Re: [R] [SOLVED] Problem building R-2.15.3 from source

On 11/07/2013 06:44, Pascal Oettli wrote: Hello, Maybe the reason why: http://www.cran.r-project.org/doc/manuals/R-admin.html#Compilation-flags And since this is a ix86 system, you really should be using -mtune=native. I do not believe the default in 2.15.3 was -O3: it is not in current R,

[R] Installing OpenBLAS in R

Hello again, I was wondering if it is possible to install OpenBLAS linear algebra library in R running under windows. I found some study saying working with OpenBLAS would significantly speed-up the calculations in R. Thanks for your pointer. Thanks and regards, [[alternative HTML

[R] GIS in R?

Hi Iam quite new to R and Iam trying to use it for GIS application. I used the maptools package to load a shapefile WVA-readShapeLines(WVA) and now I would like to fill gaps in the shape file (missing numbers) with the numbers from intersecting lines I have tried with gintersect but I can only

[R] Override setClass and setMethod in a package R 3.0.1

Hi, I am having problem to override setClass and setMethod in a package Requirement: R 3.0.1, Rtools Please find below the steps to recreate the problem: * * *#1. Create class and method* *setClass(Class=AAA,* * representation(* * name=character,* * val=numeric* *

Re: [R] Recherche de fonction

On 11-07-2013, at 09:04, Raphaëlle Carraud raphaelle.carr...@oc-metalchem.com wrote: Hello, Thank you for your reply, even though I wrote in French. In reality, the variables r1, r4, r5 are expressed as functions of A, B, C, D, E, I and H, which are the variables I wish to calculate

[R] Saving forecast.Arima as data

Hi I am setting up a simple time series model, and I need the forecast to be saved in a format I later easily can work with/load into a database. The model will run once a day on new input and hence I want how it has performed to be easy to work with. The output for forecast.Arima(ts) or for

Re: [R] Need hep for converting date data in POSIXct

Hi again , You're gonna get bored of mine and my doubts! Once I definde a función for latitude (lat=location[,1]) and other for longitude(lon=location[,2]) and I got again the same problem: vmask(lat,lon,time,vmax=25) Error en as.POSIXct.default(time1) : do not know how to convert

[R] Differential problem

Hello, I have the following differential equation system to solve, the variables I wish to obtain being A, B, C, D, E, I, G and H. 0 = -dA + dB + 2*dC - 2*r1 - 2*r5 0 = dA + dD + r1 + r4 0 = K2 - C/B^2 0 = K3 - D/(A*B) 0 = r5 + 2*r4 - dE 0 = r5 -dI 0 = -r5 - r4 - dG

Re: [R] Need hep for converting date data in POSIXct

Arun, the last email has been sent it by itself. I have just found the problem and it works. Thank very much Date: Wed, 10 Jul 2013 19:36:43 -0700 From: ml-node+s789695n4671274...@n4.nabble.com To: laila_...@hotmail.com Subject: Re: Need hep for converting date data in POSIXct

Re: [R] Help with installing a .tar.gz package on windows

On 11/07/13 17:57, Prof Brian Ripley wrote: On 11/07/2013 01:22, David Winsemius wrote: On Jul 10, 2013, at 4:37 PM, Lucy Leigh wrote: Hi, I have had a look at the manual but it makes no sense to me. I have downloaded RTools, and the InnoSetup, but I don't understand how to use these to

Re: [R] Saving forecast.Arima as data

Hello, Try the following. fr - forecast.Arima(y0,h=3) fr[[mean]] Hope this helps, Rui Barradas Em 11-07-2013 08:04, Lasse Thorst escreveu: Hi I am setting up a simple time series model, and I need the forecast to be saved in a format I later easily can work with/load into a database. The

Re: [R] Differential problem

On 11-07-2013, at 09:13, Raphaëlle Carraud raphaelle.carr...@oc-metalchem.com wrote: Hello, I have the following differential equation system to solve, the variables I wish to obtain being A, B, C, D, E, I, G and H. 0 = -dA + dB + 2*dC - 2*r1 - 2*r5 0 = dA + dD + r1 + r4 0 =

[R] Sparse matrix no longer sparse (Matrix Package)

I sent this message yesterday with an attachment allowing for reproduction of the issue. But I think the attachment is preventing the message from coming through. If anyone is interested I will forward the attachment directly allowing for you to reproduce the issue I observe. On 7/10/13 2:38 PM,

[R] calculate time from dates

My data are from 2008 to 2010, with repeated measures for same subjects. I wish to compute number of months since january 2008. The data are like the following: ID date 1 4/12/2008 1 4/13/2008 1 5/11/2008 2 3/21/2009 2 4/22/2009 2 8/05/2009 ... the date column are in the format %m/%d/%y. i wish

Re: [R] calculate time from dates

Hi. See http://stackoverflow.com/questions/1995933/number-of-months-between-two-dates Andrija On Thu, Jul 11, 2013 at 11:56 AM, Gallon Li gallon...@gmail.com wrote: My data are from 2008 to 2010, with repeated measures for same subjects. I wish to compute number of months since january

Re: [R] Reserve word in could not be used it as a dimname?

-Original Message- Reserved words outside quotes are always parsed to be references to the objects linked to in the 'Description', and hence they are not allowed as syntactic names (see make.names). They are allowed as non-syntactic names, e.g. inside backtick quotes. You

Re: [R] Differential problem

On 11-07-2013, at 12:05, Raphaëlle Carraud raphaelle.carr...@oc-metalchem.com wrote: Sorry, Here is the program I have until now: reaction-function(z, state, dval, parameters) { with(as.list(c(state)),{ K2 - 10^(2993/Tr-9.226)*(10^-3) K3 - 10^(2072/Tr-7.234)*(10^-3)

Re: [R] calculate time from dates

Hi, May be this helps: dat1- read.table(text= ID date 1 4/12/2008 1 4/13/2008 1 5/11/2008 2 3/21/2009 2 4/22/2009 2 8/05/2009 ,sep=,header=TRUE,stringsAsFactors=FALSE) library(mondate) M1- mondate(dat1[,2]) M2- mondate(01/01/2008) dat1$month-as.numeric(abs(floor(MonthsBetween(M1,M2  dat1 # 

[R] ** REMINDER ** Academic study of R users and developers

Dear all, A group of researchers from Eindhoven Univ of Technology (The Netherlands) and UC Davis (USA) is conducting a study of support activities in R. In this study, our goal is to understand how R user support activities have been evolving over time, in the presence of different information

[R] Lda - topic inference of new document

Hi, I have been playing around with 'lda' package recently and I cannot find inferencer to predict new document topic mixture I am looking for an R equivalent of a topic inferencer [ something that mallet offers ] http://mallet.cs.umass.edu/topics.php [ see Topic Inference ] Does R provide that

[R] LDA and confidence ellipse

Hi, I wish to add confidence ellipse on my LDA result of the iris data set. Therefore: Is there statistical logic to do that as I only wish it to make the species separation more visable? How can I add it to the script below (ggplot): require(MASS) require(ggplot2) iris.lda-lda(Species ~

Re: [R] Differential problem

Sorry, Here is the program I have until now: reaction-function(z, state, dval, parameters) { with(as.list(c(state)),{ K2 - 10^(2993/Tr-9.226)*(10^-3) K3 - 10^(2072/Tr-7.234)*(10^-3) K4 - 10^(-20.83/Tr-0.5012) K5 - 10^(-965.5/Tr-1.481) k1 -

Re: [R] calculate time from dates

Hello, The functions in stackoverflow need a date 'format' argument. # Functions from # http://stackoverflow.com/questions/1995933/number-of-months-between-two-dates # with a 'format' argument added # # turn a date into a 'monthnumber' relative to an origin monnb - function(d, format =

[R] Error in read.table

Hi Folks I can't see what I have done wrong in this piece of code. # Read filenames from csv file files - read.csv(file=files.csv,head=FALSE,sep=,) # for each filename read the file for (i in 1:length(files)) { # f becomes the next row inthe file f-files[i,] # the header to be used for

Re: [R] Error in read.table

Maybe you should set parameter as.is in read.csv to be false. 2013/7/11 Jannetta Steyn janne...@henning.org Hi Folks I can't see what I have done wrong in this piece of code. # Read filenames from csv file files - read.csv(file=files.csv,head=FALSE,sep=,) # for each filename read the

Re: [R] Read a txt file as numeric

Hi, May be this helps: dat1- read.table(text= 142,QUANTIZE_CAL_MIN_BAND_10,1 143,QUANTIZE_CAL_MAX_BAND_11,65535 144,QUANTIZE_CAL_MIN_BAND_11,1 145,END_GROUP,MIN_MAX_PIXEL_VALUE 146,GROUP,RADIOMETRIC_RESCALING 147,RADIANCE_MULT_BAND_1,1.2483E-02 148,RADIANCE_MULT_BAND_2,1.2730E-02

Re: [R] Differential problem

On 11-07-2013, at 13:53, Raphaëlle Carraud raphaelle.carr...@oc-metalchem.com wrote: Sorry for the bug, I had eliminated some lines to avoid making the program too big. Here is the version that works : reaction-function(z, state, dval, parameters) { with(as.list(c(state)),{ # rate

Re: [R] Differential problem

Sorry for the bug, I had eliminated some lines to avoid making the program too big. Here is the version that works : reaction-function(z, state, dval, parameters) { with(as.list(c(state)),{ # rate of change Tr - 273+90 P - 0.98*10^5 K2 - 10^(2993/Tr-9.226)*(10^-3)

[R] Differences between glmmPQL and lmer and AIC calculation

Dear R Community, I’m relatively new in the field of R and I hope someone of you can help me to solve my nerv-racking problem. For my Master thesis I collected some behavioral data of fish using acoustic telemetry. The aim of the study is to compare two different groups of fish (coded as 0

[R] Testing for weak exogeneity in a SUR ECM

Dear all, I have set up a Labour Demand Error Correction Model for some German federal states. As I expect the labour markets to be correlated I used a Seemingly Unrelated Regression using systemfit in R. My Model is: d(emp)_it = c + alpha*ln(emp)_i,t-1 + beta_1*ln(gdp)_i,t-1 + +

Re: [R] GIS in R?

Hi I suggest having a look at the R_sig_geo archives or posting to that list. On Thu, Jul 11, 2013 at 2:53 AM, ElSiebo franz.tscheikner-gr...@uibk.ac.atwrote: Hi Iam quite new to R and Iam trying to use it for GIS application. I used the maptools package to load a shapefile

Re: [R] Error in read.table

On Jul 11, 2013, at 13:50 , Dante.py wrote: Maybe you should set parameter as.is in read.csv to be false. TRUE more likely... However, there's another issue: files[i,] is a data frame, therefore so is f[1] (a telltale sign is that it has rows and column labels). So f[[1]] is probably needed.

[R] [R-pkgs] Major Update to rms package

The rms (Regression Modeling Strategies) package has undergone a massive update. The entire list of updates is at the bottom of this note. CRAN has the update for linux and will soon have it for Windows and Mac - check http://cran.r-project.org/web/packages/rms/ for availability. This rms

[R] Fwd: Error in read.table

Maybe I should rephrase my question. What would be the best way to read a list of filenames and headings from a csv file? The CSV file is structured as two columns, with column one being the filename and column two being a heading e.g.: ANA110915004A_3PERIOD_TmAvg-rdata.csv,Pre-DA

Re: [R] Differential problem

Ok, now it's good (Pt was in my workplace so it worked for me, I am not used to R using these value to make the program run so I hadn't looked...) reaction-function(z, state, dval, parameters) { with(as.list(c(state,dval,parameters)),{ # rate of change Tr - 273+90 P - 0.98*10^5

Re: [R] Error in read.table

I'll post the rephrasing of the question as a new thread. I hope that is okay. On 11 July 2013 13:40, Jannetta Steyn janne...@henning.org wrote: Maybe I should rephrase my question. What would be the best way to read a list of filenames and headings from a csv file? The CSV file is

[R] Reading a list of filenames from a csv file

What would be the best way to read a list of filenames and headings from a csv file? The CSV file is structured as two columns, with column one being the filename and column two being a heading e.g.: ANA110915004A_3PERIOD_TmAvg-rdata.csv,Pre-DA ANA110915006A_3PERIOD_TmAvg-rdata.csv,DA-10^-6

Re: [R] problem with BootCV for coxph in pec after feature selection with glmnet (lasso)

pec accepts only R-objects for which a predictSurvProb method exists and glmnet is not such an object. Currently, predictSurvProb methods are available for the following R-objects: matrix aalen, cox.aalen from library(timereg) mfp from library(mfp) phnnet, survnnet from

Re: [R] coxph won't converge when including categorical (factor) variables

I have found the answer for my second question and am posting here for the benefit of the community: pec accepts only R-objects for which a predictSurvProb method exists and glmnet is not such an object. Currently, predictSurvProb methods are available for the following R-objects:

Re: [R] Reading a list of filenames from a csv file

Hi Janetta, At a first guess, you need: files - read.csv(file=files.csv,head=FALSE,sep=,, stringsAsFactors=FALSE) str(files) would clear up any confusion as to whether the contents of the first column of files are character or not. If that doesn't help, then setting i - 1 and running each

Re: [R] Fwd: Error in read.table

On Jul 11, 2013, at 14:40 , Jannetta Steyn wrote: Maybe I should rephrase my question. What would be the best way to read a list of filenames and headings from a csv file? Just follow the hints already given, I think. E.g files - read.csv(file=files.csv, head=FALSE, sep=,, as.is=TRUE) # for

Re: [R] Reading a list of filenames from a csv file

Hi, Try this: files1-read.csv(files.csv,header=TRUE,stringsAsFactors=FALSE)  str(files1) #'data.frame':    2 obs. of  2 variables: # $ Col1: chr  ANA110915004A_3PERIOD_TmAvg-rdata.csv ANA110915006A_3PERIOD_TmAvg-rdata.csv # $ Col2: chr  Pre-DA DA-10^-6 files1 #  

Re: [R] Sparse matrix no longer sparse (Matrix Package)

The message got through but not the attachment. The R help list tends to strip off attachements for security reasons. Files of types txt, png, pdf should get through. In most cases the accepted method of sending data is to use the dput() function to output a file in the console and then

Re: [R] PCA and gglot2

Not sure why the problem. I think I'd need see your actual data and give it a try. If you want to supply your data or a sample of it see ?dput for a convenient way to do so. I see thought that you've found a dedicated ggplot biplot so if may not be worth your while. John Kane Kingston ON

Re: [R] Sparse matrix no longer sparse (Matrix Package)

Thank you, John. I originally used dput() but the output is huge. However, here is a reproducible example of what I think very unexpected behavior of some matrix functions. ### Create a symmetric matrix of class dsCMatrix A - as(diag(5, 10), 'dsCMatrix') A[1, 5] - A[5,1] - 2 ### Create a

[R] FW: Nested and/or crossed and 2 level random factor

Dear All, I have two quick questions about my study design. For 4 years, once every season, we destructively sampled larvae on bushes (the same bushes every time) and measured parasitism on these larvae. We had 10 bushes per location and two locations. We are interested in whether

Re: [R] Help with installing a .tar.gz package on windows

Since you are clearly out of your league with respect to compiling from source We are all beginners at something. Telling Windows users that building packages from source is beyond them is walling them off from a very productive area. Here is how I set things up to build R packages from either

Re: [R] FW: Nested and/or crossed and 2 level random factor

This is not the best place for this post. Post instead to r-sig-mixed-models or r-sig-ecology . Cheers, Bert On Thu, Jul 11, 2013 at 8:48 AM, Linda Bürgi patili_bue...@thotmail.com wrote: Dear All, I have two quick questions about my study design. For 4 years, once every season, we

[R] mgcv: GAM with clustered standard errors

Dear Help list, I am relatively new to the mgcv package, which I am using to model prices of housing transactions as a function of the characteristics of a home and a neighborhood. I have several smooth terms to capture price evolution over time, but also to non-parametrically fit the

[R] Cannot access PDF manuals from R console

Hello, We are currently using R for an enterprise build here on campus. However after install we noticed an issue when testing the program. We cannot access the PDF manuals from the console. Instead we get the following error: Error: Access to 'doc\manual\R-intro.pdf' denied. The same error

Re: [R] Sparse matrix no longer sparse (Matrix Package)

This is a terrible example as I didn't realize my code actually does create a non-symmetric matrix and in this case the function behaves as expected. Nonetheless, my original issue stands and that issue still does not make sense. Apologies for bad example code. -Original Message-

Re: [R] Cannot access PDF manuals from R console

No, have not encountered this. If you want further help, you will have to be quite a bit more specific about the steps you have taken, version of R, source of install files. and the operating system used and configuration thereof. Carefully read the footer on this or any other list email and

Re: [R] Sparse matrix no longer sparse (Matrix Package)

Just about anything I knew about matrices, I forgot years ago so I'm no help here but I'd suggest putting the matrix on something like Mediafire http://www.mediafire.com/ or Dropbox https://www.dropbox.com so people can download it and have a look. I agree that dput() is not really good for

Re: [R] LDA and confidence ellipse

Hi, May be this helps: require(MASS) require(ggplot2) iris.lda-lda(Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width,  data = iris) datPred-data.frame(Species=predict(iris.lda)$class,predict(iris.lda)$x) library(ellipse) dat_ell - data.frame() for(g in levels(datPred$Species)){

Re: [R] Installing OpenBLAS in R

[cc-ing the list] On Wed, Jul 10, 2013 at 11:36 PM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Hello again, I was wondering if it is possible to install OpenBLAS linear algebra library in R running under windows. You will have to re-compile R from source and re-install it.

Re: [R] mgcv: GAM with clustered standard errors

I think it's going to be a problem to have different sized groups in your second model. ?corSymm says that a general correlation matrix is being estimated (i.e. the correlation between each pair of observations is being estimated - for this to be meaningful across groups you need the jth

Re: [R] LDA and confidence ellipse

Hi, Thanks works like magic. BTW What is the confidence ellipses probability used? -- View this message in context: http://r.789695.n4.nabble.com/LDA-and-confidence-ellipse-tp4671308p4671357.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Help with installing a .tar.gz package on windows

On Jul 11, 2013, at 1:37 AM, Rolf Turner wrote: On 11/07/13 17:57, Prof Brian Ripley wrote: On 11/07/2013 01:22, David Winsemius wrote: On Jul 10, 2013, at 4:37 PM, Lucy Leigh wrote: Hi, I have had a look at the manual but it makes no sense to me. I have downloaded RTools, and the

Re: [R] LDA and confidence ellipse

Hi, No problem. The default should be 0.95 ?ellipse() level: The confidence level of a pairwise confidence region.  The   default is 0.95, for a 95% region.  This is used to control   the size of the ellipse being plotted.  A vector of levels   may be used. A.K. -

Re: [R] Sparse matrix no longer sparse (Matrix Package)

It seems to me that this issue should be reproducible with a small matrix, since the concern is the representation rather than the values. --- Jeff NewmillerThe . . Go Live...

Re: [R] Installing OpenBLAS in R

On 11/07/2013 19:26, Peter Langfelder wrote: [cc-ing the list] On Wed, Jul 10, 2013 at 11:36 PM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Hello again, I was wondering if it is possible to install OpenBLAS linear algebra library in R running under windows. You will have to

Re: [R] create new matrix from user-defined function

Dan and Arun, thank you very much for your replies. They are both very helpful and I love to get different versions of an answer so I can learn more R code. You both used indexing to refer to the columns needed in the function, but since my real data frame will be much larger I'm assuming I

Re: [R] create new matrix from user-defined function

Hi, Not sure I understand you correctly. I found it easier to index using number than replace it by lengthy column names. You could do it similar to the one below.

Re: [R] create new matrix from user-defined function

Oh, also thanks for the speed comparisons. Missed that in my first read-through. Very interesting and informative. BNC -Original Message- From: Crombie, Burnette N Sent: Thursday, July 11, 2013 4:40 PM To: 'arun' Cc: R help Subject: RE: [R] create new matrix from user-defined

Re: [R] create new matrix from user-defined function

Hi BNC, No problem. You could also use ?with() data.frame(MW_EEsDue_ERRORS=with(dat3,A_CaseID[D_MW_EEsDueTotal!=rowSums(cbind(B_MW_EEsDue1,C_MW_EEsDue2))])) #  MW_EEsDue_ERRORS #1 1882 #2 1884 #3 1885 A.K. - Original Message - From: Crombie,

Re: [R] Announcing TIBCO Enterprise Runtime for R

Hi Louis, I apologize in advance if this isn't the right forum; feel free to direct me elsewhere. Can you say a bit more about what exactly constitute the advantages of TERR over R as most readers of this list know it? Some random points of interest to me: 1. Do you have concrete benchmarks of

Re: [R] results of robust regression vs. OLS regression

One way to get standardized beta coefficients is to center and scale all of the x variables (subtract the mean then divide by the standard deviation), then fit the regression on the standardized x's. You could do the same thing with a robust regression (these values may not be meaningful if there

Re: [R] results of robust regression vs. OLS regression

Also see fortune(254) and others about r-squared in general. On Thu, Jul 11, 2013 at 3:35 PM, Greg Snow 538...@gmail.com wrote: One way to get standardized beta coefficients is to center and scale all of the x variables (subtract the mean then divide by the standard deviation), then fit the

Re: [R] Power of Kruskal-Wallis Test?

If there were a canned function for power for a non-parametric test, I would not trust it. This is because there are many assumptions that would need to be made and I would not know if those in a canned function were reasonable for my study. I would compute power by simulation. Simulate data

Re: [R] Help with installing a .tar.gz package on windows

Hi everyone, Thanks to everyone for all the advice. I should have been clearer in my first email, the version of 'PReMiuM' I have is not the one available on CRAN at the moment, but a version I was sent by one of the authors, Silvia Liveriani, with a small bug fixed. I don't know if this is

[R] Standardize GLS coefficients in R

Hello, I have estimated the coefficients for my model using the 'pggls' function from the 'plm' package. Now I want to see the relative influence of those X's. How can some please tell me how to standardize those my results in R? Thank you! -- View this message in context:

Re: [R] Differences between glmmPQL and lmer and AIC calculation

Tonio Pieterek t.pieterek at googlemail.com writes: [snip] This is really more appropriate for r-sig-mixed-mod...@r-project.org : please refer any followup questions there. For my Master thesis I collected some behavioral data of fish using acoustic telemetry. The aim of the study is to

Re: [R] Help with IF command strings

HI, Try this: set.seed(485) dat1- as.data.frame(matrix(sample(0:10,26*10,replace=TRUE),ncol=26)) mean(dat1$V21[dat1$V2==1|dat1$V2==0]) #[1] 3.8 #or with(dat1,mean(V21[V2==1|V2==0])) #[1] 3.8 A.K. I have data in 26 columns, I'm trying to get a mean for column 21 only for the participants that

[R] error of betadiver in vegan

Hello, I am using betadiver (vegan) to calculate beta diversity. However, an error message shows Error in ifelse(x 0, 1, 0) : (list) object cannot be coerced to type 'double' R version: 3.0.0 Please kindly advise how to solve the issue. Also, please kindly tell if any more information is

Re: [R] Sending carbon copy mails from R

updated code pasted here. So I guess CC is not an option at all? In that case is there any other package that would be useful? require(sendmailR) to - c(v...@abc.com) header - list(cc=c(a...@abc.com)) x - sendmail(t...@abc.com, to, test, testing,

[R] [XML packages] how to get the sub-node according to the sub-node's attribute?

For example fileName - system.file(exampleData, mtcars.xml, package=XML) doc - xmlTreeParse(fileName) r-xmlRoot(doc) record-r[[record]] record the result : record id=Mazda RX421.0 6 160.0 110 3.90 2.620 16.46 0 14 4/record but in the mecars.xml there are 32 sub-nodes called

Re: [R] Sending carbon copy mails from R

Note that sendmailR is not 'from R'. There are other possibilities, and I use create.post() from R itself, modified as I need. On 12/07/2013 02:48, Alok Jadhav wrote: updated code pasted here. So I guess CC is not an option at all? In that case is there any other package that would be