Re: [R] Tukey HSD Test als Post Hoc Test nach einem GLM inkl. Anova

2010-10-04 Thread Spencer Graves
install.packages('sos') # if you do not already have it library(sos) TH <- ???TukeyHSD #found 27 matches; retrieving 2 pages TH # The print method displays the results in a table in a web browser This suggests you might also be interested in "multcompView". Unfortunately, I failed to

Re: [R] R-help

2010-10-04 Thread Jeffrey Spies
As Joshua said, in your example sim isn't be declared anywhere (neither in the environment nor as an argument in a function), but you might try something more R-ish: prop.doubles <- function(sim){ sum(sample(1:6, sim,replace=T)==sample(1:6,sim,replace=T))/sim } prop.doubles(1000) Cheers, Jef

Re: [R] Tukey HSD Test als Post Hoc Test nach einem GLM inkl. Anova

2010-10-04 Thread Peter Dalgaard
Please, the language of the mailing list is English. A majority of readers do not understand what you are talking about. The Tukey test was designed for comparing means in equal replication ANOVA. Some "folklore" suggests that it may work reasonably for not-too-unequal replication cases, but I wou

Re: [R] R-help

2010-10-04 Thread Joshua Wiley
On Mon, Oct 4, 2010 at 9:13 PM, Lemarian WallaceIII wrote: > Im trying to simulate the rolling of a pair of dice > > this is my function: > #function to simulate tosses of a pair of dice > #from the simulation, the program returns the empirical probability of > #observing a double > count <- 0 > f

Re: [R] accessing elements located after $ symbol

2010-10-04 Thread Joshua Wiley
Dear Lorenzo, This is the trade off that comes with convenience. The `$` operator passes its argument directly as I understand it. This is what lets you pass unquoted names that not variables. The way around it is to use the `[` extraction operator. Look at these examples: test[interest] #or

[R] Petit traité de programmation orienté obje t sous R

2010-10-04 Thread Christophe Genolini
Bonjour (English below) J'ai le plaisir de vous annoncer la naissance de : "Petit traité de programmation orienté objet sous R", aux éditions De Boeck. J'y raconte comment faire de la programmation orienté objet S4, mais aussi comment construire un package. Le style est volontairement léger,

[R] Tukey HSD Test als Post Hoc Test nach einem GLM inkl. Anova

2010-10-04 Thread Lena Neuenkamp
Hallo, zur Analyse von Daten zum Artenreichtum von Pflanzen, habe ich ein Glm (glm) und anschlieÃend eine Anova (anova) durchgeführt. Nun möchte ich für die signifikanten Einflussfaktoren einen Post Hoc Tukey Test durchführen, um zu ermitteln in wie weit die einzelnen Fakt

[R] R-help

2010-10-04 Thread Lemarian WallaceIII
Im trying to simulate the rolling of a pair of dice   this is my function: #function to simulate tosses of a pair of dice #from the simulation, the program returns the empirical probability of #observing a double count <- 0 for(j in 1:sim){#begin loop die1 <- sample(1:6,1) print(die1) die2 <- samp

[R] binary tree construction in R

2010-10-04 Thread kateg
Hi all, I'm very new to R and I'm trying to construct a threaded binary tree using recursive functions. I'm very confused was wondering if anyone had any R sample code they would share. I've come across a lot of C++ code(nothing in R) and this is not helping. best, MK -- View this message

[R] accessing elements located after $ symbol

2010-10-04 Thread Lorenzo Cattarino
Hi R-users I am having troubles accessing elements after the $ symbol. Reproducible example: >test <- data.frame (first=1:10, second=11:20, third=21:30) >test$first #this works fine but when I try >interest <- "first" >test$interest # does not seem to work Could you tell me w

Re: [R] Creating R objects in Java

2010-10-04 Thread Michael Bedward
Nice ! I didn't know about RCaller. Michael On 5 October 2010 15:57, bytecode wrote: > > you can use RCaller to call R scripts and handle R variables from Java > using > a simple way. > http://www.mhsatman.com/rcaller.php > > -- > View this message in context: > http://r.789695.n4.nabble.com

Re: [R] Read file

2010-10-04 Thread Gabor Grothendieck
On Sat, Oct 2, 2010 at 11:31 PM, Nilza BARROS wrote: > Dear R-users, > > I would like to know how could I read a file with different lines lengths. > I need read this file and create an output to feed my database. > So after reading I'll need create an output like this > > "INSERT INTO TEMP (DATA,

Re: [R] R squared for lm prediction

2010-10-04 Thread Jeff Newmiller
Or use the summary function on the lm object. "Thomas Stewart" wrote: >I'm not sure I understand what you want, but here is a guess. > >Let y be the hold out response values. Let y.hat be the model predictions >for the corresponding ys. > >The key is to remember that R^2 = cor( y , y.hat )^2. >

Re: [R] Creating R objects in Java

2010-10-04 Thread bytecode
you can use RCaller to call R scripts and handle R variables from Java using a simple way. http://www.mhsatman.com/rcaller.php -- View this message in context: http://r.789695.n4.nabble.com/Creating-R-objects-in-Java-tp2904497p2955419.html Sent from the R help mailing list archive at Nabble.co

Re: [R] adding a legend to the plot (but outside of it)

2010-10-04 Thread Thomas Stewart
Right before the plot statement add: par(mar=c(5,4,4,6),xpd=F) then at the end add legend(par()$usr[2], mean(par()$usr[3:4]), c("Blue","Yellow","Green","Orange"), xpd=T, bty="n", pch=15, col=c("Blue","Yellow","Green","Orange")) On Mon, Oct 4, 2010 at 5:16 PM, Dimitri Liakhovitski <

Re: [R] R squared for lm prediction

2010-10-04 Thread Thomas Stewart
I'm not sure I understand what you want, but here is a guess. Let y be the hold out response values. Let y.hat be the model predictions for the corresponding ys. The key is to remember that R^2 = cor( y , y.hat )^2. So, cor( cbind(y,y.hat))[1,2]^2 should give you a measure you want. -tgs On

Re: [R] R squared for lm prediction

2010-10-04 Thread Joshua Wiley
Hi Brima, # Fit model model.lm <- lm(Sepal.Length ~ Petal.Length, data = iris[1:75,]) # Predict data for some new data pred.dat <- predict(model.lm, newdata = iris[76:150,]) # Calculate correlation between predicted values for new data # and actual values, then square cor(iris[1:75,"Sepal.Lengt

[R] R squared for lm prediction

2010-10-04 Thread Brima
Hi all, I have used a hold out sample to predict a model but now I want to compute an R squared value for the prediction. Any help is appreciated. Best regards -- View this message in context: http://r.789695.n4.nabble.com/R-squared-for-lm-prediction-tp2955328p2955328.html Sent from the R help

Re: [R] forecasting from a linear regression

2010-10-04 Thread Brima
Hi all, I have used the predict function to forecast values but now I would like to compute an R squared value for the prediction based on the original model. Any suggestions? -- View this message in context: http://r.789695.n4.nabble.com/forecasting-from-a-linear-regression-tp2717125p2955325.

Re: [R] Combinations

2010-10-04 Thread Arun.stat
Dear , 15 is very big number for me (perhaps for R as well :() so I have tried following: mat <- expand.grid(rep(list(c("1", "X", "2")),4)); mat[mat[,3]=="2",] -- View this message in context: http://r.789695.n4.nabble.com/Combinations-tp2955065p2955338.html Sent from the R help mailing l

Re: [R] Read file

2010-10-04 Thread jim holtman
Is this what you are looking for: > input <- readLines(textConnection(" 2010 10 01 00 + *82599 -35.25 -5.91 52 1* + 1008.0 -115 3.1 298.6 294.6 64 + 2010 10 01 00 + *83649 -40.28 -20.26 4 7 + *1011.0 - 0 0.0 298.4 296.1 64 + 1000.0 96 40

Re: [R] Reading data into

2010-10-04 Thread jim holtman
try this: > input <- readLines(textConnection("a1 89 2 > 79 392 + b 3 45 4 65")) > closeAllConnections() > # now parse each line to create a dataframe with each row being the score > result <- NULL > for

Re: [R] Read file

2010-10-04 Thread Nilza BARROS
Sorry, guys I couldn`t explain what I really wanted. I have a file with many station and many information for each one. I need identified the line where the station information start. After that I`d like to store that data (related to the station) so as to it could be work in separate way. If I w

Re: [R] Using as.polynomial() over a matrix

2010-10-04 Thread Nikhil Kaza
it looks like as. polynomial merely stores the coefficients of the polynomial. "Internally, polynomials are simply numeric coefficient vectors of class "polynomial". " If you really want to print it in the form you want try this. m <- matrix(rnorm(3000),1000,3) apply(m, 1, function(x){

[R] Using as.polynomial() over a matrix

2010-10-04 Thread Raznahan, Armin (NIH/NIMH) [E]
Hello All First - a warning. I'm not very R or programming savvy. I am trying to do something without much luck, and have scoured help-pages, but nothing has come up. Here it is: I have a matrix (m) of approx 40,000 rows and 3 columns, filled with numbers. I would like to convert the contents

Re: [R] For help on Open .tar.gz file in R under Windows

2010-10-04 Thread Jeffrey Spies
read.table('path.to.file.tar.gz') or any of its derivatives (read.csv, read.csv2, etc.). Of course you'll need to set the arguments appropriately. For example: read.table('path.to.comma.delimited.tar.gz', sep=",", header=T) Cheers, Jeff. On Mon, Oct 4, 2010 at 6:48 PM, wenyue sun wrote: > Hey

Re: [R] For help on Open .tar.gz file in R under Windows

2010-10-04 Thread Ben Bolker
wenyue sun gmail.com> writes: > I am new in R. Need help on code that can open the .tar.gz file in R under > Windows. Can any one help. Maybe untar(tarfile,compressed="gzip") ? According to ?untar it seems that just untar(tarfile) might work ... ___

Re: [R] how to make list() return a list of *named* elements

2010-10-04 Thread Hans Ekbrand
On Mon, Oct 04, 2010 at 04:10:46PM +0200, Christophe Pallier wrote: > See llist from Hmisc package: > > library(Hmisc) > a=rnorm(10) > b=rnorm(5) > llist(a,b) Ah, that seems like what I want! My old, ugly and redunant code looked like this list(utdrag=utdrag, n.fires.at.sites.with.one

Re: [R] how to make list() return a list of *named* elements

2010-10-04 Thread Gabor Grothendieck
On Mon, Oct 4, 2010 at 8:27 PM, Hans Ekbrand wrote: > On Mon, Oct 04, 2010 at 10:07:06AM -0400, Gabor Grothendieck wrote: >> Some small tweaks.   If you use simplify=FALSE then it will guarantee >> that a list is returned: >> >>    sapply(my.names, get, simplify = FALSE) >> >> for example, compare

Re: [R] how to make list() return a list of *named* elements

2010-10-04 Thread Hans Ekbrand
On Mon, Oct 04, 2010 at 10:07:06AM -0400, Gabor Grothendieck wrote: > Some small tweaks. If you use simplify=FALSE then it will guarantee > that a list is returned: > >sapply(my.names, get, simplify = FALSE) > > for example, compare the outputs of: > >sapply(c("letters", "LETTERS"), ge

Re: [R] Simultaneous equation with one ordinal reponses

2010-10-04 Thread Bill.Venables
R packages do not solve modelling problems. They can be used to solve computational problems. Wouldn't it be a better plan to sort out what kind of models you want to investigate to address your research questions first? Then, and only then, can you sensibly look around for packages that migh

[R] Fixed variance structure for lme

2010-10-04 Thread joanne ellis
I have a data set with 50 different x values and 5 values for the sampling variance; each of the 5 sampling variances corresponds to 10 particular x values. I am trying to fit a mixed effect linear model and I'm not sure about the syntax for specifying the fixed variance structure. In Pinheiro's

[R] Simultaneous equation with one ordinal reponses

2010-10-04 Thread Zhiyuan Jason ZHENG
Dear R users, I had a research question which involves a simultaneous equation system, one is the common continuous dependent variable, y1, say wage, or log wage, another one is a latent variable, y*, which I only observe up to a ordinal scale, say attitudes toward a problem, taking values as y

[R] For help on Open .tar.gz file in R under Windows

2010-10-04 Thread wenyue sun
Hey All, I am new in R. Need help on code that can open the .tar.gz file in R under Windows. Can any one help. Thanks in Advance. Wayne [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/l

Re: [R] Loop too slow for Bid calc - BUT cannot figure out how to do with matrix

2010-10-04 Thread Martin Morgan
On 10/04/2010 02:29 PM, rivercode wrote: > > Hi, > > I am trying to create Bid/Ask for each second from a high volume stock and > the only way I have been able to solve this is using loops to create the > target matrix from the source tick data matrix. Looping is too slow and > not practical to

Re: [R] Script auto-detecting its own path

2010-10-04 Thread steven mosher
in the package R.utils getAbsolutePath() or you can do a file.list(.. full.names=TRUE, recursive=TRUE,pattern="(.R)") the rest will require grep and pulling the file name and directory path apart If its not evident just ask and I'll write something for you. basically you want a call t

Re: [R] trouble with RODBC -- chopping off part of column names

2010-10-04 Thread Mike Williamson
Marc, et. al, Below are all of the pertinent version info. However, I think versions, etc., are somewhat irrelevant. Instead, somewhere there must be an environment variable or something that 'R' is talking to that is forcing the column name to fit within a set column width, and I need to ei

Re: [R] source package build/installation with subdirectory-lib

2010-10-04 Thread Murat Tasan
so i've narrowed it down to a case that works, and one that doesn't (but i think should?) here's the working Makevars file (copied directly): -- WORKING EXAMPLE JANSSON_DIR = $(PWD)/jansson-1.3 JANSSON_LIB_DIR = $(PWD)/jansson-1.3/lib JANSSON_INCLUDE_DIR =

Re: [R] Ranked Set Sampling

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 5:22 PM, Ahmed Albatineh wrote: > Thanks to all who took the time to write. I have done my job of > searching before posting the query, ... but offered no evidence of such efforts in your posting > I am a graduate of Western Michigan University and Joe McKean is my

Re: [R] Loop too slow for Bid calc - BUT cannot figure out how to do with matrix

2010-10-04 Thread Duncan Murdoch
On 04/10/2010 5:29 PM, rivercode wrote: Hi, I am trying to create Bid/Ask for each second from a high volume stock and the only way I have been able to solve this is using loops to create the target matrix from the source tick data matrix. Looping is too slow and not practical to use on multip

[R] Loop too slow for Bid calc - BUT cannot figure out how to do with matrix

2010-10-04 Thread rivercode
Hi, I am trying to create Bid/Ask for each second from a high volume stock and the only way I have been able to solve this is using loops to create the target matrix from the source tick data matrix. Looping is too slow and not practical to use on multiple stocks. For example: Bids Matrix (a r

Re: [R] source package build/installation with subdirectory-lib

2010-10-04 Thread Murat Tasan
i've simplified this process to illustrate what i'm not getting (i.e. doing wrong) regarding Makevars: take any R source package of yours (best to pick one that hasn't ever needed a Makevars file), and add a Makevars in src with: .PHONY: all testtarget all: $(SHLIB) $(SHLIB): testtarget testta

Re: [R] Ranked Set Sampling

2010-10-04 Thread Ahmed Albatineh
Thanks to all who took the time to write. I have done my job of searching before posting the query, I am a graduate of Western Michigan University and Joe McKean is my adviser and studied his book "Robust Nonparametric Statistical Methods" "as Robust class textbook. THERE IS NOTHING there that disc

Re: [R] vectorizing problem

2010-10-04 Thread Gabor Grothendieck
On Mon, Oct 4, 2010 at 2:39 PM, Gabor Grothendieck wrote: > On Mon, Oct 4, 2010 at 1:54 PM, Dylan Miracle wrote: >> Hello, >> >> I have a two column dataframe that >> has entries that look like this: >> >> 2315100       NR_024005,NR_024004,AK093685 >> 2315106       DQ786314 >> >> and I want to ch

Re: [R] Ridge regression and mixed models

2010-10-04 Thread Dimitri Liakhovitski
Curious - what would be the purpose of this regression? On Mon, Oct 4, 2010 at 4:39 PM, harez...@post.harvard.edu wrote: > Dear R users, >  An equivalence between linear mixed model formulation and penalized > regression > models (including the ridge regression and penalized regression splines)

[R] adding a legend to the plot (but outside of it)

2010-10-04 Thread Dimitri Liakhovitski
Hello! My code below creates a data frame and a plot for it. However, I can't figure out how to add a legend that is not ON the plot itself, but outside of it (e.g., to the right of my graph or below it). I tried something: I put a line par(xpd=T, mar=par()$mar+c(0,0,0,4)) right before my plot com

Re: [R] reducing distances between tickmarks

2010-10-04 Thread Dimitri Liakhovitski
Thanks a lot, David. It helped. Here is my solution: Instead of 2 last lines of the code: grid(nx=NULL,ny=NULL,col = "lightgray", lty = "dotted",lwd = par("lwd")) axis(1, las = 2) I have now: axis(1, labels =format(as.Date(my.data$date, origin="1970-01-01"), "%Y-%m-%d"), at=my.data$date, las=2,c

[R] Combinations

2010-10-04 Thread Trying To learn again
Hi all, I´ve been ill and I have lost a lot of time without seen the pc. I want you to help if you can if you want. Only I need an initial guide. I´ve been out a lot of time and I need a hope. Is only for "joby" purposes. The problem: I want to simulate each of the posible combination in a pla

[R] Globbing inconsistencies, dir() vs. unlink()

2010-10-04 Thread Ken Williams
I was trying to remove a directory and couldn't figure out why it was failing: > dir("~/p4/r-packages/IREval/Users", recursive=T) [1] "u0048513/p4/r-packages/IREval/DESCRIPTION" [2] "u0048513/p4/r-packages/IREval/R/IREval.R" [3] "u0048513/p4/r-packages/IREval/Read-and-delete-me" [4] "u0048513/p4/r

Re: [R] Fisher exact test?

2010-10-04 Thread Peter Dalgaard
On 10/04/2010 09:09 PM, James Nead wrote: > Hi Thomas, > > Thanks for the reply. > > 1. In the first pick, I draw 'A' genes from N, without replacement. > 2. Similarly, in the second pick, I draw 'B' genes from N, without > replacement > (and 'C' genes from 'N' etc.) > 3. Order does not matter

[R] source package build/installation with subdirectory-lib

2010-10-04 Thread Murat Tasan
hi all - i have a source package i'm writing that i'd like to be able to install with a special library that my R src files rely on. to be more precise, i have a normal R package directory structure (i.e. src/ R/ man/ DESCRIPTION NAMESPACE etc.). i also have another directory here called depPkg, an

Re: [R] Format of Output of Residuals

2010-10-04 Thread Michael Just
Thank you this was worked great. Thank you for the additional information as well. Knowledge is power. Cheers, Michael On Fri, Oct 1, 2010 at 5:34 AM, Dennis Murphy wrote: > > Hi: > > CW.lm <- lm(weight ~ Diet, ChickWeight) > resid.CW.lm <- resid(CW.lm) > as.data.frame(resid(CW.lm))[1:10, ] 

[R] Ridge regression and mixed models

2010-10-04 Thread harez...@post.harvard.edu
Dear R users, An equivalence between linear mixed model formulation and penalized regression models (including the ridge regression and penalized regression splines) has proven to be very useful in many aspects. Examples include the use of the lme() function in the library(nlme) to fit smooth

[R] Reading data into

2010-10-04 Thread Federman, Douglas
I have data in the following form: judge poster score poster score poster score a1 89 2 79 392 b 3 45 4 65 and am trying to get it to the following: Poster Judge_A Judge_B Judge_C 1

Re: [R] reducing distances between tickmarks

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 3:28 PM, Dimitri Liakhovitski wrote: Hello, everybody! I have a code below that creates a data set and then a stacked bar chart based on that data set. No need to look at it - just notice please that my horizontal axis is a date varible (x=my.data$date). I have a question abo

Re: [R] Debye function

2010-10-04 Thread Christophe Dutang
Thank you for your time. I'm looking for another package than the gsl package. But it does not seem to be implemented anywhere else. Christophe Le 4 oct. 2010 à 19:10, Bert Gunter a écrit : > Well, not really ... > > Google on "R package Debye" . The 5th hit lists the gsl package with > the d

[R] reducing distances between tickmarks

2010-10-04 Thread Dimitri Liakhovitski
Hello, everybody! I have a code below that creates a data set and then a stacked bar chart based on that data set. No need to look at it - just notice please that my horizontal axis is a date varible (x=my.data$date). I have a question about the last 2 lines of this code: grid(nx=NULL,ny=NULL,col =

Re: [R] Script auto-detecting its own path

2010-10-04 Thread Hadley Wickham
> I'm not sure this will solve the issue because if I move the script, I would > still have to go into the script and edit the "/path/to/my/script.r", or do > I misunderstand your workaround? > I'm looking for something like: > file.path.is.here("myscript.r") > and which would return something like

Re: [R] Fisher exact test?

2010-10-04 Thread James Nead
Hi Thomas, Thanks for the reply. 1. In the first pick, I draw 'A' genes from N, without replacement. 2. Similarly, in the second pick, I draw 'B' genes from N, without replacement (and 'C' genes from 'N' etc.) 3. Order does not matter - so the two cases you cited are equivalent. I would like to

Re: [R] Plot for Binomial GLM

2010-10-04 Thread Joshua Wiley
Hi, Dennis was kind of enough to remind me that glm() can take a two column matrix, which is probably what you did with deadalive. He also gave a rather elegant graphing solution using xyplot: xyplot(Alive/20 ~ Dose, data = rat.toxic, groups = Sex, type = c('p', 'a')) Josh On Mon, Oct 4, 2010

Re: [R] Plot for Binomial GLM

2010-10-04 Thread Peter Ehlers
On 2010-10-04 8:21, klsk89 wrote: Hi i would like to use some graphs or tables to explore the data and make some sensible guesses of what to expect to see in a glm model to assess if toxin concentration and sex have a relationship with the kill rate of rats. But i cant seem to work it out as i

Re: [R] Help with apply

2010-10-04 Thread Joshua Wiley
Hi, It seemed to me like the calculations were implemented in a bit of a redundant way, so I tried to simplify it algebraically. doit1 is Phil's version of your original calculations, and doit2 is my simplified way. doit1 <- function(i, j) { exp(sum(log((exp(tmp[i,] * (qq$nodes[j]-b)))/

Re: [R] Generating weekdays only

2010-10-04 Thread Greg Snow
Here is one way: > mydays <- seq(as.Date("2010-01-01"), as.Date("2010-02-01"), by="1 day") > myweekdays <- mydays[ ! weekdays(mydays) %in% c('Saturday','Sunday') ] > myweekdays [1] "2010-01-01" "2010-01-04" "2010-01-05" "2010-01-06" "2010-01-07" [6] "2010-01-08" "2010-01-11" "2010-01-12" "2010-0

Re: [R] Generating weekdays only

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 2:07 PM, Ron Michael wrote: Dear all, can anyone please tell me how to generate a sequence of days continuously, however without considering weekends i.e. Saturday and Sunday? I am aware of following code: seq(as.Date("2010-01-01"), as.Date("2010-02-01"), by="1 day") [

Re: [R] title and axis labels placement with layout

2010-10-04 Thread Greg Snow
You might want to look at the addtable2plot function in the plotrix package as an alternative for your tables. For placing titles/labels/etc. look at the grconvertX and grconvertY functions for ways to get coordinates based on the device converted to other coordinate systems. You can use those

Re: [R] Include externally generated pdf in output (without Sweave)

2010-10-04 Thread Greg Snow
Importing as pixel image then replotting will probably reduce the quality of the graph. Another approach is to use the pdftk program (I have seen versions for unix and windows) to add/insert the original pdf page into your document. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Inter

[R] Generating weekdays only

2010-10-04 Thread Ron Michael
Dear all, can anyone please tell me how to generate a sequence of days continuously, however without considering weekends i.e. Saturday and Sunday? I am aware of following code: > seq(as.Date("2010-01-01"), as.Date("2010-02-01"), by="1 day")  [1] "2010-01-01" "2010-01-02" "2010-01-03" "2010-01-0

[R] title and axis labels placement with layout

2010-10-04 Thread Daryl Morris
Hello, I'm writing a set of functions which we will use with a bunch of different datasets. The functions create a set of graphics pages, with each page split into an upper panel with plots and a lower panel with tables. The plots part might have one plot, or might have multiple. I'm usin

Re: [R] vectorizing problem

2010-10-04 Thread Gabor Grothendieck
On Mon, Oct 4, 2010 at 1:54 PM, Dylan Miracle wrote: > Hello, > > I have a two column dataframe that > has entries that look like this: > > 2315100       NR_024005,NR_024004,AK093685 > 2315106       DQ786314 > > and I want to change this to look like this: > > 2315100       NR_024005 > 2315100    

Re: [R] Inserting a plot into another

2010-10-04 Thread Filoche
Hi Greg. Thank you for the time you took to look at my problem. I'll try your solution until CRAN is updated. With regards, Phil -- View this message in context: http://r.789695.n4.nabble.com/Inserting-a-plot-into-another-tp2720936p2954769.html Sent from the R help mailing list archive at Na

Re: [R] Reading Strings in R

2010-10-04 Thread Greg Snow
Use scan whith what='' or read.table with colClasses='character'. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behal

Re: [R] input matrix for leaps algorithm

2010-10-04 Thread Greg Snow
The regsubsets function in the leaps package can work with fewer points than variables. Though the meaning will be questionable. The lasso (lasso2 or lars packages) may be more informative for your situation. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare gre

[R] Roxygen not truncating files

2010-10-04 Thread Ken Williams
I'm trying to use Roxygen for the first time, but I'm running into trouble. I call it like so: roxygenize('~/p4/r-packages/IREval', '~/p4/r-packages/IREval', unlink.target=T) But it seems that it's only appending to files in ~/p4/r-packages/IREval/man/, not overwriting them. So fo

[R] Null values from DBI connection

2010-10-04 Thread Albert Vernon Smith
I am connecting to an Oracle database with RJDBC, and creating a data frame with dbGetQuery. When I get values return, values which are NULL in the database are being returned as 0 from my query. How can I have them returned as ? I am query like the following. -- require(RJDBC) drv <- JDBC

Re: [R] Help with apply

2010-10-04 Thread Doran, Harold
A, I see that you wrapped apply around mapply. I was toying with both; but didn't think to use mapply inside apply. As always, thank you, Phil -Original Message- From: Phil Spector [mailto:spec...@stat.berkeley.edu] Sent: Monday, October 04, 2010 2:20 PM To: Doran, Harold Cc: Gabriel

Re: [R] Help with apply

2010-10-04 Thread Phil Spector
Harold - The first way that comes to mind is doit = function(i,j)exp(sum(log((exp(tmp[i,]*(qq$nodes[j]-b))) / (factorial(tmp[i,]) * exp(exp(qq$nodes[j]-b)) * ((1/(s*sqrt(2*pi))) * exp(-((qq$nodes[j]-0)^2/(2*s^2/ dnorm(qq$nodes[j]) * qq$weights[j] t(outer(1:3,1:2,V

[R] glmer or not - glmer model specification

2010-10-04 Thread Atle Torvik Kristiansen
Hello, I'm having some trouble figuring out the correct model specification for my data. The system consists of multiple populations of an organism, which have been genetically sampled for several years. The problem is this: A minority of individuals are found in more than one sample, either they

Re: [R] vectorizing problem

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 2:02 PM, Henrique Dallazuanna wrote: Try this: do.call(rbind.data.frame, mapply(cbind, DF$V1, strsplit(as.character(DF$V2), ","))) Also try: > txt V1 V2 1 2315100 NR_024005,NR_024004,AK093685 2 2315106 DQ786314 > st

Re: [R] vectorizing problem

2010-10-04 Thread Dimitris Rizopoulos
try this: GPL <- data.frame(x = c(2315100, 2315106), y = c("NR_024005,NR_024004,AK093685", "DQ786314")) sp <- strsplit(as.character(GPL$y), ",") ni <- sapply(sp, length) data.frame(x = rep(GPL$x, ni), y = unlist(sp)) I hope it helps. Best, Dimitris On 10/4/2010 7:54 PM, Dylan Miracle wr

Re: [R] vectorizing problem

2010-10-04 Thread Henrique Dallazuanna
Try this: do.call(rbind.data.frame, mapply(cbind, DF$V1, strsplit(as.character(DF$V2), ","))) On Mon, Oct 4, 2010 at 2:54 PM, Dylan Miracle wrote: > Hello, > > I have a two column dataframe that > has entries that look like this: > > 2315100 NR_024005,NR_024004,AK093685 > 2315106 DQ7

[R] vectorizing problem

2010-10-04 Thread Dylan Miracle
Hello, I have a two column dataframe that has entries that look like this: 2315100 NR_024005,NR_024004,AK093685 2315106 DQ786314 and I want to change this to look like this: 2315100 NR_024005 2315100 NR_024004 2315100 AK093685 2315106 DQ786314 I can do this

Re: [R] Help with apply

2010-10-04 Thread Joshua Wiley
On Mon, Oct 4, 2010 at 10:44 AM, Gabriela Cendoya wrote: > You are missing "s" in your definitions so I can't reproduce your code. When he uses apply(), he sets s = 1. > >> tmp <- data.frame(var1 = sample(c(0:10), 3, replace = TRUE), var2 = >> sample(c(0:10), 3, replace = TRUE), var3 = sample(c

Re: [R] Help with apply

2010-10-04 Thread Doran, Harold
Sorry about that; s <- 1 -Original Message- From: Gabriela Cendoya [mailto:gabrielacendoya.rl...@gmail.com] Sent: Monday, October 04, 2010 1:44 PM To: Doran, Harold Cc: R-help Subject: Re: [R] Help with apply You are missing "s" in your definitions so I can't reproduce your code. > tmp

Re: [R] Help with apply

2010-10-04 Thread Gabriela Cendoya
You are missing "s" in your definitions so I can't reproduce your code. > tmp <- data.frame(var1 = sample(c(0:10), 3, replace = TRUE), var2 = > sample(c(0:10), 3, replace = TRUE), var3 = sample(c(0:10), 3, replace = TRUE)) > > str(tmp) 'data.frame': 3 obs. of 3 variables: $ var1: int 9 3 9

Re: [R] Inserting a plot into another

2010-10-04 Thread Greg Snow
OK, I found the bug in subplot (it was never tested with multiple figures). The bug has been fixed, but probably won't make it to CRAN any time soon. In the meantime there are a couple of work arounds. 1. create your own local copy of subplot and edit it so that the 1st 3 lines of the body ar

Re: [R] Error message with scan() function

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 12:51 PM, Tariq Perwez wrote: Hi Everyone, I am new R user and am trying to learn by reading the online manual "An Introduction to R" from the R web site. I am trying to practice using the scan() function as explained in the manual. For this I first created three vect

Re: [R] Debye function

2010-10-04 Thread Bert Gunter
OOPs. I Only read Spencer's reply. Sorry for repeating the poster's original comment. -- Bert On Mon, Oct 4, 2010 at 10:10 AM, Bert Gunter wrote: > Well, not really ... > > Google on "R package Debye" . The 5th hit lists the gsl package with > the debye() function. > > Moral: DO make use of stan

Re: [R] Debye function

2010-10-04 Thread Bert Gunter
Well, not really ... Google on "R package Debye" . The 5th hit lists the gsl package with the debye() function. Moral: DO make use of standard professional search tools, also. -- Bert On Mon, Oct 4, 2010 at 9:13 AM, Spencer Graves wrote: > > install.packages('sos') # if not already installed >

[R] Help with apply

2010-10-04 Thread Doran, Harold
Suppose I have the following data: tmp <- data.frame(var1 = sample(c(0:10), 3, replace = TRUE), var2 = sample(c(0:10), 3, replace = TRUE), var3 = sample(c(0:10), 3, replace = TRUE)) I can run the following double loop and yield what I want in the end (rr1) as: library(statmod) Q <- 2 b <- runif

[R] Error message with scan() function

2010-10-04 Thread Tariq Perwez
Hi Everyone, I am new R user and am trying to learn by reading the online manual "An Introduction to R" from the R web site. I am trying to practice using the scan() function as explained in the manual. For this I first created three vectors (one a character vector and two numeric one) and saved f

[R] read columns of quoted numbers as factors

2010-10-04 Thread james hirschorn
Suppose I have a data file (possibly with a huge number of columns), where the columns with factors are coded as "1", "2", "3", etc ... The default behavior of read.table is to convert these columns to integer vectors. Is there a way to get read.table to recognize that columns of quoted number

Re: [R] Debye function

2010-10-04 Thread Spencer Graves
install.packages('sos') # if not already installed library(sos) Debye <- ???Debye #found 4 matches Debye # "Print method opens table in a web browser Conclusions: 1. There are references to Debye in the "CHNOSZ" package, but it may not be what you want. 2.

[R] Error during scp transfer

2010-10-04 Thread wesley mathew
Dear all I am implement one grid computing system using GridR package. I am working on windows platform. I did all the configuration according to the GridR tutorial. But it has some errors when I execute grid.apply function. Here is the output from stderr: R: not found java.io.IOException: Error d

[R] Debye function

2010-10-04 Thread Christophe Dutang
Dear list, Is there another package than gsl* where the Debye function (of first order) is implemented? Google only finds the gsl package. Thanks in advance Christophe * page 12 of reference manual of gsl. http://cran.r-project.org/web/packages/gsl/gsl.pdf -- Christophe DUTANG Ph. D. student a

Re: [R] plotmath: how to use greek symbols in expression(integral(f(tau)*dtau, 0, t))?

2010-10-04 Thread David Winsemius
On Oct 4, 2010, at 10:11 AM, Thomas Stewart wrote: Try expression(paste(integral(),"f(",tau,") d",tau,sep=""))) it works for me. It does "work" (albeit without properly including the requested limits of integrations), but if it is used as a teaching example, it will obscure the syntax o

Re: [R] Splitting a DF into rows according to a column

2010-10-04 Thread peter dalgaard
On Oct 4, 2010, at 16:57 , Johannes Graumann wrote: > Hi, > > I'm turning my wheels on this and keep coming around to the same wrong > solution - please have a look and give a hand ... > > The premise is: a DF like so > >> loremIpsum <- "Lorem ipsum dolor sit amet, consectetur adipiscing elit

Re: [R] Plot for Binomial GLM

2010-10-04 Thread Joshua Wiley
On Mon, Oct 4, 2010 at 7:21 AM, klsk89 wrote: > > Hi i would like to use some graphs or tables to explore the data and make > some sensible guesses of what  to expect to see in a glm model to assess if > toxin concentration and sex have a relationship with the kill rate of rats. > But i cant seem

Re: [R] Issue with match.call

2010-10-04 Thread Hadley Wickham
> RFF<-function(qtype, qOpt,...){} > i.e., I have two args that are compulsary and the rest are optional. Now when > my user passes the function call, I need to see what optional args are > defined and process accordingly...what I have so far is.. > > RFF<-function(qtype, qOpt,...){ >        mc <

Re: [R] How many R packages are not free?

2010-10-04 Thread Paul Miller
Thanks to everyone who replied to my post. One person indicated that this question treads on "dangerous terrain." I had that sense too but really wanted to know how many packages might not be "free" in the sense that they could be used at no cost by everyone. I was a little disappointed to learn

[R] Plot for Binomial GLM

2010-10-04 Thread klsk89
Hi i would like to use some graphs or tables to explore the data and make some sensible guesses of what to expect to see in a glm model to assess if toxin concentration and sex have a relationship with the kill rate of rats. But i cant seem to work it out as i have two predictor variables~help?Th

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