Re: [R] Help understanding cutree used for Dunn Index

2011-12-09 Thread kbrownk
I found a way to draw rectangles around whatever cutree cuts, so I think I now have a better idea, which is that it looks for the largest k distances and cuts there, where k is the # clusters you want defined. Then, I assume Dunn index uses the same defined #clusters to determine within vs.

Re: [R] generalized procrustes analysis without translation

2011-12-09 Thread Meyners, Michael
I’m not aware of any, but if you really want this, it should be possible to modify the code of any of the functions you propose and delete the part doing the translation. I’m not sure that this is a good idea, though; either your matrices are *truly* centered, then it doesn’t make a difference,

Re: [R] Need to calculate standard deviation by groups

2011-12-09 Thread Gerrit Eichner
Hello, Zsuzsa, does ave() with its argument FUN supplied with sd not do what you want? Something like with( Dataset, ave( x = B, C, D, FUN = sd)) should do it. Hth -- Gerrit On Fri, 9 Dec 2011, Zsuzsanna Papp wrote: Hello, please help me with this basic question, I already spent two

Re: [R] R packages for pathway analysis?

2011-12-09 Thread Mohamed Lajnef
Hi Karena, Ask your question in bionconductor mailing list (bioconduc...@r-project.org) Regards ML Le 09/12/11 03:36, karena a écrit : What R packages do you guys use for 'pathway analysis'? By 'pathway analysis', I mean to check the enrichment of certain genes in KEGG | GO pathways.

Re: [R] Help with study guide for R exam

2011-12-09 Thread peter dalgaard
On Dec 8, 2011, at 20:34 , 343GS wrote: Hi there. I have a final exam coming up in a class that is heavily based in the R programming language. The teacher has provided to us a few questions to study in preparation for the exam. I was looking to see if anyone could help answer any or all of

Re: [R] Hinton Diagram for a matrix of weights

2011-12-09 Thread Xavier Fernández i Marín
Jim Lemon vas escriure el dia dj, 08 des 2011: The Hinton diagram looks fairly close to an image plot, or the color2D.matplot function. The difference is that the area of the squares in the Hinton plot are proportional to some value rather than the color, which indicates the sign of the

Re: [R] Hinton Diagram for a matrix of weights

2011-12-09 Thread Wet Bell Diver
Xavier, Perhaps this would be of help, you could use it as a starting point: http://www.cs.princeton.edu/~mimno/factor-analysis.R This page provides a function for Hinton diagrams. -Peter Op 7-12-2011 17:45, Xavier Fernández i Marín schreef: Hello, Although I have used a general search

[R] ggplot with geom_tile

2011-12-09 Thread Pelt van, Saskia (KNMI)
Dear R-users, I am trying to make a plot with ggplot-geom_tile(), but cannot remove some unwanted (white) lines through my plot. Below a reproducible example: # library(ggplot2) tot=as.data.frame(rep(seq(-50,50,5),each=21)) names(tot)=precip temp=rep(seq(-5,5,0.5),21) tot$temp=temp

Re: [R] How to load the data set from an URL Link?

2011-12-09 Thread Tal Galili
Hello dear Henser, You seem to be asking a homework question, which you will not get answers for here. In short, have a look at: ?read.table For reading the data. And: ?mean For the mean... And go read through an introductory book on R. There is a long list here:

Re: [R] ggplot with geom_tile

2011-12-09 Thread Paul Hiemstra
Dear Saskia, Thank you for the reproducible example, that helps a lot. I pasted you code into R and got a perfectly fine image. You need to provide us with your sessionInfo(). Mine is listed at the end of the mail. I seem to remember having this problem with R 2.12. Therefore updating R might be

Re: [R] stop messages

2011-12-09 Thread Sarah Goslee
The answer to that question appears at the bottom of each and every message posted to the list. On Thu, Dec 8, 2011 at 8:09 PM, nur mohd nurm1...@gmail.com wrote: Dear sir how to stop the messages from r-help to appear in my email.tq __

Re: [R] axis line width in boxplots

2011-12-09 Thread S Ellison
How can I control only the width of the axis line? Or, other option, how can I get rid of the axis line without getting rid of the tickmarks (as below the axis, there is the line from the frame, I don't really need the axis line)? Not sure which boxplot you;re using; on mine (R 3.13.1)

[R] apply on function with vector as result

2011-12-09 Thread Christof Kluß
Hi, a have some code like myfunc - function(x) { ...; return c(a,b) } ys - sapply(0:100,myfunc) so I get something like c(c(a1,b1),c(a2,b2),...) But now I need the as and bs in one vector as - apply(ys, function(c(a,b)) a) bs - apply(ys, function(c(a,b)) b) Can you help me with the

Re: [R] ggplot with geom_tile

2011-12-09 Thread Pelt van, Saskia (KNMI)
Dear Paul and others, It also happens with the examples from Hadley geom_tile() on: http://had.co.nz/ggplot2/geom_tile.html http://had.co.nz/ggplot2/geom_tile.html With this example I do not get the white lines: p - ggplot(data = tot, mapping = aes(x = temp, y = precip)) p + layer(data =

Re: [R] ggplot with geom_tile

2011-12-09 Thread Frederic Andrieu
Dear Saskia, If you mean the grid lines around the edge then they can be removed by using the following: p - ggplot(tot, aes(x=temp, y=precip,group=dis)) p+geom_tile(aes(fill=dis)) + scale_fill_gradientn(colours=cols) + scale_x_continuous(expand = c(0,0)) + scale_y_continuous(expand = c(0,0))

Re: [R] apply on function with vector as result

2011-12-09 Thread Sarah Goslee
This would be a whole lot easier if we had a reproducible example, or at least knew what your output data actually looked like, and an example of what you *wanted* it to look like. For instance, I'm confused by your description of your output data: c(c(1,2), c(3,4)) [1] 1 2 3 4 c(c(), c()) is a

[R] how to add an edgetext to a dendrogram?

2011-12-09 Thread barbara costa
Hello to all, I'd like to colour the different labels of my dendrogram. How can I do? I guess I could to using *edgetext* and then* t.col* or *lab.col* but I don't know how to add edgetext to my dendrogram. Can you help me please? Example: require(graphics); require(utils) hc -

[R] display memory usage

2011-12-09 Thread bcdc
Does anybody knows how can I display the memory usage in R? I'd like to know how much RAM R is using to store a data set that I'm reading, is it possible? Thanks in advance, Beatriz -- View this message in context: http://r.789695.n4.nabble.com/display-memory-usage-tp4175898p4175898.html Sent

[R] Making outregs in R

2011-12-09 Thread David .
Dear r-Gods! I am interesting in making an equivalent command like outreg in stata where I get all my 8 regressions in one table. Does R have an easy command to that? MVH Dave [[alternative HTML version deleted]]

Re: [R] how to add an edgetext to a dendrogram?

2011-12-09 Thread Sarah Goslee
Hi, On Fri, Dec 9, 2011 at 6:57 AM, barbara costa rbarbar...@gmail.com wrote: Hello to all, I'd like to colour the different labels of my dendrogram. How can I do? I guess I could to using *edgetext* and then* t.col* or *lab.col* but I don't know how to add edgetext to my dendrogram. Can you

[R] Error using function MVN in package MCLUST: Fortran symbol name not in DLL for package

2011-12-09 Thread Natalie Franklin
Hi All, I need to fit a mutlivariate normal model to a dataset in order to obtain the mean and covariance parameters. I see that the MVN function in the MCLUST package can do this, however when I try to run even the simplest example provided in the documentation, as below, I get the following

Re: [R] Making outregs in R

2011-12-09 Thread Sarah Goslee
Er, *what* eight regressions would that be? Can you provide an example of what you're looking for: data, anticipated output? Many of us have never used stata and have no idea what you're asking, so you'll need to explain it to us in more detail. Sarah On Fri, Dec 9, 2011 at 5:22 AM, David .

[R] Summary model with observations taken out and dummied back in - not working

2011-12-09 Thread RRRRRRRRRRR
I have a data set with 35 observations and 4 variables. I have removed 4 observations as they were skewing the data analysis but I want to dummy them back in, (not entirely sure on the reason, but have been told I should try). I have used this in order to do it, but I am not getting any

Re: [R] display memory usage

2011-12-09 Thread Sarah Goslee
Typing ??memory at an R prompt lists several functions that might be helpful, depending on exactly what you want to know. Sarah On Fri, Dec 9, 2011 at 4:29 AM, bcdc bia@gmail.com wrote: Does anybody knows how can I display the memory usage in R? I'd like to know how much RAM R is using to

Re: [R] Error using function MVN in package MCLUST: Fortran symbol name not in DLL for package

2011-12-09 Thread Sarah Goslee
I suspect at a minimum we need the basic information requested in the posting guide: your OS, version of R version of the package in question. sessionInfo() is a useful command. You shouldn't need to load anything beyond the package itself. Sarah On Fri, Dec 9, 2011 at 4:01 AM, Natalie

Re: [R] cannot access the functions in the package

2011-12-09 Thread Duncan Murdoch
On 11-12-08 1:30 PM, Weizeng Ni wrote: hi, I am using the package of Fslector which contains a function named information.gain. I want to see the detailed code of this function. the result shows information.gainfunction (formula, data) { information.gain.body(formula, data, type =

[R] mclust

2011-12-09 Thread Sarah Goslee
While looking at someone's question on this list led me to the mclust package, and from there to its license. Excerpts: Except for strict academic use, use of MCLUST (by itself or through other packages) requires payment of an annual license fee and completion of a license agreement found at the

Re: [R] bwplot title size

2011-12-09 Thread S Ellison
Check the Intro page for Lattice and note the bit that says 'In particular, changing par() settings usually has no effect on Lattice plots' By and large, lattice uses things like cex inside a list of options and only in a few cases (when passed to panel.bwplot) does it use what look like

Re: [R] ggplot with geom_tile

2011-12-09 Thread Pelt van, Saskia (KNMI)
Dear Frederic, No this was not the problem, the problem are horizontal and vertical white lines in the figure. But the problem is gone when I save the figure and reopen it (in another program), so I think the problem is only with my direct plot outputs. Thanks for your help. Kind regards,

Re: [R] read.table performance

2011-12-09 Thread Petr PIKAL
By the way, here's my original session information. (I can never remember the name of that command when I want it). It's strange that Petr is having the problem with 2.14. It's relatively fast on my machine with R 2.14. Probably I use inferior PC based on nowadays standards. WXP,

[R] Retrieving samples when ussing BRugs.

2011-12-09 Thread Thiago Guerrera
Hello R users, I have used the R package BRugs in some applications but one thing that annoy me is the functions to retrieve samples (samplesSample) or summary statistics (samplesStats). They take a really long time to return the values if the size of the chains in question is moderate, for

Re: [R] what is the difference between using function predict() and coef() in prediction

2011-12-09 Thread Petr PIKAL
Hi Did you find any difference? The results shall be same (with only rounding error). Can you show us some example where you get substantial difference? Regards Petr i do not know what is the difference between predict() and coef() i use the two function give me different result zz =

Re: [R] mclust

2011-12-09 Thread Prof Brian Ripley
On Fri, 9 Dec 2011, Sarah Goslee wrote: While looking at someone's question on this list led me to the mclust package, and from there to its license. Excerpts: Except for strict academic use, use of MCLUST (by itself or through other packages) requires payment of an annual license fee and

Re: [R] Error using function MVN in package MCLUST: Fortran symbol name not in DLL for package

2011-12-09 Thread Prof Brian Ripley
On Fri, 9 Dec 2011, Natalie Franklin wrote: Hi All, I need to fit a mutlivariate normal model to a dataset in order to obtain the mean and covariance parameters. I see that the MVN function in the MCLUST package can do this, however when I try to run even the simplest example provided in

[R] Titelpage pdf-manual, packaging

2011-12-09 Thread Johannes Radinger
Hi, I am trying to get write my first own package. I followed the instructions in Creating R Packages: A Tutorial and Writing R Extensions. So far everything works really fine, the script works and even the man-pages don't show any problems during the check process. During check there is also

Re: [R] display memory usage

2011-12-09 Thread jim holtman
? object.size On Dec 9, 2011 4:13 AM, bcdc bia@gmail.com wrote: Does anybody knows how can I display the memory usage in R? I'd like to know how much RAM R is using to store a data set that I'm reading, is it possible? Thanks in advance, Beatriz -- View this message in context:

Re: [R] how to add an edgetext to a dendrogram?

2011-12-09 Thread barbara costa
I'm sorry. (dend1 - as.dendrogram(hc)) On 9 December 2011 12:10, Sarah Goslee sarah.gos...@gmail.com wrote: Hi, On Fri, Dec 9, 2011 at 6:57 AM, barbara costa rbarbar...@gmail.com wrote: Hello to all, I'd like to colour the different labels of my dendrogram. How can I do? I guess I

[R] [R-pkgs] stringr 0.6

2011-12-09 Thread Hadley Wickham
# stringr Strings are not glamorous, high-profile components of R, but they do play a big role in many data cleaning and preparations tasks. R provides a solid set of string operations, but because they have grown organically over time, they can be inconsistent and a little hard to learn.

Re: [R] Align expression and text in mtext()

2011-12-09 Thread David Winsemius
On Dec 8, 2011, at 9:53 PM, Remko Duursma wrote: Dear R-helpers, I have trouble aligning an expression with a subscript, and text, in margin text: par(mar=c(6,6,1,1)) b - barplot(1:3) mtext(c(A,B,C), at=b, side=1, line=1, cex=1.3) mtext(expression(italic(C)[a]~(more~text)), at=0, line=1,

Re: [R] read.table question

2011-12-09 Thread Pavan G
Thanks All! On Thu, Dec 8, 2011 at 7:41 PM, Robert Baer rb...@atsu.edu wrote: Hello All, This works, results - read.table(plink.txt,T) while this doesn't. results - read.table(plink.txt) The T is the value for the second parameter which you show from the help file

Re: [R] Making outregs in R

2011-12-09 Thread Sarah Goslee
Please copy the whole list on your replies. On Fri, Dec 9, 2011 at 8:26 AM, David . loove...@hotmail.com wrote: Hey Sarah! Outreg in stata is like a table with all your regressions. In the first row its the first regression and in the second row its the second regression with some added

[R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Jannis
Dear R users, the way I understand the documentation of sub() and regexp the following code: sub('[[:digit:]]{1,2}', '', '9ewww') ... should yield: 'ewww' It returns, however: 'www' Why is this the case? My code should just substitute 1 (minimum) or up to 2 (maximum) digits, i.e.

Re: [R] minor allele frequency comparison

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 2:44 AM, Scott Harding wrote: Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with

Re: [R] Making outregs in R

2011-12-09 Thread Sarah Goslee
And the *whole list* might like to see that. So you want some way to display pre-existing regressions in that format, not a stepwise procedure that performs the regressions and displays them, right? On Fri, Dec 9, 2011 at 9:17 AM, David . loove...@hotmail.com wrote: You're right! A picture says

Re: [R] apply on function with vector as result

2011-12-09 Thread Christof Kluß
Am 09-12-2011 12:54, schrieb Sarah Goslee: myfunc- function(x) {a=x; b=x-1; c(a, b) } ys- sapply(1:5, myfunc) ys [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]01234 And from there, it's not at all clear what you mean by one vector - in what order?

Re: [R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Duncan Murdoch
On 09/12/2011 9:20 AM, Jannis wrote: Dear R users, the way I understand the documentation of sub() and regexp the following code: sub('[[:digit:]]{1,2}', '', '9ewww') ... should yield: 'ewww' It returns, however: 'www' Why is this the case? My code should just substitute 1

Re: [R] Making outregs in R

2011-12-09 Thread Sarah Goslee
On Fri, Dec 9, 2011 at 9:23 AM, David . loove...@hotmail.com wrote: A whole list? You are replying to me personally. You should be sending your messages to the *R help email list*. But yeah thats is basically what I want to be able to do. I don't know how to do exactly what you want, but

Re: [R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Prof Brian Ripley
This is AFAICS an instance of bug PR#14408 : it seems that in UTF-8 locales the grammar generated by the TRE engine for repetitions is in odd cases buggy. And as the author has vanished, our hopes of his fixing it are slim. Try perl=TRUE . On 09/12/2011 14:20, Jannis wrote: Dear R users,

Re: [R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Sarah Goslee
But I do get the incorrect result on R 2.14.0 on linux: sub('[[:digit:]]{1,2}', '', '9ewww') [1] www And also: sub('[[:digit:]]{1,2}', '', '9ewww') [1] www sub('[[:digit:]]{1,2}', '', 'ewww9') [1] ww9 sub('\\d{1,2}', '', 'ewww9') [1] ww9 But: sub('\\d', '', 'ewww9') [1] ewww sub('\\d*',

Re: [R] mclust

2011-12-09 Thread Sarah Goslee
Thank you for the suggestions. I've generally relied on task views to simplify package installation, and not paid much attention to other options. I also see that mclust does notify the user when loaded: library(mclust) by using mclust, invoked on its own or through another package, you accept

[R] R: prop.test() and the simultaneous confidence interval for multiple proportions in R

2011-12-09 Thread angelo.arc...@virgilio.it
Hello, is there anyone who has some ideas about the problem I posted? Help! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Jannis
Thanks to all who replied. perl = TRUE indeed seems to fix the problem. It would be great, however, to prevent others from stumbling in this pitfall by fixing the issue if this is possible. But as Prof. Ripley mentioned fixing this might be difficult/impossible so we might have to live with it.

Re: [R] cannot access the functions in the package

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 7:27 AM, Duncan Murdoch wrote: On 11-12-08 1:30 PM, Weizeng Ni wrote: hi, I am using the package of Fslector which contains a function named information.gain. I want to see the detailed code of this function. the result shows information.gainfunction (formula, data)

Re: [R] ggplot with geom_tile

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 7:47 AM, Pelt van, Saskia (KNMI) wrote: Dear Frederic, No this was not the problem, the problem are horizontal and vertical white lines in the figure. But the problem is gone when I save the figure and reopen it (in another program), so I think the problem is only

Re: [R] unexpected behaviour of sub() / usage of regexp

2011-12-09 Thread Prof Brian Ripley
On 09/12/2011 14:49, Jannis wrote: Thanks to all who replied. perl = TRUE indeed seems to fix the problem. It would be great, however, to prevent others from stumbling in this pitfall by fixing the issue if this is possible. But as Prof. Ripley mentioned fixing this might be

[R] gam, what is the function(s)

2011-12-09 Thread Ben quant
Hello, I'd like to understand 'what' is predicting the response for library(mgcv) gam? For example: library(mgcv) fit - gam(y~s(x),data=as.data.frame(l_yx),family=binomial) xx - seq(min(l_yx[,2]),max(l_yx[,2]),len=101) plot(xx,predict(fit,data.frame(x=xx),type=response),type=l) I want to see

Re: [R] gam, what is the function(s)

2011-12-09 Thread Bert Gunter
There is an extensive list of references given in ?gam, including an R-news article and Simon Woods's (gam's author) website. Would that not be the logical place to start? -- Bert On Fri, Dec 9, 2011 at 7:05 AM, Ben quant ccqu...@gmail.com wrote: Hello, I'd like to understand 'what' is

Re: [R] gam, what is the function(s)

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 10:05 AM, Ben quant wrote: Hello, I'd like to understand 'what' is predicting the response for library(mgcv) gam? For example: library(mgcv) fit - gam(y~s(x),data=as.data.frame(l_yx),family=binomial) xx - seq(min(l_yx[,2]),max(l_yx[,2]),len=101)

[R] question about spaces in r

2011-12-09 Thread Matt Spitzer
Hello, I would like to please ask if someone would explain how r reads characters and numbers differently. Using read.csv, I had a matrix that resembled the following, only with many more ids and data: ID Visit variable 2 1 5 2 1 3 2 3 4 2 41 1 2 42 34 2 5 54 2 9 1 2

[R] rgl.postscript() failure when saving a scene

2011-12-09 Thread ppiras
Dear all, I write to the community to know if other people expierenced the same problem. I want to save a rgl scene where I plotted a 3d cloud of spheres whose radius is set proportional to a given variable and coloured by another group variable and with 95% ellipsoids for distribution of any

Re: [R] Retrieving samples when ussing BRugs.

2011-12-09 Thread Sacha Epskamp
If you obtain an output object with openbugs(), e.g.: samples - openbugs( ... ) Then this is a list with all the parameters and samples. See names(samples). You can obtain the samples in a list with: samples[['sims.list']] Is this what you mean? On Fri, Dec 9, 2011 at 2:00 PM, Thiago Guerrera

Re: [R] question about spaces in r

2011-12-09 Thread MacQueen, Don
First of all, it's R, not r, and on this mailing list people care about this kind of thing. Second, you will need to provide more information in order to get better help. Please read the posting guide. There are a number of introductory level documents available via CRAN, please pick one and

Re: [R] gam, what is the function(s)

2011-12-09 Thread Simon Wood
See help(mgcv-FAQ), item 2. best, Simon On 09/12/11 15:05, Ben quant wrote: Hello, I'd like to understand 'what' is predicting the response for library(mgcv) gam? For example: library(mgcv) fit- gam(y~s(x),data=as.data.frame(l_yx),family=binomial) xx-

Re: [R] rgl.postscript() failure when saving a scene

2011-12-09 Thread Duncan Murdoch
On 09/12/2011 9:49 AM, ppi...@uniroma3.it wrote: Dear all, I write to the community to know if other people expierenced the same problem. I want to save a rgl scene where I plotted a 3d cloud of spheres whose radius is set proportional to a given variable and coloured by another group variable

[R] 'callNextMethod' in a '[-' function does not work ?

2011-12-09 Thread cgenolin
Hi the list, I try to use callNextMethod in a setteur ([-) but it does not work. Any raison ? Any other option ? --- 8 -- ### Class B0 ### setClass(B0 , representation(b0 = numeric)) setReplaceMethod([,B0,function(x,i,j,value){x@b0 - -value}) a - new(B0) a@b0 - 3 a a[b0] - 3 a

Re: [R] Making outregs in R

2011-12-09 Thread Jakson Alves de Aquino
On Fri, Dec 9, 2011 at 7:22 AM, David . loove...@hotmail.com wrote: I am interesting in making an equivalent command like outreg in stata where I get all my 8 regressions in one table. Does R have an easy command to that? The function of mtable() of memisc package may be what you want. There

[R] Anyone See a Problem with my Header/Data?

2011-12-09 Thread Lost in R
First time using R. Having problems importing my data. Can anyone take a look at my data to see if there is something stupid that I'm doing? This is the error that I'm getting. - read.table(C:\\CM3_DATASET.out.txt, + sep=\t,header=TRUE) Error in scan(file, what, nmax, sep, dec, quote, skip,

[R] HELP

2011-12-09 Thread Gabrielle Gauthier
I was wondering if anyone could help me with my R homework. I have using the R tutorials and help options but it just is not helping me at all. I have some questions completed but these are the ones i need help on: A.) Plot the values in vector MyNumbers in a scatterplot. B.) Create a new

[R] matrix calculation

2011-12-09 Thread Junyu Lee
Hello, I have a matrix animaltime A01 A02 A d0 -5.4 2.7 A d1124.6 5.9 A d224 3.96.3 B

[R] scatterplot to boxplot translation?

2011-12-09 Thread Vining, Kelly
attachment: C_count_vs_RPKM.PNG__ 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 provide commented, minimal, self-contained, reproducible

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread Vining, Kelly
My apologies if anyone is seeing this twice...looks like my previous message didn't come through... Dear UseRs, I have a feeling this is a relatively simple question, but I'm having a hard time getting my head around it. I have a simple x-y scatterplot with many points, as shown

Re: [R] HELP

2011-12-09 Thread Sarah Goslee
On Fri, Dec 9, 2011 at 1:35 PM, Gabrielle Gauthier gauthiergabrie...@yahoo.com wrote: I was wondering if anyone could help me with my R homework. No. This list is not for doing homework, though I applaud your honesty in admitting it. Your instructor is being paid to teach you; that's who you

Re: [R] Anyone See a Problem with my Header/Data?

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 12:57 PM, Lost in R wrote: First time using R. Having problems importing my data. Can anyone take a look at my data to see if there is something stupid that I'm doing? This is the error that I'm getting. - read.table(C:\\CM3_DATASET.out.txt, + sep=\t,header=TRUE) Error

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 2:11 PM, Vining, Kelly wrote: My apologies if anyone is seeing this twice...looks like my previous message didn't come through... Dear UseRs, I have a feeling this is a relatively simple question, but I'm having a hard time getting my head around it. I have a simple x-y

Re: [R] HELP

2011-12-09 Thread Sarah Goslee
From the bottom of every email on this list: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html And from the posting guide: Basic statistics and classroom homework: R-help is not intended for these. I'm not sure how being from your lab professor makes it any less

Re: [R] gam, what is the function(s)

2011-12-09 Thread Ben quant
Thank you Simon. I already ordered your book. Regards, Ben On Fri, Dec 9, 2011 at 10:49 AM, Simon Wood s.w...@bath.ac.uk wrote: See help(mgcv-FAQ), item 2. best, Simon On 09/12/11 15:05, Ben quant wrote: Hello, I'd like to understand 'what' is predicting the response for

Re: [R] Anyone See a Problem with my Header/Data?

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 2:12 PM, David Winsemius wrote: On Dec 9, 2011, at 12:57 PM, Lost in R wrote: First time using R. Having problems importing my data. Can anyone take a look at my data to see if there is something stupid that I'm doing? This is the error that I'm getting. -

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread Vining, Kelly
Thanks for the tip on cut, seems like it should work. I must still be missing something, though. Here, I'm cutting on the y variable, then attempting the boxplot: cutRPKM - cut(count$RPKM, breaks=4) head(cutRPKM) [1] (-0.0995,24.8] (-0.0995,24.8] (-0.0995,24.8] (-0.0995,24.8] (-0.0995,24.8]

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread Uwe Ligges
On 09.12.2011 20:41, Vining, Kelly wrote: Thanks for the tip on cut, seems like it should work. I must still be missing something, though. Here, I'm cutting on the y variable, then attempting the boxplot: cutRPKM- cut(count$RPKM, breaks=4) head(cutRPKM) [1] (-0.0995,24.8] (-0.0995,24.8]

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread Tom Fletcher
You need to create some grouping for your cut points (0-100, etc). See ?cut Then, you can use boxplot and formula (y ~ NEWVARIABLE from cut) boxplot(y ~ cut(x)) There may be other ways to do this, but the above should work. TF -Original Message- From: r-help-boun...@r-project.org

[R] Help with the Mice Function

2011-12-09 Thread Richard J. Buning
Hi, I am attempting to impute my data for missing values using the mice function. However everytime I run the function it freezes or lags. I have tried running it over night, and it still does not finish. I am working with 17000 observations across 32 variables. here is my code: imputed.data =

Re: [R] scatterplot to boxplot translation?

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 2:50 PM, Uwe Ligges wrote: On 09.12.2011 20:41, Vining, Kelly wrote: Thanks for the tip on cut, seems like it should work. I must still be missing something, though. Here, I'm cutting on the y variable, then attempting the boxplot: cutRPKM- cut(count$RPKM, breaks=4)

[R] Fixed! Thanks all:RE: scatterplot to boxplot translation?

2011-12-09 Thread Vining, Kelly
Thanks to David and Jorge - both of your helpful suggestions got me to the desired endpoint. In case anyone else has this question: I boxplotted my y variable data, but did the cut operation on the x variable in order to conserve the order of the y data. I see another suggestion coming in from

Re: [R] Help with study guide for R exam

2011-12-09 Thread B77S
343GS You should consider dropping out of college; I don't think you belong there. McDonalds is hiring. 343GS wrote Thanks for nothing, jerk! DENMARK IS POO -- View this message in context: http://r.789695.n4.nabble.com/Help-with-study-guide-for-R-exam-tp4173951p4178139.html Sent from

Re: [R] curve fitted ... how to retreive data

2011-12-09 Thread Mintewab Bezabih
THanks so much Gene, it worked mintewab Från: gley...@gmail.com [gley...@gmail.com] f#246;r Gene Leynes [gleyne...@gmail.com] Skickat: den 7 december 2011 18:43 Till: Mintewab Bezabih Kopia: r-help@r-project.org Ämne: Re: [R] curve fitted ... how to

Re: [R] 'callNextMethod' in a '[-' function does not work ?

2011-12-09 Thread Martin Morgan
On 12/09/2011 10:15 AM, cgenolin wrote: Hi the list, I try to use callNextMethod in a setteur ([-) but it does not work. Any raison ? Any other option ? --- 8 -- ### Class B0 ### setClass(B0 , representation(b0 = numeric)) setReplaceMethod([,B0,function(x,i,j,value){x@b0-

Re: [R] Fixed! Thanks all:RE: scatterplot to boxplot translation?

2011-12-09 Thread Bert Gunter
Kelly: Glad you got what you were looking for, but this whole thread begs the question; (Why) should you do this? You lose information in binning the continuous data, of course. Perhaps your answer is that the point scatter in the data is too noisy to clearly discern what's going on, a legitimate

Re: [R] profile likelihood

2011-12-09 Thread Ben Bolker
plocq less.is.mo_ at hotmail.com writes: Hi, I try to use the function profile() of the SpatialExtremes' package to obtain the profile likelihood of parameters for an extreme values fit based on Poisson process : fit-fpot(data, threshold, model=pp, npp=365). But when I call

Re: [R] optimize()

2011-12-09 Thread Ben Bolker
dnz.marcio dnz.marcio at gmail.com writes: [snip] # Logaritmo da distribuição condicional de alpha[i] lp_alphai - function(alphai, i, beta, tau, N){ t1 - (N[i+1] - N[i])*log(alphai) t2 - - (N[i+1] - N[i])*alphai*log(beta[i]) t3 - (alphai - 1)*sum(log(times[(N[i] + 1):N[i+1]]))

Re: [R] Help with the Mice Function

2011-12-09 Thread Ben Bolker
Richard J. Buning rbuning at ufl.edu writes: Hi, I am attempting to impute my data for missing values using the mice function. However every time I run the function it freezes or lags. I have tried running it over night, and it still does not finish. I am working with 17000

Re: [R] Help with the Mice Function

2011-12-09 Thread Ken
Try reducing the maximum iterations. Probably won't make your call instantaneous, but might be worth the slack gained over a day or so. Ken Hutchison On Dec 9, 2554 BE, at 1:59 PM, Richard J. Buning rbun...@ufl.edu wrote: Hi, I am attempting to impute my data for missing values using the

[R] Bayesian Neural Networks

2011-12-09 Thread Felipe Bhering
I wanted to do a modelling like this, many variables, will simplificate for understanding y1 in [a1,b1] = (weight 1) = number 1.1 y2 in [a1,b1] = (weight 1) = number 1.2 y3 in [a1,b1] = (weight 1) = number 1.3 y4 in [a1,b1] = (weight 1) = number 1.4 y5 in [a1,b1] = (weight 2) = number 2.1 y6 in

[R] Can not install doBy

2011-12-09 Thread jdef
Every time I try to install the doBy package I receive this error message: Warning in install.packages : error 1 in extracting from zip file Warning in install.packages : cannot open compressed file 'mvtnorm/DESCRIPTION', probable reason 'No such file or directory' Error in install.packages

[R] installing binary packages across windows cluster

2011-12-09 Thread Benjamin Tyner
Hi Given a cluster of identical windows machines all running the same version of R, are there any circumstances where using install.packages() to install a package (say, one that doesn't have any dependencies) on just a single machine, then copying the resulting installed package

Re: [R] Can not install doBy

2011-12-09 Thread David Winsemius
On Dec 9, 2011, at 5:13 PM, jdef wrote: Every time I try to install the doBy package I receive this error message: Warning in install.packages : error 1 in extracting from zip file Warning in install.packages : cannot open compressed file 'mvtnorm/DESCRIPTION', probable reason 'No