Re: [R] The R Journal, Vol.2 Issue 1

2010-07-01 Thread Peter Dalgaard
Peter Dalgaard wrote: > The first issue of the second volume of The R Journal will shortly be > available at jour...@r-project.org/current.html. Thanks to everyone As no less than 16 people has informed me, that of course wants to be http://journal.r-project.org/current.html (That's what you get

[R] Export data frame of high dimension to txt

2010-07-01 Thread Loukia Spin.
I managed with success to export a data frame of 367 columns and 37 rows to a txt file, but unfortunately I couldn't manage the same with the transposed data frame. Specifically, it seems like the notebook cannot "read" correctly 367 columns, so it reads the first 145 columns and it folds down

[R] Stacked Restricted Boltzmann Machine

2010-07-01 Thread Matthew OKane
Hi, Are there any implementations of stacked RBMs either complete or planned in R? Thanks, Matthew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the postin

Re: [R] Assigning entries to categories

2010-07-01 Thread LogLord
As requested, here is some example data: a=c("x","y","z") b=c(1,5,8) c=c(200010,535388,19929) data=data.frame(a,b,c) d=c("cat1","cat2","cat3") b1=c(1,5,8) c_start=c(20,50,60) c_stop=c(201000,55,70) category=data.frame(d,b1,c_start,c_stop) I want to add a variable into data, w

[R] Sweave function

2010-07-01 Thread n.via...@libero.it
Dear list, I have a question about the interaction between R code and Latex language trough the Sweave function in the package "utils". What I'm trying to do is to write a report. Contrary to the examples shown in the Sweave Manual in which table already constructed by R are "exported" on Lat

Re: [R] Sweave function

2010-07-01 Thread Allan Engelhardt
In general, use cat (see help("cat")) for printing your output, e.g. <>= cat(levels(mydata$Firms)[mydata$Firms], "\n") cat(mydata$Year, "\n") # etc. @ For your specific case you may also be interested in help("xtable", package="xtable") along with the <<...,results=tex>>= Sweave construct. F

Re: [R] plain text in Chinese can not be set

2010-07-01 Thread Jinsong Zhao
On 2010-7-1 12:16, Jinsong Zhao wrote: Hi there, The following code can produce the correct type face, however, the Latin character are displayed in GB1 font. pdf("test_1.pdf", family = c("GB1")) plot(1:10) text(5,1, "\u4F60\u597D", font = 1) text(5,2, "\u4F60\u597D", font = 2) text(5,3, "\u4F6

Re: [R] Export data frame of high dimension to txt

2010-07-01 Thread Allan Engelhardt
On 01/07/10 08:50, Loukia Spin. wrote: I managed with success to export a data frame of 367 columns and 37 rows to a txt file, but unfortunately I couldn't manage the same with the transposed data frame. Specifically, it seems like the notebook cannot "read" correctly 367 columns, so it reads

Re: [R] Stacked Restricted Boltzmann Machine

2010-07-01 Thread Allan Engelhardt
I don't know of a native implementation, but you could probably use MDP along with RPy or R/S Plus as suggested here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628591/ Allan. On 01/07/10 09:01, Matthew OKane wrote: Hi, Are there any implementations of stacked RBMs either complete or plann

[R] question regarding panel data analysis

2010-07-01 Thread amatoallah ouchen
Good day R-users, I apologize for asking such an elementary question, but I could not find an adequate response . I'm currently running a panel data analysis i've used the plm package to perform the Tests of poolability as results intercepts and coefficients are assumed different. so my question

Re: [R] Why software fails in scientific research

2010-07-01 Thread Jim Lemon
On 07/01/2010 03:29 AM, Dr. David Kirkby wrote: On 03/ 1/10 12:23 AM, Sharpie wrote: John Maindonald wrote: I came across this notice of an upcoming webinar. The issues identified in the first paragraph below seem to me exactly those that the R project is designed to address. The claim that

Re: [R] Plot map Brazil and documentation

2010-07-01 Thread Jakson A. Aquino
2010/7/1 Pablo Cerdeira : > *If not, can someone help me to find some brazilian map (with states)?* You may look at: http://www.gismaps.com.br/divpol/divpol.htm and ftp://geoftp.ibge.gov.br/mapas/malhas_digitais/ __ R-help@r-project.org mailing list

[R] question regarding panel data analysis

2010-07-01 Thread amatoallah ouchen
Good day R-users, I apologize for asking such an elementary question, but I could not find an adequate response . I'm currently running a panel data analysis i've used the plm package to perform the Tests of poolability as results intercepts and coefficients are assumed different. so my question

Re: [R] What is wrong with this code?

2010-07-01 Thread Jim Lemon
On 07/01/2010 07:56 AM, Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: Okay, here is a reproducible example of a possible solution (actually it probably does not do what you want but it's a start for discussion. Note it is actual code and data which is what is needed. ===

Re: [R] Export data frame of high dimension to txt

2010-07-01 Thread Jan van der Laan
Loukia, Do you mean that the lines are wrapped when you open the file in Notepad? Notepad seems to wrap lines after 1024 characters. Try to open the file in a more decent editor, e.g. notepad++, gvim, ... and there are probably plenty more editors available. Hope this helps. Jan On Thu, Jul 1,

[R] possible to plot number line in R?

2010-07-01 Thread Kroepfl, Julia (julia.kroe...@uni-graz.at)
Hallo! Is there a possibility to plot a number line in R? I would like to display 3 different Intervals on the same number line. Ideally, it would be possible to add a name to each number (e.g. Interval 1, lower cut-off...and so on). I have not found a command for this. Thank you for your help.

Re: [R] possible to plot number line in R?

2010-07-01 Thread jim holtman
?segments Do provide an example of the data and what you what to do with it. On Thu, Jul 1, 2010 at 7:18 AM, Kroepfl, Julia (julia.kroe...@uni-graz.at) wrote: > Hallo! > > Is there a possibility to plot a number line in R? > I would like to display 3 different Intervals on the same number line.

Re: [R] question regarding panel data analysis

2010-07-01 Thread Liviu Andronic
Hello On Thu, Jul 1, 2010 at 1:12 AM, amatoallah ouchen wrote: > serious  issue for me . I'm currently running a panel data analysis > i've used the plm package to perform the Tests of poolability as > results intercepts and coefficients are assumed different. so my > The above is not very clear

[R] left end or right end

2010-07-01 Thread ravikumar sukumar
Dear all, I am a biologist. I have two sets of distance P(start1, end1) and Q(start2, end2). The distance will be like this. P Q I want to know whether P falls closely to the right end or left end of Q. P and Q are of dif

Re: [R] Factor Loadings in Vegan's PCA

2010-07-01 Thread Gavin Simpson
On Wed, 2010-06-30 at 18:02 -0300, afso...@unisinos.br wrote: > Hi all, > >I am using the vegan package to run a prcincipal components analysis > on forest structural variables (tree density, basal area, average > height, regeneration density) in R. > >However, I could not find out how t

Re: [R] possible to plot number line in R?

2010-07-01 Thread Carlos Ortega
Hello, If I understood well, you can compose that with "text" or "mtext" functions. Regards, Carlos. On Thu, Jul 1, 2010 at 1:38 PM, jim holtman wrote: > ?segments > > Do provide an example of the data and what you what to do with it. > > On Thu, Jul 1, 2010 at 7:18 AM, Kroepfl, Julia > (julia

Re: [R] possible to plot number line in R?

2010-07-01 Thread Jim Lemon
On 07/01/2010 09:18 PM, Kroepfl, Julia (julia.kroe...@uni-graz.at) wrote: Hallo! Is there a possibility to plot a number line in R? I would like to display 3 different Intervals on the same number line. Ideally, it would be possible to add a name to each number (e.g. Interval 1, lower cut-off.

Re: [R] possible to plot number line in R?

2010-07-01 Thread John Kane
Here is a simple 'brute force' way to do it (assuming I understand what you want) == text1 <- "Interval 1" text2 <- "Inteval 2" text3 <- "Interval 3" ycord <- 3.3 plot(1:21, rep(3,21), type="l", xlab="Number Line", ylab="",yaxt="n")

Re: [R] Mac OS X R.app has trouble rendering certain fonts.

2010-07-01 Thread David Winsemius
On Jun 30, 2010, at 11:10 PM, Carlo Tambuatco wrote: I noticed this running a few graphics demos the other day. In particular the plotmath and the persp graphics demos, certain fonts don't seem to render on the demos. Three points: 1) The correct venue for questions that are likely due to fe

Re: [R] left end or right end

2010-07-01 Thread Joris Meys
First of all, read the posting guide carefully : http://www.R-project.org/posting-guide.html Your question is far from clear. When you say that the lengths of P and Q are different, you mean the length of the data or the difference between start and end? That makes a world of difference. Regarding

Re: [R] left end or right end

2010-07-01 Thread Matt Shotwell
Suku, It looks like you might want to consult with a [bio]statistician, but I'm interested in what these distances represent. Can you give some additional context for your problem? How were these distances collected? Is it a collection of pairs of intervals, like this: P

Re: [R] left end or right end

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 7:53 AM, ravikumar sukumar wrote: Dear all, I am a biologist. I have two sets of distance P(start1, end1) and Q(start2, end2). The distance will be like this. P Q I want to know whether P falls clo

Re: [R] left end or right end

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 9:00 AM, David Winsemius wrote: On Jul 1, 2010, at 7:53 AM, ravikumar sukumar wrote: Dear all, I am a biologist. I have two sets of distance P(start1, end1) and Q(start2, end2). The distance will be like this. P Q --

[R] rms::ols & I(.) in formulas

2010-07-01 Thread Otto Kässi
Dear R-helpers, To start I would like to thank Prof. Harrell for package rms. It is one of the most useful packages for R that I have encountered. Turning to my problem, I encountered a surprising problem when working with rms::ols. It seems that insulating terms in a formula by using I() to insu

Re: [R] left end or right end

2010-07-01 Thread ravikumar sukumar
Sorry for posting to the R list. P Q 12, 28 10, 42 2, 5 1, 55 32, 50 22, 63 . there are 1 points of P and Q. The number of points of P and Q are equal (i,e 1). The interval P always overlaps with Q. i,e start1https://stat.ethz.ch/mailman/listinfo

Re: [R] Using coxph with Gompertz-distributed survival data.

2010-07-01 Thread Terry Therneau
Try using psurvreg(x, mean=fit2$coef, scale=fit2$scale, dist='extreme') The psurvreg and qsurvreg functions inherit the same parameterizations as survreg. I have trouble myself matching the location/scale form of survreg to default parameterizations used in the weibull, extreme, etc distributions

Re: [R] left end or right end

2010-07-01 Thread Jonathan Christensen
Hi, You need to define what you want more exactly--what are the possible conclusions (hypotheses) you want to reach? Based on what you've said, I can think of several different approaches you might want, but I'm not sure which one of them you're actually after. For example: Hypothesis A: The dist

Re: [R] left end or right end

2010-07-01 Thread ravikumar sukumar
There are three possibilities: Case1: Left end P-- Q-- Case2: Right end P-- Q-- Case3: At mid position P- A-- My q

[R] coefficients poolability (was: question regarding panel data analysis)

2010-07-01 Thread Millo Giovanni
Hello. Not an easy question at all, and it has little to do with software, alas! Veery loosely speaking: if the homogeneity hypothesis is rejected, then, depending on data availability, you may still be able to treat the data like a panel by: a) ignoring the results of the poolability test b

Re: [R] generate irregular series of dates

2010-07-01 Thread Simon Kiss
Dear Gabor, Yours worked really well. For what it's worth, here is the final product. I also added a line or two to reconvert the dates back to written form (October 15 2010). require(chron) dd <- seq(as.Date("INSERT FIRST DATE OF CLASSES IN TERM HERE"), as.Date("INSERT LAST DAY OF CLASSE

[R] Cholmod warning when fitting a poisson GLMM

2010-07-01 Thread Aïda Nitsch
Hi, I am getting a warning message when I am fitting a generalized mixed model (mod_2) and I don't understand why because when I add just an interaction factor the model works perfectly (mod_1). Does anyone know what it happpens ? Thanks, Aïda   > mod_1<-lmer(sur15~soeviv15_4plus+frviv1

Re: [R] Axes intercept

2010-07-01 Thread Gavin Simpson
On Wed, 2010-06-30 at 15:24 -0700, Bert Gunter wrote: > I nominate the below for a Fortune. Seconded! G > > -- Bert > > Bert Gunter > Genentech Nonclinical Biostatistics > > > > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behal

Re: [R] Why software fails in scientific research

2010-07-01 Thread Gavin Simpson
On Wed, 2010-06-30 at 11:17 -0700, Bert Gunter wrote: > Just one small additional note below ... > > Bert Gunter > Genentech Nonclinical Biostatistics > > > "But a lot of academics are not going to "waste" their time documenting code > > properly, so others can reap the benefits of it. They wo

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Liaw, Andy
You have not shown any code on exactly how you use na.roughfix(), so I can only guess. If you are doing something like: randomForest(y ~ ., mybigdata, na.action=na.roughfix, ...) I would not be surprised that it's taking very long on large datasets. Most likely it's caused by the formula inter

Re: [R] parameterization of glm nested design

2010-07-01 Thread Charles C. Berry
On Wed, 30 Jun 2010, Huso, Manuela wrote: Dear R community, I am new to R, a reforming SAS user :) Welcome aboard! I am running R 2.10.1 on a Windows XP machine. I would like to write linear functions of my coefficient parameter estimates from a glm, but am having a difficult time underst

[R] How best to set library search path so user libraries come first

2010-07-01 Thread Allan Engelhardt
I want my local libraries to have priority over the system installed ones, which, as far as I can make out from help(".libPaths"), means they have to come first in that list (it doesn't actually_say_ so, but that seems to be the idea). We have R_LIBS_USER which looks made for specifying where

Re: [R] Why software fails in scientific research

2010-07-01 Thread Murray M Cooper, PhD
For what its worth! A good friend who also happens to be an ecologist told me "An ecologist is a statistician who likes to be outside". Murray M Cooper, Phd Richland Statistics - Original Message - From: "Gavin Simpson" To: "Bert Gunter" Cc: Sent: Thursday, July 01, 2010 11:57 AM S

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Mike Williamson
Andy, You're right, I didn't supply any code, because my call was very simple and it was the call itself at question. However, here is the associated code I am using: naFixTime <- system.time( { if (fltrResponse) { ## TRUE: there are no NA's in the response... cleared v

Re: [R] Assigning entries to categories

2010-07-01 Thread Charles C. Berry
On Thu, 1 Jul 2010, LogLord wrote: As requested, here is some example data: a=c("x","y","z") b=c(1,5,8) c=c(200010,535388,19929) data=data.frame(a,b,c) d=c("cat1","cat2","cat3") b1=c(1,5,8) c_start=c(20,50,60) c_stop=c(201000,55,70) category=data.frame(d,b1,c_start,c_stop)

Re: [R] left end or right end

2010-07-01 Thread Steve Lianoglou
Hi, On Thu, Jul 1, 2010 at 10:24 AM, ravikumar sukumar wrote: > There are three possibilities: > > Case1: Left end > > P-- > Q-- > > Case2: Right end > > P                        -- > Q-- > > > Case3:

[R] Double Integration

2010-07-01 Thread Sarah Sanchez
Dear R helpers I am working on the Bi-variate Normal distribution probabilities. I need to double integrate the following function (actually simplified form of bivariate normal distribution) f(x, y) = exp [ - 0.549451 * (x^2 + y^2 - 0.6 * x * y) ] where 2.696 < x < 3.54 and -1.51 < y < 1.98 I

[R] identifying odd or even number

2010-07-01 Thread Yemi Oyeyemi
Hi, I run into problem when writing a syntax, I don't know syntax that will return true or false if an integer is odd or even. Thanks OYEYEMI, Gafar Matanmi Department of Statistics University of Ilorin P.M.B 1515 Ilorin, Kwara State Nigeria Tel: +2348052278655 Tel: +2348068241885

[R] s.e. of arima

2010-07-01 Thread speretti
Hi, I'm using the function arima() from the ts package. when the function gives me the output I can see the s.e. of the coefficients. However I cannot find a way to collect them in a object estimate<-arima(x, order=c(1,0,1)) estimate$se does not work in fact str(estimate) does not contain $se.

[R] Calculate area under a curve

2010-07-01 Thread suse
Hi, I want to know the area under a curve, which is not given as a function, but as values in a time series. It is not a smooth curve, but switches often between positive values and zero (the values describe the moisture in the soil over a year, one entry is one day). I already tried area.betwee

Re: [R] left end or right end

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 10:24 AM, ravikumar sukumar wrote: There are three possibilities: Case1: Left end P-- Q-- Case2: Right end P-- Q-- Case3: At mid position P--

[R] ROC curve in R

2010-07-01 Thread ashu6886
Hi, i have a fairly large amount of genomic data. I have created a dataframe which has "Reference" as one column and "Variation" as another. I want to plot a ROC curve based on these 2 columns. I have serached the R manual but I could not understand. Can anybody help me with the R code for plotti

Re: [R] identifying odd or even number

2010-07-01 Thread Charles C. Berry
On Thu, 1 Jul 2010, Yemi Oyeyemi wrote: Hi, I run into problem when writing a syntax, I don't know syntax that will return true or false if an integer is odd or even. Thanks See ?"%%" example("%%") ?"==" HTH, Chuck OYEYEMI, Gafar Matanmi [snip] Charles C. Berry

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Liaw, Andy
You need to isolate the problem further, or give more detail about your data. This is what I get: R> nr <- 2134 R> nc <- 14037 R> x <- matrix(runif(nr*nc), nr, nc) R> n.na <- round(nr*nc/10) R> x[sample(nr*nc, n.na)] <- NA R> system.time(x.fixed <- na.roughfix(x)) user system elapsed 8.4

Re: [R] ROC curve in R

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 12:50 PM, ashu6886 wrote: Hi, i have a fairly large amount of genomic data. I have created a dataframe which has "Reference" as one column and "Variation" as another. I want to plot a ROC curve based on these 2 columns. I have serached the R manual but I could not und

Re: [R] ROC curve in R

2010-07-01 Thread Bert Gunter
Did you try googling on "R ROC function" (or something similar) or using the RSiteSearch() function? ?RSiteSearch RSiteSearch("ROC",restr="func") Learn to use R's various search capabilities before posting, please! Bert Gunter Genentech Nonclinical Biostatistics -Original Message-

Re: [R] Double Integration

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 8:30 AM, Sarah Sanchez wrote: Dear R helpers I am working on the Bi-variate Normal distribution probabilities. I need to double integrate the following function (actually simplified form of bivariate normal distribution) f(x, y) = exp [ - 0.549451 * (x^2 + y^2 - 0.6 *

Re: [R] identifying odd or even number

2010-07-01 Thread Marc Schwartz
On Jul 1, 2010, at 10:40 AM, Yemi Oyeyemi wrote: > Hi, I run into problem when writing a syntax, I don't know syntax that will > return true or false if an integer is odd or even. > Thanks x <- 1:10 > x [1] 1 2 3 4 5 6 7 8 9 10 # modulo division > x %% 2 == 0 [1] FALSE TRUE FALSE

Re: [R] Calculate area under a curve

2010-07-01 Thread stephen sefick
simp() in the StreamMetabolism package may do the trick. I have used this on time series of chemical constituent masses. hth, Stephen Sefick On Thu, Jul 1, 2010 at 9:56 AM, suse wrote: > > Hi, > > I want to know the area under a curve, which is not given as a function, but > as values in a time

Re: [R] identifying odd or even number

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 11:40 AM, Yemi Oyeyemi wrote: Hi, I run into problem when writing a syntax, I don't know syntax that will return true or false if an integer is odd or even. Thanks > 1:12 %% 2 == 0 [1] FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE OYEYEMI,

Re: [R] ROC curve in R

2010-07-01 Thread Saeed Abu Nimeh
Try the ROCR package. http://rocr.bioinf.mpi-sb.mpg.de/ROCR.pdf Saeed On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote: > > Hi, > > i have a fairly large amount of genomic data. I have created a dataframe > which has "Reference" as one column and "Variation" as another. I want to > plot a ROC curve

Re: [R] Calculate area under a curve

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 10:56 AM, suse wrote: Hi, I want to know the area under a curve, which is not given as a function, but as values in a time series. It is not a smooth curve, but switches often between positive values and zero (the values describe the moisture in the soil over a year

Re: [R] ROC curve in R

2010-07-01 Thread Tal Galili
Regarding search, There is also the "sos" packege. And yesterday someone wrote a nice R code to enable searching inside the description of all packages: http://www.r-bloggers.com/cran-search/ Cheers, Tal Contact Details:---

Re: [R] identifying odd or even number

2010-07-01 Thread Bernardo Rangel Tura
On Thu, 2010-07-01 at 08:40 -0700, Yemi Oyeyemi wrote: > Hi, I run into problem when writing a syntax, I don't know syntax that will > return true or false if an integer is odd or even. > Thanks > > OYEYEMI, Gafar Matanmi > > Department of Statistics > > University of Ilorin Hi Yemi! Your pro

[R] Documentation for library() and how to specify missing arguments

2010-07-01 Thread Allan Engelhardt
I can, after carefully reading about the returned values, see why library("MASS", "MASS", character.only=TRUE) has to chose between loading the package and displaying the help (I thought I had found a nice shortcut), but wouldn't the documentation be better if it said that the two are incompat

Re: [R] Documentation for library() and how to specify missing arguments

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 1:24 PM, Allan Engelhardt wrote: I can, after carefully reading about the returned values, see why library("MASS", "MASS", character.only=TRUE) has to chose between loading the package and displaying the help (I thought I had found a nice shortcut), but wouldn't the docum

Re: [R] Calculate area under a curve

2010-07-01 Thread suse
Thank you, seems to be the right thing for me. But what is this "n" for? The number of iteration steps as mentioned on other pages for the simpson rule? "number of divisions" as said on the help page I don't understand. ("a" and "b" can be ignored, if I got it right?!). Thanks again! stephen sef

Re: [R] Calculate area under a curve

2010-07-01 Thread stephen sefick
Don't sorry about n it is only necessary for using a and b which are the upper and lower limit of integration and n is the # of sub-intervals. You can ignore all else and use x and y. I will fix the documentation soon. I did a rather bad job on that help document. kindest regards, Stephen Sefic

Re: [R] Why software fails in scientific research

2010-07-01 Thread Thomas Adams
OK… My Grandfather, who was a farmer, was outstanding in his field… Cheers… Murray M Cooper, PhD wrote: For what its worth! A good friend who also happens to be an ecologist told me "An ecologist is a statistician who likes to be outside". Murray M Cooper, Phd Richland Statistics - Orig

Re: [R] left end or right end

2010-07-01 Thread Matt Shotwell
Suku, Just to clarify, in your table and each of your images, it appears that the start position of P (start1) is _after_ or at the start position of Q (start2), and the end position of P (end1) is _before_ or at the end position of Q (end2). If these positions represent increasing integers, then

Re: [R] ROC curve in R

2010-07-01 Thread Changbin Du
Read the ROCR package, it is very good. On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote: > > Hi, > > i have a fairly large amount of genomic data. I have created a dataframe > which has "Reference" as one column and "Variation" as another. I want to > plot a ROC curve based on these 2 columns

Re: [R] Double Integration

2010-07-01 Thread Hans W Borchers
Sarah Sanchez yahoo.com> writes: > > Dear R helpers > > I am working on the Bi-variate Normal distribution probabilities. > I need to double integrate the following function > (actually simplified form of bivariate normal distribution) > > f(x, y) = exp [ - 0.549451 * (x^2 + y^2 - 0.6 * x * y)

Re: [R] Why software fails in scientific research

2010-07-01 Thread steven mosher
Thomas, How popular is R inside of NOAA? On Thu, Jul 1, 2010 at 11:25 AM, Thomas Adams wrote: > OK… > > My Grandfather, who was a farmer, was outstanding in his field… > > Cheers… > > > Murray M Cooper, PhD wrote: > >> For what its worth! >> >> A good friend who also happens to be an ecol

[R] Command Line Arguments

2010-07-01 Thread Bierbryer, Andrew
Do you know to pass named command line arguments into an R script? I have used littler and argv to pass a vector of arguments, but this requires you to maintain the order of the arguments. I'm wondering if there is a way to do this when you do not know the order of the arguments being passed in.

Re: [R] Command Line Arguments

2010-07-01 Thread Steve Lianoglou
Hi, On Thu, Jul 1, 2010 at 2:49 PM, Bierbryer, Andrew wrote: > Do you know to pass named command line arguments into an R script? > > I have used littler and argv to pass a vector of arguments, but this > requires you to maintain the order of the arguments. > > I'm wondering if there is a way to

Re: [R] Command Line Arguments

2010-07-01 Thread Dirk Eddelbuettel
On Thu, Jul 01, 2010 at 02:49:20PM -0400, Bierbryer, Andrew wrote: > Do you know to pass named command line arguments into an R script? > > I have used littler and argv to pass a vector of arguments, but this > requires you to maintain the order of the arguments. Install the getopt package from C

Re: [R] Double Integration

2010-07-01 Thread Ravi Varadhan
Here is another approach using `integrate': fvec = function(x, y) sapply(x, function(z, y) exp(-0.549451*(z^2+y^2-0.6*z*y)), y=y) gvec = function(x) sapply(x, function(y) integrate(fvec, lower=-1.51, upper=2.696, subdivisions=1, rel.tol=1.e-08, y=y)$val) > integrate(gvec, lower=1.98, upp

[R] Modelling survival with time-dependent covariates

2010-07-01 Thread Ben Rhelp
Hi all, I am looking at the tutorial/appendix from John Fox on “Cox Proportional-Hazards Regression for Survival Data” available here: http://cran.r-project.org/doc/contrib/Fox-Companion/appendix-cox-regression.pdf I am particularly interested in modelling survival with time-dependent covariates

Re: [R] Embed function strips out date index

2010-07-01 Thread Manussawee Sukunta
Thank you for all your help. After some sleep last night, I started fresh on the problem with a little clearer thinking. I thought over what Jonathan had said... and I just decided to bypass indexing my data after passing it through the embed function all together. I still was able to perform t

Re: [R] ROC curve in R

2010-07-01 Thread Frank E Harrell Jr
On 07/01/2010 01:33 PM, Changbin Du wrote: Read the ROCR package, it is very good. Just be sure you really need an ROC curve. More often than not it gets in the way of understanding. Frank On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote: Hi, i have a fairly large amount of genomi

[R] how to display the clock time in the loop

2010-07-01 Thread Jack Luo
Hi, I am doing some computation which is pretty time consuming, I want R to display CPU time after each iteration using the command Sys.time(). However, I found that the code only began to display the CPU time after quite a while and several iterations have finished. Is there a way to ask R to dis

[R] Coloring axis labels on lattice xyplot

2010-07-01 Thread Andrew Liu
Hello, First let me apologize for replying/changing subject when I initially asked this question. Its my first time using a mailing list of any sort! I am trying to color particular labels on my lattice xyplot. For example: library(lattice) z = data.frame(x = 1:5) xyplot(x~x, z) Is there an

Re: [R] how to display the clock time in the loop

2010-07-01 Thread Matt Shotwell
Try to flush output after printing: cat(paste(Sys.time()),"\n"); flush(stdout()) On Thu, 2010-07-01 at 16:17 -0400, Jack Luo wrote: > Hi, > > I am doing some computation which is pretty time consuming, I want R to > display CPU time after each iteration using the command Sys.time(). However, > I

Re: [R] how to display the clock time in the loop

2010-07-01 Thread Nikhil Kaza
explicit call to print usually works for me. library(audio) for (i in 1:5){ wait(60) print(Sys.time()) } On Jul 1, 2010, at 4:30 PM, Matt Shotwell wrote: > Try to flush output after printing: > > cat(paste(Sys.time()),"\n"); flush(stdout()) > > On Thu, 2010-07-01 at 16:1

Re: [R] Coloring axis labels on lattice xyplot

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 4:29 PM, Andrew Liu wrote: Hello, First let me apologize for replying/changing subject when I initially asked this question. Its my first time using a mailing list of any sort! I am trying to color particular labels on my lattice xyplot. For example: library(lattice)

Re: [R] s.e. of arima

2010-07-01 Thread Peter Ehlers
On 2010-07-01 8:55, speretti wrote: Hi, I'm using the function arima() from the ts package. when the function gives me the output I can see the s.e. of the coefficients. However I cannot find a way to collect them in a object estimate<-arima(x, order=c(1,0,1)) estimate$se does not work in f

Re: [R] Link to a pdf document

2010-07-01 Thread cgenolin
Hmmm. I guess I did something wrong since it does not work. The file r2lhOutput.pdf is in the folder \inst\doc\ In the Rd file (for example in rthb.Rd) I add "See \url{/library/r2lh/doc/r2lhOutput.pdf} for display detail." But the link leads to a dead link. I did not manage to find the file r2l

Re: [R] Documentation for library() and how to specify missing arguments

2010-07-01 Thread Gabor Grothendieck
On Thu, Jul 1, 2010 at 1:24 PM, Allan Engelhardt wrote: > > Is there in the language a lexical x such that f(x, ...) is the same as f(, > ...)? > Try this: > mx <- formals(identity)$x > missing(mx) [1] TRUE > sin(mx) Error in sin(mx) : 'mx' is missing ___

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Mike Williamson
Jim, Andy, Thanks for your suggestions! I found some time today to futz around with it, and I found a "home made" script to fill in NA values to be much quicker. For those who are interested, instead of using: dataSet <- na.roughfix(dataSet) I used:

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Hadley Wickham
Here's another version that's a bit easier to read: na.roughfix2 <- function (object, ...) { res <- lapply(object, roughfix) structure(res, class = "data.frame", row.names = seq_len(nrow(object))) } roughfix <- function(x) { missing <- is.na(x) if (!any(missing)) return(x) if (is.numer

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-07-01 Thread Mike Williamson
Hadley, Thanks! Yes... as.data.frame() is quite slow. (And it forces the column names to become "acceptable" names, which is a hassle to fix all the time.) I just hadn't thought of something as clever as what you wrote below. I'll try out this suggestion. :)

[R] Files with Missing Data

2010-07-01 Thread Norman Jessup
I'm a new R user so this is possibly a naive question. I'm trying to load an external CSV file into a dataframe using: df_name<-read.table("myfile.csv") myfile.csv should have 5 elements per row, though a percentage are missing the last two elements (the commas are present as placemarkers).

[R] is there a way to do dense rank in R

2010-07-01 Thread Suresh Singh
I have not been able to find a way to do dense rank in R Here is an example of what I need rank() gives the following 5 rank 1 7 rank 2 7 rank 2 9 *rank 4* but I want 5 rank 1 7 rank 2 7 rank 2 9 *rank 3* * * thanks SS [[alternative HTML version deleted]]

Re: [R] Files with Missing Data

2010-07-01 Thread Peter Alspach
Tena koe Norman The default separator for read.table is '' so you need to specify it as a comma: dfName <- read.table("myfile.csv", sep=',') or use read.csv(). HTH Peter Alspach > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On

Re: [R] Files with Missing Data

2010-07-01 Thread Erik Iverson
Norman Jessup wrote: I'm a new R user so this is possibly a naive question. I'm trying to load an external CSV file into a dataframe using: df_name<-read.table("myfile.csv") myfile.csv should have 5 elements per row, though a percentage are missing the last two elements (the commas are pre

Re: [R] Files with Missing Data - Thanks

2010-07-01 Thread Norman Jessup
Thanks to Peter and Erik - This advice resolved my problem. regards Norman Jessup On 2/07/10 11:43 AM, Erik Iverson wrote: Norman Jessup wrote: I'm a new R user so this is possibly a naive question. I'm trying to load an external CSV file into a dataframe using: df_name<-read.table("myf

Re: [R] is there a way to do dense rank in R

2010-07-01 Thread David Winsemius
On Jul 1, 2010, at 9:30 PM, Suresh Singh wrote: I have not been able to find a way to do dense rank in R Here is an example of what I need rank() gives the following 5 rank 1 7 rank 2 7 rank 2 9 *rank 4* but I want 5 rank 1 7 rank 2 7 rank 2 9 *rank 3 > tst <- read.table(textConnection("

Re: [R] is there a way to do dense rank in R

2010-07-01 Thread Matt Shotwell
> x <- c(5,7,7,9) > rank(unique(x))[match(x, unique(x))] [1] 1 2 2 3 On Thu, 2010-07-01 at 21:30 -0400, Suresh Singh wrote: > I have not been able to find a way to do dense rank in R > > Here is an example of what I need > > rank() gives the following > > 5 rank 1 > 7 rank 2 > 7 rank 2 > 9 *ran

[R] Good Package(s) for String and URL processing?

2010-07-01 Thread Ralf B
Are there packages that allow improved String and URL processing? E.g. extract parts of a URLs such as sub-domains, top-level domain, protocols (e.g. https, http, ftp), file type based on endings, check if a URL is valid or not, etc... I am currently only using split and paste. Are there better an

Re: [R] Good Package(s) for String and URL processing?

2010-07-01 Thread Erik Iverson
Ralf B wrote: Are there packages that allow improved String and URL processing? E.g. extract parts of a URLs such as sub-domains, top-level domain, protocols (e.g. https, http, ftp), file type based on endings, check if a URL is valid or not, etc... I am currently only using split and paste. Are

[R] help with the xtable package

2010-07-01 Thread Changbin Du
HI, Dear R community, I am using the xtable to create the table, but how can I see the table? The following is the codes I used: > data(tli) > tli.table <- xtable(tli[1:10, ]) > digits(tli.table)[c(2, 6)] <- 0 > print(tli.table, floating = FALSE) % latex table generated in R 2.11.0 by xtable

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