Re: [R] Coding of categorical variables for logistic regression?

2010-03-29 Thread Daniel Malter
This is about the covariates, not the dependent variable. So a polynomial logistic regression seems hardly appropriate. David is right with his latest statement, just because they are ordered does not assure that the effect is monotonic. If the low, medium, and high groups had even spacing

Re: [R] a vectorized solution to some simple dataframe math?

2010-03-29 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 27.03.2010 11:53:30: Hi: Does this do what you want? # Create some fake data... df - data.frame(id = factor(rep(c('cell1', 'cell2'), each = 10)), cond = factor(rep(rep(c('A', 'B'), each = 5), 2)), time =

[R] create space for a matrix

2010-03-29 Thread leobon
Hello all, I want to creat a space for a matrix. For example, I have a matrix with the dimension of 1(row)*3(col), which is (2,3,4). Then I want to put this matrix into a new and larger matrix. The dimension of the new matrix is 3*3. So what I want is creating a new larger matrix which allows me

Re: [R] create space for a matrix

2010-03-29 Thread Giovanni Azua Garcia
Hi Leo, see the matrix function e.g. m - matrix(0, nrow=1, ncol=3) then you can use functions like rbind or cbind to create bigger ones. I am a newbie so double check everything :) HTH, Best regards, Giovanni On Mar 29, 2010, at 8:37 AM, leobon wrote: Hello all, I want to creat a space

Re: [R] Page width figures in Latex

2010-03-29 Thread Jim Lemon
bRotheRs (and sisteRs who might have responded after I posted this), My heartfelt thanks to you all. I had interpreted figure* as the command 'figure' with a wildcard after it, and assumed that I had to discover what arcane suffixes might be appended to figure. The following lines got the

Re: [R] create space for a matrix

2010-03-29 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 29.03.2010 08:41:15: Hi Leo, see the matrix function e.g. m - matrix(0, nrow=1, ncol=3) then you can use functions like rbind or cbind to create bigger ones. I am a newbie so double check everything :) HTH, Best regards, Giovanni

[R] Problem comparing logistic regression output with SPSS.

2010-03-29 Thread Ravi Kulkarni
Hello, I have a logistic regression model contrasts(z) = contr.helmert(4) mylogit = glm(binvar~x+y+z, family=binomial(logit)) summary(mylogit) where x is a ratio variable, y is categorical with two levels, z

[R] Need help on matrix manipulation

2010-03-29 Thread Ron_M
Dear all, Ket say I have 3 matrices : mat1 - matrix(rnorm(16), 4) mat2 - matrix(rnorm(16), 4) mat3 - matrix(rnorm(16), 4) Now I want to merge those three matrices to a single one with dimension 4*3=12 and 4 wherein on resulting matrix, row 1,4,7,10 will be row-1,2,3,4 of mat1, row 2,5,8,11

[R] Odp: Need help on matrix manipulation

2010-03-29 Thread Petr PIKAL
Hi One option (probably not the best one) is index an aggregate matrix mat - rbind(mat1, mat2, mat3) idx - seq(1,12, 4)+rep(0:3, each=3) mat - mat[idx, ] Regards Petr r-help-boun...@r-project.org napsal dne 29.03.2010 09:44:12: Dear all, Ket say I have 3 matrices : mat1 -

Re: [R] Need help on matrix manipulation

2010-03-29 Thread Dennis Murphy
Hi: This seems to work for your example: matrix(t(cbind(mat1, mat2, mat3)), ncol = 4, byrow = TRUE) HTH, Dennis On Mon, Mar 29, 2010 at 12:44 AM, Ron_M ron_michae...@yahoo.com wrote: Dear all, Ket say I have 3 matrices : mat1 - matrix(rnorm(16), 4) mat2 - matrix(rnorm(16), 4) mat3 -

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Barry Rowlingson
On Mon, Mar 29, 2010 at 4:02 AM, Ben Bolker bol...@ufl.edu wrote:  I'll be interested to hear what others come up with.  I'm not sure the problem as you have stated it is well-posed, or necessarily possible. Suppose there is a true unknown bivariate probability distribution with a

Re: [R] Simulation of VAR

2010-03-29 Thread Pfaff, Bernhard Dr.
Dear Ron, have you had a look at the package dse? Here, ARMA models can be specified and simulated. The only exercise left for you, is to transform the VECM coefficients into their level-VAR values. Best, Bernhard | -Original Message- | From: r-help-boun...@r-project.org |

Re: [R] cacheSweave fails when used in conjunction with rjags

2010-03-29 Thread Martyn Plummer
Hi Roger, If you do not supply an explicit data list, the jags.model() function will try to get the data from the calling environment. This is obviously not working with cacheSweave, but if you do supply an explicit list, like this: m - jags.model(j.bug, data=list(y=y)) it will work. Martyn

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Jim Lemon
On 03/29/2010 07:17 PM, Barry Rowlingson wrote: ... I think the problem as posed doesn't produce a unique ellipse. You could start with a circle of radius 0 centered on mean(x),mean(y) and then increase the radius until it has 95% of the points in it. As long as your points are in continuous

Re: [R] Simulation of VAR

2010-03-29 Thread Ron_M
Yes I looked into dse package. Here I have implemented two approach for simulation like following : library(dse) A1 - matrix(rnorm(16),4) A2 - matrix(rnorm(16),4) mu - rnorm(4) sigma - matrix(c(0.006594712, 0.006467731, -0.000254914, 0.005939934, 0.006467731, 0.006654184, -0.000384097,

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread S Ellison
The bagplot at http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=112 gives a nonparametric 2-d view analagous to a boxplot. S Ellison I can take the results of a simulation with one random variable and generate an empirical interval that contains 95% of the observations, e.g.,

[R] add sd to a plot

2010-03-29 Thread karine heerah
Hi, I would like to add sd bar to an existing plot. How can i do that? For example: library(MASS) x - rnorm(100) mean - mean(x) sd - sd(x) plot(mean) ## How can i add the sd bar around the mean point? thanks a lot Karine HEERAH Master 2 , océanographie et

[R] Error of a fit parameter, of the data set has errors itself?

2010-03-29 Thread Markus Schmotz
Hi out there, imagine you have a dataset (x,y) with errors f, so that each y_i is y_i +- f_i. This is the normal case for almost all measurements, since one quantity y can only be measured with a certain accuracy f. x-c(1,2,3) y-c(1.1,0.8,1.3) f-c(0.2,0.2,0.2) plot(x,y) #whereas every y has

[R] errors in package nortest

2010-03-29 Thread Robert Offinger
There are two errors in the R package nortest. I tried to contact the maintainer Juergen Gross but to no avail. How should one progress if the mail address is still valid but the maintainer does not answer or react in any way, e.g. since he left the university? The automatic R checking system for

Re: [R] Page width figures in Latex

2010-03-29 Thread Duncan Murdoch
Sharpie wrote: Jim Lemon wrote: bRotheRs sisteRs, I am once again attempting to learn enough Latex voodoo to get something done, and failing comically. The document RJAuthorguide.pdf mentions that one can get page width figures through the use of the figure* or table* environments, but

Re: [R] add sd to a plot

2010-03-29 Thread Jim Lemon
On 03/29/2010 08:45 PM, karine heerah wrote: Hi, I would like to add sd bar to an existing plot. How can i do that? Hi Karine, bar.err (agricolae) plotCI (gplots) xYplot (Hmisc) error.bars (psych) dispersion (plotrix) plotCI (plotrix) and probably a few more. Jim

[R] Combing

2010-03-29 Thread Val
Hi all, I want to combine two data sets (ZA and ZB to get ZAB). The common variable between the two data sets is ID. Data ZA ID F M 1 0 0 2 0 0 3 1 2 4 1 0 5 3 2 6 5 4 Data ZB ID v1 v2 v3 3 2.5 3.4 302 4 8.6 2.9 317 5 9.7 4.0 325 6 7.5 1.9 296 Output (ZAB) ID F M v1 v2

[R] inverse function of SSlogis

2010-03-29 Thread Kay Cichini
hello, is there a more convenient way to get the inverse of SSlogis than transforming the function by hand? thanks, kay -- View this message in context: http://n4.nabble.com/inverse-function-of-SSlogis-tp1694995p1694995.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Combing

2010-03-29 Thread jim holtman
?merge On Mon, Mar 29, 2010 at 7:13 AM, Val valkr...@gmail.com wrote: Hi all, I want to combine two data sets (ZA and ZB to get ZAB). The common variable between the two data sets is ID. Data ZA ID F M 1 0 0 2 0 0 3 1 2 4 1 0 5 3 2 6 5 4 Data ZB ID v1 v2 v3 3

[R] multiple plots on the same chart - zipf.fnc

2010-03-29 Thread ivrit
Hello, I have used the zipf.fnc several times and would like to draw now the Zipf curve of four different corpora on the same chart, present them one on top of the other. How do I go about it? Thanks a lot, Noam -- View this message in context:

[R] getting CI's for certain y of nls fitted curve

2010-03-29 Thread Kay Cichini
hello, i managed to get CI's for my curve - but now I need the intervall for a certain y point (y_tenth) of the curve.. can anyone help me with this? #data: por-data.frame(list(structure(list(run = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L), .Label = c(1, 3, 4), class =

[R] package earth - forward pass: out of memory error, how to resolve this?

2010-03-29 Thread vibha patel
Hello, while using earth function, I'm getting the out of memory error: the dataset is too small(dimension is displayed in code). how to resole this error? tr.sub1 - sample(1:nrow(HCMauto), .8 * nrow(HCMauto)) tst.sub1 - (1:nrow(HCMauto))[-tr.sub1] HCMm1 - earth(V1 ~ ., data =

[R] xyplot second y-xis and legend

2010-03-29 Thread robbert blonk
Dear list, I try to set a secondary y-axis in a lattice xyplot. This works. However, I am unable to set a proper legend/key together with the 2nd y-axis under general xyplot procedures. See example below. The combination of the par.settings with simpleTheme and other settings seems to go

Re: [R] inverse function of SSlogis

2010-03-29 Thread Gabor Grothendieck
Try this. More info at http://ryacas.googlecode.com : library(Ryacas) Asym - Sym(Asym); xmid - Sym(xmid); scal - Sym(scal) x - Sym(x); y - Sym(y) Solve(Asym/(1+exp((xmid-x)/scal))==y, x) expression(list(x == xmid - log(Asym/y - 1) * scal)) On Mon, Mar 29, 2010 at 7:24 AM, Kay Cichini

Re: [R] inverse function of SSlogis

2010-03-29 Thread Kay Cichini
hello gabor, thanks a lot for that. i'll try. best wishes, kay -- View this message in context: http://n4.nabble.com/inverse-function-of-SSlogis-tp1694995p1695061.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

[R] Legends for line and point data

2010-03-29 Thread Steve Murray
Dear all, I have a plot which contains 4 data series displayed using solid, dashed and dotted lines, and also points. How do I use lty and pch together to signify that the first legend item is a solid line, the second is point data (pch=16), the third is dashed and the fourth is dotted? Many

[R] naming consecutive objects

2010-03-29 Thread dgallego
Dear list, I would generate a loop: a-c(1:98) for (i in a ) { cbind(vor.tile[[i]]$x, vor.tile[[i]]$y)-p rbind(p,c(p[1,]))-p.c Polygon(p.c)-pc.p Polygons(list(pc.p),sprintf(p%s,i))-pc.ps sprintf(pc.ps%s,i)-pc.ps } I need to obtain 98 pc.ps objects (like: pc.ps1,

[R] Fw: similarity measure

2010-03-29 Thread karuna m
  hi all, I am doing hierarchical clustering using similarity measures for binary data using package ade4 and hclust function. For method=8 and method = 9 of dist.binary, I am getting Na values. Hence, hclust function is giving error as Error in hclust(d8, method = ward) :   NA/NaN/Inf in

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Tom La Bone
Concisely, here is what I am trying to do: #I take a random sample of 300 measurements. After I have the measurements #I post stratify them to 80 type A measurements and 220 type B measurements. #These measurements tend to be lognormally distributed so I fit them to #determine the geometric

[R] about data export

2010-03-29 Thread meghana kulkarni
Hello all, This is Meghana. Well, I have some analysis output in 3 dimensional array form. for example: , , type1 A B C D 1 2 3 4 1 2 3 4 , , type2 etc. This array is very big. and I want to export this to either text form or excel(csv is preffered) so that different

Re: [R] about data export

2010-03-29 Thread Mark Knecht
?WriteXLS On Mon, Mar 29, 2010 at 6:29 AM, meghana kulkarni msk2...@gmail.com wrote: Hello all, This is Meghana. Well, I have some analysis output in 3 dimensional array form. for example: , , type1      A B C D      1 2 3  4      1 2 3 4  , , type2 etc. This array is very big.

Re: [R] about data export

2010-03-29 Thread Ivan Calandra
Hi, I've never worked with 3d arrays so I'm not sure what to do. Have you tried write.csv()? The function write.xls() from package xlsReadWrite can be really useful too, as well as RODBC which allow appending new spreadsheets to an existing Excel file (works on Windows). Without more on your

[R] Odp: naming consecutive objects

2010-03-29 Thread Petr PIKAL
Hi It is really a nice example. You managed to break probably all rules specified in posting guide No reproducible example No structure of data No explain what you really want No effort on your side even to look to docs. You maybe want some object of type list. obj - vector(98, mode=list you

Re: [R] naming consecutive objects

2010-03-29 Thread Ivan Calandra
Hi, what about: assign()? I don't know if it's really important, but I've always seen the assignment operator the other way (-) HTH, Ivan Le 3/29/2010 13:14, dgallego a écrit : Dear list, I would generate a loop: a-c(1:98) for (i in a ) { cbind(vor.tile[[i]]$x,

Re: [R] Legends for line and point data

2010-03-29 Thread Ivan Calandra
Hi, Your question is really vague. What about legend(lty=, pch=)? Ivan Le 3/29/2010 12:45, Steve Murray a écrit : Dear all, I have a plot which contains 4 data series displayed using solid, dashed and dotted lines, and also points. How do I use lty and pch together to signify that the first

Re: [R] similarity measure

2010-03-29 Thread Steve Lianoglou
Hi, On Fri, Mar 26, 2010 at 7:12 AM, karuna m m_karuna2...@yahoo.com wrote: hi all, I am doing hierarchical clustering using similarity measures for binary data using package ade4 and hclust function. For method=8 and method = 9 of dist.binary, I am getting Na values. Hence, hclust function

Re: [R] Combing

2010-03-29 Thread Matthew Dowle
Val, Type combine two data sets (text you wrote in your post) into www.rseek.org. The first two links are: Quick-R: Merge and Merging data: A tutorial. Isn't it quicker for you to use rseek, rather than the time it takes to write a post and wait for a reply ? Don't you also get more

Re: [R] Legends for line and point data

2010-03-29 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 29.03.2010 16:13:31: Hi, Your question is really vague. What about legend(lty=, pch=)? Well, it is probably not mentioned explicitly in ?legend but he is probably seeking legend(..., lty=c(1,NA, 2,3), pch=c(NA, 16, NA,NA)) Regards Petr Ivan

Re: [R] help in matlab - r code

2010-03-29 Thread Susanne Schmidt
Dear Marta, I did it in Matlab, and fiddled around with R code until I had *almost* the same result. The almost is probably due to R handling the picture values (ranging from 0 to 1) differently than Matlab (ranging from 0 to 255), and simply multiplying the R picture values by 255 did NOT

[R] Question about 'logit' and 'mlogit' in Zelig

2010-03-29 Thread Mathew, Abraham T
I'm running a multinomial logit in R using the Zelig packages. According to str(trade962a), my dependent variable is a factor with three levels. When I run the multinomial logit I get an error message. However, when I run 'model=logit' it works fine. any ideas on whats wrong? ## MULTINOMIAL

[R] Error grid must have equal distances in each direction

2010-03-29 Thread maddy
Hello all, I am trying to create a grid of large number of points 4096*4096, on processing the data I am writing it into a file. phi - 0.5 N - 4096 mu - 90 sim-grf(N*N,grid=reg,cov.model=spherical,cov.pars=c(1,phi),method=RF) sim$data - (sim$data - mean(sim$data)) / sd(sim$data) local -

[R] how to prove that the factor makes no difference

2010-03-29 Thread Xiang Gao
Dear R-helper, Please suggest some methods for my question below. We measured the amount of protein A in patient blood in pre-treatment and post-treatment condition from 32 patients. Pre-treatment Post-treatment Pat1 25

[R] how to update R files included assource ?

2010-03-29 Thread arnaud chozo
Hi all, I have a main file main.R in which I include some other R files. For example, in main.R I have: source(functions.R). When I modify the file functions.R, I'd like R to take into account the changes and to reload the file functions.R when I run main.R Is it possible? Thanks, Arnaud

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread David Freedman
for a picture of the bagplot, try going to http://www.statmethods.net/graphs/boxplot.html -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1695236.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] how to update R files included assource ?

2010-03-29 Thread Erik Iverson
Hello, arnaud chozo wrote: Hi all, I have a main file main.R in which I include some other R files. For example, in main.R I have: source(functions.R). When I modify the file functions.R, I'd like R to take into account the changes and to reload the file functions.R when I run main.R Is it

[R] Plotting individual points on a surface plot

2010-03-29 Thread Guadalupe García Rubio
Hi all, I'm trying to plot individual points on a surface plot. I want the points to be hidden by the surface if they are below it. AFAIK points() doesn't fulfill this requirement, so on the following plot the point (50,50,0) is visible and it shouldn't: x - 1:100 y - 1:100 pn - persp(x, y,

[R] one way to write scripts in R

2010-03-29 Thread Jason E. Aten
Dear R users, A colleague of mine asked me how to write a script (an executable text file containing R code) in R. After I showed him, he said that after extensive searching of the R archives, he had not found anything like these techniques. He suggested that I share these methods to enable

Re: [R] about data export

2010-03-29 Thread David Winsemius
On Mar 29, 2010, at 9:29 AM, meghana kulkarni wrote: Hello all, This is Meghana. Well, I have some analysis output in 3 dimensional array form. for example: , , type1 A B C D 1 2 3 4 1 2 3 4 , , type2 ?write.table arr - array(1:27, c(3,3,3)) write.table(arr[, , 1]) V1

Re: [R] Convert number to Date

2010-03-29 Thread anna
Hi Joshua, thank you this worked pretty well. I don't understand all the details of the dates on excel and R so sorry for not participating more on my own post. - Anna Lippel -- View this message in context: http://n4.nabble.com/Convert-number-to-Date-tp1691251p1695267.html Sent from the R

Re: [R] Convert number to Date

2010-03-29 Thread Gabor Grothendieck
There is a discussion of excel dates in R News 4/1. On Mon, Mar 29, 2010 at 11:47 AM, anna lippelann...@hotmail.com wrote: Hi Joshua, thank you this worked pretty well. I don't understand all the details of the dates on excel and R so sorry for not participating more on my own post. -

Re: [R] one way to write scripts in R

2010-03-29 Thread Steve Lianoglou
Hi Jason, Thanks for sharing your solution(s). For other alternatives for running R scripts, you (or your colleague) might want to look into: * Rscript (comes installed with R (these days)) * littler (http://code.google.com/p/littler/) Also, there are some libraries that deal with parsing

Re: [R] one way to write scripts in R

2010-03-29 Thread Gabor Grothendieck
Thanks. You might want to repost it as a text attachment since many of the lines wrapped around. Another more permanent possibility would be to put it on the R wiki at http://rwiki.sciviews.org/doku.php Note that the gsubfn package has a facility for quasi-perl type string interpolation as

Re: [R] how to update R files included assource ?

2010-03-29 Thread Keith Jewell
Hi, I'm afraid I really don't have time to enter into a dialogue :-{ but this fragment from a function of mine might help... -- outfile - sub(Rd$, html, hfile, ignore.case=TRUE) # name of corresponding html out.mod - file.info(outfile)[,mtime] # if html absent

Re: [R] one way to write scripts in R

2010-03-29 Thread Jason E. Aten
Thanks Gabor. I didn't realize you could. Here is the scriptdemo.rsh file as a text attachment, in case the line wraps made it hard to read/use. - Jason On Mon, Mar 29, 2010 at 11:19 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Thanks. You might want to repost it as a text

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Bert Gunter
Easy. See below. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tom La Bone Sent: Monday, March 29, 2010 6:56 AM To: r-help@r-project.org Subject: Re: [R] Ellipse that Contains 95%

Re: [R] how to update R files included assource ?

2010-03-29 Thread Dieter Menne
arnaud chozo wrote: When I modify the file functions.R, I'd like R to take into account the changes and to reload the file functions.R when I run main.R source again, and you old definitions will be overwritten. Dieter -- View this message in context:

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Tom La Bone
I know what get a bigger sample means. I have no clue what ask a more statistically meaningful question means. Can you elaborate a bit? Tom -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1695357.html Sent from the R help mailing

Re: [R] how to prove that the factor makes no difference

2010-03-29 Thread Dieter Menne
Xiang Gao-2 wrote: How can we prove that the treatment did not make any difference in the amount of protein A. In another word, Pre- and post- are the same. There is no way to prove that there is no difference. While you could use some alternative hypothesis, people rarely understand the

Re: [R] one way to write scripts in R

2010-03-29 Thread Tsjerk Wassenaar
Hi, That seems quite neat. To make it a bit more flexible, and maybe do some argument acrobatics with bash, you could change the first few lines to something like #!/bin/bash exec R --vanilla -q --slave -e source(file=pipe(\sed -n /^##RSTART/,\$p $0\)) --args $@ ##RSTART # Script here

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Bert Gunter
Tom: You asked whether two groups have the same underlying population 1st and 2nd moments. The answer is: no they don't. Nothing is ever exactly the same as anything else (indeed, I think this is the Paul Exclusion Principle ;-) ). So quoting Jim Holtman: What is the question? That certainly

[R] too many arguments error

2010-03-29 Thread Euphoria
Hi all! I keep getting the too many arguments error when I insert the xaxt=n, axis(1, at=seq (0, 183, 365, 549, 732, 915, 1095)) statement in the code below for a survival plot. How can I go around this issue? Is there another way for me to change the x-axis? Also, I would prefer the y-axis

Re: [R] too many arguments error

2010-03-29 Thread Sarah Goslee
seq (0, 183, 365, 549, 732, 915, 1095) should be c(0, 183, 365, 549, 732, 915, 1095) see ?seq and ?c for why. Sarah On Mon, Mar 29, 2010 at 2:11 PM, Euphoria yeshapate...@gmail.com wrote: Hi all! I keep getting the too many arguments error when I insert the xaxt=n, axis(1, at=seq (0, 183,

Re: [R] Ellipse that Contains 95% of the Observed Data

2010-03-29 Thread Bert Gunter
Typo: **Paul_i** Exclusion Principle Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and

Re: [R] too many arguments error

2010-03-29 Thread Euphoria
that was way too simple (and completely dumb on my part!) Thanks! =) -- View this message in context: http://n4.nabble.com/too-many-arguments-error-tp1695431p1695461.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] one way to write scripts in R

2010-03-29 Thread Jason E. Aten
Okay, I'll try again with .txt extension. Thanks David. On Mon, Mar 29, 2010 at 12:50 PM, David Winsemius dwinsem...@comcast.netwrote: I would have made it through the mail-server had you given it an extension of .txt but not so with the .rsh extension. On Mar 29, 2010, at 12:31 PM, Jason

[R] plm package duplication problem

2010-03-29 Thread serdal
hi, i am writing my master thesis and i am dealing with 146474 observations (panel data), i have just learned the R so i am a beginner!! i am trying to use the plm package and i have a duplication problem; i have written the following commands to read my data and create my model

Re: [R] one way to write scripts in R

2010-03-29 Thread Muhammad Rahiz
I've been calling R from shell using the following (as example) ... #!/bin/bash for dir in $(ls *.txt); do R CMD BATCH script.R done Muhammad Tsjerk Wassenaar wrote: Hi, That seems quite neat. To make it a bit more flexible, and maybe do some argument acrobatics with bash, you could

[R] Reshaping a data frame with a series of factors and 23 repeated measures

2010-03-29 Thread wclapham
I have a data frame that I created using read.table on a csv spreadsheet. The data look like the following: Steer.ID stocker.trt Finish.trt Date Days Wt .. Steer.Id, stocker.trt, Finish.trt are factors-- Date, Days, Wt are data that are repeated 23 times (wide format). I want

[R] Finding common an unique elements in character vectors

2010-03-29 Thread Thomas Jensen
Dear R-list, I have a problem which I think is quite basic, but so far google has not helped me. I have two vectors like this: vector_1 - c(Belgium, Spain, Greece, Ireland, Luxembourg, Netherlands, Portugal) vector_2 - c(Denmark, Luxembourg) I would like to find the elements in vector_1 that

[R] zero standard errors with geeglm in geepack

2010-03-29 Thread miriza
Hi! I am using geeglm to fit a Poisson model to a timeseries of count data as follows. Since there are no clusters I use 73 values of 1 for the ids. The problem I have is that I am getting standard errors of zero for the parameters. What am I doing wrong? Thanks, Michelle N_Base [1] 95

Re: [R] Finding common an unique elements in character vectors

2010-03-29 Thread Henrique Dallazuanna
Try this: setdiff(vector_1, vector_2) On Mon, Mar 29, 2010 at 2:53 PM, Thomas Jensen thomas.jen...@eup.gess.ethz.ch wrote: Dear R-list, I have a problem which I think is quite basic, but so far google has not helped me. I have two vectors like this: vector_1 - c(Belgium, Spain, Greece,

Re: [R] Finding common an unique elements in character vectors

2010-03-29 Thread Bert Gunter
?setdiff Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Thomas Jensen Sent: Monday, March 29, 2010 10:53 AM To: r-help@r-project.org Subject: [R] Finding common an unique

Re: [R] Finding common an unique elements in character vectors

2010-03-29 Thread Stephan Kolassa
Hi Thomas, %in% does the trick: vector_1 - c(Belgium, Spain, Greece, Ireland, Luxembourg, Netherlands,Portugal) vector_2 - c(Denmark, Luxembourg) vector_1[!(vector_1 %in% vector_2)] HTH, Stephan Thomas Jensen schrieb: Dear R-list, I have a problem which I think is quite basic, but so far

Re: [R] Finding common an unique elements in character vectors

2010-03-29 Thread Chuck Cleland
On 3/29/2010 1:53 PM, Thomas Jensen wrote: Dear R-list, I have a problem which I think is quite basic, but so far google has not helped me. I have two vectors like this: vector_1 - c(Belgium, Spain, Greece, Ireland, Luxembourg, Netherlands, Portugal) vector_2 - c(Denmark,

Re: [R] Finding common an unique elements in character vectors

2010-03-29 Thread David Winsemius
On Mar 29, 2010, at 1:53 PM, Thomas Jensen wrote: Dear R-list, I have a problem which I think is quite basic, but so far google has not helped me. I have two vectors like this: vector_1 - c(Belgium, Spain, Greece, Ireland, Luxembourg, Netherlands, Portugal) vector_2 - c(Denmark,

Re: [R] Reshaping a data frame with a series of factors and 23 repeated measures

2010-03-29 Thread Ista Zahn
Hi Bill, Without an example dataset it's hard to see exactly what you need to do. But you can get started by looking at the documentation for the reshape function (?reshape), and by looking at the reshape package. The reshape package has an associated web page (http://had.co.nz/reshape/) with

Re: [R] Inverse plot colors?

2010-03-29 Thread Lukas Schefczyk
Hi I think ?bxp ( the pars section of it) is what you are searching for. x - rnorm(100) par(bg = white) boxplot(x, col = white, notch=T,medcol=black,whiskcol=white,boxfill=TRUE) HTH Lukas Schefczyk -- From: Frostygoat frostyg...@gmail.com

Re: [R] large dataset

2010-03-29 Thread Thomas Lumley
On Sun, 28 Mar 2010, kMan wrote: This was *very* useful for me when I dealt with a 1.5Gb text file http://www.csc.fi/sivut/atcsc/arkisto/atcsc3_2007/ohjelmistot_html/R_and_la rge_data/ Two hours is a *very* long time to transfer a csv file to a db. The author of the linked article has not

Re: [R] Competing with SPSS and SAS: improving code that loops throughrows (data manipulation)

2010-03-29 Thread Dimitri Liakhovitski
Would like to thank every one once more for your great help. I was able to reduce the time from god knows how many hours to about 2 minutes! Really appreciate it! Dimitri On Sat, Mar 27, 2010 at 11:43 AM, Martin Morgan mtmor...@fhcrc.org wrote: On 03/26/2010 06:40 PM, Dimitri Liakhovitski wrote:

Re: [R] plm package duplication problem

2010-03-29 Thread Achim Zeileis
On Mon, 29 Mar 2010, serdal wrote: hi, i am writing my master thesis and i am dealing with 146474 observations (panel data), i have just learned the R so i am a beginner!! i am trying to use the plm package and i have a duplication problem; i have written the following commands to read my

[R] question for posting

2010-03-29 Thread mswilliams77
Does anyone know of courses to learn R programming in the DC area? I know there is the conference in Gaithersburg, but I was curious if there was anything sooner. Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing

[R] stuck with affy / limma

2010-03-29 Thread Maxim
Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the

Re: [R] Design of a survey using the survey package

2010-03-29 Thread Thomas Lumley
On Sun, 28 Mar 2010, Tom La Bone wrote: So, am I missing something obvious here or is the survey package meant only for analyzing survey data once you have it in hand? Yes, basically. The package title is analysis of complex survey samples, and the book is a guide to analysis using R, and

Re: [R] large dataset

2010-03-29 Thread Gabor Grothendieck
On Mon, Mar 29, 2010 at 4:12 PM, Thomas Lumley tlum...@u.washington.edu wrote: On Sun, 28 Mar 2010, kMan wrote: This was *very* useful for me when I dealt with a 1.5Gb text file http://www.csc.fi/sivut/atcsc/arkisto/atcsc3_2007/ohjelmistot_html/R_and_la rge_data/ Two hours is a *very*

Re: [R] large dataset

2010-03-29 Thread Douglas Bates
On Sat, Mar 27, 2010 at 4:19 AM, n.via...@libero.it n.via...@libero.it wrote: Hi I have a question, as im not able to import a csv file which contains a big dataset(100.000 records) someone knows how many records R can handle without giving problems? What im facing when i try to import the

Re: [R] large dataset

2010-03-29 Thread Thomas Lumley
On Mon, 29 Mar 2010, Gabor Grothendieck wrote: On Mon, Mar 29, 2010 at 4:12 PM, Thomas Lumley tlum...@u.washington.edu wrote: On Sun, 28 Mar 2010, kMan wrote: This was *very* useful for me when I dealt with a 1.5Gb text file

[R] GLM / large dataset question

2010-03-29 Thread geelman
LS, How large a dataset can glm fit with a binomial link function? I have a set of about 100.000 observations and about 8000 explanatory variables (a factor with 8000 levels). Is there a way to find out how large datasets R can handle in general? Thanks in advance, geelman

[R] mixed effects models for grouped time survival data

2010-03-29 Thread HAKAN DEMIRTAS
How do I fit a mixed effects model with two crossed random effects for grouped time survival data? I tried coxme with no luck. Suppose that y is survival time, uncens is censoring indicator, trt is treatment below. ran.eff1 and ran.eff2 below are two crossed random effects. This way, it

[R] single quotes and double quotes in a system() command. What to do?

2010-03-29 Thread Matthew Keller
Hi all, I would like to run the following from within R: awk '{$3=$4=;gsub( ,);print}' myfile outfile However, this obviously won't work: system(awk '{$3=$4=;gsub( ,);print}' myfile outfile) and this won't either: system(awk '{$3=$4='';gsub(' ','');print}' myfile outfile) Can anyone

[R] mcmcglmm starting value example

2010-03-29 Thread ping chen
Hi R-users: Can anyone give an example of giving starting values for MCMCglmm? I can't find any anywhere. I have 1 random effect (physicians, and there are 50 of them) and family=ordinal. How can I specify starting values for my fixed effects? It doesn't seem to have the option to do so.

Re: [R] single quotes and double quotes in a system() command. What to do?

2010-03-29 Thread Duncan Murdoch
On 29/03/2010 5:14 PM, Matthew Keller wrote: Hi all, I would like to run the following from within R: awk '{$3=$4=;gsub( ,);print}' myfile outfile However, this obviously won't work: system(awk '{$3=$4=;gsub( ,);print}' myfile outfile) and this won't either: system(awk '{$3=$4='';gsub('

[R] Decision Trees

2010-03-29 Thread Per
Hi, Does R have a Decision Tree functionality akin to 'Precision Tree' by Palisade? When I search, I end up with 'rpart' but this does not appear to be what I am looking for. Kind regards, Per Bak Copenhagen __ R-help@r-project.org mailing list

[R] generating samples by Monte Carlo

2010-03-29 Thread Jin
Hello Dear, I am trying to generate samples by using Monte Carlo simulation. For example, 1000 samples, Exponential distribution (f(x), lambda=0.0005, 0=x=360) Is there any package for Monte Carlo or just use random sample generation function? Many thank you for your help in advance, Jin --

[R] Data sets with usage in documentation object 'data' but not in the code

2010-03-29 Thread shruti
Hi, My name is shruti,When I was trying to check the package I got this error Data sets with usage in documentation object 'data' but not in the code Can any one help me with this.I'm attaching the file for your reference http://n4.nabble.com/file/n1695616/dataset.jpg Thank you -- View this

Re: [R] Data sets with usage in documentation object 'data' but not in the code

2010-03-29 Thread David Winsemius
On Mar 29, 2010, at 4:49 PM, shruti wrote: Hi, My name is shruti,When I was trying to check the package I got this error Data sets with usage in documentation object 'data' but not in the code Can any one help me with this.I'm attaching the file for your reference

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