Re: [R] x86 SSE* Pointer Favors

Hi Ivo, On Friday 13 June 2008 12:23:06 am ivo welch wrote: > Dear Statisticians--- This is not even an R question, so please > forgive me. I have so much ignorance in this matter that I do not > know where to begin. I hope someone can point me to documentation > and/or a sample. You will sure

Re: [R] Getting Batch mode to continue running a script after running into errors

?stop explains why this happens and how to change it. You can also set options(error=expression(NULL)) to ignore all errors, and use tryCatch() (or its wrapper try()) skip particular expressions if tjhey fail. But surely in your example your script should check for existence of the file by fi

Re: [R] Regex for Special Characters under Grep

On Thu, 12 Jun 2008, Henrik Bengtsson wrote: A regular set is given by "[]". The complementary set is given by "[^]" where is a set of symbols. I don't think you have to escape symbols in (but I might be wrong). This covered in ?regexp. The metacharacters in character classes (the offici

Re: [R] Rprintf and "C stack usage is too close to the limit"

Rprintf is the right function, but this is the wrong list (please see the posting guide). The issue is related to your 'C++ program', not to R itself and we have no details. Non-R programming questions should go to R-devel, as the posting guide says. On Thu, 12 Jun 2008, Youyi Fong wrote:

Re: [R] Regex for Special Characters under Grep

A regular set is given by "[]". The complementary set is given by "[^]" where is a set of symbols. I don't think you have to escape symbols in (but I might be wrong). In any case, this does what you want: > lines <- c("abc", "!abc", "#abc", "^abc", " #abc") > pattern <- "^[^!#^]"; > grep(patt

Re: [R] MCA in R

Dear John, thanks for Your quick reply. John Fox wrote: Dear Kimmo, MCA is a rather old name (introduced, I think, in the 1960s by Songuist and Morgan in the OSIRIS package) for a linear model consisting entirely of factors and with only additive effects -- i.e., an ANOVA model will no interac

[R] x86 SSE* Pointer Favors

Dear Statisticians--- This is not even an R question, so please forgive me. I have so much ignorance in this matter that I do not know where to begin. I hope someone can point me to documentation and/or a sample. I want to compute a covariance as quickly as non-humanly possible on an Intel core

Re: [R] Regex for Special Characters under Grep

on 06/12/2008 08:42 PM Gundala Viswanath wrote: Hi all, I am trying to capture lines of a file that DO NOT start with the following header: !, #, ^ But somehow my regex used under grep doesn't work. Please advice what's wrong with my code below. __BEGIN__ in_fname <- paste("mydata.txt,".soft"

[R] Regex for Special Characters under Grep

Hi all, I am trying to capture lines of a file that DO NOT start with the following header: !, #, ^ But somehow my regex used under grep doesn't work. Please advice what's wrong with my code below. __BEGIN__ in_fname <- paste("mydata.txt,".soft",sep="") data_for_R <- paste("data_for_R/", args[3

Re: [R] alternative to matching/merge?

It would be nice if you at least included the code that you are using and a subset of the data. Have you run Rprof to determine which of the functions is consuming the time? On Thu, Jun 12, 2008 at 3:25 PM, Lana Schaffer <[EMAIL PROTECTED]> wrote: > > Greetings, > I am doing matching/merge for a

Re: [R] piper diagram

Sorry no previous message text or addresses, but I just cleaned my mailbox and then found something relevant. Regarding the Piper diagram. I just noticed the 'hydrogeo' package on CRAN, courtesy of one Myles English. That should be what you need or close to it. Best regards, Michael Grant

Re: [R] Limiting size of pairs plots

Hi Sébastien wrote: > Dear R-users, > > This is a follow-up on a quite old post of mine which dealt with margins > in the pairs function. I thought my problem was solved, but it doesn't > seem so (see the code below). > > I use the pairs function to produce matrix plots, where distinct groups

Re: [R] Problem with rowMeans()

ss wrote: Thanks, Erik. I will try your code soon. I did this first: > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > class(data[[3]]) [1] "factor" > is.numeric(data[[3]]) [1] FALSE > So it is not numeric but

Re: [R] Problem with rowMeans()

Dear Erik and Wacek, I would request that you stop working on my problem. I had the second column deleted and the problem is gone. I don't know why but apparently the second column somehow interfered with the third column such that the third column is regarded as 'factor' not 'numeric'. I can rec

Re: [R] Problem with rowMeans()

Thanks, Erik. I will try your code soon. I did this first: > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > class(data[[3]]) [1] "factor" > is.numeric(data[[3]]) [1] FALSE > So it is not numeric but 'factor' instead. Can

Re: [R] Getting Batch mode to continue running a script after running into errors

There is a "try" function that you can wrap around functions. Hope this helps! Sincerely, Erin On 6/12/08, Josh <[EMAIL PROTECTED]> wrote: > I'm invoking R in batch mode from a bash script as follows: > > R --no-restore --no-save --vanilla > <$TARGET/$directory/o2sat-$VERSION.R> > $TARGET/$dire

Re: [R] Problem with rowMeans()

ss wrote: It is: > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > class(data[3]) [1] "data.frame" > Oops, should have said class(data[[3]]) and is.numeric(data[[3]]) See ?Extract And if I try to use as.ma

Re: [R] Problem with rowMeans()

It is: > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > class(data[3]) [1] "data.frame" > And if I try to use as.matrix(read.table()), I got: >data <-as.matrix(read.table('E-TABM-1-processed-data-1342561271_log2_with_sy

Re: [R] Problem with rowMeans()

ss wrote: Hi Wacek, Yes, data is data frame not a matrix. is.numeric(data[3]) [1] FALSE what is class(data[3]) But I looked at the column 3 and it looks okay though. There are few NAs and I did find anything strange. Any suggestions? Thanks, Allen On Thu, Jun 12, 2008 at 7:0

Re: [R] Generate Random Samples

To answer your specific question, you can use mvrnorm (from MASS, i.e. library(MASS)) to generate each component. To generate a mixture with three components (Prob(1 st component) = p1, Prob(2nd component) = p2, Prob(3rd component) = p3, p1+p2+p3=1), you can generate a uniformly distributed varia

Re: [R] Problem with rowMeans()

Hi Wacek, Yes, data is data frame not a matrix. > is.numeric(data[3]) [1] FALSE But I looked at the column 3 and it looks okay though. There are few NAs and I did find anything strange. Any suggestions? Thanks, Allen On Thu, Jun 12, 2008 at 7:01 PM, Wacek Kusnierczyk < [EMAIL PROTECTE

Re: [R] Problem with rowMeans()

ss wrote: > Thank you very much, Wacek! It works very well. > But there is a minor problem. I did the following: > > >data <- > read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', > +row.names = NULL ,header=TRUE, fill=TRUE) looks like you have a data frame, not a matrix > > d

Re: [R] numbers as part of long character

On Jun 12, 2008, at 6:34 PM, Hua Li wrote: Thanks, Marc and Haris! I didn't know the values of the numbers beforehand, so the scan method won't work, but "[^+-\\d.]+" will do! And Haris, I didn't intend to keep the information of which number is B, which is C etc when asking the question,

[R] Getting Batch mode to continue running a script after running into errors

I'm invoking R in batch mode from a bash script as follows: R --no-restore --no-save --vanilla <$TARGET/$directory/o2sat-$VERSION.R> $TARGET/$directory/o2sat-$VERSION.Routput When R comes across some error in the script however it seems to halt instead of running subsequent lines in the script:

Re: [R] numbers as part of long character

Oh, Sorry, Marc. The scan method does work! Hua --- On Thu, 6/12/08, Charilaos Skiadas <[EMAIL PROTECTED]> wrote: > From: Charilaos Skiadas <[EMAIL PROTECTED]> > Subject: Re: [R] numbers as part of long character > To: [EMAIL PROTECTED] > Cc: [EMAIL PROTECTED], r-help@r-project.org > Date: Thu

Re: [R] numbers as part of long character

Thanks, Marc and Haris! I didn't know the values of the numbers beforehand, so the scan method won't work, but "[^+-\\d.]+" will do! And Haris, I didn't intend to keep the information of which number is B, which is C etc when asking the question, as I had a tedious way to do it (use strspilt

[R] rJava classpath issues

I'm having some issues with getting my own jars to work properly with rJava. Bear with me as I explain my scenario: I have a java package called rjbridge, with the following classes: RJBridge.class ObjectInfo.class Each of the classes has the following line on top: package com.rjbridge

Re: [R] numbers as part of long character

On Jun 12, 2008, at 5:06 PM, Marc Schwartz wrote: on 06/12/2008 03:46 PM Hua Li wrote: Hi, I'm looking for some way to pick up the numbers which are contained and buried in a long character. For example, outtree.new="(((B:1204.25,E:1204.25):7581.11,F:8785.36):8353.85,C: 17139.21);" num.char

[R] Problems with mars in R in the case of nonlinear functions

Hi, I'm trying to use mars function in R to interpolate nonlinear multivariate functions. However, it seems that mars gives me a fit which uses only very few basis function and it underfits very badly. For example, I have tried the following code to test mars: require("mda") f <- function(x

Re: [R] Problem with rowMeans()

ss wrote: Dear Erik, Thanks! The 'data' is matrix but all(apply(data[,3:85], 2, class) == "numeric") is false. > class(data) [1] "matrix" > a<- rowMeans(data[,3:85],na.rm = TRUE) Error in rowMeans(data[, 3:85], na.rm = TRUE) : 'x' must be numeric > all(apply(data[,3:85], 2, class) == "nu

Re: [R] numbers as part of long character

on 06/12/2008 03:46 PM Hua Li wrote: Hi, I'm looking for some way to pick up the numbers which are contained and buried in a long character. For example, outtree.new="(((B:1204.25,E:1204.25):7581.11,F:8785.36):8353.85,C:17139.21);" num.char = unlist(strsplit(unlist(strsplit(unlist(strsplit

Re: [R] Problem with rowMeans()

ss wrote: > Hi all, > > I have a matrix called 'data', which looks like: > > >> data[1:4,1:4] >> > Probe_ID Gene_Symbol M1601 M1602 > 1 A_23_P10586213CDNA73-1.60.16 > 2 A_23_P76435 15E1.20.180.59 > 3 A_24_P402

Re: [R] Problem with rowMeans()

Dear Erik, Thanks! The 'data' is matrix but all(apply(data[,3:85], 2, class) == "numeric") is false. > class(data) [1] "matrix" > a<- rowMeans(data[,3:85],na.rm = TRUE) Error in rowMeans(data[, 3:85], na.rm = TRUE) : 'x' must be numeric > all(apply(data[,3:85], 2, class) == "numeric") [1] FALSE >

Re: [R] Problem with rowMeans()

Hello - ss wrote: Hi all, I have a matrix called 'data', which looks like: data[1:4,1:4] Probe_ID Gene_Symbol M1601 M1602 1 A_23_P10586213CDNA73-1.60.16 2 A_23_P76435 15E1.20.180.59 3 A_24_P402115 15E1.2

[R] numbers as part of long character

Hi, I'm looking for some way to pick up the numbers which are contained and buried in a long character. For example, outtree.new="(((B:1204.25,E:1204.25):7581.11,F:8785.36):8353.85,C:17139.21);" num.char = unlist(strsplit(unlist(strsplit(unlist(strsplit(unlist(strsplit(unlist(strsplit(outtre

[R] Problem with rowMeans()

Hi all, I have a matrix called 'data', which looks like: > data[1:4,1:4] Probe_ID Gene_Symbol M1601 M1602 1 A_23_P10586213CDNA73-1.60.16 2 A_23_P76435 15E1.20.180.59 3 A_24_P402115 15E1.21.63

[R] Rprintf and "C stack usage is too close to the limit"

Hi, I would appreciate if someone could comment on this problem I am experiencing. I am writing a C++ program to be called from R. In this program, there is a verbose switch that decides whether to print some debugging info using Rprintf. On windows, things work ok. On linux, things are fine in no

Re: [R] overall title

Check out this previous post from years ago. http://tolstoy.newcastle.edu.au/R/help/00a/2237.html Bill> Date: Thu, 12 Jun 2008 10:38:03 -0500> From: [EMAIL PROTECTED]> To: r-help@r-project.org> Subject: [R] overall title> > I have a 2x2 plot set up using: par(mfrow=c(2,2))> I'd like to put a

Re: [R] Subset in cast: compact form?

On Thu, Jun 12, 2008 at 2:27 PM, Agustin Lobo <[EMAIL PROTECTED]> wrote: > Hi! > > How can I subset several variables in cast? > > For example, I can do it for one, (ie, ph): > cast(am, organismo +arriba ~ variable,subset=variable=="ph",mean,na.rm=T) > > For selecting ph, temperature and Ba I'm usi

[R] using MCLUST package to estimate a poisson-gaussian process

Hi All, I am using em() function to estimate a poisson-gaussian process from a univariate one dimension time series, but not sure how to do. In the help manual, it specify that in "pro" of the argument "parameter", if the model includes a Poisson term for noise, there should be one more mixing pro

[R] Subset in cast: compact form?

Hi! How can I subset several variables in cast? For example, I can do it for one, (ie, ph): cast(am, organismo +arriba ~ variable,subset=variable=="ph",mean,na.rm=T) For selecting ph, temperature and Ba I'm using: cast(am, organismo +arriba ~ variable,subset=variable=="ph" variable=="temperatu

[R] alternative to matching/merge?

Greetings, I am doing matching/merge for a table (40919x3) to data which is in the form of a list of 1268 data.frames. Using lapply this is taking ~5 minutes. I know that the match/merge functions are time consuming, so is there an alternative to this accomplish this goal? is lapply not efficie

Re: [R] save workspace while running R on a cluster

Hi Manisha, How about you incluse something like this on your script.R: setwd("/your/full/working/directory") # ?setwd save.image()# or save.image("your_workspace.RDA"). By the way, I don´t know if you added the line below to run in background: R --save < calculate.R >& script.out May be

[R] save workspace while running R on a cluster

Hello, I have a question about running R in a cluster environment. The shell script I am running looks like this: #!/bin/bash cd /nfs/apollo/2/c2b2/users/mb0001/Data /nfs/apollo/1/shares/software/core_facility/local/x86_64_rocks/R/current/bin/ R --save < calculate.R >& script.out I ha

Re: [R] How to increase the for() loop speed?

The first thing to do is to run Rprof and determine where time is being spent. It may be that it is one of the functions that you are calling inside the loop that is taking the majority of time and if that is the case, there may not be any improvement other than coming up with a different algorith

Re: [R] adding horizontal lines to a trellis plot

Please read about panel functions in ?xyplot and ?panel.abline In particular, you do this sort of thing in panel functions where you must use grid graphics functions or various lattice forms (wrappers) thereof. The standard graphics constructions will not work (as you found out).Suggested refere

[R] adding horizontal lines to a trellis plot

I would like to add two horizontal lines representing acceptible drug levels to a trellis plot. I tried using abline and I get an error that "plot.new has not been called." See below. xyplot(FK~WEEK|Event1/MRN, data=FKdat.o1) abline(h=5) abline(h=10) Error in int_abline(a = a, b = b, h = h,

Re: [R] problem with function "rep"

I believe this might do what you want a bit faster. I replaced the while loop with something that is likely to be faster. I saw no reason for the rounding you were doing, better to use as.integer at the end. test <- function(t){ x <- rexp(t,0.1) while(sum(x) <= t) { x <- c(x, rexp(

Re: [R] How to increase the for() loop speed?

We would certainly need more information about your function to offer any specific advice, therefore I'll fall back on the general. First there is no command that will increase a for loop speed, it is not as if they are artificially slowed down. In general, you may be able to do whatever it i

Re: [R] overall title

?title, see 'outer' (and you will need to make room for an outer margin). This is described in 'An Introduction to R' (and in all good books on R). On Thu, 12 Jun 2008, [EMAIL PROTECTED] wrote: I have a 2x2 plot set up using: par(mfrow=c(2,2)) I'd like to put an overall title on the page, but

Re: [R] How to increase the for() loop speed?

My routine is on Financial Econometrics (Yield Curve Modeling). It is very intensive. And I have heard that the for() loop speed could be increased with a command. I want to know if there a way to do it. Best regards. Rafael Barros de Rezende -- Original Message

Re: [R] About Mcneil Hanley test for a portion of AUC!

Dukka k.c. wrote: Dear all I am trying to compare the performances of several methods using the AUC0.1 and not the whole AUC. (meaning I wanted to compare to AUC's whose x axis only goes to 0.1 not 1) I came to know about the Mcneil Hanley test from Bernardo Rangel Tura and I referred to the o

Re: [R] overall title

Please try this: > z1 <- rexp(100) > z2 <- rexp(100) > z3 <- rexp(100) > z4 <- rexp(100) > par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) > curve(dexp,from=0,to=5) > hist(z1,main="first") > hist(z2,main="second") > hist(z3,main="third") > mtext("Densities", outer = TRUE, cex = 1.5) > Hope this helps. Sin

Re: [R] overall title

See mtext: mtext("Title", outer = T, side = 3, line = -2) On Thu, Jun 12, 2008 at 12:38 PM, <[EMAIL PROTECTED]> wrote: > I have a 2x2 plot set up using: par(mfrow=c(2,2)) > I'd like to put an overall title on the page, but I cannot figure out how. > Any ideas? > > >[[alternative HTML

Re: [R] How to increase the for() loop speed?

13 minutes is a long time for a loop to simply send an email, what other calculations are going on? Rafael Barros de Rezende wrote: Dear R users, I would like to know if there is a way to increase the for() loop speed because in my routine the calculations are too slow. Best regar

Re: [R] XML parameters to Column Headers for importing into a dataset

Hi Ajay -- "ajay ohri" <[EMAIL PROTECTED]> writes: > Dear List, > > Do you know any way I can convert XML parameters into column headers. My In R, the XML package will help you... > data is in a csv file with each row containing a xml form of data , and > multiple parameters ( > > data_val1 ,

Re: [R] shell command

samitj wrote: Hi, Can we execute a unix shell command from within R shell? thanks, Sam ?system hth, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax:+31302

Re: [R] shell command

Yes, see ?system samitj wrote: Hi, Can we execute a unix shell command from within R shell? thanks, Sam __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/post

[R] overall title

I have a 2x2 plot set up using: par(mfrow=c(2,2)) I'd like to put an overall title on the page, but I cannot figure out how. Any ideas? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/li

Re: [R] problem with function "rep"

Hi I believe this should provide an example of the confusing behavior. Run this with t=100 for example: test=function(t){ x=c() while(sum(x)<=t){ ###I simply generate some numbers from an exponential until the sum of these numbers gets to 100(without loss of generality) x=c(x,round(rexp(1,0.1)

[R] shell command

Hi, Can we execute a unix shell command from within R shell? thanks, Sam -- View this message in context: http://www.nabble.com/shell-command-tp17803089p17803089.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org ma

[R] How to increase the for() loop speed?

Dear R users, I would like to know if there is a way to increase the for() loop speed because in my routine the calculations are too slow. Best regards. Rafael Barros de Rezende Cedeplar - Center for Development and Regional Planning Face, UFMG ([1]http://www.cedeplar.ufmg.

[R] Problem with Freq function {prettyR}

Dear list, I have a problem with freq from prettyR. Please have a look at my syntax with a litte example: library(prettyR) #Version 1 test.df<-data.frame(q1=sample(1:4,8,TRUE), gender=sample(c("f","m"),8,TRUE)) test.df freq(test.df) #No error message #Version 2 test.df<-data.frame(gender=sampl

Re: [R] problem with function "rep"

Berwin appears to be correct here. After you do x <- x / 0.0001, I inserted a call to round(x) - x, and received round(x) - x [1] 7.275958e-12 0.00e+00 0.00e+00 This is basically a case of FAQ 7.31. Julien Hunt wrote: Hi I believe this should provide an example of the confusing behav

[R] How to increase the for() loop speed?

Dear R users, I would like to know if there is a way to increase the for() loop speed because in my routine the calculations are too slow. Best regards. Rafael Barros de Rezende Cedeplar - Center for Development and Regional Planning Face, UFMG ([1]http://www.cedeplar.ufmg.

Re: [R] case-cohort

Jin Wang had an error. My original note specified a variable that was 1 for subjects NOT in the subcohort, so the correct coxph call is coxph(Surv(edrel, rel) ~ stage + histol + age + offset(-100*(subcohort==0)) + cluster(seqno), data =ccoh.data) This gives the same coeffici

[R] Generate Random Samples

Hi, I am a newbie to R and I am working with a Mac. Is there any package that I can use to generate random samples from a user defined distribution ? That is , I define a distribution function ( maybe multi dimension ) and I want some random samples generated from my this distribution.

Re: [R] cch function and time dependent covariates

same subject id has to be multiple in mutiple times like following format, Multiple records per id not allowed in cch() so it's difficult to use cch() for time dependent covariate. Maybe coxph() is alternative, but seems difficult because coxph() and cch() return different estimate for same data "n

Re: [R] problem with function "rep"

on 06/12/2008 09:48 AM Julien Hunt wrote: To whom it may concern, I am currently writing a program where I need to use function rep. The results I get are quite confusing. Given two vectors A and B, I want to replicate a[1] b[1] times, a[2] b[2] times and so on. All the entries of vector B ar

Re: [R] problem with function "rep"

G'day Julien, On Thu, 12 Jun 2008 16:48:43 +0200 Julien Hunt <[EMAIL PROTECTED]> wrote: > I am currently writing a program where I need to use function rep. > The results I get are quite confusing. Given two > vectors A and B, I want to replicate a[1] b[1] > times, a[2] b[2] times and so on. >

Re: [R] controlling location of labels in axis()

Thanks for the reply. I think I've figured it out, you can set this with the mgp parameter. So I'd use the following statement instead: axis(1, at=foo$plot.x, labels=foo$plot.x, mgp=c(3,0.5,1)) #this brings the axis labels closer to the axis line Andrew On Thu, Jun 12, 2008 at 9:53 AM, Toby Ma

Re: [R] problem with function "rep"

We need a reproducible example of this to tell you what is going on. Find a small example that exhibits the confusing behavior, and share it with the list. Julien Hunt wrote: To whom it may concern, I am currently writing a program where I need to use function rep. The results I get are quite

Re: [R] problem with function "rep"

On Jun 12, 2008, at 10:48 AM, Julien Hunt wrote: Do you need more information on my specific program. Thanks for your time and help, Yes, as the posting guide says, we would probably need a reproducible self-contained example. Emphasis on "reproducible" and "self-contained. Best regards,

[R] problem with function "rep"

To whom it may concern, I am currently writing a program where I need to use function rep. The results I get are quite confusing. Given two vectors A and B, I want to replicate a[1] b[1] times, a[2] b[2] times and so on. All the entries of vector B are positive integers. My problem comes from th

Re: [R] model simplification using Crawley as a guide

on 06/12/2008 09:37 AM Peter Dalgaard wrote: Simon Blomberg wrote: Good points Ben. For now I'd recommend simply that the allergic reaction to insignificant statistical tests be treated with an antihistamine :-) A vote for Frank's comment to be added to the 'fortunes' package. S

Re: [R] model simplification using Crawley as a guide

Simon Blomberg wrote: >>> Good points Ben. For now I'd recommend simply that the allergic >>> reaction to insignificant statistical tests be treated with an >>> antihistamine :-) >>> >> A vote for Frank's comment to be added to the 'fortunes' package. >> >> > Seconded! :-) > > Tha

Re: [R] cch function and time dependent covariates

I tried your alternative method on the example in cch() description manual. The example data "nwtco" has not time-dependent covariates yet. I test cch() and coxph() on the same data. But the estimation result is different. I don't know if I did anything wrong. subcoh <- nwtco$in.subcohort selccoh

[R] R/S course in *** New York City *** July 28-29 by XLSolutions Corp

Our July *** New York City *** R/S Fundamentals and Programming Techniques is scheduled for: New York City / July 28-29, 2008 *** Please direct enquiries to Sue Turner: [EMAIL PROTECTED] Ask for Group Discount --- Looking for R Advanced course? It's comming up in Seattle on

Re: [R] p-value

Not sure if this is what you are looking for but you can get the p-value with something like this: # Create a vector mydata<- c(132968364, 135945080, 156539568, 157817896, 162399496, 168344072, 173146584, 176302744, 182878168, 183946152, 18506

[R] About Mcneil Hanley test for a portion of AUC!

Dear all I am trying to compare the performances of several methods using the AUC0.1 and not the whole AUC. (meaning I wanted to compare to AUC's whose x axis only goes to 0.1 not 1) I came to know about the Mcneil Hanley test from Bernardo Rangel Tura and I referred to the original paper for th

Re: [R] p-value

Something like. . . > midpoint <- c(132968364, 135945080, 156539568, 157817896, + 162399496, 168344072, 173146584, 176302744, + 182878168, 183946152, 185068720, 190791232, + 84317660, 93708872, 106810172, 12684, + 148519056, 150945112, 155771432, 181069984, + 87104384 + ) > shapiro.test(

Re: [R] p-value

Here's a sample: > unif_rand_1 <- runif(1000); > unif_rand_2 <- runif(1000); > ks.test(unif_rand_1,unif_rand_2); Two-sample Kolmogorov-Smirnov test data: unif_rand_1 and unif_rand_2 D = 0.021, p-value = 0.9802 alternative hypothesis: two-sided So in your case: > ks.test( runif( length( you

[R] p-value

Dear R User, say I have this sample of data ( attach with). What i'm going to do is to test whether this data is uniformly distributed or not by finding the p-value. I've tried using the punif command but it gave me the value of 1 of all the data. Any suggestion on R command to find the p-

Re: [R] controlling location of labels in axis()

Hi Andrew, Perhaps this example would help. You can add in spaces to the mtext text to move the text sideways. par(mai=c(0.5,0.5,0.5,0.5),oma=c(2,2,2,2)) #mai units are INCHES, oma units are LINES plot(runif(50),xlab="xlab",ylab="ylab",bty="l") #n.b. these labels don't appear mtext("First in

Re: [R] How to change the class of data?

Try this workaround: library(methods) setClass("of") setAs("character", "of", function(from) as.ordered(from)) Input <- "A B b 1 c 2 a 3 " DF <- read.table(textConnection(Input), header = TRUE, colClasses = c("of", "numeric")) str(DF) On Thu, Jun 12, 2008 at 4:57 AM, Birgitle <[EMAIL PROTECTE

[R] controlling location of labels in axis()

Here's a naive question about axis() How do you control the location of the labels with the axis() command? In the following example: foo <- data.frame(plot.x=seq(1:3), plot.y=seq(4:6)) plot(foo$plot.x, foo$plot.y, type='n', axes=FALSE) points(foo$plot.x, foo$plot.y) axis(1, at=foo$plot.x, label

Re: [R] cch function and time dependent covariates

- begin included message In case cohort study, we can fit proportional hazard regression model to case-cohort data. In R, the function is cch() in Survival package Now I am working on case cohort analysis with time dependent covariates using cch() of "Survival" R package. I wonder if cch() pro

Re: [R] applying a function recursively

Wrap each element in an environment, flatten that and then extact the element in each environment. (Be sure not to use an old version of R since sufficiently far back R had a bug when environments were stored in lists that was since fixed.) L <- rapply(test.list, function(el) environment(), how =

Re: [R] Predicting from an nls model

Thanks. As a (relatively) new user of R and programming in general, I tend to miss things like that. I appreciate your patience. SR Steven H. Ranney Graduate Research Assistant (Ph.D) USGS Montana Cooperative Fishery Research Unit Montana State University PO Box 173460 Bozeman, MT 59717-3460

Re: [R] Predicting from an nls model

To predict from Weight~alpha*Length^beta you need to specify Length, not Weight. It is most likely finding Length from your workspace. On Thu, 12 Jun 2008, Ranney, Steven wrote: I keep running up against the same error when I try to plot a line from a nls model. The data is fisheries length

Re: [R] Predicting from an nls model

Ranney, Steven montana.edu> writes: > plot(Weight~Length, data = wae, pch=19, > xlab="Length (mm)", ylab="Weight (g)", > xlim = c(150,1000), ylim = c(0, 10050)) > mod = seq(150, 1000)

Re: [R] as.numeric(".") returns 0

On Thu, 12 Jun 2008, Peter Dalgaard wrote: Paul Johnson wrote: In R version 2.7.0 (2008-04-22) as.numeric(".") returns zero. as.numeric(".") [1] 0 This must be a bug. Splus and previous versions of R (<= 2.6.0) return NA, as you might expect. Depends who is doing the expecting. Americans

[R] Predicting from an nls model

I keep running up against the same error when I try to plot a line from a nls model. The data is fisheries length/weight data. Code follows: require(graphics) pow = nls(Weight~alpha*Length^beta, data=wae, start=list(alpha=0.001, beta=3.0), trace=TRUE) pre

Re: [R] Close Window Button Problems

You have failed to provide the most basic of information as requested in the posting guide. As you mention 'i create a x11 window and plot' I will assume you mean that you open an X11() device and hence this is some Unix-alike OS. This has come up several times before, so please search the ar

Re: [R] as.numeric(".") returns 0

Paul Johnson wrote: > In R version 2.7.0 (2008-04-22) as.numeric(".") returns zero. > > >> as.numeric(".") >> > [1] 0 > > This must be a bug. Splus and previous versions of R (<= 2.6.0) return NA, > as you might expect. > > I'm running R version 2.7.0 (2008-04-22) on Windows XP. > > I su

[R] read and write stdout() to tktext window

I've been trying to write the consoles output to a tktext window, but have not succeeded... Does anybody know if that works? Any help would be highly appreciated. Thanks in advance, Andreas Posch __ R-help@r-project.org mailing list https://stat.ethz.

Re: [R] as.numeric(".") returns 0

Paul Johnson: > In R version 2.7.0 (2008-04-22) as.numeric(".") returns zero. > >> as.numeric(".") > [1] 0 Seems to be fixed already. In R version 2.7.0 Patched (2008-06-12 r45898): $ as.numeric(".") [1] NA Warning message: NAs introduced by coercion -- Karl Ove Hufthammer __

Re: [R] applying a function recursively

Prof Brian Ripley wrote: > > See ?rapply Golly, the things one learns when least expecting it. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guid

Re: [R] applying a function recursively

Hi, thanks a lot for your help. Somehow rapply had escaped my notice. I also have a follow-up question on that. I would like to "flatten" my output list to a list with only one level. Option "unlist" in rapply returns a character vector, in my example: > rapply(test.list, rev, how="unlist")

[R] as.numeric(".") returns 0

In R version 2.7.0 (2008-04-22) as.numeric(".") returns zero. > as.numeric(".") [1] 0 This must be a bug. Splus and previous versions of R (<= 2.6.0) return NA, as you might expect. I'm running R version 2.7.0 (2008-04-22) on Windows XP. Paul ___

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