other model parameters will also vary in the same way. Am I right? * what would be the ideal chunksize? should it be the maximum possible size R and my system's RAM is able to handle? Any comments will be helpful. Example of AIC variation with chunksize: I ran the following code on my data which has 1 observations and 3 independent variables chunksize = 500 fit = biglm(y~x1+x2+x3, data=xx[1:chunksize,]) for(i in seq(chunksize,1,chunksize)) fit=update(fit, data=xx[(i+1):(i+chunksize),]) AIC(fit) [1] 30647.79 Here are the AIC for other chunksizes: chunksizeAIC 500 30647.79 100029647.79 200027647.79 250026647.79 500021647.79 1 11647.79 Regards Utkarsh utkarshsinghal wrote: Thank you Mr. Lumley and Mr. Greg. That was helpful. Regards Utkarsh Thomas Lumley wrote: On Fri, 3 Jul 2009, utkarshsinghal wrote: Hi Sir, Thanks for making package available to us. I am facing few problems if you can give some hints: Problem-1: The model summary and residual deviance matched (in the mail below) but I didn't understand why AIC is still different. AIC(m1) [1] 532965 AIC(m1big_longer) [1] 101442.9 That's because AIC.default uses the unnormalized loglikelihood and AIC.biglm uses the deviance. Only differences in AIC between models are meaningful, not individual values. Problem-2: chunksize argument is there in bigglm but not in biglm, consequently, udate.biglm is there, but not update.bigglm Is my observation correct? If yes, why is this difference? Because update.bigglm is impossible. Fitting a glm requires iteration, which means that it requires multiple passes through the data. Fitting a linear model requires only a single pass. update.biglm can take a fitted or partially fitted biglm and add more data. To do the same thing for a bigglm you would need to
Re: [R] cor vs cor.test
?cor says that cor() can be applied to
'numeric vector, matrix or data frame'
?cor.test requires
'numeric vectors of data values'
So, what's your q?
As to na.action:
?cor.test makes no reference to na.action for the default method.
Looking at the code of cor.test.default shows that only complete
cases are used. The formula method does have an argument na.action
and it works just fine for me.
Try getOption('na.action') and you'll probably find that it is set
^^
to 'na.omit'.
-Peter Ehlers
Godmar Back wrote:
Hi,
I am trying to use R for some survey analysis, and need to compute the
significance of some correlations. I read the man pages for cor and
cor.test, but I am confused about
- whether these functions are intended to work the same way
- about how these functions handle NA values
- whether cor.test supports 'use = complete.obs'.
Some example output may explain why I am confused:
---
WORKS:
cor(q[[9]], q[[10]])
perceivedlearningcurve
overallimpression 0.7440637
---
DOES NOT WORK:
cor.test(q[[9]], q[[10]])
Error in `[.data.frame`(x, OK) : undefined columns selected
---
(I assume that's because of R's generous type coercions does R
have a typeof operator to learn what the type of q[[9]] is?)
---
WORKS:
cor.test(q[[9]][,1], q[[10]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[10]][, 1]
t = 12.9877, df = 136, p-value 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.6588821 0.8104055
sample estimates:
cor
0.7440637
---
WORKS, but propagates NAs:
cor(q[[9]], q[[51]])
usefulnessautodetectionbox_ord
overallimpression NA
---
WORKS, and uses complete observations only
cor(q[[9]], q[[51]], use=complete.obs)
usefulnessautodetectionbox_ord
overallimpression 0.2859895
---
WORKS, apparently, but does not require 'use=complete.obs' (!?)
cor.test(q[[9]][,1], q[[51]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[51]][, 1]
t = 3.1016, df = 108, p-value = 0.002456
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.1043351 0.4491779
sample estimates:
cor
0.2859895
---
The help page for cor.test states that 'getOption('na.action')'
describes the action taken on NAs:
getOption(na.option)
NULL
---
No action is taken, yet cor.test appears to only use complete observations (!?)
Others believe that cor.test accepts 'use=complete.obs':
http://markmail.org/message/nuzqeouqhbb7f6ok
--
Needless to say, this makes writing robust code very hard.
I'm wondering what the rationale for the inconsistencies between cor
and cor.test is.
Thanks!
- Godmar
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Uncorrelated random vectors
Be careful to be clear what you are referring to when you say correlation is zero. The commands x - rnorm(100) y - rnorm(100) will produce two vectors of given length (100) which (to within the effectively ignorable limitations of the ransom number generator) will have been produced independently. Hence the *theoretical* correlation is zero. If that is what you meant, then it is already answered. When you compute cor(x,y), however, the answer will in general be non-zero (though only rarely significantly so). This is because the numbers produced by the second independent run of rnrom() have an almost zero probability of producing two vectors for which the value of cor(x,y) = 0. However, possibly you mean that you want two vectors for which the result of cor(x,y) = 0. One way to achieve this is along the following lines: set.seed(54321) x - rnorm(100) y0 - rnorm(100) My - mean(y0) Sy - sd(y0) y1 - lm(y0 ~ x)$res ; y1 - y1/sd(y1) y - My + y1*Sy mean(y0) # [1] 0.04497584 mean(y) # [1] 0.04497584 sd(y0) # [1] 0.848231 sd(y) # [1] 0.848231 cor(x,y0) # [1] 0.05556468 cor(x,y) # [1] 6.451072e-18 [effectively 0, to within rounding error] In this case, however, note that [A]: The 100 elements of y, given the values of x, are NOT independent of each other, since they satisfy the linear constraint x[1]*y[1] + x[2]*y[2] + ... + x[100]*y[100] - (sum(x))*[y[1] + y[2] + ... + y[100])/100 = 0 and therefore can vary only in 99 dimensions, not 100. Nor are they independent of the values of x (even though the numerical correlation is 0). On the other hand, the values of y0 are independent of the values of x, and of each other. You need to be very clear why you want to have two vectors x,y such that cor(x,y) = 0, since otherwise you are at risk of carrying out an invalid analysis. Hoping this helps, Ted. On 07-Jul-09 14:26:02, Stein, Luba (AIM SE) wrote: Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Gesendet: Dienstag, 7. Juli 2009 15:51 An: Stein, Luba (AIM SE); r-help@r-project.org Betreff: RE: [R] Uncorrelated random vectors cor.test(rnorm(1), rnorm(1)) ir. Thierry Onkelinx ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Stein, Luba (AIM SE) Verzonden: dinsdag 7 juli 2009 15:46 Aan: r-help@r-project.org Onderwerp: [R] Uncorrelated random vectors Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jul-09 Time: 16:48:06 -- XFMail -- __ 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] Solving quadratic equations with covariance term
On Tue, 7 Jul 2009, Stein, Luba (AIM SE) wrote: Hi, more precisely I consider a matrix with three column vectors a_i (i=1,2,3), i.e. A=(a_1,a_2,a_3). On the other hand x should take vectors as values, i.e. x=v_j, while j goes also from 1 till 3. Now I just want to calculate the equation Cov(a_i,x_j) = 0, where Cov(a_i,x_j) is the covariance matrix. A is a given value and x is the variable I am looking for. In my opinion this is an quadratic equation and makes sense. Well, x_j = (0,0,...,0)' will satisfy Cov( A, x_j ) = (0,...0)'. Suggest you Google 'orthogonal complement' for nontrivial solutions. Then peruse ?qr HTH, Chuck p.s. Don't lose sight of FAQ 7.31 http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Best wishes, Luba -Urspr?ngliche Nachricht- Von: Rolf Turner [mailto:r.tur...@auckland.ac.nz] Gesendet: Montag, 6. Juli 2009 23:16 An: Stein, Luba (AIM SE) Cc: R-help@r-project.org Betreff: Re: [R] Solving quadratic equations with covariance term On 7/07/2009, at 2:15 AM, Stein, Luba (AIM SE) wrote: Hi, I would like to solve the following equation with R: Cov(A,x)=0. A is a given matrix, x is the an unknown vector. Is there any nice solution for this? What on earth do you mean by ``Cov(A,x)''? This makes no sense at all. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ 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] Mathematical annotation axis in lattice
Hi Albart, This bugged me also for quite some time. After some experiments the following syntax worked best: library(lattice) a = 0.11 xyplot(1:10~10:11, xlab = as.expression(bquote(R^2~ equals ~.(a With the combination of as.expression and bquote you can mix text, math expression and the content of objects (in the case here of a). Read the documentation of bquote for more details. cheers, Paul Coster, Albart wrote: Dear list, making mathematical expressions in plots is not difficult: expression(phi[1]) for example. At this moment I am stuck in creating a vector of expressions: pos - 1:10 lab - letters[pos] Now, I would like to create a vector of expressions which I could use for labeling the x-axis of a lattice plot. ll - as.expression(paste(pos, phi[,lab,],sep = ) xyplot(1:10~11:10,scales = list(x = list(labels = ll,at = 1:10))) does not work. I read about the function substitute, but that did not solve it. Could you recommend me how I should do this? Thanks in advance, Albart Coster Wageningen Universiteit Netherlands __ 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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Uncorrelated random vectors
Here are some examples that may get you started (note that there is no guarantee that a variable follows a given distribution after it has been adjusted to have 0 correlation with another variable): library(MASS) tmp - mvrnorm(25, c(0,0), diag(2), empirical=TRUE) zapsmall(cor(tmp)) tmp2 - exp(tmp) zapsmall(cor(tmp2)) x - rexp(100, 3) y - rexp(100, 2) par(mfrow=c(2,1)) plot(x,y) tmp3 - cbind(x,y) zapsmall(cor(tmp3)) tmp4 - tmp3 %*% solve(chol(var(tmp3))) zapsmall(cor(tmp4)) plot(tmp4) hist(tmp4[,1]) hist(tmp4[,2]) plot(tmp4[,1], x) plot(tmp4[,2], y) Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Stein, Luba (AIM SE) Sent: Tuesday, July 07, 2009 8:26 AM To: ONKELINX, Thierry; r-help@r-project.org Subject: Re: [R] Uncorrelated random vectors Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Gesendet: Dienstag, 7. Juli 2009 15:51 An: Stein, Luba (AIM SE); r-help@r-project.org Betreff: RE: [R] Uncorrelated random vectors cor.test(rnorm(1), rnorm(1)) --- - ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Stein, Luba (AIM SE) Verzonden: dinsdag 7 juli 2009 15:46 Aan: r-help@r-project.org Onderwerp: [R] Uncorrelated random vectors Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba [[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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get R to print only one column per line when outputting a matrix?
It looks like you are printing a matrix and that you want to print all rows of the first column before all rows of the second column. Apply should do it. Assume the matrix is named AA apply(AA, c(2,1), cat, \n) # the \n is the line-feed character -- DW On Jul 7, 2009, at 10:06 AM, Godmar Back wrote: Hi, I'm trying to make it easier for my survey evaluators to read the results of my survey analysis. To that end, I'd like to suppress R's habit of filling every line up to width columns. How do I do that? For instance, using 'print()', R outputs something like: But you have not offered the code that produced this. [,1] [,2] var2 someshortname someothershortname r0.33417550.3275274 N136 136 [,3] var2 somereallyreallyreallyreallyreallylongname r0.323306 N136 [,4] var2 someotherreallyreallyreallyreallyreallylongname r0.3121291 N101 How can I get it to place every column on a new line to avoid confusing the reader? I read the help for print, print.default, format, cat, and options(width) and wasn't able to find an answer. Thanks! - Godmar __ 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 Heritage Laboratories 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] Thanks!
Hi all, I just wanted to send a general word of thanks to the list for making my first week using R successful (by my measures) and reasonably pleasurable. (Not a single literal RTFM!) ;-) I appreciate all the help I've received from folks. I have a long way to go but I'm starting to get data and plots that look interesting and I couldn't have gotten there this fast without your help. Cheers, Mark __ 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] error: no such index at level 2
Hi, I am confused about how to select elements from a list. I'm trying to select all rows of a table 'crossRsorted' such that the mean of a related vector is 0. The related vector is accessible as a list element l[[i]] where i is the row index. I thought this would work: crossRsorted[mean(q[[ crossRsorted[,1] ]], na.rm = TRUE) 0, ] Error in q[[crossRsorted[, 1]]] : no such index at level 2 How can I express: select only those rows 'r_i' from crossRsorted where mean(q[[r_i[1]]]) 0? Thanks, - Godmar __ 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] cor vs cor.test
Thanks, Peter.
You're right, I mistyped and getOption('na.action') shows na.omit.
Perhaps my question was more commentary about my perceived lack of
rationale and orthogonality in R than it should have been. Presumably,
q[[i]] is a data frame and q[[i]][,1] is a numeric vector, so cor and
cor.test work differently. The interfaces for how to handle NAs
between the two functions are completely different. Why design things
this way, though.
- Godmar
On Tue, Jul 7, 2009 at 11:42 AM, Peter Ehlersehl...@ucalgary.ca wrote:
?cor says that cor() can be applied to
'numeric vector, matrix or data frame'
?cor.test requires
'numeric vectors of data values'
So, what's your q?
As to na.action:
?cor.test makes no reference to na.action for the default method.
Looking at the code of cor.test.default shows that only complete
cases are used. The formula method does have an argument na.action
and it works just fine for me.
Try getOption('na.action') and you'll probably find that it is set
^^
to 'na.omit'.
-Peter Ehlers
Godmar Back wrote:
Hi,
I am trying to use R for some survey analysis, and need to compute the
significance of some correlations. I read the man pages for cor and
cor.test, but I am confused about
- whether these functions are intended to work the same way
- about how these functions handle NA values
- whether cor.test supports 'use = complete.obs'.
Some example output may explain why I am confused:
---
WORKS:
cor(q[[9]], q[[10]])
perceivedlearningcurve
overallimpression 0.7440637
---
DOES NOT WORK:
cor.test(q[[9]], q[[10]])
Error in `[.data.frame`(x, OK) : undefined columns selected
---
(I assume that's because of R's generous type coercions does R
have a typeof operator to learn what the type of q[[9]] is?)
---
WORKS:
cor.test(q[[9]][,1], q[[10]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[10]][, 1]
t = 12.9877, df = 136, p-value 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.6588821 0.8104055
sample estimates:
cor
0.7440637
---
WORKS, but propagates NAs:
cor(q[[9]], q[[51]])
usefulnessautodetectionbox_ord
overallimpression NA
---
WORKS, and uses complete observations only
cor(q[[9]], q[[51]], use=complete.obs)
usefulnessautodetectionbox_ord
overallimpression 0.2859895
---
WORKS, apparently, but does not require 'use=complete.obs' (!?)
cor.test(q[[9]][,1], q[[51]][,1])
Pearson's product-moment correlation
data: q[[9]][, 1] and q[[51]][, 1]
t = 3.1016, df = 108, p-value = 0.002456
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.1043351 0.4491779
sample estimates:
cor
0.2859895
---
The help page for cor.test states that 'getOption('na.action')'
describes the action taken on NAs:
getOption(na.option)
NULL
---
No action is taken, yet cor.test appears to only use complete observations
(!?)
Others believe that cor.test accepts 'use=complete.obs':
http://markmail.org/message/nuzqeouqhbb7f6ok
--
Needless to say, this makes writing robust code very hard.
I'm wondering what the rationale for the inconsistencies between cor
and cor.test is.
Thanks!
- Godmar
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Re: [R] how to get R to print only one column per line when outputting a matrix?
On Tue, Jul 7, 2009 at 12:20 PM, David Winsemiusdwinsem...@comcast.net wrote: It looks like you are printing a matrix and that you want to print all rows of the first column before all rows of the second column. Apply should do it. Assume the matrix is named AA apply(AA, c(2,1), cat, \n) # the \n is the line-feed character I thought along these lines, too, but: AA [,1][,2][,3] [1,] overallimpression yourinitialimpression managementprocess_as_ord [2,] 0.7440637 0.7270246 0.5550202 [,4] [1,] userinterfacechangedisplayorder:It was very easy to use with either option [2,] -0.4476622 [ remainder deleted ] apply(AA, c(2,1), cat, \n) Error in cat(list(...), file, sep, fill, labels, append) : argument 1 (type 'list') cannot be handled by 'cat' This may give more information about what AA is: attributes(AA) $dim [1] 2 13 is.matrix(AA) [1] TRUE - Godmar __ 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 get R to print only one column per line when outputting a matrix?
On Tue, Jul 7, 2009 at 1:22 PM, Godmar Backgod...@gmail.com wrote:
apply(AA, c(2,1), cat, \n)
Error in cat(list(...), file, sep, fill, labels, append) :
argument 1 (type 'list') cannot be handled by 'cat'
ps: but your idea of using 'apply' led me to this:
dummy - apply(AA, c(2), function (r) { cat(sprintf(%f - %s\n, r[2],
format(r[1]))) })
0.744064 - overallimpression
0.727025 - yourinitialimpression
0.555020 - managementprocess_as_ord
[...]
which is exactly what I'd like.
Thanks!
- Godmar
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[R] Error due to non-conformable arrays
Hello,
Consider this function for generalized ridge regression:
gre - function (X,y,D){
n - dim(X)[1]
p - dim(X)[2]
intercept - rep(1, n)
X - cbind(intercept, X)
X2D - crossprod(X,X)+ D
Xy - crossprod(X,y)
bth - qr.solve(X2D, Xy)
}
# suppose X is an (nxp) design matrix and y is an (nx1) response vector
p - dim(x)[2]
D- diag(rep(1.5,p))
bt - gre(X,y,D)
I am getting following error:
Error in crossprod(X, X) + D : non-conformable arrays
But when i define D within the function 'gre()' then everything is fine.
What wrong i have done?
thanks.
--
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Re: [R] Error due to non-conformable arrays
I think that is because X in your function has (n + 1) columns and D with
only n coluimns:
matrix(1:9, ncol = 3) + matrix(1:8, ncol = 2)
On Tue, Jul 7, 2009 at 2:30 PM, spime saby...@gmail.com wrote:
Hello,
Consider this function for generalized ridge regression:
gre - function (X,y,D){
n - dim(X)[1]
p - dim(X)[2]
intercept - rep(1, n)
X - cbind(intercept, X)
X2D - crossprod(X,X)+ D
Xy - crossprod(X,y)
bth - qr.solve(X2D, Xy)
}
# suppose X is an (nxp) design matrix and y is an (nx1) response vector
p - dim(x)[2]
D- diag(rep(1.5,p))
bt - gre(X,y,D)
I am getting following error:
Error in crossprod(X, X) + D : non-conformable arrays
But when i define D within the function 'gre()' then everything is fine.
What wrong i have done?
thanks.
--
View this message in context:
http://www.nabble.com/Error-due-to-non-conformable-arrays-tp24377781p24377781.html
Sent from the R help mailing list archive at Nabble.com.
__
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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Re: [R] Error due to non-conformable arrays
Incomplete code leaves us able to do naught but guess;
Perhaps you are unaware that x != X
--
DW
On Jul 7, 2009, at 1:30 PM, spime wrote:
Hello,
Consider this function for generalized ridge regression:
gre - function (X,y,D){
n - dim(X)[1]
p - dim(X)[2]
intercept - rep(1, n)
X - cbind(intercept, X)
X2D - crossprod(X,X)+ D
Xy - crossprod(X,y)
bth - qr.solve(X2D, Xy)
}
# suppose X is an (nxp) design matrix and y is an (nx1) response
vector
p - dim(x)[2]
D- diag(rep(1.5,p))
bt - gre(X,y,D)
I am getting following error:
Error in crossprod(X, X) + D : non-conformable arrays
But when i define D within the function 'gre()' then everything is
fine.
What wrong i have done?
thanks.
--
View this message in context:
http://www.nabble.com/Error-due-to-non-conformable-arrays-tp24377781p24377781.html
Sent from the R help mailing list archive at Nabble.com.
__
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] Error due to non-conformable arrays
Hi spime,
What is x? Did you have any other X defined in your R-session? Be aware
that R is case-sensitive.
Best,
Jorge
On Tue, Jul 7, 2009 at 1:30 PM, spime saby...@gmail.com wrote:
Hello,
Consider this function for generalized ridge regression:
gre - function (X,y,D){
n - dim(X)[1]
p - dim(X)[2]
intercept - rep(1, n)
X - cbind(intercept, X)
X2D - crossprod(X,X)+ D
Xy - crossprod(X,y)
bth - qr.solve(X2D, Xy)
}
# suppose X is an (nxp) design matrix and y is an (nx1) response vector
p - dim(x)[2]
D- diag(rep(1.5,p))
bt - gre(X,y,D)
I am getting following error:
Error in crossprod(X, X) + D : non-conformable arrays
But when i define D within the function 'gre()' then everything is fine.
What wrong i have done?
thanks.
--
View this message in context:
http://www.nabble.com/Error-due-to-non-conformable-arrays-tp24377781p24377781.html
Sent from the R help mailing list archive at Nabble.com.
__
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[[alternative HTML version deleted]]
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[R] how to read point shp file to R?
I am new with R and want do some analysis with a point vector data file. Any help is appreciate. Sunny [[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] object .trPaths not found
Uwe Ligges schrieb: Maybe, but the may depend on your script, your OS, your R version, used packages and so on. Hence please read and follow the posting guide and provide commented, minimal, self-contained, reproducible code. Hi Uwe, I was just asked the same question and hat the same problem before. It seem that it is a Tinn_R installation problem . I do not now what I changed to get it working, but the single line (R send line) mode is working, the R send selection and Rsend file mode not. System Windows XP new installed TinnR File permissions should not a problem on windows systems. Maybe any file is set to read only? The same srcipt which is working at home is not working at the new system. Regards Knut __ 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] Quantitative Risk Management by McNeil
Dear Andriy:
1. The help file for fit.NH says the first argument should be
a vector of data. Consider the following modification of the example
on that help page:
rs - matrix(rseries, 10, 202, dimnames=list(letters[1:10], 1:202))
rs. - fit.NH(rs)
Error: cannot allocate vector of size 238 Kb
In addition: Warning messages:
1: In sqrt(3/(variance * ekurt)) : NaNs produced
2: In optim(par = theta, fn = negloglik, gr = NULL, datavector = data, :
Reached total allocation of 3583Mb: see help(memory.size)
3: In optim(par = theta, fn = negloglik, gr = NULL, datavector = data, :
Reached total allocation of 3583Mb: see help(memory.size)
2. This suggests you try the following:
fit.NH(as.numeric(Transpose), case=NIG, symmetric=FALSE, se=FALSE)
3. If this doesn't work, I suggest you look at str(Transpose):
Is this character?
4. If this does not solve your problem, have you tried emailing
directly Scott Ulman scottul...@hotmail.com for Alexander McNeil?
5. You could make it easier for others to reply to a question
like this by helping your readers find the fit.NH function. I have
not seen Quantitative Risk Management by McNeil, but it sounded
interesting, so I looked at your question. I found fit.NH as follows:
library(RSiteSearch)
fitNH - RSiteSearch.function('fit.NH')
HTML(fitNH)
This last line opened a web browser with links to 6 different help
pages in the QRMlib package.
Hope this helps.
Spencer Graves
Andriy Fetsun wrote:
Dear Specialists in R,
May be somebody has experiment in using pakage for the book Quantitative
Risk Management by McNeil?
This package is writen in R.
I have run this package for fitting the data to Nornal Inverse Gaussian
distribution and fased with following problem.
Return-read.csv(data.csv)
Transpose-t(Return)
fit.NH(Transpose, case=NIG, symmetric=FALSE, se=FALSE)
Error: cannot allocate vector of size 57 Kb
In addition: Warning messages:
1: In var.default(data) :
Reached total allocation of 222Mb: see help(memory.size)
2: In optim(par = theta, fn = negloglik, gr = NULL, datavector = data, :
Reached total allocation of 222Mb: see help(memory.size)
3: In optim(par = theta, fn = negloglik, gr = NULL, datavector = data, :
Reached total allocation of 222Mb: see help(memory.size)
In the attachment you can find the description of the function.
the link where I took this soft is
http://cran.r-project.org/web/packages/QRMlib/index.html
Thank you in advance!
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[R] how to count number of elements in a vector that are not NA ?
Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
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Re: [R] how to count number of elements in a vector that are not NA ?
Dear Godmar,
Yes. One way would be
sum( !is.na( yourvector ) )
HTH,
Jorge
On Tue, Jul 7, 2009 at 2:56 PM, Godmar Back god...@gmail.com wrote:
Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
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[[alternative HTML version deleted]]
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Re: [R] how to count number of elements in a vector that are not NA ?
another option should be:
length(na.omit(v))
On Tue, Jul 7, 2009 at 3:56 PM, Godmar Back god...@gmail.com wrote:
Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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[R] Test for X=1 fails, test for 0 works, data in text file is 1
Hi, I am apparently not understanding some nuance about either the use of subset or more likely my ability to test for a numerical match using '='. Which is it? Thanks in advance. I've read a data file, reshaped it and then created MyResults by keeping only lines where the value column is greater than 0. So far so good. The data in MyResults looks good to me by eye. The problem comes in when I try to further subset MyResults into two files, one with PosType=1 and the other with PosType=-1. Looking at the dimension of the results there's no change. It didn't work which is verified by eye. However if I test for PosType=1 by actually testing for PosType0 then it does work. Is this the general case in R that if I've read data that was written into a csv file as 1 - it is 1 if I look into the file with a text editor - that I cannot test for that? Or is some case where I need to use maybe as.numeric or something else first to ensure R sees the number the way I'm thinking about the number? Cheers, Mark dim(X) [1] 25 425 ReShapeX - melt(X, id = c(Trade, PosType, EnDate, EnTime, ExDate, ExTime, PL_Pos, Costs, Save2)) dim(ReShapeX) [1] 1040011 MyResults - subset(ReShapeX, value 0) dim(MyResults) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType = 1) dim(MyResults.GroupA) [1] 1105 11 MyResults.GroupB - subset(MyResults, PosType = -1) dim(MyResults.GroupB) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType 0) dim(MyResults.GroupA) [1] 432 11 MyResults.GroupB - subset(MyResults, PosType 0) dim(MyResults.GroupB) [1] 673 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to count number of elements in a vector that are not NA ?
How about
countN - function ( v ) {
sum ( !is.na ( v ) ) - sum ( is.na ( v ) )
}
--
David
-
David Huffer, Ph.D. Senior Statistician
CSOSA/Washington, DC david.huf...@csosa.gov
-
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Godmar Back
Sent: Tuesday, July 07, 2009 2:57 PM
To: R-help@r-project.org
Subject: [R] how to count number of elements in a vector that are not NA ?
Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
__
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and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] Test for X=1 fails, test for 0 works, data in text file is 1
Try this: MyResults.GroupA - subset(MyResults, PosType == 1) On Tue, Jul 7, 2009 at 4:06 PM, Mark Knecht markkne...@gmail.com wrote: Hi, I am apparently not understanding some nuance about either the use of subset or more likely my ability to test for a numerical match using '='. Which is it? Thanks in advance. I've read a data file, reshaped it and then created MyResults by keeping only lines where the value column is greater than 0. So far so good. The data in MyResults looks good to me by eye. The problem comes in when I try to further subset MyResults into two files, one with PosType=1 and the other with PosType=-1. Looking at the dimension of the results there's no change. It didn't work which is verified by eye. However if I test for PosType=1 by actually testing for PosType0 then it does work. Is this the general case in R that if I've read data that was written into a csv file as 1 - it is 1 if I look into the file with a text editor - that I cannot test for that? Or is some case where I need to use maybe as.numeric or something else first to ensure R sees the number the way I'm thinking about the number? Cheers, Mark dim(X) [1] 25 425 ReShapeX - melt(X, id = c(Trade, PosType, EnDate, EnTime, ExDate, ExTime, PL_Pos, Costs, Save2)) dim(ReShapeX) [1] 1040011 MyResults - subset(ReShapeX, value 0) dim(MyResults) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType = 1) dim(MyResults.GroupA) [1] 1105 11 MyResults.GroupB - subset(MyResults, PosType = -1) dim(MyResults.GroupB) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType 0) dim(MyResults.GroupA) [1] 432 11 MyResults.GroupB - subset(MyResults, PosType 0) dim(MyResults.GroupB) [1] 673 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Test for X=1 fails, test for 0 works, data in text file is 1
Hi Mark, X = 1 assings the number 1 to X whereas X == 1 test if X is equal to 1. I suspect you want to do this :-) Here is an example: # R code X = 1 X # [1] 1 X == 1 # [1] TRUE HTH, Jorge On Tue, Jul 7, 2009 at 3:06 PM, Mark Knecht markkne...@gmail.com wrote: Hi, I am apparently not understanding some nuance about either the use of subset or more likely my ability to test for a numerical match using '='. Which is it? Thanks in advance. I've read a data file, reshaped it and then created MyResults by keeping only lines where the value column is greater than 0. So far so good. The data in MyResults looks good to me by eye. The problem comes in when I try to further subset MyResults into two files, one with PosType=1 and the other with PosType=-1. Looking at the dimension of the results there's no change. It didn't work which is verified by eye. However if I test for PosType=1 by actually testing for PosType0 then it does work. Is this the general case in R that if I've read data that was written into a csv file as 1 - it is 1 if I look into the file with a text editor - that I cannot test for that? Or is some case where I need to use maybe as.numeric or something else first to ensure R sees the number the way I'm thinking about the number? Cheers, Mark dim(X) [1] 25 425 ReShapeX - melt(X, id = c(Trade, PosType, EnDate, EnTime, ExDate, ExTime, PL_Pos, Costs, Save2)) dim(ReShapeX) [1] 1040011 MyResults - subset(ReShapeX, value 0) dim(MyResults) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType = 1) dim(MyResults.GroupA) [1] 1105 11 MyResults.GroupB - subset(MyResults, PosType = -1) dim(MyResults.GroupB) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType 0) dim(MyResults.GroupA) [1] 432 11 MyResults.GroupB - subset(MyResults, PosType 0) dim(MyResults.GroupB) [1] 673 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Test for X=1 fails, test for 0 works, data in text file is 1
On 7/7/2009 3:06 PM, Mark Knecht wrote: Hi, I am apparently not understanding some nuance about either the use of subset or more likely my ability to test for a numerical match using '='. Which is it? Thanks in advance. I've read a data file, reshaped it and then created MyResults by keeping only lines where the value column is greater than 0. So far so good. The data in MyResults looks good to me by eye. The problem comes in when I try to further subset MyResults into two files, one with PosType=1 and the other with PosType=-1. Looking PosType = 1 is an assignment. The test is PosType == 1. Duncan Murdoch at the dimension of the results there's no change. It didn't work which is verified by eye. However if I test for PosType=1 by actually testing for PosType0 then it does work. Is this the general case in R that if I've read data that was written into a csv file as 1 - it is 1 if I look into the file with a text editor - that I cannot test for that? Or is some case where I need to use maybe as.numeric or something else first to ensure R sees the number the way I'm thinking about the number? Cheers, Mark dim(X) [1] 25 425 ReShapeX - melt(X, id = c(Trade, PosType, EnDate, EnTime, ExDate, ExTime, PL_Pos, Costs, Save2)) dim(ReShapeX) [1] 1040011 MyResults - subset(ReShapeX, value 0) dim(MyResults) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType = 1) dim(MyResults.GroupA) [1] 1105 11 MyResults.GroupB - subset(MyResults, PosType = -1) dim(MyResults.GroupB) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType 0) dim(MyResults.GroupA) [1] 432 11 MyResults.GroupB - subset(MyResults, PosType 0) dim(MyResults.GroupB) [1] 673 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 count number of elements in a vector that are not NA ?
On Tuesday, July 07, 2009 3:20 PM, Godmar Back wrote:
...That would be wrong, wouldn't it, if the
other replies are correct
Yes. It was wrong. This isn't:
countN - function ( v ) {
length ( v ) - sum ( is.na ( v ) )
}
But there are really tons of ways to do it. Even your way is not
wrong...
--
David
-
David Huffer, Ph.D. Senior Statistician
CSOSA/Washington, DC david.huf...@csosa.gov
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[R] find duplicates... need help!
Hi all,
Suppose I have x = c('a', 't', 'c', 'y', 'g')
and also y = c('a', 'a', 'g', 's')
If I do something like x%in%y, I obtain a vector like this: [TRUE, FALSE,
FALSE, FALSE, TRUE] which I can easily turn into this: [1, 0, 0, 0, 1].
I was wondering is there anyway for me to get a vector back in return in the
form of: [2, 0, 0, 0, 1]? Essentially, the 2 will tell me that in the first
position of vector 'x', there were two matches found with vector y.
Thanks a ton in advance!
--
View this message in context:
http://www.nabble.com/find-duplicates...-need-help%21-tp24379828p24379828.html
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Re: [R] Test for X=1 fails, test for 0 works, data in text file
On 07-Jul-09 19:06:59, Mark Knecht wrote: Hi, I am apparently not understanding some nuance about either the use of subset or more likely my ability to test for a numerical match using '='. Which is it? Thanks in advance. It looks as though you have tripped over the distinction between = and ==. The first is (in effect) an assignment operator (like -). The second is a comparison operator: X==Y is TRUE if X equals Y. So, for example, to select rows from MyResults according to your criteria below, you could do something like: MyResultsNeg - MyResults[(MyResults$PosType==(-1)),] MyResultsPos - MyResults[(MyResults$PosType==1 ),] [Note: the parentheses (...) are in fact logically superfluous, but I like to use them (a) to make it absolutely clear, visually, how things are being evaluated; (b) (not relevant in this particular context) to avoid falling into traps like N - 10 ; X - 1:N-1 which results in X == (0:9) = (1:10) - 1. The correct syntax for the latter would be X - 1:(N-1).] Hoping this helps, Ted. I've read a data file, reshaped it and then created MyResults by keeping only lines where the value column is greater than 0. So far so good. The data in MyResults looks good to me by eye. The problem comes in when I try to further subset MyResults into two files, one with PosType=1 and the other with PosType=-1. Looking at the dimension of the results there's no change. It didn't work which is verified by eye. However if I test for PosType=1 by actually testing for PosType0 then it does work. Is this the general case in R that if I've read data that was written into a csv file as 1 - it is 1 if I look into the file with a text editor - that I cannot test for that? Or is some case where I need to use maybe as.numeric or something else first to ensure R sees the number the way I'm thinking about the number? Cheers, Mark dim(X) [1] 25 425 ReShapeX - melt(X, id = c(Trade, PosType, EnDate, EnTime, ExDate, ExTime, PL_Pos, Costs, Save2)) dim(ReShapeX) [1] 1040011 MyResults - subset(ReShapeX, value 0) dim(MyResults) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType = 1) dim(MyResults.GroupA) [1] 1105 11 MyResults.GroupB - subset(MyResults, PosType = -1) dim(MyResults.GroupB) [1] 1105 11 MyResults.GroupA - subset(MyResults, PosType 0) dim(MyResults.GroupA) [1] 432 11 MyResults.GroupB - subset(MyResults, PosType 0) dim(MyResults.GroupB) [1] 673 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jul-09 Time: 20:28:44 -- XFMail -- __ 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 count number of elements in a vector that are not NA ?
Thank you for the many replies! This is really a very friendly and helpful community! On Tue, Jul 7, 2009 at 3:06 PM, Henrique Dallazuannawww...@gmail.com wrote: another option should be: length(na.omit(v)) I think the above is what I was looking for since, presumably, it uses the very same test as other methods that exploit na.*, such as cor.test. ... so I tried it out and, of course, R's typing trips me over: length(na.omit(q[[51]])) [1] 1 Why? I think I know: q[[51]] is a data frame with 1 component, and 'length' applied to a data frame counts its components. Not a problem, I can do: length(na.omit(q[[51]][,1])) [1] 110 or length(na.omit(q[[51]])[,1]) [1] 110 for this data frame of 1 components. Do other functions act like length()? Let's look at sum(): sum(na.omit(q[[51]])) [1] 132 sum(na.omit(q[[51]][,1])) [1] 132 sum(na.omit(q[[51]])[,1]) [1] 132 Nope. Easy to get wrong. I buy the last two, but the first? I assume sum() applied to a data frame reduces all its elements across all components(?). Letting the call sum(na.omit(q[[51]])) fail would have been a sensible design decision too, IMO. One needs to be really careful in R. Thank you again, - Godmar __ 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] Test for X=1 fails, test for 0 works, data in text file is 1
On Tue, Jul 7, 2009 at 12:17 PM, Henrique Dallazuannawww...@gmail.com wrote: Try this: MyResults.GroupA - subset(MyResults, PosType == 1) SNIP Darn those small screen fonts. I never noticed that! Every example I'm looking at jsut looks like a single '=' until you pointed it out! Thanks to everyone who responded. Cheers, Mark __ 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] find duplicates... need help!
Dear njhuang86,
Here is one way:
x - c('a', 't', 'c', 'y', 'g')
y - c('a', 'a', 'g', 's')
table(factor(y, levels = x))
# a t c y g
# 2 0 0 0 1
HTH,
Jorge
On Tue, Jul 7, 2009 at 3:28 PM, njhuang86 njhuan...@yahoo.com wrote:
Hi all,
Suppose I have x = c('a', 't', 'c', 'y', 'g')
and also y = c('a', 'a', 'g', 's')
If I do something like x%in%y, I obtain a vector like this: [TRUE, FALSE,
FALSE, FALSE, TRUE] which I can easily turn into this: [1, 0, 0, 0, 1].
I was wondering is there anyway for me to get a vector back in return in
the
form of: [2, 0, 0, 0, 1]? Essentially, the 2 will tell me that in the first
position of vector 'x', there were two matches found with vector y.
Thanks a ton in advance!
--
View this message in context:
http://www.nabble.com/find-duplicates...-need-help%21-tp24379828p24379828.html
Sent from the R help mailing list archive at Nabble.com.
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[[alternative HTML version deleted]]
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[R] vectorizing a function
I'm sure I'm missing something obvious but I'm not seeing how to simply vectorize a function of two or more variables. Say I have f - function(x,y) if (x0) y else -y Now I have vectors x and y of equal length and I'd like to apply f element-wise. I.e. conceptually z - f(x,y) where x, y, z are vectors of the same length Some magic involving apply? Thanks -- View this message in context: http://www.nabble.com/vectorizing-a-function-tp24380064p24380064.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] vectorizing a function (NEVERMIND)
Nevermind, indeed it is obvious: Vectorize ! Steve Jaffe wrote: I'm sure I'm missing something obvious but I'm not seeing how to simply vectorize a function of two or more variables. -- View this message in context: http://www.nabble.com/vectorizing-a-function-tp24380064p24380136.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] how to count number of elements in a vector that are not NA ?
how about sum(!is.na(x)) ?
On Tue, Jul 7, 2009 at 2:56 PM, Godmar Backgod...@gmail.com wrote:
Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
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Re: [R] vectorizing a function
For this case it is quite simple, see ?ifelse z - ifelse( x 0, y, -y ) Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Steve Jaffe Sent: Tuesday, July 07, 2009 1:42 PM To: r-help@r-project.org Subject: [R] vectorizing a function I'm sure I'm missing something obvious but I'm not seeing how to simply vectorize a function of two or more variables. Say I have f - function(x,y) if (x0) y else -y Now I have vectors x and y of equal length and I'd like to apply f element-wise. I.e. conceptually z - f(x,y) where x, y, z are vectors of the same length Some magic involving apply? Thanks -- View this message in context: http://www.nabble.com/vectorizing-a- function-tp24380064p24380064.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] vectorizing a function
?ifelse Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Steve Jaffe Sent: Tuesday, July 07, 2009 12:42 PM To: r-help@r-project.org Subject: [R] vectorizing a function I'm sure I'm missing something obvious but I'm not seeing how to simply vectorize a function of two or more variables. Say I have f - function(x,y) if (x0) y else -y Now I have vectors x and y of equal length and I'd like to apply f element-wise. I.e. conceptually z - f(x,y) where x, y, z are vectors of the same length Some magic involving apply? Thanks -- View this message in context: http://www.nabble.com/vectorizing-a-function-tp24380064p24380064.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] Solving quadratic equations with covariance term
It is not clear to me whether you are talking about a covariance (a theoretical quantity depending on the distribution of A and x) or an empirical covariance, estimated from some data. In the first case you don't need to solve anything because, as long as A is fixed, i.e. non-random, its covariance with anything else is zero. Best, Giovanni Date: Tue, 07 Jul 2009 09:37:53 +0200 From: Stein, Luba (AIM SE) luba.st...@allianz.com Sender: r-help-boun...@r-project.org Cc: R-help@r-project.org R-help@r-project.org Accept-Language: en-US, de-DE Precedence: list Thread-topic: [R] Solving quadratic equations with covariance term Thread-index: Acn+fxCBg0P+0HykRKGeDofFN9YatQAVYRSw acceptlanguage: en-US, de-DE Hi, more precisely I consider a matrix with three column vectors a_i (i=1,2,3), i.e. A=(a_1,a_2,a_3). On the other hand x should take vectors as values, i.e. x=v_j, while j goes also from 1 till 3. Now I just want to calculate the equation Cov(a_i,x_j) = 0, where Cov(a_i,x_j) is the covariance matrix. A is a given value and x is the variable I am looking for. In my opinion this is an quadratic equation and makes sense. Best wishes, Luba -Urspr?ngliche Nachricht- Von: Rolf Turner [mailto:r.tur...@auckland.ac.nz] Gesendet: Montag, 6. Juli 2009 23:16 An: Stein, Luba (AIM SE) Cc: R-help@r-project.org Betreff: Re: [R] Solving quadratic equations with covariance term On 7/07/2009, at 2:15 AM, Stein, Luba (AIM SE) wrote: Hi, I would like to solve the following equation with R: Cov(A,x)=0. A is a given matrix, x is the an unknown vector. Is there any nice solution for this? What on earth do you mean by ``Cov(A,x)''? This makes no sense at all. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.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] Test for X=1 fails, test for 0 works, data in text file is 1
subset(), like many R methods, has an argument list that ends with '...', meaning that it will not tell you that an argument you gave it by name= is not in the official list of arument names. If the ... were not there then you would have gotten an error message. E.g., the following makes a version of subset.data.frame without the ... argument: sb-subset.data.frame formals(sb) - formals(sb)[1:4] data(cars) sb(cars, speed==19) speed dist 3619 36 3719 46 3819 68 sb(cars, speed=19) Error in sb(cars, speed = 19) : unused argument(s) (speed = 19) subset(cars, speed=19) silently ignores the argument you named speed and returns the entire cars dataset. I think that it is unfortunate that the method system requires these ... arguments, as it leads users to waste time tracking down typing errors that would otherwise be flagged. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Mark Knecht Sent: Tuesday, July 07, 2009 12:39 PM To: Henrique Dallazuanna Cc: r-help Subject: Re: [R] Test for X=1 fails, test for 0 works,data in text file is 1 On Tue, Jul 7, 2009 at 12:17 PM, Henrique Dallazuannawww...@gmail.com wrote: Try this: MyResults.GroupA - subset(MyResults, PosType == 1) SNIP Darn those small screen fonts. I never noticed that! Every example I'm looking at jsut looks like a single '=' until you pointed it out! Thanks to everyone who responded. Cheers, Mark __ 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] Uncorrelated random vectors
Here is one way: x - rnorm(100) y - rnorm(100) z - residuals(lm(y ~ x)) cor(x, z) [1] 3.610290e-17 Best, Giovanni Date: Tue, 07 Jul 2009 16:26:02 +0200 From: Stein, Luba (AIM SE) luba.st...@allianz.com Sender: r-help-boun...@r-project.org Accept-Language: en-US, de-DE Precedence: list Thread-topic: [R] Uncorrelated random vectors Thread-index: Acn/CUJmE2gw3SggRTqBPK7cXE4i5QAAMBVwAAE0SfA= acceptlanguage: en-US, de-DE Thank you for your help! But is it possible to produe two vectors x and y with a given length such that there correlation is zero. For me ist not enough just to simulate two vectors with there correlation. Thank you, Luba -Urspr?ngliche Nachricht- Von: ONKELINX, Thierry [mailto:thierry.onkel...@inbo.be] Gesendet: Dienstag, 7. Juli 2009 15:51 An: Stein, Luba (AIM SE); r-help@r-project.org Betreff: RE: [R] Uncorrelated random vectors cor.test(rnorm(1), rnorm(1)) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Stein, Luba (AIM SE) Verzonden: dinsdag 7 juli 2009 15:46 Aan: r-help@r-project.org Onderwerp: [R] Uncorrelated random vectors Hello, is it possible to create two uncorrelated random vectors for a given distribution. In fact, I would like to have something like the function rnorm or rlogis with the extra property that they are uncorrelated. Thanks for your help, Luba [[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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] building 2.0.6 on Win32/Py2.5
After I posted the previous message, I repeated the process on a windows machine with Python 2.6 and still get the same error. I would appreciate any help. __ 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] Dump plots to powerpoint?
Hi, Is it possible to dump a series of plots directly into a powerpoint presentation (as is possible in Splus)? Thank you, Thomas [[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] subscripted assignment of grid units
Hi You have encountered the fact that, while there are [ methods for grid unit objects, there are NOT any [- methods for grid unit objects. I guess that needs to go (back) onto my todo list. A workaround for your simple example is ... unit.c(testUnits[1:2], testUnit2, testUnits[4:5]) ... though I can imagine that getting pretty tedious in more complex cases. Paul pbarros wrote: Hi, I want to do subscripted assignment of grid units, but I cannot find a straightforward way of doing it (and I have searched all forums and places I could think about, including Paul Murrell,s page). The usual subscripted assignment operator does replace the numeric part, but does not update the attributes. Before I write my own function, manipulating attributes etc I would like to know if such a function already exists (I am sure it does). What I want to do can be reflected as in the code below: testUnit - unit(1, lines) testUnit [1] 1lines testUnits - rep(testUnit, 5) testUnits [1] 1lines 1lines 1lines 1lines 1lines testUnit2 - unit(0.5, grobwidth, textGrob(Testing)) testUnits[3] - testUnit2 testUnits [1] 1lines 1lines 0.5lines 1lines 1lines I would like to obtain [1] 1lines 1lines 0.5grobwidth 1lines 1lines Any tips? Thanks, Pedro -- View this message in context: http://www.nabble.com/subscripted-assignment-of-grid-units-tp24371172p24371172.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. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ 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] Numbering sequences of non-NAs in a vector
Greetings, I have a vector of the form: [10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9...] That is, a combination of sequences of non-missing values and missing values, with each sequence possibly of a different length. I'd like to create another vector which will help me pick out the sequences of non-missing values. For the example above, this would be: [1,1,1,1,1,1,NA,NA,NA,NA,2,2,2,NA,NA,NA,3,3,3,3...]. The goal ultimately is to calculate means separately for each sequence. Your help is appreciated. If I'm making this more complicated than necessary, I'd appreciate knowing that as well! Many thanks. [[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] object .trPaths not found
I have to admit that I have no idea what we are talking about here (yes, I tend to forget many things these days) - and you have not cited the original message, unfortunately (nor have you specifies R versions, Tinn-R versions and both OS versions, but just one) ... Best wishes, Uwe Knut Krueger wrote: Uwe Ligges schrieb: Maybe, but the may depend on your script, your OS, your R version, used packages and so on. Hence please read and follow the posting guide and provide commented, minimal, self-contained, reproducible code. Hi Uwe, I was just asked the same question and hat the same problem before. It seem that it is a Tinn_R installation problem . I do not now what I changed to get it working, but the single line (R send line) mode is working, the R send selection and Rsend file mode not. System Windows XP new installed TinnR File permissions should not a problem on windows systems. Maybe any file is set to read only? The same srcipt which is working at home is not working at the new system. Regards Knut __ 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] Dump plots to powerpoint?
I generate PDF images and then rasterise using imagemagick to large, high quality JPG files. Then manually insert into powerpoint. Former two can definitely be automated, I'm sure the latter insertion could be automated with judicious use of scripting if really necessary. 2009/7/7 Thomas aikto...@yahoo.com: Hi, Is it possible to dump a series of plots directly into a powerpoint presentation (as is possible in Splus)? Thank you, Thomas [[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. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] building 2.0.6 on Win32/Py2.5
Which previous message? Should we all look up the archives now? Please cite and stay within the same thread. Thank you, Uwe LIgges Chuck White wrote: After I posted the previous message, I repeated the process on a windows machine with Python 2.6 and still get the same error. I would appreciate any help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to count number of elements in a vector that are not NA ?
sum(!is.na(x))
Date: Tue, 07 Jul 2009 14:56:54 -0400
From: Godmar Back god...@gmail.com
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Hi,
is there a simpler way to count the number of elements in a vector
that are not NA than this:
countN - function (v) {
return (Reduce(function (x, y) x + y, ifelse(is.na(v), 0, 1)))
}
?
- Godmar
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[R] ReShape to create Time from Observations?
Here is a couple of very simple data.frames: X-data.frame(A=1:10, B=0, C=1, Ob1=1:10, Ob2=2:11, Ob3=3:12, Ob4=4:13, Ob5=3:12, Ob6=2:11) Y-data.frame(A=1:20, B=0, C=1, D=5, Ob1=1:10, Ob2=2:11, Ob3=3:12, Ob4=4:13, Ob5=3:12, Ob6=2:11, Ob7=5:9) Z-data.frame(A=1:30, B=0, C=1, D=6, E=1:2, Ob1=1:10, Ob2=2:11, Ob3=3:12, Ob4=4:13, Ob5=3:12, Ob6=2:11, Ob7=1:10, Ob8=3:12) Each row in the data.frame is a unique experiment. The fields Ob1:Ob6 (in the case of the first data.frame) represent observations taken at fixed intervals for specific that experiment. (Observation 1, Observation2, etc.) IMPORTANT - Different data files have different numbers of both experiments and observations as well as different observation rates. Some data.frames might have 50 observations/experiment at 10 minute intervals (a work day) while others might have 2000 observations/experiment at daily intervals representing years of data. The number of columns preceding OB1 varies from file to file but once I get to Ob1 I have set it up so that the names to the right are consecutive to the end of the row, so 2000 observations will have names Ob1:Ob2000. How could I use ReShape to create a generic new data.frame where all of the ObX columns become 'time' for the experiments in that data.frame? I.e. - Ob1:ObX become s single variable called time incrementing from 1:X. The generic answer cannot use any numbers like 1:3 or 4:12 because every file is different. I think I need to discover the dimensions of the data.frames and locations of Ob1 as well as the name of the last column, etc., to construct the right fields. We could (if it's legal in R) say things like Ob1:Ob11 but it doesn't seem legal. I do see I can say things like names(X[4]) to discover Ob1, and cute things like names(X[dim(X)[2]]) to get the last name, etc., but I cannot put it together how to use this to drive ReShape into making all the Observations into a single variable called time. I hope this is clear. Thanks, Mark __ 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] Numbering sequences of non-NAs in a vector
Dear Krishna,
Here is one way. It is not very elegant, but seems to work:
# x is the vector you want to change
foo - function(x){
R1 - rle(!is.na(x))
R2 - rle(is.na(x))
len - R1$lengths[!R2$values]
x[!is.na(x)] - rep(1:length(len), len)
x
}
# Example
x - c(10, 8, 1, 3, 0, 8, NA, NA, NA, NA, 2, 1, 6, NA, NA, NA, 0, 5, 1, 9)
foo(x)
# [1] 1 1 1 1 1 1 NA NA NA NA 2 2 2 NA NA NA 3 3 3 3
HTH,
Jorge
On Tue, Jul 7, 2009 at 5:08 PM, Krishna Tateneni taten...@gmail.com wrote:
Greetings, I have a vector of the form:
[10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9...] That is, a
combination
of sequences of non-missing values and missing values, with each sequence
possibly of a different length.
I'd like to create another vector which will help me pick out the sequences
of non-missing values. For the example above, this would be:
[1,1,1,1,1,1,NA,NA,NA,NA,2,2,2,NA,NA,NA,3,3,3,3...]. The goal ultimately
is
to calculate means separately for each sequence.
Your help is appreciated. If I'm making this more complicated than
necessary, I'd appreciate knowing that as well!
Many thanks.
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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[R] R2WinBUGS under Linux/WINE fails
Hi, I'm running wine-1.0.1, OpenBUGS 3.0.3, R 2.9.0, and R2WinBUGS on a Redhat Enterprise Linux machine. Following various peoples' suggestions... This works perfectly (yay!): wine Z:/opt/OpenBUGS/winbugs.exe Within R, however, I get this: (setup the example from ?bugs, then) R schools.sim - bugs(data, inits, parameters, model.file, n.chains=3, n.iter=5000,bugs.directory=Z:/opt/OpenBUGS/) Error in file(con, rb) : cannot open the connection In addition: Warning message: In file(con, rb) : cannot open file '/home/harlan/.wine/dosdevices/z:/opt/OpenBUGS//System/Rsrc/Registry.odc': No such file or directory Error in bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, : WinBUGS executable does not exist in /home/harlan/.wine/dosdevices/z:/opt/OpenBUGS/ Trying to figure out these path issues: ls /home/harlan/.wine/dosdevices/z:/opt/OpenBUGS/ BackBUGS.lnk CompareDocu Graph Lindev OleRandnumseeds.odc Std Updater brugs.dllCorrel DoodleHost Manuals OpenBUGS.zip Ranks Summary Win brugs.so DevExamples Html Maps Plots Samples System winbugs.exe Bugs Developer Form libtaucs.dll Math randnumseeds0.bmp Script.odcTest Xhtml classicbugs.exe Deviance GeoBUGS Lin Monitors Randnumseeds.html Spatial Text ls /home/harlan/.wine/dosdevices/z:/opt/OpenBUGS//System/Rsrc/Registry.odc ls: /home/harlan/.wine/dosdevices/z:/opt/OpenBUGS//System/Rsrc/Registry.odc: No such file or directory So, the warning message is correct, but the error is not. winbugs.exe clearly exists, and I'd expect bugs.run to find it... If I add program=openbugs, then I get the warning to install BRugs, which no longer exists. (But it's not clear if that's necessary.) Is it possible to make this work? If not, I'm extremely thankful that I can use Bugs under Wine, but I'd really prefer to use the R interface if possible! Thank you for any guidance! -Harlan [[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] Numbering sequences of non-NAs in a vector
Here's one possibility: vv - c(10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9) (1+cumsum(diff(is.na(c(vv[1],vv)))==1)) * !is.na(vv) [1] 1 1 1 1 1 1 0 0 0 0 2 2 2 0 0 0 3 3 3 3 On Tue, Jul 7, 2009 at 5:08 PM, Krishna Tateneni taten...@gmail.com wrote: Greetings, I have a vector of the form: [10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9...] That is, a combination of sequences of non-missing values and missing values, with each sequence possibly of a different length. I'd like to create another vector which will help me pick out the sequences of non-missing values. For the example above, this would be: [1,1,1,1,1,1,NA,NA,NA,NA,2,2,2,NA,NA,NA,3,3,3,3...]. The goal ultimately is to calculate means separately for each sequence. Your help is appreciated. If I'm making this more complicated than necessary, I'd appreciate knowing that as well! Many thanks. [[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] Numbering sequences of non-NAs in a vector
On Jul 7, 2009, at 4:08 PM, Krishna Tateneni wrote: Greetings, I have a vector of the form: [10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9...] That is, a combination of sequences of non-missing values and missing values, with each sequence possibly of a different length. I'd like to create another vector which will help me pick out the sequences of non-missing values. For the example above, this would be: [1,1,1,1,1,1,NA,NA,NA,NA,2,2,2,NA,NA,NA,3,3,3,3...]. The goal ultimately is to calculate means separately for each sequence. Your help is appreciated. If I'm making this more complicated than necessary, I'd appreciate knowing that as well! Many thanks. Here is one possibility: Vec - c(10,8,1,3,0,8,NA,NA,NA,NA,2,1,6,NA,NA,NA,0,5,1,9) Vec [1] 10 8 1 3 0 8 NA NA NA NA 2 1 6 NA NA NA 0 5 1 9 Use rle() to get the runs of NA and non-NA values. See ?rle Runs - rle(is.na(Vec)) Runs Run Length Encoding lengths: int [1:5] 6 4 3 3 4 values : logi [1:5] FALSE TRUE FALSE TRUE FALSE Create grouping values for each run: Grps - rep(seq(length(Runs$lengths)), Runs$lengths) Grps [1] 1 1 1 1 1 1 2 2 2 2 3 3 3 4 4 4 5 5 5 5 Now get the means for each run, split by Grps. See ?aggregate aggregate(Vec, list(Grps = Grps), mean) Grpsx 11 5.00 22 NA 33 3.00 44 NA 55 3.75 If you don't want the NA runs included in the result, you could use subset(): subset(aggregate(Vec, list(Grps = Grps), mean), !is.na(x)) Grpsx 11 5.00 33 3.00 55 3.75 HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] r-project.org address blacklisted by anti-spam software
Dear List: An e-mail mentioning the r-project.org address and sent to a friend at a German university was considered spam by the local spam filter. Its reasoning: the URL r-project.org is blacklisted at uribl.swinog.ch resp. at antispam.imp.ch. I checked the list http://antispam.imp.ch/swinog-uri-rbl.txt [caution: long list] and indeed, there it was. Can anybody explain how or why the R project made its way onto the list? Is it reasonable to file a protest? --Hans Werner __ 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] wordStem problems in R 2.9, Fedora 11; Linux Kernel 2.6.29.5-191.fc11.i586
Dear All, I just updated from Fedora 9 to Fedora 11, kernel version 2.6.29.5-191.fc11.i586. I'm running R 2.9. I successfully installed package Rstem from source (it always ran fine for me in F9). However: wordStem(c(This,is,a,test)) Error in wordStem(c(This, is, a, test)) : VECTOR_ELT() can only be applied to a 'list', not a 'character' Any idea what causes this / how I can fix this? RR __ 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] Question in using e1071 svm routine
Hi all,
I've got the following error message in using e1071 svm routine...
Could anybody please help me?
Thank you!
-
model - svm(y=factor(mytraindata[, 1]), x=mytraindata[, -1], probability=T)
Error in if (any(co)) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In FUN(newX[, i], ...) : NAs introduced by coercion
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] building 2.0.6 on Win32/Py2.5
My sincere apologies. This message was intended for the rpy2 mailing list. Thanks. Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Which previous message? Should we all look up the archives now? Please cite and stay within the same thread. Thank you, Uwe LIgges Chuck White wrote: After I posted the previous message, I repeated the process on a windows machine with Python 2.6 and still get the same error. I would appreciate any help. __ 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] odfWeave: odt-file damaged
Hi,
I think, I can answer my own posting. I found out, that the directory
structure
of the ODT-file created by odfWeave causes the error message.
The file structure of the unzipped odt-file looks like this:
DIR Pictures
content_1-Boxplot.png
content.xml
current.xml
manifest.xml
meta.xml
mimetype
settings.xml
styles.xml
thumbnail.png
But it should look like this:
DIR META-INF
manifest.xml
DIR Thumbnails
thumbnail.png
DIR Pictures
content_1-Boxplot.png
meta.xml
mimetype
settings.xml
styles.xml
content.xml
Now I know. what causes the message odt file damaged,
but I don´t know a solution. Does anyone do so?
Thanks, Udo
Dear all,
I am doing my first steps with odfWeave.
After running the r code (see below), I am trying to open the ODF-document
with open office, but I am getting the error message:
The file is damaged, but it can be repaired. If I confirm the question and
repair the file with open office, I can open it with the desired output,
which seems to be fine.
My system:
R Version 2.9.1
Open Office 3.0.1
7-Zip 4.65
Windows XP
Using zip (http://www.info-zip.org/, zip232xN.zip) had the same result.
What causes the error message? Is the structure of the ODF document
as it should be (for the structure please have a look at the bottom of
this mail)?
I'd greatly appreciate any help.
Udo K o e n i g
Clinic for Child and Adolescent Psychiatry
Philipps University of Marburg, Germany
###
#R code
library(odfWeave)
#odfWeave call
odfWeave(c:/temp/odfWeave-test.odt, c:/temp/odfWeave-test-out.odt,
control=odfWeaveControl(zipCmd = c(7z a -tzip $$file$$ .,
7z e -tzip $$file$$)))
###
# Contents of my Open office document
Initiate, results = hide, echo= FALSE=
#First steps with odfWeave
attach(iris)
@
There are \Sexpr{length(iris[, 1])} observations.
Table, echo=FALSE, results= xml=
odfTable(iris[1:5,])
@
Table2, echo=FALSE, results= xml=
tab - round(apply(iris[, 1:4], 2, mean), 2)
odfTable(tab, horizontal= TRUE)
@
Boxplot, echo=FALSE, fig=TRUE=
boxplot(Sepal.Length~Species)
@
###
#Log
odfWeave(c:/temp/odfWeave-test.odt, c:/temp/odfWeave-test-out.odt,
+ control=odfWeaveControl(zipCmd = c(7z a -tzip $$file$$ .,
+ 7z e -tzip $$file$$)))
Copying c:/temp/odfWeave-test.odt
Setting wd to
C:\DOCUME~1\Udo_2\LOCALS~1\Temp\Rtmp6QrXgk/odfWeave05190748330
Unzipping ODF file using 7z e -tzip odfWeave-test.odt
7-Zip 4.65 Copyright (c) 1999-2009 Igor Pavlov 2009-02-03
Processing archive: odfWeave-test.odt
Extracting mimetype
Extracting Configurations2\statusbar
Extracting Configurations2\accelerator\current.xml
Extracting Configurations2\floater
Extracting Configurations2\popupmenu
Extracting Configurations2\progressbar
Extracting Configurations2\menubar
Extracting Configurations2\toolbar
Extracting Configurations2\images\Bitmaps
Extracting content.xml
Extracting styles.xml
Extracting meta.xml
Extracting Thumbnails\thumbnail.png
Extracting settings.xml
Extracting META-INF\manifest.xml
Everything is Ok
Folders: 7
Files: 8
Size: 28518
Compressed: 8768
Removing odfWeave-test.odt
Creating a Pictures directory
Pre-processing the contents
Sweaving content.Rnw
Writing to file content_1.xml
Processing code chunks ...
1 : term hide(label=Initiate)
2 : term xml(label=Table)
3 : term xml(label=Table2)
4 : term verbatim(label=Boxplot)
'content_1.xml' has been Sweaved
Removing content.xml
Post-processing the contents
Removing content.Rnw
Removing styles.xml
Renaming styles_2.xml to styles.xml
Removing extra files
Packaging file using 7z a -tzip odfWeave-test.odt .
7-Zip 4.65 Copyright (c) 1999-2009 Igor Pavlov 2009-02-03
Scanning
Creating archive odfWeave-test.odt
Compressing content.xml
Compressing current.xml
Compressing manifest.xml
Compressing meta.xml
Compressing mimetype
Compressing Pictures\content_1-Boxplot.png
Compressing settings.xml
Compressing styles.xml
Compressing thumbnail.png
Everything is Ok
Copying odfWeave-test.odt
Resetting wd
Removing C:\DOCUME~1\Udo_2\LOCALS~1\Temp\Rtmp6QrXgk/odfWeave05190748330
Done
###
#Structure of the unzipped odf-document that produced the error message
05.07.2009 11:43DIR Bitmaps
05.07.2009 19:0713.820 content.xml
05.07.2009 11:43 0 current.xml
05.07.2009 11:43DIR floater
05.07.2009 11:43 1.889 manifest.xml
05.07.2009 11:43DIR menubar
05.07.2009 11:43 968 meta.xml
05.07.2009 11:4339 mimetype
05.07.2009 22:18DIR Pictures
05.07.2009 11:43DIR
Re: [R] r-project.org address blacklisted by anti-spam software
On 07/07/2009 5:59 PM, Hans W Borchers wrote: Dear List: An e-mail mentioning the r-project.org address and sent to a friend at a German university was considered spam by the local spam filter. Its reasoning: the URL r-project.org is blacklisted at uribl.swinog.ch resp. at antispam.imp.ch. I checked the list http://antispam.imp.ch/swinog-uri-rbl.txt [caution: long list] and indeed, there it was. Can anybody explain how or why the R project made its way onto the list? Is it reasonable to file a protest? Presumably you should be asking those questions to someone at the antispam site, or at the university you can't send email to. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tex fonts in R plots
Hello, R users. I would like to display the font of Math Mode of MikTex 2.3, WinEdt 5.4 in R plots, e.g. in xlab, ylab or legend. How can I do that? Thank you in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
