Re: [R] ordiellipse

2011-05-25 Thread Mark Difford
On May 26, 2011 Andrew Halford wrote: > I am using ordiellipse to plot the ellipses and it works fine except one > of my groups > contains only 2 sites and I cannot get an ellipse around them. I'm > assuming > that 2 points is not enough to perform the relevant calculations here, > however I wo

Re: [R] What am I doing wrong with sapply ?

2011-05-25 Thread Joshua Wiley
Hi Eric, Hopefully the following addresses your question: library(XML) ## please do not include rm(list=ls()) in code other's might copy and paste ## it could remove things precious to them url <- "http://webapp.montcopa.org/sherreal/salelist.asp?saledate=05/25/2011"; tbl <-data.frame(readHTMLTab

Re: [R] What am I doing wrong with sapply ?

2011-05-25 Thread Steve Lianoglou
Hi, On Thu, May 26, 2011 at 12:49 AM, eric wrote: > Statement 9 using sapply does not seem to give the correct answer (or at > least to me). Yet I do what I think is the same thing with statement 11 and > I get the answer I'm looking for. > > 9 : s <-sapply(unlist(v[c(1:length(v))]), max) > 11: f

[R] likelihood ratio test

2011-05-25 Thread karuna m
Dear R-help, Can anybody tell me which R package has Lo-Mendell Rubin LR test and Bootstrap LR test to compare the model fit between k class and k+1 class model for Latent class analysis? Thanks in advance,  warn regards,Ms.Karunambigai M PhD Scholar Dept. of Biostatistics NIMHANS Bangalore India

[R] all possible regression

2011-05-25 Thread Mufira Fitria
hi, I want to know how about r package  Robust CP in all possible regression   method...can you help me?? thanks before... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PL

[R] What am I doing wrong with sapply ?

2011-05-25 Thread eric
Statement 9 using sapply does not seem to give the correct answer (or at least to me). Yet I do what I think is the same thing with statement 11 and I get the answer I'm looking for. 9 : s <-sapply(unlist(v[c(1:length(v))]), max) 11: for(i in 1 :length(v)) v1[i] <- max(unlist(v[i])) Shouldn't I

[R] ordiellipse

2011-05-25 Thread Andrew Halford
Hi Users, I am trying to plot 95% confidence ellipses around the 4 groupings found in a PCA ordination and identified a-priori by clustering. I am using ordiellipse to plot the ellipses and it works fine except one of my groups contains only 2 sites and I cannot get an ellipse around them. I'm ass

Re: [R] problems getting the splm package installed

2011-05-25 Thread David Winsemius
On May 25, 2011, at 10:21 PM, Rafael Terra wrote: Dear R-project members, I'm a newbie in R and I'm trying to install the "splm" package to analyze spatial panel data. I have the R x64 2.12.0 beta version installed in my computer. When I try to install the package from within R typing "

[R] problems getting the splm package installed

2011-05-25 Thread Rafael Terra
Dear R-project members, I'm a newbie in R and I'm trying to install the "splm" package to analyze spatial panel data. I have the R x64 2.12.0 beta version installed in my computer. When I try to install the package from within R typing ">install.packages("splm", repos="http://R-Forge.R-project

[R] Thiel's Uncertainty Coefficient

2011-05-25 Thread Sparks, John James
Dear R Helpers, I was looking at the email help threads in trying to find a calculation in R of Thiel's uncertainty coefficient. One of the writers offered to send the function in custom code to the inquirer. Can I get a copy of that code, or does anyone know if the calculation is now available

[R] Using deriv3() in a separated nonlinear regression model

2011-05-25 Thread Walmes Zeviani
Hi all, I'm adjusting a nonlinear regression model for data that has a categorigal variable present. So, I can use nls() to do this considering the categorical variable, like this # da <- expand.grid(tr=gl(2,1,la=c("tr")), x=1:12) da$y <

[R] R svm prediction kernlab

2011-05-25 Thread kjkartik
Hi All, I am using ksvm method in kernlab R package for support vector machines. I learned the multiclass one-against-one svm from training data and using it to classify new datapoints. But I want to update/finetune the 'svm weights' based on some criteria and use the updated svm weights

Re: [R] L-BFGS-B and parscale in optim()

2011-05-25 Thread Sebastian P. Luque
On Wed, 25 May 2011 19:33:24 -0500, "Sebastian P. Luque" wrote: > which shows me that the estimate for at least one parameter is outside > the bounds. I'll try to prepare a simplified example to reproduce. I got it, it turned out to be the ndeps being too large so it pushed the L-BFGS-B over th

Re: [R] L-BFGS-B and parscale in optim()

2011-05-25 Thread Sebastian P. Luque
On Wed, 25 May 2011 19:33:24 -0500, "Sebastian P. Luque" wrote: > which shows me that the estimate for at least one parameter is outside > the bounds. I meant the value for the parameter during the failing iteration, not the estimate, of course. -- Seb

[R] Thiessen Method

2011-05-25 Thread federico eccel
Dear Users, I would like to know if any of you know some R packages for appling the Thiessen method; in my case I would like to interpolete with this method some rain gauges. Tanks a lot [[alternative HTML version deleted]] __ R-help@r-project

Re: [R] panel.first problem when plotting with formula

2011-05-25 Thread Gene Leynes
David, Peter (and others), If you're interested, I submitted this as a bug, and was informed of the error of my ways by Professor Ripley * His informative reply is copied below. * The short answer is that panel.first is not a documented function of "plot.formula", which is called by the generic "

Re: [R] L-BFGS-B and parscale in optim()

2011-05-25 Thread Sebastian P. Luque
On Wed, 25 May 2011 23:46:02 +, Ben Bolker wrote: > Sebastian P. Luque gmail.com> writes: >> Hi, >> When using method L-BFGS-B along with a parscale argument, should the >> lower and upper bounds provided be on the scaled or unscaled values? >> Thanks. > I think you can figure this out b

Re: [R] L-BFGS-B and parscale in optim()

2011-05-25 Thread Ben Bolker
Sebastian P. Luque gmail.com> writes: > > Hi, > > When using method L-BFGS-B along with a parscale argument, should the > lower and upper bounds provided be on the scaled or unscaled values? > Thanks. I think you can figure this out by experimentation on your own, but I believe that all of t

[R] Time and db precision

2011-05-25 Thread Mikkel Grum
I have a loop that regularly checks for new data to analyse in my database. In order to facilitate this, the database table has a timestamp column with the time that the data was inserted into the database. Something like this: while () { load(timetoken.Rdata) df <- sqlQuery(con, pas

[R] L-BFGS-B and parscale in optim()

2011-05-25 Thread Sebastian P. Luque
Hi, When using method L-BFGS-B along with a parscale argument, should the lower and upper bounds provided be on the scaled or unscaled values? Thanks. Cheers, -- Seb __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PL

Re: [R] Using dates on axis with Grid plots

2011-05-25 Thread Paul Murrell
Hi On 15/05/2011 2:01 a.m., Larry White wrote: Hi, I'm trying to use Grid plots and would like to have an X axis that represents dates. I have several years of data so I would like to be able to have labeled tick marks only intermittently (not one per date). I can transform the initial data fr

Re: [R] panel.first problem when plotting with formula

2011-05-25 Thread David Winsemius
On May 25, 2011, at 5:56 PM, Gene Leynes wrote: David, Peter (and others), If you're interested, I submitted this as a bug, and was informed of the error of my ways by Professor Ripley * His informative reply is copied below. * The short answer is that panel.first is not a documented funct

Re: [R] Subtracting rows by id

2011-05-25 Thread Sara Maxwell
That worked perfectly. Thank you Dennis - I very much appreciate the help! Sara Maxwell, PhD, Postdoctoral Fellow Marine Conservation Institute University of California Santa Cruz Long Marine Laboratory 100 Shaffer Road Santa Cruz CA 95060 USA +1 206 355 3249 sara.maxw...@marine-conservation.or

Re: [R] how to compute the inverse percentile of a given observation w.r.t. a reference distribution

2011-05-25 Thread David Winsemius
On May 25, 2011, at 5:50 PM, Dennis Murphy wrote: Hi: On Wed, May 25, 2011 at 12:42 PM, rudi wrote: Hi, can anyone help me to figure out how to compute the percentile of an individual observation with respect to a reference distribution. What I mean is. Let's assume I have a vector consi

Re: [R] Fwd: Opening R in 64-bit version by default

2011-05-25 Thread Duncan Murdoch
On 25/05/2011 5:43 PM, John C Frain wrote: I have no problems configuring .r files to start in Emacs or RStudio and then use Emacs or RStudio to call the required version of R. You might check when you open with other from Windows Explorer that the check box "Always open with this program is tic

Re: [R] how to compute the inverse percentile of a given observation w.r.t. a reference distribution

2011-05-25 Thread Dennis Murphy
Hi: On Wed, May 25, 2011 at 12:42 PM, rudi wrote: > Hi, > > can anyone help me to figure out how to compute the percentile of an > individual observation with respect to a reference distribution. > > What I mean is. Let's assume I have a vector consisting of 10 numbers > {3,5,8,1,9,5,4,3,5.5,7} a

Re: [R] What are the common Standard Statistical methods used for the analysis of a dataset

2011-05-25 Thread Stephan Kolassa
Dear all, may I suggest the acronym IOTT for the inter-ocular trauma test? Now we just need someone to implement iot.test(). I assume it will appear on CRAN within the next 24 hours. Looking forward to yet another base package, Stephan Am 25.05.2011 23:36, schrieb Greg Snow: How can anyon

Re: [R] Fwd: Opening R in 64-bit version by default

2011-05-25 Thread John C Frain
I have no problems configuring .r files to start in Emacs or RStudio and then use Emacs or RStudio to call the required version of R. You might check when you open with other from Windows Explorer that the check box "Always open with this program is ticked. If you are using Windows 7 you can set

Re: [R] What are the common Standard Statistical methods used for the analysis of a dataset

2011-05-25 Thread Greg Snow
How can anyone overlook the intra-ocular trauma test (or sometimes called the inter-ocular concussion test). But the i-o trauma test needs either a small data set or an appropriate graph of the data (or can you look at a dataset of a hundred columns and a million rows and do an intra-ocular tra

Re: [R] how to compute the inverse percentile of a given observation w.r.t. a reference distribution

2011-05-25 Thread Jorge Ivan Velez
Hi Rudi, Take a look at ?ecdf HTH, Jorge On Wed, May 25, 2011 at 3:42 PM, rudi <> wrote: > Hi, > > can anyone help me to figure out how to compute the percentile of an > individual observation with respect to a reference distribution. > > What I mean is. Let's assume I have a vector consisting

Re: [R] how to compute the inverse percentile of a given observation w.r.t. a reference distribution

2011-05-25 Thread David Winsemius
On May 25, 2011, at 3:42 PM, rudi wrote: Hi, can anyone help me to figure out how to compute the percentile of an individual observation with respect to a reference distribution. What I mean is. Let's assume I have a vector consisting of 10 numbers {3,5,8,1,9,5,4,3,5.5,7} and I want figure ou

[R] how to compute the inverse percentile of a given observation w.r.t. a reference distribution

2011-05-25 Thread rudi
Hi, can anyone help me to figure out how to compute the percentile of an individual observation with respect to a reference distribution. What I mean is. Let's assume I have a vector consisting of 10 numbers {3,5,8,1,9,5,4,3,5.5,7} and I want figure out what percentile the number 4.9 corresponds

Re: [R] Data Frame housekeeping

2011-05-25 Thread Scott Hatcher
Hello Dr. Winsemius, First of all, thank you for your prompt and helpful reply. Also, for providing something I hoped would be produced from joining this mailing list: a means of discovering incredibly useful packages such as the "reshape2" one you have introduced me too. I have a follow up

Re: [R] Processing large datasets

2011-05-25 Thread Mike Marchywka
> Date: Wed, 25 May 2011 12:32:37 -0400 > Subject: Re: [R] Processing large datasets > From: mailinglist.honey...@gmail.com > To: marchy...@hotmail.com > CC: ro...@bestroman.com; r-help@r-project.org > > Hi, > > On Wed, May 25, 2011 at 11:00 AM, Mike

Re: [R] What are the common Standard Statistical methods used fo

2011-05-25 Thread Ted Harding
[See in-line below] On 25-May-11 19:14:11, Michael Dewey wrote: > At 00:41 25/05/2011, Greg Snow wrote: >>The only statistical method that I know of that can be >>applied to any dataset without further definition of the >>nature of the data or the question being asked is >>SnowsCorrectlySizedButOt

Re: [R] Subtracting rows by id

2011-05-25 Thread Dennis Murphy
Hi: Interesting problem. Here's one approach: library(plyr) # Read in your datasets as data frames rather than matrices dataset1 <- data.frame(id1 = rep(1:3, each = 10), value1 = sample(seq_len(100), 30, replace = TRUE)) dataset2 <- data.frame(id2 = 1:3, subtract.value = c(

Re: [R] Accessing elements of a list

2011-05-25 Thread David Winsemius
On May 25, 2011, at 3:25 PM, Seth W Bigelow wrote: I have a list that is made of lists of varying length. I wish to create a new vector that contains the last element of each list. So far I have used sapply to determine the length of each list, but I'm stymied at the part where I index the

Re: [R] Accessing elements of a list

2011-05-25 Thread Marc Schwartz
On May 25, 2011, at 2:25 PM, Seth W Bigelow wrote: > I have a list that is made of lists of varying length. I wish to create a > new vector that contains the last element of each list. So far I have used > sapply to determine the length of each list, but I'm stymied at the part > where I index

Re: [R] Accessing elements of a list

2011-05-25 Thread David Winsemius
On May 25, 2011, at 3:25 PM, Seth W Bigelow wrote: I have a list that is made of lists of varying length. I wish to create a new vector that contains the last element of each list. So far I have used sapply to determine the length of each list, but I'm stymied at the part where I index the

[R] Accessing elements of a list

2011-05-25 Thread Seth W Bigelow
I have a list that is made of lists of varying length. I wish to create a new vector that contains the last element of each list. So far I have used sapply to determine the length of each list, but I'm stymied at the part where I index the list to make a new vector containing only the last item

Re: [R] What are the common Standard Statistical methods used for the analysis of a dataset

2011-05-25 Thread Michael Dewey
At 00:41 25/05/2011, Greg Snow wrote: The only statistical method that I know of that can be applied to any dataset without further definition of the nature of the data or the question being asked is SnowsCorrectlySizedButOtherwiseUselessTestOfAnything which is found in the TeachingDemos packa

[R] Job opening at Harvard Business School

2011-05-25 Thread Ao, Xiang
Dear Colleagues, I'd like to draw your attention to the following job available at the Harvard Business School. We are looking for a candidate with strong statistical/econometrical background, with strong programming skills in R or Stata. Please apply through the following link. If you know

Re: [R] Importing fixed-width data

2011-05-25 Thread Dennis Murphy
I get a data frame on my end: lines <- "2011-05-13 00:00:00 EONAAL330 dfa13002516PSCNONA 2011-05-13 00:00:01 EONAAL223 laa13044510AS.NONM 2011-05-13 00:00:05 EONBHS229 mia13001621NON" df = read.fwf(textConnection(lines), widths=c(19,-4,7,3,8,2,1,3,1), col.names=c("DateTime","Flight","Dest","ArrTi

Re: [R] matrix Manipulation...

2011-05-25 Thread Sarah Goslee
It's very easy to do in two steps: > testmat <- matrix(c(.2, .3, 1, -1, 3, .2, .4, 5, .5, -1), byrow=TRUE, nrow=2) > testmat [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.31 -1.03 [2,] 0.2 0.45 0.5 -1 > testmat[testmat >= 1] <- 1 > testmat[testmat < 0] <- 0 > testmat [,1] [,2] [,

Re: [R] matrix Manipulation...

2011-05-25 Thread Jim Silverton
Hello everyone, I have a 2 x 5 matrix: say 0.2 0.3 1 -1 3 0.2. 0.4 5 0.5 -1 I want to replace all the values greater than or equal to 1 with 1 and those less than or equal to 0 with 0. So I should end up with a mtrix looking like: 0.2 0.3 1 0 1 0.2. 0.4 1 0.5 0 An

Re: [R] grep pattern

2011-05-25 Thread jim holtman
try this using strsplit: > x <- round(runif(10)*10, digits=0) > y <- as.Date(x, origin="1970-01-01") > str(y) Class 'Date' num [1:10] 26551 37212 57285 90821 20168 ... > y1 <- as.character(y) > str(y1) chr [1:10] "2042-09-11" "2071-11-19" "2126-11-04" "2218-08-30" "2025-03-21" "2215-12-22" .

Re: [R] What does "smaller than" comparison do on strings?

2011-05-25 Thread Dennis Murphy
Hi: Here are two alternatives that do work as you expect; sprintf() is your friend: > sprintf("%2d", 1:12) [1] " 1" " 2" " 3" " 4" " 5" " 6" " 7" " 8" " 9" "10" "11" "12" > sprintf("%02d", 1:12) [1] "01" "02" "03" "04" "05" "06" "07" "08" "09" "10" "11" "12" > sprintf("%2d", 1:12) < 10 [1] TR

Re: [R] Fwd: transpose ?

2011-05-25 Thread Dennis Murphy
Hi: Does this work? dd <- read.table(textConnection(" C C C C T T G G A A C C G G C C G G T T A A A A T A T T C C G G C C C C T T G G A A C C G G C C "), stringsAsFactors = FALSE) # Convert the data frame to a ch

Re: [R] Data Frame housekeeping

2011-05-25 Thread David Winsemius
On May 25, 2011, at 1:16 PM, Scott Hatcher wrote: Hello Dr. Winsemius, First of all, thank you for your prompt and helpful reply. Also, for providing something I hoped would be produced from joining this mailing list: a means of discovering incredibly useful packages such as the "reshape

Re: [R] barplot groups of different size i.e. height is NOT a matrix

2011-05-25 Thread Walmes Zeviani
You can produce a graph similar to the ggplot with lattice::barchart, require(lattice) dataset <- data.frame(Main=c("A","A","A","B","B"), Detail=c("a","b","c","1","2"), value=runif(5, min= 0.5, max=1)) barchart(value~Detail|Main, data=dataset, s

[R] Subtracting rows by id

2011-05-25 Thread Sara Maxwell
Dear R users, I have two datasets: id1 <- c(rep(1,10), rep(2,10), rep(3,10)) value1 <- sample(1:100, 30, replace=TRUE) dataset1 <- cbind(id1,value1) id2 <- c(1,2,3) subtract.value <- c(1,3,5) dataset2 <- cbind(id2, subtract.value) I want to subtract the number of rows in the subtract.value that

Re: [R] stepwise selection cox model

2011-05-25 Thread linda Porz
Many thanks for your reply. I have run a stepwise selection in Stata and R using the function fastbw (rule="p") from Design package. Both functions give the same results. Is this because both functions do the same job or can it be that for different data one will have different results? Many thank

Re: [R] How do I assign boolean (o,1) values to a column?

2011-05-25 Thread Xenimes
Thankyou very much, I managed to count he numbr of Markers 2 linked to Markers 3. And Markers 1 to Markers 3 with the aggregate function: with(data,aggregate(Marker1,list(Marker2=Marker2),length)) data2<-with(data,aggregate(Marker1,list(Marker2=Marker2,Marker3=Merker3),length)) So, now is easy I

Re: [R] How to intantiate a list of data.frames?

2011-05-25 Thread Rui Maximo
Hi Josh, You are definitely right. And were all time. Yes, the problem was always with the write.csv(). I though it was with the "ds". Thank you very much. Cheers, Rui > Date: Tue, 24 May 2011 14:30:56 -0700 > Subject: Re: [R] How to intantiate a list of data.frames? > From: jwiley.ps...@gmail.

Re: [R] stepwise selection cox model

2011-05-25 Thread David Winsemius
On May 25, 2011, at 12:11 PM, linda Porz wrote: Many thanks for your reply. I have run a stepwise selection in Stata and R using the function fastbw (rule="p") from Design package. Both functions give the same results. Is this because both functions do the same job or can it be that for di

Re: [R] Adjusted Rate Ratios in R

2011-05-25 Thread Walmes Zeviani
Matthew, You can change the matrix (restriction) involved. Start from help(contr.sum) to know how specify this. Walmes. == Walmes Marques Zeviani LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W) D

Re: [R] Processing large datasets

2011-05-25 Thread Steve Lianoglou
Hi, On Wed, May 25, 2011 at 11:00 AM, Mike Marchywka wrote: [snip] >> > If your datasets are *really* huge, check out some packages listed >> > under the "Large memory and out-of-memory data" section of the >> > "HighPerformanceComputing" task view at CRAN: >> >> > http://cran.r-project.org/web/v

Re: [R] Trouble Combining With Paste

2011-05-25 Thread Phil Spector
John - Try infert[,toolong] = sapply(infert[,toolong],cut2,g=10,levels.mean=TRUE) - Phil Spector Statistical Computing Facility Department of Statistics

[R] [Fwd: Re: the mgcv package can not be loaded]

2011-05-25 Thread gbrenes
Sorry, I forgot to be more specific. I am using Windows XP. I am using R.12.2 I installed both packages from the install packages menu. I always write library(name.of.library), and it is enough. But when I write library(nlme), R does not find nlme right away I load nlme first and it says pac

Re: [R] barplot groups of different size i.e. height is NOT a matrix

2011-05-25 Thread Walmes Zeviani
Victor, I agree with Marc's point of view. So, if you can use another representation of you data, like points, considering looking at http://lmdvr.r-forge.r-project.org/figures/figures.html figures 10.20 and 10.21 for a start point. Walmes. ===

Re: [R] Trouble Combining With Paste

2011-05-25 Thread Sarah Goslee
You need to use get() so that you are acting on the dataframe, and not the string that names the dataframe. Sarah On Wed, May 25, 2011 at 12:02 PM, Sparks, John James wrote: > Dear R Helpers, > > I am having trouble combining some pieces of programming that work fine > individually, but fall dow

Re: [R] Trouble Combining With Paste

2011-05-25 Thread Joshua Wiley
Hi John, The issue is that: "infert$age" != infert$age One is a text string, the other references the information stored in the age variable of the infert object. If you need to pass the names as a string, use "[" instead: ## for a data frame infert[, "age"] ## for a list infert[["age"]] It l

Re: [R] the mgcv package can not be loaded

2011-05-25 Thread Sarah Goslee
Well, that answered some of my questions, though you forgot to send your answer to the r-help list rather than just to me. I don't use windows, so someone else may have better advice. On Wed, May 25, 2011 at 12:02 PM, wrote: > Sorry, I forgot to be more specific. > > I am using Windows XP. > > I

[R] Trouble Combining With Paste

2011-05-25 Thread Sparks, John James
Dear R Helpers, I am having trouble combining some pieces of programming that work fine individually, but fall down when I try to get them to work together. The end goal is to take a data frame, and if any of the variables has more than 10 values, then use cut2 to reduce the number of (effective)

Re: [R] Processing large datasets

2011-05-25 Thread Hugo Mildenberger
With PostgreSQL at least, R can also be used as implementation language for stored procedures. Hence data transfers between processes can be avoided alltogether. http://www.joeconway.com/plr/ Implemention of such a procedure in R appears to be straighforward: CREATE OR REPLACE FUNCTION

Re: [R] stepwise selection cox model

2011-05-25 Thread Bert Gunter
See the Vignette in the glmnet package for one alternative approach to variable selection. Of course, you need to gain some background to know what you're doing here. -- Bert On Wed, May 25, 2011 at 8:38 AM, Marc Schwartz wrote: > Hi, > > You are unlikely to find one, as fundamentally, stepwise

Re: [R] Importing fixed-width data

2011-05-25 Thread Ian Gow
Everything looks OK. Does this help? > test <- >data.frame(alpha=as.factor(c("A","A","B","B","C")),number=c(1,2,3,4,5)) > mode(test) [1] "list" > class(test) [1] "data.frame" > sapply(test, mode) alphanumber "numeric" "numeric" > sapply(test, class) alphanumber "factor" "numeric

[R] Importing fixed-width data

2011-05-25 Thread James Rome
I have a data set where the lines look like: 2011-05-13 00:00:00 EONAAL330 dfa13002516PSCNONA 2011-05-13 00:00:01 EONAAL223 laa13044510AS.NONM Some lines are missing the field before and after the NON: 2011-05-13 00:00:05 EONBHS229 mia13001621NON I read them into R using df = read.fwf(file, wi

Re: [R] stepwise selection cox model

2011-05-25 Thread Marc Schwartz
Hi, You are unlikely to find one, as fundamentally, stepwise procedures are a bad way to engage in covariate selection. Search the list archives at rseek.org using 'stepwise' as the keyword to see a plethora of discussion on this point. This is not a new issue BTW, as I happened to stumble upon

Re: [R] Processing large datasets

2011-05-25 Thread Mike Marchywka
> Date: Wed, 25 May 2011 10:18:48 -0400 > From: ro...@bestroman.com > To: mailinglist.honey...@gmail.com > CC: r-help@r-project.org > Subject: Re: [R] Processing large datasets > > > Hi, > > If your datasets are *really* huge, check out some packages list

Re: [R] Print the content of several columns in only one

2011-05-25 Thread Scott Chamberlain
Or use melt in the reshape2 package to melt all columns to one with an indexing column to boot... __Scott Chamberlain Rice University, EEB Dept. On Wednesday, May 25, 2011 at 7:06 AM, zoe.cryocla wrote: > Ok, I found how to do, > with the function paste() > > -- > View th

Re: [R] the mgcv package can not be loaded

2011-05-25 Thread Sarah Goslee
We really need some more information to be able to help you (as requested in the posting guide): What OS? What version of R? How did you install nlme? Were there any messages? What happens when you type library(nlme) at the R prompt? How did you install mgcv? Were there any messages? On Wed,

Re: [R] R as.numeric()

2011-05-25 Thread David Winsemius
On May 25, 2011, at 7:25 AM, Lutz Fischer wrote: Thanks a lot for both replies. If I setup the option as proposed everything works as I wanted it to. I guess as.character would work as well. Only then I guess I would need to loop through the data frame. as.character is vectorized. You

Re: [R] stepwise selection cox model

2011-05-25 Thread David Winsemius
On May 25, 2011, at 5:28 AM, linda Porz wrote: Sorry, I have wrote a wrong subject in the first email! Regards, Linda -- Forwarded message -- From: linda Porz Date: 2011/5/25 Subject: combined odds ratio To: r-help@r-project.org Cc: r-help-requ...@stat.math.ethz.ch Dear all

[R] the mgcv package can not be loaded

2011-05-25 Thread gbrenes
Hi. I have been trying to load the mgcv package but I always get the error message: there is no package called 'nlme' Error: package/namespace load failed for 'mgcv' I load the package nlme and still I get the same message. I have noticed that there are some problems in using nlme in recent v

Re: [R] Multinomial Logistical Model

2011-05-25 Thread Frank Harrell
I suggest a couple of courses before proceeding. Multinomial logistic models have special challenges. And note that you have two nomenclature errors in your note, which is usually a sign of not having taken the relevant coursework. Frank Belle wrote: > > Does anyone know how to run Multinomial

Re: [R] plotting texas school district using shape files

2011-05-25 Thread Ben Bolker
Shant Ch yahoo.com> writes: > > Yes I had included the library(maptools) in my code, it is already > installed in > my computer. but still it is showing the same error. > In that case you should (1) read the posting guide, (2) copy and paste the code you ran, and the precise error you got,

Re: [R] barplot groups of different size i.e. height is NOT a matrix

2011-05-25 Thread Marc Schwartz
On May 25, 2011, at 7:56 AM, Victor Gabillon wrote: > Hello, > > I want to use the function barplot do display several group of bars. > A standard example is given at this link > http://onertipaday.blogspot.com/2007/05/make-many-barplot-into-one-plot.html > > But in their example the 4 groups of

Re: [R] Processing large datasets/ non answer but Q on writing data frame derivative.

2011-05-25 Thread Mike Marchywka
> Date: Wed, 25 May 2011 09:49:00 -0400 > From: ro...@bestroman.com > To: biomathjda...@gmail.com > CC: r-help@r-project.org > Subject: Re: [R] Processing large datasets > > Thanks Jonathan. > > I'm already using RMySQL to load data for couple of days.

Re: [R] Processing large datasets

2011-05-25 Thread Steve Lianoglou
Hi, On Wed, May 25, 2011 at 10:18 AM, Roman Naumenko wrote: [snip] > I don't think data.table is fundamentally different from data.frame type, but > thanks for the suggestion. > > http://cran.r-project.org/web/packages/data.table/vignettes/datatable-intro.pdf > "Just like data.frames, data.table

Re: [R] select levels of factor variables

2011-05-25 Thread David Winsemius
On May 25, 2011, at 4:46 AM, zoe.cryocla wrote: Hi again, I've got another question... I often use the symbol == to select some levels of factor variables like : data[data$var=="blabla", [ But this time, I'd like to select all the levels of my variable wich contain the letter "B", is t

Re: [R] Processing large datasets

2011-05-25 Thread Marc Schwartz
Take a look at the High-Performance and Parallel Computing with R CRAN Task View: http://cran.us.r-project.org/web/views/HighPerformanceComputing.html specifically at the section labeled "Large memory and out-of-memory data". There are some specific R features that have been implemented in a

Re: [R] What does "smaller than" comparison do on strings?

2011-05-25 Thread Duncan Murdoch
On 25/05/2011 6:06 AM, Niklaus Kuehnis wrote: What's the logic behind the following, and where can I find any documentation about it? In particular, why are 2:9 - as characters - not regarded as being smaller than 10? # R-Code: a<- as.character(1:12) a< 10 # [1] TRUE FALSE FALSE FALSE FALSE

Re: [R] panel.first problem when plotting with formula

2011-05-25 Thread David Winsemius
On May 24, 2011, at 11:42 PM, Gene Leynes wrote: Peter, Good idea! (why didn't I think of that?) If it stumped the r-list, I think there is probably a slight bug with the plot formula. Problems like this make me realize how amazingly full featured and relatively bug free R is. A problem

Re: [R] Fwd: transpose ?

2011-05-25 Thread Jeff Newmiller
Then use as.matrix. Transpose is not a well-defined operation for data frames. --- Jeff Newmiller The . . Go Live... DCN: Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries

Re: [R] Processing large datasets

2011-05-25 Thread Roman Naumenko
Thanks Jonathan. I'm already using RMySQL to load data for couple of days. I wanted to know what are the relevant R capabilities if I want to process much bigger tables. R always reads the whole set into memory and this might be a limitation in case of big tables, correct? Doesn't it use te

Re: [R] Processing large datasets

2011-05-25 Thread Roman Naumenko
> Hi, > On Wed, May 25, 2011 at 12:29 AM, Roman Naumenko > wrote: > > Hi R list, > > > > I'm new to R software, so I'd like to ask about it is capabilities. > > What I'm looking to do is to run some statistical tests on quite > > big > > tables which are aggregated quotes from a market feed. > >

[R] Adjusted Rate Ratios in R

2011-05-25 Thread matthew.benigni
I am trying to calculate Poisson regression based adjusted rate ratios in R, but R's default in glm does not code the intercept as the global rate. In SAS I use "cell means" coding so that the intercept is the global rate, but I do not know how to do this in R. If anyone knows a way to make glm u

Re: [R] plotting texas school district using shape files

2011-05-25 Thread Shant Ch
Yes I had included the library(maptools) in my code, it is already installed in my computer. but still it is showing the same error. From: Ben Bolker To: r-h...@stat.math.ethz.ch Sent: Wed, May 25, 2011 8:06:19 AM Subject: Re: [R] plotting texas school distric

Re: [R] R as.numeric()

2011-05-25 Thread Lutz Fischer
Thanks a lot for both replies. If I setup the option as proposed everything works as I wanted it to. I guess as.character would work as well. Only then I guess I would need to loop through the data frame. Lutz On 24/05/11 22:42, Ista Zahn wrote: > This is a FAQ: > > http://cran.r-project.org

Re: [R] Multinomial Logistical Model

2011-05-25 Thread Mark Difford
On May 24, 2011; 11:06pm Belle wrote: > Does anyone know how to run Multinomial logistical Model in R in order to > get predicted probability? Yes. I could stop there but you shouldn't. The author of the package provides plenty of examples (and two good vignettes) showing you how to do this. Sugg

[R] What does "smaller than" comparison do on strings?

2011-05-25 Thread Niklaus Kuehnis
What's the logic behind the following, and where can I find any documentation about it? In particular, why are 2:9 - as characters - not regarded as being smaller than 10? # R-Code: a <- as.character(1:12) a < 10 # [1] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE

Re: [R] Print the content of several columns in only one

2011-05-25 Thread zoe.cryocla
Ok, I found how to do, with the function paste() -- View this message in context: http://r.789695.n4.nabble.com/Print-the-content-of-several-columns-in-only-one-tp3549114p3549514.html Sent from the R help mailing list archive at Nabble.com. __ R-help

[R] stepwise selection cox model

2011-05-25 Thread linda Porz
Sorry, I have wrote a wrong subject in the first email! Regards, Linda -- Forwarded message -- From: linda Porz Date: 2011/5/25 Subject: combined odds ratio To: r-help@r-project.org Cc: r-help-requ...@stat.math.ethz.ch Dear all, I am looking for an R function which does stepwi

[R] connection problem

2011-05-25 Thread rgui
Hi, I have a problem during choosing a Cran mirror, a&n error messages comes: > In open.connection (con, "r") connection to 'cran.r-project.org' impossible to prt 80. I don't know why? can you help me to choose a cran mirror. thanks for any suggestion. -- View this message in contex

[R] approximate function and find local peaks (Maxima or Minima)

2011-05-25 Thread Michael S.
Hi, I have a data-matrix: > CB                    Zeit                Low 2   2011-05-02 08:05:05 7596.0 3   2011-05-02 08:10:06 7593.5 4   2011-05-02 08:15:11 7594.5 5   2011-05-02 08:20:15 7597.5 6   2011-05-02 08:25:18 7595.0 7   2011-05-02 08:30:20

[R] combined odds ratio

2011-05-25 Thread linda Porz
Dear all, I am looking for an R function which does stepwise selection cox model in r (delta chisq likelihood ratio test) similar to the stepwise, pe (0.05) lr: stcox in STATA. I am very thankful for any reply. Regards, Linda [[alternative HTML version deleted]] ___

[R] Print the content of several columns in only one

2011-05-25 Thread zoe.cryocla
Hi, I’m an R beginner and I'd really appreciate an hand… I'd like to create a new column in a dataframe in wich will be print the content of several other columns. For instance : I’ve got 2 columns : "site" – "sampling number" and I would like to create a third column "ID", in wich will appear b

[R] select levels of factor variables

2011-05-25 Thread zoe.cryocla
Hi again, I've got another question... I often use the symbol == to select some levels of factor variables like : data[data$var=="blabla", [ But this time, I'd like to select all the levels of my variable wich contain the letter "B", is that a way to determine this conditions ? Thanks a lot !

[R] issues with rJava; cannot run JRI example

2011-05-25 Thread Ajaya Mishra
Hello, I am trying to run JRI example from rJava, but I have some issues. I have read many posts and didn't find any solution to my problem. I have the following code: Rengine re = new Rengine(null, false, null); System.out.println("Rengine created, waiting for R"); if (!re.waitForR()

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