[R] different results of fisher.test function in R2.8.1 and R2.6.0

2009-03-26 Thread 马传香
Hi; I use the function fisher.test to compute in R2.8.1 and R2.6.0,and the results are not identical.the last number is different. why? thank you ! Merry [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.e

[R] Combining multiple dataframes in a list

2009-03-26 Thread Daren Tan
I have a list containing multiple dataframes. Depending on whether the dataframes have 1 column or more than 1 columns, the column names are named differently. How can I force single column dataframes to have prefixed column names ? > m<- list(fc=data.frame(A=1:3)) > do.call(cbind, m) A 1 1 2 2

Re: [R] Physical or Statistical Explanation for the "Funnel" Plot?

2009-03-26 Thread Mike Miller
On Thu, 26 Mar 2009, Jason Rupert wrote: The R code below produces (after running for a few minutes on a decent computer) the plot shown at the following location: http://n2.nabble.com/Is-there-a-physical-and-quantitative-explanation-for-this-plot--td2542321.html I'm just taking the mean of a

[R] Installing Rmpi on Centos 5.2

2009-03-26 Thread Rick Bilonick
I am trying to install the R package "Rmpi" which needs libmpi. I've installed openmpi and lam in Centos 5.2: [r...@rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [r...@rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 I'm using this to install Rmpi: R CMD INSTALL /h

[R] Need some help at interfacing R with Fortran-90

2009-03-26 Thread mauede
I browsed through ch.5 of R manual "Writing R extensions". It seems to be written for experienced programmers rathern than for people who occasionally face this problem. A table summarising the main ley points for each supported platform would be very useful. Something like: Supported languages:

Re: [R] how to quit mailing list

2009-03-26 Thread Jorge Ivan Velez
Dear Jiang, Go to https://stat.ethz.ch/mailman/listinfo/r-help and follow the instructions at the end. HTH, Jorge On Thu, Mar 26, 2009 at 11:27 PM, Jiang Peng wrote: > Dear list, > I will not use this account later, so i have to quit this list. > > >I don't know how to quit this list,

Re: [R] how to quit mailing list

2009-03-26 Thread Rolf Turner
On 27/03/2009, at 4:27 PM, Jiang Peng wrote: Dear list, I will not use this account later, so i have to quit this list. I don't know how to quit this list, I search the official website and find no answer. Well you didn't search very hard. Go to Mailing Lists ---> R.help web int

Re: [R] Bug? FORTTRAN help

2009-03-26 Thread Berwin A Turlach
G'day Kevin, On Thu, 26 Mar 2009 13:42:20 -0700 wrote: > I was feeling masochistic the other day [...] Welcome to the club. :) > and we have been having some wierd memory problems so I started > digging into the source for L-BFGS-B. In the lbgfsb.c file I see the > following code: > > /*

[R] how to quit mailing list

2009-03-26 Thread Jiang Peng
Dear list, I will not use this account later, so i have to quit this list. I don't know how to quit this list, I search the official website and find no answer. thanks very much !! [[alternative HTML version deleted]] __ R-help@r-p

Re: [R] Conerned about Interfacing R with Fortran

2009-03-26 Thread Berwin A Turlach
G'day Maura, On Thu, 26 Mar 2009 18:21:01 +0100 wrote: > I am reading the manual sections illustrating how to call a Fortran > subroutine from R. I feel uneasy at the explicit statement about > ".Fortran" interface working with Fortran 77. I would like to call a > Fortran-90 subroutine from my R

Re: [R] Some install package fixes for Ubuntu Hardy

2009-03-26 Thread Dirk Eddelbuettel
On 26 March 2009 at 09:45, John C Nash wrote: | I encountered some failures in using install.packages() to install rgl | and rJava in some of my (multiple) Ubuntu Hardy systems. A quick search | of the 'Net did not show any debian packages for these. The | install.packages messages said header

[R] Physical or Statistical Explanation for the "Funnel" Plot?

2009-03-26 Thread Jason Rupert
The R code below produces (after running for a few minutes on a decent computer) the plot shown at the following location: http://n2.nabble.com/Is-there-a-physical-and-quantitative-explanation-for-this-plot--td2542321.html I'm just taking the mean of a given set of random variables, where the s

[R] Overlying a map on top of an image [SEC=UNCLASSIFIED]

2009-03-26 Thread Augusto.Sanabria
Good day everyone, I have a *.jpeg map and I want to display it on top of an existing image (created using 'image'), Is there an easy way to do it? "map" does the job but only with pre-existing maps (from its database) not with my map. I would greatly appreciate any help in this matter. Thanks,

Re: [R] use of "@" character in variable name

2009-03-26 Thread Rolf Turner
On 27/03/2009, at 2:52 PM, Marc Schwartz wrote: On Mar 26, 2009, at 8:40 PM, Rolf Turner wrote: On 27/03/2009, at 2:04 PM, Mike Miller wrote: Importing data with a header row using read.delim, one variable should be named @5HTT but it is automatically renamed to X.5HTT, presumably because

Re: [R] use of "@" character in variable name

2009-03-26 Thread John Fox
Dear Mike, As a slight simplification, a legal R name can start with a period (.), upper- or lower-case letter (A-Z, a-z), and can contain periods, underscores (_), letters, and numerals; depending upon the locale, some other characters may also be allowed. This information *is* in the R manuals,

Re: [R] use of "@" character in variable name

2009-03-26 Thread Marc Schwartz
On Mar 26, 2009, at 8:40 PM, Rolf Turner wrote: On 27/03/2009, at 2:04 PM, Mike Miller wrote: Importing data with a header row using read.delim, one variable should be named @5HTT but it is automatically renamed to X.5HTT, presumably because the "@" is either unacceptable or misunderstood

Re: [R] pgmm (blundell-bond) help needed

2009-03-26 Thread ivo welch
I have been playing with more examples, and I now know that with larger NF's my example code actually produces a result, instead of a singular matrix error. interestingly, stata's xtabond2 command seems ok with these sorts of data sets. either R has more stringent requirements, or stata is too ca

Re: [R] use of "@" character in variable name

2009-03-26 Thread Rolf Turner
On 27/03/2009, at 2:04 PM, Mike Miller wrote: Importing data with a header row using read.delim, one variable should be named @5HTT but it is automatically renamed to X.5HTT, presumably because the "@" is either unacceptable or misunderstood. I've tried to find out what the rules are on v

[R] ROCR package finding maximum accuracy and optimal cutoff point

2009-03-26 Thread Saeed Abu Nimeh
If we use the ROCR package to find the accuracy of a classifier pred <- prediction(svm.pred, testset[,2]) perf.acc <- performance(pred,"acc") Do we find the maximum accuracy as follows (is there a simplier way?): > max(perf@x.values[[1]]) Then to find the cutoff point that maximizes the accur

Re: [R] use of "@" character in variable name

2009-03-26 Thread Krzysztof Sakrejda-Leavitt
The '@' character is an operator used for accessing slots in S4 classes. Similarly the '$' character is the operator for accessing elements of lists, etc... Although R allows periods, SQL databases will choke on them. LaTeX will (sometimes?) choke on underscores, and of course any native R o

[R] use of "@" character in variable name

2009-03-26 Thread Mike Miller
Importing data with a header row using read.delim, one variable should be named @5HTT but it is automatically renamed to X.5HTT, presumably because the "@" is either unacceptable or misunderstood. I've tried to find out what the rules are on variable names but have been unsuccessful. I'll bet

[R] Trellis barchart help

2009-03-26 Thread jimdare
Hi, I apologise if this sounds like a really simple problem. I have a time-series data set with two columns of data: Catch and TACC. I want Catch plotted as a barchart and TACC plotted on the same graph as a series of points with an overlaying a line. I have created the code for a barchart usi

[R] Snow Parallel R: makeCluster with more nodes than available

2009-03-26 Thread Ubuntu Diego
Hi all, I would like to know what would happen if using snow I create a cluster of size 50, for example using makeCluster(50,type='SOCK') on a machine with 2 Cores and run a function. Does snow run 25 and 25 functions on each of my 2 "real" processors or it just run 50 functions in one proc

[R] [R-pkgs] New CRAN Package: WriteXLS

2009-03-26 Thread Marc Schwartz
A new package called WriteXLS (Version 1.5.0), containing a single function of the same name, is now available via CRAN. The package is made available under the GPL, version >=2. The function is based upon a Perl script that I have previously posted on r-help, now wrapped in R for convenien

[R] R 2.8.1 and 2.9 alpha crash when running survest of Design package

2009-03-26 Thread Nguyen Dinh Nguyen
Dear Prof Harrell and everyone, My PC: Window XP service pack 3 and service pack 2 R version 2.8.1 and 2.9 alpha For the last 3 days, after updating R, my two computers have been facing problems when running existing and runable R commands that involves with Design package I attempt to

Re: [R] ApEn (Approximate Entropy), Total Corr, Information Interaction

2009-03-26 Thread Stephan Kolassa
Hi Vishal, re 1]: Ben Bolker very kindly shared an R reimplementation of Kaplan's Matlab code a little while ago: http://www.nabble.com/Approximate-Entropy--to21144062.html#a21149402 Best wishes Stephan Vishal Belsare schrieb: Is there any existing implementation in R/S of : 1] Pincus & Ka

[R] for Interaction of continous var and categorical var, any way approach the categorical var to continous ?

2009-03-26 Thread Yong Wang
Dear list, This is NOT a techical question ragrding use of R. I have a linear model where the response variable is neigborhood safety . It is projected poverty deteriorate safety and number of officers per thousand residents improve safety. The focal hypothesis is poverty poses less safety threat

Re: [R] Column name assignment problem

2009-03-26 Thread Tal Galili
Way are you taking the forth argument of the paste ?paste("arunoff_",table_year, sep="")[4] Either way, way not use something like: colnames(x)[column to change] <- "text, or pasted text" Cheers, Tal On Thu, Mar 26, 2009 at 2:33 PM, Steve Murray wrote: > > Dear all, > > I'm trying to assign

[R] pgmm (Blundell-Bond) sample needed

2009-03-26 Thread ivowel
Dear R Experts--- Sorry for all the questions yesterday and today. I am trying to use Yves Croissant's pgmm function in the plm package with Blundell-Bond moments. I have read the Blundell-Bond paper, and want to run the simplest model first, d[i,t] = a*d[i,t-1] + fixed[i] + u[i,t] . no thir

[R] ApEn (Approximate Entropy), Total Corr, Information Interaction

2009-03-26 Thread Vishal Belsare
Is there any existing implementation in R/S of : 1] Pincus & Kalman's approximate entropy (ApEn) measure 2] Total Correlation / Multiinformation 3] Information Interaction A search doesn't quite reveal anything, but I'd be keen to not reinvent in case someone has worked on it. Many thanks in anti

[R] VGAM and cnstraints

2009-03-26 Thread Raffaello Vardavas
Dear R-Users, I am learning how to use the package VGAM to do multinomial regressions. I have worked through the example provided by UCLA stats group: http://www.ats.ucla.edu/stat/r/dae/mlogit.htm However - what I would like to learn is how to use the constraint option. So in the example give

[R] Bug? FORTTRAN help

2009-03-26 Thread rkevinburton
I was feeling masochistic the other day and we have been having some wierd memory problems so I started digging into the source for L-BFGS-B. In the lbgfsb.c file I see the following code: /* Cholesky factorization of (2,2) block of wn. */ F77_CALL(dpofa)(&wn[*col + 1 + (*col + 1) * wn_d

[R] ICC question: Interrater and intrarater variability (intraclass correlation coefficients)

2009-03-26 Thread Tal Galili
Hello dear R help group. I encountered this old thread (http://tinyurl.com/dklgsk) containing the a similar question to the one I have, but left without an answer. I am and hoping one of you might help. A simplified situation: I have a factorial design (with 2^3 experiment combinations), for 167

[R] Hazard rate estimation by smoothing baseline cumulative hazard from Cox model - Was: RE: Competing risks Kalbfleisch & Prentice method

2009-03-26 Thread Ravi Varadhan
Hi Eleni, I will take a look at this. I have some preliminary comments. You estimate the hazard function from the Cox model baseline cumulative hazard by differencing successive jumps. It seems that a better approach might be to estimate this using kernel smoothing, i.e. as the derivative of ke

Re: [R] Analogy for %in% for the whole columns (rather than individual values)

2009-03-26 Thread Dimitri Liakhovitski
Thank you very much! I tried %in% and it did not work. However == works! Thank you! On Thu, Mar 26, 2009 at 3:05 PM, Fredrik Karlsson wrote: > Hi Dimitri, > > What about this: > > >> with(a, x == y) -> a$equal >> a > x    y equal > 1 john mary FALSE > 2 mary mary  TRUE > 3 mary john FALSE >

Re: [R] Reading in files with variable parts to names

2009-03-26 Thread Jorge Ivan Velez
Dear Steve, Another option would be using list() to storage your files into R: # Year/Month year <- 1986:1995 month <- sprintf("%02d", 1:12) # Names Files <- paste(year,month,'.asc',sep="") # Data ListFiles <- sapply(Files, read.table, header=TRUE,sep="") # To access the fist file ListFiles[[1

Re: [R] Reading in files with variable parts to names

2009-03-26 Thread Dieter Menne
Steve Murray hotmail.com> writes: > I'm trying to read in a whole directory of files which have two variable > parts to the file name: year and month. E.g. comp198604.asc represents < April of 1986 - 'comp' is fixed in each case. Years range between > 1986 to 1995 and months are between 1 and

Re: [R] Analogy for %in% for the whole columns (rather than individual values)

2009-03-26 Thread Fredrik Karlsson
Hi Dimitri, What about this: > with(a, x == y) -> a$equal > a xy equal 1 john mary FALSE 2 mary mary TRUE 3 mary john FALSE 4 john john TRUE /Fredrik On Thu, Mar 26, 2009 at 7:48 PM, Dimitri Liakhovitski wrote: > Hello! > > I have a matrix a with 2 variables (see below) that contai

Re: [R] Reading in files with variable parts to names

2009-03-26 Thread Rowe, Brian Lee Yung (Portfolio Analytics)
Try this to generate your year/month combinations: > expand.grid(year=1986:1995, month=1:12) Obviously you'll have to format the months. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Steve Murray Sent: Thursday, March 26, 2009 2

Re: [R] Reading in files with variable parts to names

2009-03-26 Thread baptiste auguie
Hi, If your directory contains only files you want to load anyway, then list.files() is your friend, list.files(pattern = "comp") # or pattern =".asc" for example If you do need to create the names manually, then you could create the combinations with expand.grid, as in, do.call(paste

Re: [R] Analogy for %in% for the whole columns (rather than individual values)

2009-03-26 Thread Jorge Ivan Velez
Dear Dimitri: Try this: a<-data.frame(x=c("john", "mary", "mary","john"),y=c("mary","mary","john","john")) a$x<-as.character(a$x) a$y<-as.character(a$y) a$TEST<-apply(a,1,function(x) x[1]==x[2]) a See ?apply for more details. HTH, Jorge On Thu, Mar 26, 2009 at 2:48 PM, Dimitri Liakhovitski w

[R] Analogy for %in% for the whole columns (rather than individual values)

2009-03-26 Thread Dimitri Liakhovitski
Hello! I have a matrix a with 2 variables (see below) that contain character strings. I need to create a 3rd variable that contains True if the value in column x is equal to the value in column y. The code below does it. a<-data.frame(x=c("john", "mary", "mary", "john"),y=c("mary","mary","john","

[R] Reading in files with variable parts to names

2009-03-26 Thread Steve Murray
Dear all, I'm trying to read in a whole directory of files which have two variable parts to the file name: year and month. E.g. comp198604.asc represents April of 1986 - 'comp' is fixed in each case. Years range between 1986 to 1995 and months are between 1 and 12. Just to be clear, there are

Re: [R] boxplot in subgroups

2009-03-26 Thread Pooja Jain
Thank you very much Annette, With your help I can do exactly what I wanted to. Best wishes, -Pooja On 26 Mar 2009, at 06:59, Annette Heisswolf wrote: Hei, the error message below just tells you that you have specified nine places along the axis where you want to have labels (i.e. at=1:9)

[R] Conerned about Interfacing R with Fortran

2009-03-26 Thread mauede
I am reading the manual sections illustrating how to call a Fortran subroutine from R. I feel uneasy at the explicit statement about ".Fortran" interface working with Fortran 77. I would like to call a Fortran-90 subroutine from my R script. Is that supported at all ? Thank you, Maura tutti i

Re: [R] problem with "choose.files" command & interactive functions

2009-03-26 Thread O'Farrell, Shay
Perfect. That's fixed the problem. Thanks very much for the advice. Shay If you don't specify where to open the dialog, it will open in the last location where it was opened. This saves time if you are running it more than once, because often you wil

Re: [R] Competing risks Kalbfleisch & Prentice method

2009-03-26 Thread Eleni Rapsomaniki
Ravi, I agree with you, that the Fine & Gray method does much more than calculating the cumulative incidence. The Kalbfleisch & Prentice formula relies on the strong assumption that the coefficients for the cause specific hazard models are valid in the presence of competing risks. You will find my

Re: [R] Density estimation: scale back for calendar time

2009-03-26 Thread David Winsemius
Pradeep Raje gmail.com> writes: > > Thanks David for your response.I had done that. But not shared it. > Problem is not with the > computations, but in the interpretation. > Assume that x ordinates are 'time' [1:3472], and y are associated parameter > values. > Now density gives me 512/1024/2

Re: [R] programming creating different functions in a loop

2009-03-26 Thread Bert Gunter
Good point, Greg. So to handle i as a vector, you'd probably want something like f <- function(x,i)outer(x,i,"+") -- Bert Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf O

Re: [R] programming creating different functions in a loop

2009-03-26 Thread Greg Snow
But wrong questions requiring complicated answers are sometimes more fun :-). One difference though is in my last example, your function will give a different answer for f(1:3, 1:10), but for the simpler cases, yours is probably the better. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Cent

[R] Locale problem between WinXP and Ubuntu

2009-03-26 Thread Harsh
Hi R list, I have a peculiar problem in trying to Sweave a document in Ubuntu. The error message I get is the following: Error in gsub("\\n", "_", dd_name_level_nominal[k, 1], perl = TRUE) : input string 1 is invalid in this locale dd_name_level_nominal[k, 1] is a character object. I initially

Re: [R] programming creating different functions in a loop

2009-03-26 Thread Bert Gunter
... but perhaps even more straightforward is: f <- function(i,x)x+i Of course, we don't know exactly what the poster is after with his rather arcane construction, so this may not suit. But you know the rule: if the question requires a complex, tricky answer, it's probably the wrong question. C

Re: [R] Way to rotate a histogram?

2009-03-26 Thread Mike Lawrence
In case anyone is still interested, a slight improvement is to plot both density and normal distributions on top of the empirical histogram (previous version plotted only density): library(ggplot2) test_data<-rnorm(100,mean=10,sd=4) a = data.frame(obs = test_data,condition = 'None') p1 = ggplot(

Re: [R] How to rotate axis labels? 2009

2009-03-26 Thread Ben Bolker
Usuario R gmail.com> writes: > > Hi, > > What you want is done with argument srt of par function. See ?par and then > look for srt argument. > > Regards > To clarify: if you just want labels rotated parallel/perpendicular to axes, then par("las") will do everything you need. If you need a

Re: [R] programming creating different functions in a loop

2009-03-26 Thread Greg Snow
Anytime that you are tempted to use assign and a loop, you should consider using lapply (or sapply) and a list instead. Consider this alternative: > f <- lapply( 1:3, function(i){ force(i); function(x) x+i} ) > > f[[1]](3) [1] 4 > f[[2]](10) [1] 12 > f[[3]](0) [1] 3 > > sapply( f, function(f)

Re: [R] installing contributed programs

2009-03-26 Thread Duncan Murdoch
On 3/26/2009 10:11 AM, David Covell wrote: Dear R-help, I'm sure this is contained within the documentation, but I have not yet located it (with good effort nonetheless). I am attempting to install the binary for randomForests. After unpacking the zip, I extracted the contents to my R-2.8.1 fold

Re: [R] programming creating different functions in a loop

2009-03-26 Thread Florin Maican
Thanks Luke! It works! My mistake was that I used "local binding" only for "i" and not for the whole function. Best regards, Florin On Thu, 26 Mar 2009 10:57:21 -0500 (CDT) l...@stat.uiowa.edu wrote: > for() does not creae separete bindings for the index each iteration, > so the function bodi

Re: [R] How to rotate axis labels? 2009

2009-03-26 Thread Usuario R
Hi, What you want is done with argument srt of par function. See ?par and then look for srt argument. Regards 2009/3/26 Jonas Stein > Hi, > > while searching for a solution i found many solutions in the internet. > But the postings seemed to be many years old and the workaround was a > dirty

Re: [R] standard plot font

2009-03-26 Thread Uwe Ligges
Martin Batholdy wrote: hi, I was wondering what font-type R uses in plots (title etc.). Is that depending on the system you are working on? (working with mac OS) In fact, it is dependent on the *Device* you are plotting to. See ?Devices and the help page for the device you are going to plot

Re: [R] How to rotate axis labels? 2009

2009-03-26 Thread Uwe Ligges
Jonas Stein wrote: Hi, while searching for a solution i found many solutions in the internet. But the postings seemed to be many years old and the workaround was a dirty hack like this: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-rotated-axis-labels_003f Now its the year 20

[R] Odp: installing contributed programs

2009-03-26 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 26.03.2009 15:11:32: > Dear R-help, > > I'm sure this is contained within the documentation, but I have not yet located > it (with good effort nonetheless). I am attempting to install the binary for > randomForests. After unpacking the zip, I extracte

[R] How to rotate axis labels? 2009

2009-03-26 Thread Jonas Stein
Hi, while searching for a solution i found many solutions in the internet. But the postings seemed to be many years old and the workaround was a dirty hack like this: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-rotated-axis-labels_003f Now its the year 2009 and there might have

[R] standard plot font

2009-03-26 Thread Martin Batholdy
hi, I was wondering what font-type R uses in plots (title etc.). Is that depending on the system you are working on? (working with mac OS) thanks for help! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] programming creating different functions in a loop

2009-03-26 Thread luke
for() does not creae separete bindings for the index each iteration, so the function bodies see the global binding of i, which in this case will be the final value. One possible solution is to use local(), e.g. for(i in 1:3){ assign(paste("f",i,sep=""), local({ k <- i

[R] Odp: Tables

2009-03-26 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 26.03.2009 16:39:18: > Hi, > > I am just starting using R. Hence, sorry for asking probably rather easy > questions. > > I used "read.table" to bring an .txt Table to R. Unfortunately the > columns do not have the same length. I tried "fill=TRUE", t

[R] the by function

2009-03-26 Thread Melissa2k9
Hey, I have a dataframe with subjects who have watched films. The variables of interest are Pixel number and Temperature on the face. For each subject there are 8 films, for each film for each subject I need to measure the mean number of pixels then merge this vector with the data frame. I have

[R] installing contributed programs

2009-03-26 Thread David Covell
Dear R-help, I'm sure this is contained within the documentation, but I have not yet located it (with good effort nonetheless). I am attempting to install the binary for randomForests. After unpacking the zip, I extracted the contents to my R-2.8.1 folder. However, when I try to execute the comma

Re: [R] Tables

2009-03-26 Thread jim holtman
How are you sure it moved the data? What is the column separator that you have? Is it just 'white space' as opposed to a tab or comma? It you have a CSV file with a separator, the system knows where the columns are. If it sees 'a b c' and then 'a c' as the next row, 'c' will be in column

[R] Tables

2009-03-26 Thread skrug
Hi, I am just starting using R. Hence, sorry for asking probably rather easy questions. I used "read.table" to bring an .txt Table to R. Unfortunately the columns do not have the same length. I tried "fill=TRUE", to fill the blank space with "na". In a certain kind of way it worked, but befo

[R] arima, xreg, and the armax model

2009-03-26 Thread Marc Vinyes
Hello all, I'm having fun again with the arima function. This time I read in: http://www.stat.pitt.edu/stoffer/tsa2/R_time_series_quick_fix.htm <> (by R.H. Shumway & D.S. Stoffer) This is quite surprising... Does anybody know anything about it? Marc Vinyes (AleaSoft) [[alternative

[R] package installation on OSX --- suggestion

2009-03-26 Thread ivo welch
dear R experts: I am trying to install packages in OSX, R 2.8.1. Since I do this about every 2 years, I have completely forgotten it. However, this should not be difficult: http://wiki.r-project.org/rwiki/doku.php?id=getting-started:installation:packages nice document. beautiful method.

[R] programming creating different functions in a loop

2009-03-26 Thread Florin Maican
Hi I want to create the following functions in a loop f1<-function(x){x+1} f2<-function(x){x+2} f3<-function(x){x+3} Output f1(2)=3 f2(2)=4 f3(2)=5 I tried to create the in a loop as bellow but I get wrong on answers because the value of i change for(i in 1:3){ ass

[R] Travel funding for DSC/useR 2009 for young researchers at U.S. institutions

2009-03-26 Thread luke
*** Travel and Accommodation Support *** [Deadline extended to April 15, 2009] Funds from the U.S. National Science Foundation may be available to provide partial support for travel and accommodation for some graduate students and junior faculty at U.S. post-secon

Re: [R] Competing risks Kalbfleisch & Prentice method

2009-03-26 Thread Ravi Varadhan
Hi Eleni, I would like to take a look at your R function for obtaining the cumulative incidence function (CIF) from individual Cox models for cause-specific hazards (CSH). Does your code predict the CIF (with pointwise confidence intervals and global confidence bands) for different sub-groups? H

Re: [R] Competing risks Kalbfleisch & Prentice method

2009-03-26 Thread Eleni Rapsomaniki
Thank you for your reply. It wasn't too hard to code actually, which is probably why it doesn't have a special package dedicated to it. The results are almost identical to Fine & Gray regression model. The problem with the latter is that my colleagues are not convinced that the model assumptions (

[R] Some install package fixes for Ubuntu Hardy

2009-03-26 Thread John C Nash
I encountered some failures in using install.packages() to install rgl and rJava in some of my (multiple) Ubuntu Hardy systems. A quick search of the 'Net did not show any debian packages for these. The install.packages messages said header or other files were missing, suggesting path and relat

[R] Minimal R-installation (and it's size)

2009-03-26 Thread Oliver Bandel
Hello, for very small systems (embedded devices) I think about a minimalistic R-installation. When I look at the R-binary, it has just 5472 Bytes of size. I think this will only be a small initial program, that afterwards starts other executables and also will load standard/base package(s). Can

[R] Plot the highest point in a contour plot

2009-03-26 Thread Thomas Levine
I'm plotting contour plots with contourplot. which.max gives me the index of the highest point of a matrix. I can find the point in the matrix from here, convert it to a point on a graph and add it with points, but you'd think someone's already written this. How do I plot the highest point in a c

Re: [R] problem with "choose.files" command & interactive functions

2009-03-26 Thread Duncan Murdoch
On 3/26/2009 9:09 AM, Shay O'Farrell wrote: Hi all, I’m new to R, and I’m having a small but annoying problem with the choose.files command, using version 2.8.1 in Windows XP. I am holding my data text files in C:\\Data\\, and I’m writing a short script that first resets the default directory

[R] problem with "choose.files" command & interactive functions

2009-03-26 Thread Shay O'Farrell
Hi all, I’m new to R, and I’m having a small but annoying problem with the choose.files command, using version 2.8.1 in Windows XP. I am holding my data text files in C:\\Data\\, and I’m writing a short script that first resets the default directory to this directory, then allows me to intera

Re: [R] same value in column-->delete

2009-03-26 Thread Uwe Ligges
Patrizio Frederic wrote: this works which.is.not.unique <- apply(x,2,function(x)ifelse(length(unique(x))==1,F,T)) x[,which.is.not.unique] or you simplify that idea and say x[, apply(x, 2, function(x) length(unique(x)) > 1)] Uwe Ligges patrizio 2009/3/26 Duijvesteijn, Naomi : Hi R

[R] Column name assignment problem

2009-03-26 Thread Steve Murray
Dear all, I'm trying to assign a name to the fourth column whilst using 'assign', but keep encountering errors. What have I done wrong?! > assign(colnames(c(paste("arunoff_",table_year, sep="")[4]), "COUNT")) Error in if (do.NULL) NULL else if (nc> 0) paste(prefix, seq_len(nc), : argument

Re: [R] R: Fortran-90 and R

2009-03-26 Thread jgarcia
Perhaps you should consider also the possibility of simply export the data from the R workspace to the system and make your fortran code to read these system files. > On Thu, 2009-03-26 at 11:01 +0100, mau...@alice.it wrote: >> I do hope the chapte about "Interfacing R and Fortran" is sufficient.

Re: [R] same value in column-->delete

2009-03-26 Thread Patrizio Frederic
this works which.is.not.unique <- apply(x,2,function(x)ifelse(length(unique(x))==1,F,T)) x[,which.is.not.unique] patrizio 2009/3/26 Duijvesteijn, Naomi : > >   Hi Readers, > > >   I have a question. > > >   I have a large dataset and want to throw away columns that have the same >   value in the

Re: [R] Centring variables in Cox Proportional Hazards Model

2009-03-26 Thread Frank E Harrell Jr
Laura Bonnett wrote: Dear All, I am contemplating centering the covariates in my Cox model to reduce multicollinearity between the predictors and the interaction term and to render a more meaningful interpretation of the regression coefficient. Suppose I have two indicator variables, x1 and x2

Re: [R] same value in column-->delete

2009-03-26 Thread Gustaf Rydevik
On Thu, Mar 26, 2009 at 12:15 PM, Duijvesteijn, Naomi wrote: > >   Hi Readers, > > >   I have a question. > > >   I have a large dataset and want to throw away columns that have the same >   value in the column itself and I want to know which column this was. > > >   For example > >   > x<-data.fr

Re: [R] Getting started,

2009-03-26 Thread Gabor Grothendieck
Try this: library(zoo) library(chron) my.url <- "http://www.federalreserve.gov/releases/h15/data/Business_day/H15_ED_M1.txt"; z <- read.zoo(my.url, skip = 8, header = TRUE, sep = ",", na.strings = "ND", strip.white = TRUE, FUN = as.chron) plot(z[1:50,]) # or to plot with NAs interpolate

Re: [R] same value in column-->delete

2009-03-26 Thread jim holtman
Try this: > x id snp1 snp2 snp3 1 1AGG 2 2GGG 3 3GGA > str(x) 'data.frame': 3 obs. of 4 variables: $ id : num 1 2 3 $ snp1: Factor w/ 2 levels "A","G": 1 2 2 $ snp2: Factor w/ 1 level "G": 1 1 1 $ snp3: Factor w/ 2 levels "A","G": 2 2 1 > # test fo

Re: [R] Getting started,

2009-03-26 Thread jim holtman
In answer to your first question, your statement should be: date_vec = as.Date(data_download[1:50,1],"%m/%d/%Y") Notice the capital "Y"; lower case says the year is only 2 digits, so you were pickup up the '19' from the date. Use 'plot(..., type='l')' for a line plot. Your data is being read in

[R] Centring variables in Cox Proportional Hazards Model

2009-03-26 Thread Laura Bonnett
Dear All, I am contemplating centering the covariates in my Cox model to reduce multicollinearity between the predictors and the interaction term and to render a more meaningful interpretation of the regression coefficient. Suppose I have two indicator variables, x1 and x2 which represent age cat

[R] Using JRclient in java application

2009-03-26 Thread Tomasz Spulak
Hi, I'm wondering if anyone can help me. I'm writing java application that using JRclient and Rserve to communicate with R. I want to get response from R for command: x <- rbind(matrix(rnorm(100, sd = 0.3), ncol = 2),matrix(rnorm(100, mean = 1, sd = 0.3), ncol = 2)) kmeans(x, 2, 22, algorithm = "

[R] same value in column-->delete

2009-03-26 Thread Duijvesteijn, Naomi
Hi Readers, I have a question. I have a large dataset and want to throw away columns that have the same value in the column itself and I want to know which column this was. For example > x<-data.frame(id=c(1,2,3), snp1=c("A","G", "G"),snp2=c("G","G","G"),snp3=c("G","G",

Re: [R] Manual sort in a for loop

2009-03-26 Thread Steve Murray
Thanks all - I'm fairly new to R, so I was oblivious to the pros and cons of using a data frame as opposed to a list! The 'get' command also seemed to work successfully. Thanks again, Steve _ 25GB of FREE Online Storage – Find

[R] Warning messages from quantreg

2009-03-26 Thread Daren Tan
Hi, I keep getting warning messages from quantreg about "tiny diagonals replaced with Inf when calling blkfct". Is there any cause for concern like improper codes, NAs in datasets or missing values ? Thanks Stanley __ R-help@r-project.org mailing list h

Re: [R] R: Fortran-90 and R

2009-03-26 Thread Gavin Simpson
On Thu, 2009-03-26 at 11:01 +0100, mau...@alice.it wrote: > I do hope the chapte about "Interfacing R and Fortran" is sufficient. > I have a heavy load of work from two projects and no previous experience in > either cases (analysis packages, > algorithms, and so on ...). I am a postdoc. Ranjan

[R] Getting started,

2009-03-26 Thread gug
Hello, First of all, I'm new to R and I don't have anyone who already knows the language to ask for tips, so please excuse my ignorance. I'm trying to download data direct from the Federal Reserve statistics website and graph it, using the following: #This downloads the data from the Fe

Re: [R] Density estimation: scale back for calendar time

2009-03-26 Thread Pradeep Raje
Thanks David for your response.I had done that. Problem is not with the computations, but in the interpretation. Assume that x ordinates are 'time' [1:3472], and y are associated parameter values. Now density gives me 512/1024/2048 x-ordinates, of which some (7 to be precise) are negative. What do

[R] Sort by timestamp

2009-03-26 Thread j.k
#Good morning alltogheter. I'm using R for a short time to analyse TimeSeries and I have the following Problem: #I have a bunch of Time Series: #First of all I import them from a txt File data.input01 <-read.csv("./LD/20081030.txt", header = TRUE, sep = ";", quote="\"", dec=",", fill = TRUE, comm

Re: [R] loop problem

2009-03-26 Thread Jim Lemon
Muhammad Azam wrote: Dear R members I have a problem regarding storing the lists. Let L=number of distinct values of any predictor (say L=5) P=number of predictors (say P=20) g1 <- c() for(i in 1:P){ if(L > 1){ for(j in 1:(L-1)){ g <- g1[j] <- g } } g2

Re: [R] Manual sort in a for loop

2009-03-26 Thread Simon Pickett
I would suggest avoiding the function ?assign inside a loop. I used top use this until someone here kindly pointed out that it was much easier to catch the data of interest in a list... eg. df.list <- vector("list", length(10)) for (i in 1:10)} df.list[[i]]<-data.frame(arunoff_,table_year,_tem

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