Re: [R] quantmod package

2011-10-27 Thread ATANU
the code you posted works well except that when i am using chartSeries() it does not give any graphical stuff: >chartSeries(P,type="auto") >Error in if (on == "years") { : missing value where TRUE/FALSE needed i also tried to store the entire getQuote output (OHLC object) by the above manner but

[R] Thank you

2011-10-27 Thread Roslina Zakaria
Dear r-community, Today I have completed my PhD.  I would like to take this opportunity to thank the r-community for helping me with the r-coding.  I use r to do data manipulation during my PhD and I benefit a lot through the discussion in the r-forum. I will continue using R and help the ot

Re: [R] Poblems wih EBImage

2011-10-27 Thread Prof Brian Ripley
EBImage is a Bioconductor package: please ask on their lists. You seem to be on Windows, and EBImage (like a number of other packages) needs external software installed. This is described in one of the vigettes, e.g. http://www.bioconductor.org/packages/2.8/bioc/vignettes/EBImage/inst/doc/EBI

Re: [R] 'for' in steps

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 6:29 PM, RhoR wrote: I want to use for (i in 1:time) That is insufficient to tell what sort of date or date-time object you intend. You may want to look at: ?ISOdate ?DateTimeClasses > ISOdate(2011, 1:12, 1) [1] "2011-01-01 12:00:00 GMT" "2011-02-01 12:00:00 GMT" "20

Re: [R] vis.gam zlab problem

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 6:13 PM, wildlifeduke wrote: I am using the mgcv package to develop vis.gam plots and having trouble figuring out how to relabel the z-axis (image attached). It is currently labeled as "linear predictor," but I would like to change it to a different name. Currently I

Re: [R] Poblems wih EBImage

2011-10-27 Thread diyanah
Hai, can you help me. Why am I having this lines of errors? please help me. thank you. > library("EBImage") Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/Program Files/R/R-2.13.2/library/EBImage/libs/i386/EBImage.dll': LoadLibrary failure: The s

Re: [R] Simple time series question with zoo

2011-10-27 Thread Marc Girondot
Le 27/10/11 22:18, Vinny Moriarty a écrit : New user here. My goal is pull daily averages from a long dataset. I've been working with some code I got from this list from https://stat.ethz.ch/pipermail/r-help/2009-March/191302.html The code how I have been using it is as follows: library(zoo)

Re: [R] 'for' in steps

2011-10-27 Thread Marc Girondot
Le 28/10/11 00:29, RhoR a écrit : I want to use for (i in 1:time) but I want the increments to be monthly. For example, if I'm adding interest to a virtual bank account monthly, for a total of 'time' in years which the user has entered. If I understand well the problem: for (i in 1:time) {

[R] Help with increasing the speed of script

2011-10-27 Thread a217
I actually have two questions regarding the same script: # data <- vector('list', 24) splc <- vector('list',24) df.summ <- vector('list',24) for (i in 1:length(chrData)) { data[[i]] <- read.table(file=paste('chr',i,'.nonCG.covered.out',sep=''), h

[R] 'for' in steps

2011-10-27 Thread RhoR
I want to use for (i in 1:time) but I want the increments to be monthly. For example, if I'm adding interest to a virtual bank account monthly, for a total of 'time' in years which the user has entered. Is there a simple way of doing this please? I'm not familiar with many R functions yet. --

[R] vis.gam zlab problem

2011-10-27 Thread wildlifeduke
I am using the mgcv package to develop vis.gam plots and having trouble figuring out how to relabel the z-axis (image attached). It is currently labeled as "linear predictor," but I would like to change it to a different name. Currently I am using this code: vis.gam(model1,theta=320,ticktype="det

[R] Proc Mixed to R

2011-10-27 Thread Molly Hanlon
Hi All, I'm working with some SAS code to analyze an experiment set up as follows: 66 subjects (colonies) treated with a random treatment (1-8) and measured at three time points. The data structure looks like: input colony tmt y1 y2 y3; y=y1; date=*1*; output;

Re: [R] help with parallel processing code

2011-10-27 Thread Max Kuhn
I have had issues with some parallel backends not finding functions within a namespace for packages listed in the ".packages" argument or explicitly loaded in the body of the foreach loop. This has occurred with MPI but not with multicore. I can get around this to some extent by calling the functio

Re: [R] combining pairs plot with other plots in one output

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 6:27 PM, Ulrich wrote: I would like to combine multiple plots (one of which is a pairs plot) in one output display: While this works well: layout(matrix(c(1,2,3,3,3,3), ncol=2, byrow=T)) data <- matrix(rnorm(1000), ncol=10) boxplot(data) hist(data) plot(data) This does

Re: [R] plotting large time series

2011-10-27 Thread jim holtman
Try another format (tiff, jpg, etc) to see how they look, what the sizes are for different resolutions. If you have a lot of single points, PDF files get very large because of the commands used to print each point. If you want to keep PDF, then find some way of aggregating the data points so that

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: I will be leaving work shortly, and won't be able to look at this again until tomorrow some time. However, I went back and reread the help page on dcast. Here is part of that page. fun.aggregate aggregation function needed if variables do

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 4:29 PM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RD

Re: [R] Simple time series question with zoo

2011-10-27 Thread Gabor Grothendieck
On Thu, Oct 27, 2011 at 4:18 PM, Vinny Moriarty wrote: > New user here. My goal is pull daily averages from a long dataset. > > I've been working with some code I got from this list from > > https://stat.ethz.ch/pipermail/r-help/2009-March/191302.html > > > The code how I have been using it is as

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: It appears that what you did differently was to dcast the un-melted data. In addition, you shouldn't need to turn your dates into factors. I assume that your unaltered data is in tds.anal. Dan, It's been that sort of a day when that mig

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 2:41 PM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Dennis Murphy wrote: >

[R] combining pairs plot with other plots in one output

2011-10-27 Thread Ulrich
I would like to combine multiple plots (one of which is a pairs plot) in one output display: While this works well: layout(matrix(c(1,2,3,3,3,3), ncol=2, byrow=T)) data <- matrix(rnorm(1000), ncol=10) boxplot(data) hist(data) plot(data) This doesn't: (because the pairs function seems to ove

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Rich Shepard wrote: So I did the conversion and melting the long way: tds.a <- tds.anal tds.a$sampdate <- factor(tds.a$sampdate) I didn't copy the melt command: tds.anal.m <- melt(tds.a) However, ... c.tds.anal <- dcast(tds.a, site + sampdate ~ param, value_var =

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Dennis Murphy wrote: # Define param so that all of its levels are represented: tds.a <- within(tds.a, { param = factor(param, levels = c('TDS', 'Cond', 'Mg', 'Ca', 'Cl', 'Na', 'SO4')) sampdate = as.Date(sampdate) } ) Dennis, This produces an error:

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Fri, 28 Oct 2011, Hadley Wickham wrote: See here: https://github.com/hadley/reshape Thanks, Hadley. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.or

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
If i understand correctly you mean to write the line as below: foreach(icount(itr),.combine=combine,.options.smp=smpopts,.packages='MASS')%dopar% -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-processing-code-tp3944303p3945954.html Sent from the R help mailin

Re: [R] Correllogram of Daily Time Series

2011-10-27 Thread Bazman76
I did it using the code below thank you. Will the fact I have used a ts object but the observations are not really equally spaced invalidate the results? vols=read.csv(file="C:/Documents and Settings/Hugh/My Documents/PhD/Swaption vols.csv" + , header=TRUE, sep=",") > x<-ts(vols[,2]) > x >acf(x

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
yes the library(MASS) was loaded. -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-processing-code-tp3944303p3945972.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list ht

[R] Simple time series question with zoo

2011-10-27 Thread Vinny Moriarty
New user here. My goal is pull daily averages from a long dataset. I've been working with some code I got from this list from https://stat.ethz.ch/pipermail/r-help/2009-March/191302.html The code how I have been using it is as follows: library(zoo) library(chron) DB<-read.table("/Users/me/Des

Re: [R] Using functions written in Fortran in R

2011-10-27 Thread Rolf Turner
On 28/10/11 01:13, Duncan Murdoch wrote: I think nowadays many Linux distros are no more ready than Windows for this. On Linux, you'll likely need to install development libraries and tools; on Windows, the same. The advantage of Windows is that the tools have all been collected in one plac

Re: [R] preceding X. and X

2011-10-27 Thread Ben quant
I think it is what I want. The values look OK. I do get a warning. Here is what you asked for: > dat=read.csv(file_path, header=F) Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'y:\ALL STRATEGIES\INVEST

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Hadley Wickham
>> So I was using the rshape package rather than rshape2.  I don't know the >> relationship between those two packages and/or how they differ.  I am sure >> that there are others that can help you out here. > >  I, too, don't know how the two packages 'reshape, The Orignal' and > 'reshape2, Reboote

Re: [R] loading RMySQL - location of MySQL install

2011-10-27 Thread Gabor Grothendieck
On Thu, Oct 27, 2011 at 1:46 PM, Jeff Laux wrote: > I am having trouble loading RMySQL after installing it.  I have looked at > archived r-help files and it seems many people have had issues, but I didn't > find my specific issue.  I also went to the webpage at Vanderbilt > (http://biostat.mc.vand

[R] loading RMySQL - location of MySQL install

2011-10-27 Thread Jeff Laux
(I apologize if this ends up being posted twice, I tried to post it earlier, and it didn't seem to 'take'.) I am having trouble loading RMySQL after installing it. I have looked at archived r-help files and it seems many people have had issues, but I didn't find my specific iss

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Dennis Murphy
Try this, based on your small example: > tds.a <- read.table(textConnection(" + site sampdate param quant + 1UDS-O 2006-12-06 TDS 10800 + 4 STC-FS 1996-06-14 Cond 280 + 7UDS-O 2007-10-04Mg 1620 + 9UDS-O 2007-10-04 SO4 7580 + 19 JCM-10B 2007-06-21Ca79 + 20

Re: [R] preceding X. and X

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Ben quant > Sent: Thursday, October 27, 2011 12:26 PM > To: r-help@r-project.org > Subject: Re: [R] preceding X. and X > > Figured it out. Solution: > dat=read.csv(file_path, hea

Re: [R] help with parallel processing code

2011-10-27 Thread Dennis Murphy
Did you load the class package before calling lda()? Dennis On Thu, Oct 27, 2011 at 10:14 AM, 1Rnwb wrote: > my modification gives me error >>  rows<- c(1:nrow(mat)) >>  scores <- c() >>  labels <-c() >>  itr<-1000 >>  chnksz<-ceiling(itr/getDoParWorkers()) >> smpopt=list(chunkSize=chnksz) >>  f

Re: [R] preceding X. and X

2011-10-27 Thread Ben quant
Figured it out. Solution: dat=read.csv(file_path, header=F) > dat V1 V2V3 V4 V5 V6V7 V8V9V10V11V12V13 V14 V15 V16 V17 V18 V19V20 1 0 -0.2404324 0.3554681 -0.21147 1.18128

Re: [R] NROW doesn't equal length(x)

2011-10-27 Thread R. Michael Weylandt
Data frame is list internally so length(df) = ncol(df) M On Oct 27, 2011, at 2:44 PM, Muhammad Abuizzah wrote: > Hi, > > I am converting a data.frame to xts. the data.frame is 4 columns and 1000 > rows. I get a message that "NROW (x) must match length(order.by) > class is data.frame, mode i

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 12:00 PM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/R

[R] NROW doesn't equal length(x)

2011-10-27 Thread Muhammad Abuizzah
Hi, I am converting a data.frame to xts.  the data.frame is 4 columns and 1000 rows.  I get a message that "NROW (x) must match length(order.by) class is data.frame, mode is list when I run  dim(x)   # I get  1000     4   #which is consistent with 1000 rows and 4 columns NROW (x)  # I get 1000

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: I read in the sample data that you put in an earlier post. tds.anal <- read.table('clipboard',header=TRUE) tds.anal site sampdate param quant 1UDS-O 2006-12-06 TDS 10800 4 STC-FS 1996-06-14 Cond 280 7UDS-O 2007-10-04

[R] preceding X. and X

2011-10-27 Thread Ben quant
Hello, Why do I get preceding "X." (that is a and X followed by a period) for negative numbers and an "X" for positive numbers when I read a csv file? Am I stuck with this? If so, how do I convert it to normal numbers? dat=read.csv(file_path) > dat [1] X0.0 X.0.240432350374 X0.

Re: [R] package for time series

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Mehmet Suzen wrote: This book is also pretty good: Introductory Time Series with R Paul S.P. Cowpertwait and Andrew V. Metcalfe http://www.springer.com/statistics/statistical+theory+and+methods/book/9 78-0-387-88697-8 There's also: "Time Series Analysis and its Applicati

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: What I think you want is as simple as test.melted <- melt(test) Dan, et al.: No, it's not that simple. Unfortunately. I've tried various combinations of id.vars, measure.vars, and variable, but just cannot get the dates to display in the

[R] loading RMySQL - location of MySQL install

2011-10-27 Thread Jeff Laux
I am having trouble loading RMySQL after installing it. I have looked at archived r-help files and it seems many people have had issues, but I didn't find my specific issue. I also went to the webpage at Vanderbilt (http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL) and followed the instructi

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 11:17 AM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/R

Re: [R] Trying to create a function to extract values from a matrix

2011-10-27 Thread StephenHughes
Thanks Michael, this worked great. Stephen -- View this message in context: http://r.789695.n4.nabble.com/Trying-to-create-a-function-to-extract-values-from-a-matrix-tp3944737p3945236.html Sent from the R help mailing list archive at Nabble.com. __ R-

[R] Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC

2011-10-27 Thread Thomas . Rousseaubeaumier
Hi Guys, First, English is not my native language so sorry if the question is too difficult to understand. I can rephrase it if necessary. I have 32-bit Windows Xp SP3, i use R version 2.12.0 (2010-10-15), and the question is about Redundancy canonical analysis  plot problem in 3D using VEG

Re: [R] Using optim with parameters that are factors (instead of continuous parameters)

2011-10-27 Thread Lucas Merrill Brown
Ben, Thank you for the incredibly helpful suggestions and links. I've been exploring each over the past few days, and for anyone else's future reference, here's what I've found. (1) I was able to use SANN to specify how to choose new candidate solutions, but I wasn't able to easily use SANN for a

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
my modification gives me error > rows<- c(1:nrow(mat)) > scores <- c() > labels <-c() > itr<-1000 > chnksz<-ceiling(itr/getDoParWorkers()) > smpopt=list(chunkSize=chnksz) > foreach(icount(itr),.combine=cbind,.options.smp=smpopts)%dopar% + { + train <- sample(rows, length(rows)-1) + label =

[R] plotting large time series

2011-10-27 Thread Agnes Richard
hello, I got a problem with plotting large time series, since I want to store the results in a .PDF file (I want to store several pages of plots). The PDF files get too large to be handled (> 10MB, one was even 200MB big). So I wonder, if there would be a possibilty to either - reduce the fil

Re: [R] package for time series

2011-10-27 Thread 1Rnwb
if you are a beginer then try this http://www.stat.pitt.edu/stoffer/tsa2/R_time_series_quick_fix.htm there are lots of books and their exercises available on the authors website. also search in google books http://books.google.com/books?id=0fRcUmyhUIQC&printsec=frontcover&source=gbs_ge_summary_r&c

Re: [R] help with parallel processing code

2011-10-27 Thread 1Rnwb
sorry for noise the simulated data should be like this d=data.frame(replicate(9, rnorm(40)+10),rep(c('y','n'),20)) colnames(d)<-c("LEPTIN","SAA","PTH","sEGFR","IGFBP6","MMP2","OPG","IGFBP3","PDGFAABB","group") -- View this message in context: http://r.789695.n4.nabble.com/help-with-parallel-pr

Re: [R] creating vector os zeros for simulations (beginner's question)

2011-10-27 Thread Seb
you could try this: u2=matrix(rnorm(150), nrow=5, ncol=30); u2 Seb On Thu, Oct 27, 2011 at 1:44 PM, Iara Faria wrote: > Dear R helpers, > > I know this is a simple task, but I'm new to R and I'm still havind > difficulties with the language. > I want to create 30 vectors to be used in a simu

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: You should be able to get what you want using the dcast function (I think). test.melted <- melt(tds.anal) dcast(test.melted, site + sampdate ~ param) Dan, I don't think the data frame melted properly. I tried the dcast() but sampdate is

Re: [R] package for time series

2011-10-27 Thread Mehmet Suzen
This book is also pretty good: Introductory Time Series with R Paul S.P. Cowpertwait and Andrew V. Metcalfe http://www.springer.com/statistics/statistical+theory+and+methods/book/9 78-0-387-88697-8 >-Original Message- >From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.or

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 10:56 AM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/R

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: I should apologize. I saw rshape2 and just "glossed" over that and read rshape. Dan, Apparently the 'e' in the subject line fell off. It's 'reshape2'. So I was using the rshape package rather than rshape2. I don't know the relationshi

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Nordlund, Dan (DSHS/RDA) > Sent: Thursday, October 27, 2011 10:47 AM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > > -Original Message- >

[R] regression in R

2011-10-27 Thread Ajay Ohri
1) Packages to be used- For smaller datasets use these 1. CAR Package http://cran.r-project.org/web/packages/car/index.html 2. GVLMA Package http://cran.r-project.org/web/packages/gvlma/index.html 3. ROCR Package http://rocr.bioinf.mpi-sb.mpg.de/ 4. Relaimpo Package 5. DAAG packag

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 10:22 AM > To: r-help@r-project.org > Subject: Re: [R] Syntax Check: rshape2 melt() > > On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/R

[R] creating vector os zeros for simulations (beginner's question)

2011-10-27 Thread Iara Faria
Dear R helpers,   I know this is a simple task, but I'm new to R and I'm still havind difficulties with the language. I want to create 30 vectors to be used in a simulation, each with 1 columm and 5 lines, of random numbers N(0,1). What I tried was this:   N=150 u2<-rep(1:150,0) u2<-list(matrix(0

Re: [R] Problem Installing a local package in linux

2011-10-27 Thread sambit rath
Dear Paul, Thanks for the response. I could resolve the problem. The problem, as you had rightly pointed out, was the absence of the gfortran package called libgfortran41. I located the rpm and installed it. This contains libgfortran.so.1. That does it. Thanks again. sambit On 27 October 2011

Re: [R] Correllogram of Daily Time Series

2011-10-27 Thread R. Michael Weylandt
You also might be satisfied with the output of acf() or pacf() if you are just looking at the auto-correlation of one series. Michael On Thu, Oct 27, 2011 at 11:18 AM, R. Michael Weylandt wrote: > Usually it's encouraged to use a csv or txt intermediary between Excel > and R: depending on what y

Re: [R] show.ci='FALSE' ignored in simple.lm

2011-10-27 Thread Dennis Murphy
Hi: A trip to package sos reveals that simple.lm() is in the UsingR package. Looking at the code of this function, it plots the (x, y) pairs and the fitted least squares line without an option to suppress the plot. Here's a slight hack of the function; it adds a new argument plot with default acti

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
On Thu, 27 Oct 2011, Nordlund, Dan (DSHS/RDA) wrote: What I think you want is as simple as test.melted <- melt(test) Dan, I see the difference this syntax makes; sampdate is the variable associated with the value (quant) for a specific ID pair of site and param. wanted <- cast(test.melted

[R] glmmBUGS fails to accept higher level covariates

2011-10-27 Thread dunner
Hello I am using glmmBUGS to fit a multilevel model. Treatments are nested in Course are nested in Patients. The predicted variable in total EEG duration. The predictors are: at the observation level : Medication dose at the Course level: Weight in KG and Age at the Patient level: Weight in KG a

Re: [R] Syntax Check: rshape2 melt()

2011-10-27 Thread Nordlund, Dan (DSHS/RDA)
> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Rich Shepard > Sent: Thursday, October 27, 2011 8:26 AM > To: r-help@r-project.org > Subject: [R] Syntax Check: rshape2 melt() > > >This is my first excursion into using res

Re: [R] Power mixed model ordinal logistic regression

2011-10-27 Thread Ben Bolker
Scott Raynaud yahoo.com> writes: > > Is there a package that will perform power calculations > for mixed model ordinal logistic regression?  I > searched and came up with nothing. Didn't you ask this question, and get an answer, on this list yesterday ... ?? _

[R] LATEX Command in R in Windows 7

2011-10-27 Thread Baris Demiral
Hi guys, I have 64-bit Windows 7 machine. I need to execute the "latex" and "pdflatex" commands from R to print out tables in pdf. I use R 2.13 64-bit, and I have GSView, GSScript and TexWorks installed. I remember i did this once but I forgot the next step. What shall I do? Thanks, -- Ş. Barı

[R] R.oo package, inherit two classes

2011-10-27 Thread Ben quant
Hello, How do I inherit two classes using the R.oo package. Below is kind of a silly example, but I am trying to create class PerDog from classes Dog and Person. Error at bottom. I've tried a few other ways of using extend(), but nothing seems to get me what I want. Example: setConstructorS3("Pe

Re: [R] Consistant test for NAs in a factor when exclude = NULL?

2011-10-27 Thread William Dunlap
Note that for factors with NA in the levels, is.na(f)[2] <- TRUE and is.na(f[2])<-TRUE give different results: > f <- factor(c("A","A",NA), levels=c(NA, "A"), exclude=NULL) > str(f) Factor w/ 2 levels NA,"A": 2 2 1 > is.na(f) [1] FALSE FALSE FALSE > is.na(f[2]) <- TRUE > str(f)

Re: [R] package for time series

2011-10-27 Thread Duncan Murdoch
On 27/10/2011 11:08 AM, rgui wrote: hi, I want any suggestion for a differents packages to manipulate a time series. thanks for help. See the Time Series task view on http://cran.r-project.org/web/views/. Duncan Murdoch __ R-help@r-project.org mai

[R] Power mixed model ordinal logistic regression

2011-10-27 Thread Scott Raynaud
Is there a package that will perform power calculations for mixed model ordinal logistic regression?  I searched and came up with nothing. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] FOR loop with statistical analysis for microarray data

2011-10-27 Thread Weidong Gu
Looks like you have problems with indexing. In your code, fc is a vector of length 2, pv is a scalar(it only keeps the last value of the loop), then you try to cbind different lengths of vectors (row.names(y1), fc and pv). cbind only works for vectors with the same length. I don't know what you wa

Re: [R] package for time series

2011-10-27 Thread R. Michael Weylandt
http://lmgtfy.com/?q=CRAN+time+series+analysis Michael On Thu, Oct 27, 2011 at 11:08 AM, rgui wrote: > hi, > > I want any suggestion for a differents packages to manipulate a time series. > > thanks for help. > > > -- > View this message in context: > http://r.789695.n4.nabble.com/package-for-t

[R] Syntax Check: rshape2 melt()

2011-10-27 Thread Rich Shepard
This is my first excursion into using reshape2 and I want to ensure that the melt() function call is syntactically correct. The unmodifed data frame is organized this way: head(tds.anal) site sampdate param quant 1UDS-O 2006-12-06 TDS 10800 4 STC-FS 1996-06-14 Cond 280 7

Re: [R] Trying to create a function to extract values from a matrix

2011-10-27 Thread R. Michael Weylandt
This might be an easier method: suppose your data is in MAT t(apply(MAT, 1, function(v) eigen(matrix(v, 2))$values)) Your problem is that return() automatically returns the output and ceases function execution as soon as its hit. Michael On Thu, Oct 27, 2011 at 10:44 AM, StephenHughes wrote:

Re: [R] Correllogram of Daily Time Series

2011-10-27 Thread R. Michael Weylandt
Usually it's encouraged to use a csv or txt intermediary between Excel and R: depending on what you want to do, you can either convert it once it's in R or maybe use read.zoo() to simplify a few things. Most people find the raw ts class hard to use and prefer a contributed class instead: my usual f

[R] Trying to create a function to extract values from a matrix

2011-10-27 Thread StephenHughes
My issue seems simple but I can't find any method to work... I've got a matrix with 4 columns and I want to extract the values from each row to make a new 2x2 matrix for each row. From these resultant matrices, I want to get the Eigen Values and output them from the function as usable numbers (no

[R] package for time series

2011-10-27 Thread rgui
hi, I want any suggestion for a differents packages to manipulate a time series. thanks for help. -- View this message in context: http://r.789695.n4.nabble.com/package-for-time-series-tp3944825p3944825.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Calculate the difference using ave

2011-10-27 Thread Patrick Hausmann
Thanks Dimitris, but I would like to bind the result on the dataframe, so the length should be equal to nrow(df1). BTW, sorry for the example, it wasn't very clear, next try: # options(stringsAsFactors = FALSE) set.seed(123

Re: [R] question R regarding consecutive numbers

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 9:21 AM, Duncan Murdoch wrote: On 27/10/2011 8:43 AM, Samir Benzerfa wrote: Hi everyone Do you know about any possibility in R to check for consecutive numbers in vectors? That is, I do not only want to count the number of observations in total (which can be done ta

Re: [R] FOR loop with statistical analysis for microarray data

2011-10-27 Thread Seb
thanks for the replies so, i remove the indices pv[i] and fc[i]..but when i run it like this: === fc=0 pv=0 for (i in 1:nrow(data)) { v1= c(y1[i,1], y1[i,2]) v2= c(y2[i,1], y2[1,2]) fc=v1-v2 w=t.test(v1,v2) pv=w$p.value } results =

Re: [R] show.ci='FALSE' ignored in simple.lm

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 6:58 AM, Elinor Zeev wrote: Hi, I am using PostgreSQL 9.1 and want to run loglinear_simple<-simple.lm(x$p_overPnot,x$logQuantity,show.ci =FALSE,conf.level=confidenceLevel) without showing the graph, however the show.ci=FALSE is ignored. My guess (and it is a guess si

Re: [R] minimizing device-dependent code in graphics scripts

2011-10-27 Thread Duncan Murdoch
On 27/10/2011 10:13 AM, Michael Friendly wrote: Here is a common scenario that I and probably others often face: - I write a script, test.R, to produce some graphs, viewing them on-screen and tinkering until they look right - I want to save image files (e.g., .png), so I wrap each plot in device

[R] minimizing device-dependent code in graphics scripts

2011-10-27 Thread Michael Friendly
Here is a common scenario that I and probably others often face: - I write a script, test.R, to produce some graphs, viewing them on-screen and tinkering until they look right - I want to save image files (e.g., .png), so I wrap each plot in device driver calls, e.g., png(file='test01.png', w

Re: [R] Problem Installing a local package in linux

2011-10-27 Thread Paul Hiemstra
Hi, Yea Linux! I think you are missing a library file (libgfortran.so.1), you can use locate to try and find the so file, in bash type: locate libgfortran Now three things can happen: - It doesn't find anything, than you need to install an additional gfortran package. This is often called libgfo

Re: [R] question R regarding consecutive numbers

2011-10-27 Thread Duncan Murdoch
On 27/10/2011 8:43 AM, Samir Benzerfa wrote: Hi everyone Do you know about any possibility in R to check for consecutive numbers in vectors? That is, I do not only want to count the number of observations in total (which can be done table(x)), but I also want to count for instance how many ti

[R] Correllogram of Daily Time Series

2011-10-27 Thread Bazman76
Hi there, What is the best way to get a time series of daily stock price observations into R (from excel). The time series are daily but there are spaces for w/e's and holidays etc. So I am not sure a ts object will be suitable but I am not sure what I should use? What ever package you recemmned

[R] show.ci='FALSE' ignored in simple.lm

2011-10-27 Thread Elinor Zeev
Hi, I am using PostgreSQL 9.1 and want to run loglinear_simple<-simple.lm(x$p_overPnot,x$logQuantity,show.ci =FALSE,conf.level=confidenceLevel) without showing the graph, however the show.ci=FALSE is ignored. Thank you [[alternative HTML version deleted]] _

[R] help with parallel processing code

2011-10-27 Thread 1Rnwb
Hello R gurus, I have the code below for which i need help and pointers to make it run in parallel on a dual core win7 computer with R 2.13.x, using foreach, iterators,doMC. library(scatterplot3d) # Loads 3D library. library(fields) library(MASS) library(ROCR) library(verification) library(caret)

[R] Error installing packages

2011-10-27 Thread picohan
Hello, I got an error if I try to install a package. For example package emg: R CMD check emg Everything is fine. R CMD INSTALL emg I got the following errors: * installing to library 'c:/R_2_13_1/library' * installing *source* package 'emg' ... Error in file_path_as_absolute(dfile) : Datei './

Re: [R] help with paste

2011-10-27 Thread 1Rnwb
Hi Joshua, Thanks for the suggestion. Sharad -- View this message in context: http://r.789695.n4.nabble.com/help-with-paste-tp3942818p3943753.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://s

[R] Interesting Memory Management Problem (Windows)

2011-10-27 Thread Bob
Hi, I am try to fit an eGARCH model on an expanding basis using the rugarch package. I have 6 columns of data, and I am trying refit parameters ~6000 for each column. If I run the following code, I get an error in windows on the 2nd column (this means I am getting all the way through the first inn

[R] question R regarding consecutive numbers

2011-10-27 Thread Samir Benzerfa
Hi everyone Do you know about any possibility in R to check for consecutive numbers in vectors? That is, I do not only want to count the number of observations in total (which can be done table(x)), but I also want to count for instance how many times that vector contains a certain number cons

Re: [R] FOR loop with statistical analysis for microarray data

2011-10-27 Thread Weidong Gu
In your loop, you assign, for example, pv twice pv=w$p.value # pv is scalar pv[i]= w[2] # pv is a vector give an example for the point pv=1 pv[5]=2 pv [1] 1 NA NA NA 2 This may not be what you want. Weidong On Thu, Oct 27, 2011 at 7:40 AM, Seb wrote: > y1,y2 were designed as follow,from t

[R] Problem Installing a local package in linux

2011-10-27 Thread sambit rath
Dear all, I am "still" fairly new to R and newer still to linux (opensuse). I want to install a package called "FEAR" from "http://www.clemson.edu/economics/faculty/wilson/Software/FEAR/fear-download.html";. So, I downloaded the tar.gz file called "FEAR-linux-64bit-2.6.16.60-0.21-smp.tar.gz" and

Re: [R] Consistant test for NAs in a factor when exclude = NULL?

2011-10-27 Thread David Winsemius
On Oct 27, 2011, at 12:21 AM, andrewH wrote: Thanks Jeff! I appreciate you sharing your experience. My data set is survey data, 13,209 records over nine years, collected by someone else, converted from SPSS format. It includes missing values, identified however SPSS does so, and translated

Re: [R] Fitting Maximums of data series with cubic spline

2011-10-27 Thread Paul Hiemstra
On 10/27/2011 10:46 AM, Zablone Owiti wrote: > Hi Users, > > I want to fit the maximums of a data series with a cubic spline. How do I > go about this in R. > > I failed to figure out how I can use the mgcv library to do this. > > > Thanks > > ZABLONE > > _

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