Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread Prof Brian Ripley
This is all in the help page for pdf ... including a request not to falsely blame R and two workarounds for the broken viewers. On Thu, 28 Jul 2011, Duncan Murdoch wrote: On 11-07-28 1:22 PM, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with de

[R] Different result on using apply.

2011-07-28 Thread Ashim Kapoor
Dear R-helpers, In the following example I compute ret and returns the SAME way. In ret I use compute returns for EACH column and in returns I do it for the whole data frame. Could someone please tell me why I see a lagged result,by which I mean ret and returns are different by one lag. getSymbo

Re: [R] Looping through data sets to change column from character to numeric

2011-07-28 Thread Rolf Turner
On 29/07/11 11:09, Sarah Henderson wrote: Greetings to all -- I am having a silly problem that I just can't solve. Someone has given me an .RData file will hundreds of data frames. Each data frame has a column named ResultValue, currently character when it should be numeric. I want to loop th

Re: [R] Lowest values in a vector of numbers

2011-07-28 Thread Dennis Murphy
> x <- rpois(50, 10) > which(x <= quantile(x, 0.2)) [1] 7 14 16 24 25 28 33 44 45 48 > x[which(x <= quantile(x, 0.2))] [1] 6 5 4 5 7 7 4 5 6 7 > quantile(x, 0.2) 20% 7.8 HTH, Dennis On Thu, Jul 28, 2011 at 9:42 PM, Jim Silverton wrote: > I have a vector of numbers, and I will like to find the

Re: [R] order a data frame after date and hour

2011-07-28 Thread Dennis Murphy
Hi: On Thu, Jul 28, 2011 at 1:05 AM, anglor wrote: > Hi, > > I've got a dataframe looking like this: > >                DateHour TcuvInt.A TcuvInt.B TcuvInt.C > 1757 2007-03-15 14:00:00                7.83       > 1758 2007-03-15 14:30:00      7.42      7.69       > 1759 2007-03-15 15:00:00      

Re: [R] Lowest values in a vector of numbers

2011-07-28 Thread Jim Silverton
I have a vector of numbers, and I will like to find the positions of the lowest 20% of the values. Can anyhow point out how to do this. I tried the ecdf function but to no avail. -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help

Re: [R] apply is making me crazy...

2011-07-28 Thread Dennis Murphy
Hi Gene: I would encourage you to take some time to write a general-purpose function that does exception handling and deals with one-column matrices properly. Since you have nested lists of matrices, operations like lapply() and perhaps more usefully, rapply(), could well be productive. Dennis O

Re: [R] How to adjust the order of one-way table ?

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 10:51 PM, Jeff Zhang wrote: Hi all, I wan to make a bar chart for a one-way table, but it seems the bar is in the order of alphabet which is my expectation, how can I adjust the order of the one-way table. Make it a factor with the desired order in its levels. ?fact

Re: [R] hdf5 library install issue

2011-07-28 Thread Yitping Kok
I have had the same problem. It seems that you need to configure the make option with a file. Create a file, ~/.R/Makevars, and insert "LDFLAGS=-L/share/apps/HDF5/lib" (in your case) into it. It solved my problem. __ R-help@r-project.org mailing list htt

[R] How to adjust the order of one-way table ?

2011-07-28 Thread Jeff Zhang
Hi all, I wan to make a bar chart for a one-way table, but it seems the bar is in the order of alphabet which is my expectation, how can I adjust the order of the one-way table. Thanks -- Best Regards Jeff Zhang [[alternative HTML version deleted]] __

[R] R, ctree and categorical variables

2011-07-28 Thread seanstclair
I am running the ctree function in R. My data has about 10 variables, many of which are categorical. 2 of the categorical variables have many levels (one has 900 levels, another has 1,000 levels). As an example, 1 of these variables is disease code and is structured as A, B, C,

Re: [R] unlist?

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 8:59 PM, Penny Bilton wrote: How do I unlist from the r-help email group? I have tried to follow the instrictions on the website with no success. Really?. Describe in excruciating detail what you did, please. (It has worked for everyone else.) I sent the password code

Re: [R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread John Fox
Dear Simon, On Thu, 28 Jul 2011 17:32:45 -0400 Simon Kiss wrote: > Dear John, > The Command Tab does not work for me, but I have been able to get expose to > work. I.e. it does bring up all windows, including the x11 terminal. It will > take a little getting used to, but it is functional. I

[R] unlist?

2011-07-28 Thread Penny Bilton
How do I unlist from the r-help email group? I have tried to follow the instrictions on the website with no success. I sent the password code from my confirmation email to r-help-ow...@r-project.org and received a return email with the message "unprocessed". Thank you Penny. _

Re: [R] smooth scatterplot and geo map

2011-07-28 Thread Leo Guelman
check smooth.ppp{spatstat} which performs spatial smoothing based on a Gaussian kernel...it has a plot method that may do what you are looking for hope this helps, Leo. On Thu, Jul 28, 2011 at 4:09 PM, marco wrote: > Hello everybody, > I'm trying to understand how to draw a smoothed scatterplo

Re: [R] Looping through data sets to change column from character to numeric

2011-07-28 Thread Sarah Henderson
Thanks for the explainable, Denes. Your solution worked a charm. I should have seen things more clearly, but sometimes I just get stuck in a rut. The help of this list is always appreciated -- such a fantastic resource. Cheers, Sarah 2011/7/28 "Dénes TÓTH" > > Sorry, I was wrong. Of cou

Re: [R] Looping through data sets to change column from character to numeric

2011-07-28 Thread Dénes TÓTH
Sorry, I was wrong. Of course you can assign a variable to itself, but it does not make much sense... What you misunderstood was that in the assignment you assign the data frame (e.g. "df1") to itself. You do not modify the frame object which remains a character string. > > The problem is that y

Re: [R] Looping through data sets to change column from character to numeric

2011-07-28 Thread Dénes TÓTH
The problem is that you can not assign a variable to itself. rm(list=ls()) df1 <- data.frame(ResultValue=as.character(1:5)) df2 <- data.frame(ResultValue=as.character(1:10)) frames = ls() for (frame in frames){ temp <- get(frame) temp[,"ResultValue"] = as.numeric(temp[,"ResultValue"])

Re: [R] Reading name-value data

2011-07-28 Thread Hadley Wickham
Use plyr::rbind.fill? That does match up columns by name. Hadley On Thu, Jul 28, 2011 at 5:23 PM, Stavros Macrakis wrote: > I have a file of data where each line is a series of name-value pairs, but > where the names are not necessarily the same from line to line, e.g. >    a=1,b=2,d=5 >    b=4

Re: [R] not working yet: Re: lattice overlay

2011-07-28 Thread Duncan Mackay
At 21:50 28/07/2011, you wrote: Hi Dieter and R community: I tried both of these three versions with ylim as suggested, none work: I am getting only single (pch = 16) not overlayed (pch =3) everytime. *vs 1* require(lattice) xyplot(Sepal.Length ~ Sepal.Width | Species , data= iris, panel=

Re: [R] Can R (without GUI) be compiled with static linking?

2011-07-28 Thread Duncan Murdoch
On 28/07/2011 5:54 PM, Jonathan Callahan wrote: I have a potential client that is considering R for data analysis and visualization modules within a larger framework. The host systems run either Solaris or a version of Linux. Hopefully this client will respect the R license, and license their

[R] Looping through data sets to change column from character to numeric

2011-07-28 Thread Sarah Henderson
Greetings to all -- I am having a silly problem that I just can't solve. Someone has given me an .RData file will hundreds of data frames. Each data frame has a column named ResultValue, currently character when it should be numeric. I want to loop through all of the data frames to change the v

Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread selwyn quan
On Fri, 29 Jul 2011, Rolf Turner wrote: On 29/07/11 09:51, selwyn quan wrote: On Thu, 28 Jul 2011, Duncan Murdoch wrote: On 11-07-28 1:22 PM, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (ope

Re: [R] How to use as.Date (or something else) with "31-Jul-2010 23:59:00"

2011-07-28 Thread Eduardo M. A. M.Mendes
Hello Many thanks. Sorry for not replying earlier but I have followed advice and read as much documentation as I could. I managed to get a zoo object the way I want dadoszoo : 'zoo' series from 2010-06-27 to 2010-08-05 Data: num [1:56161, 1:14] 74 74.2 74.2 74.1 73.9 ... Index: POSIXct[1:5

[R] Why won't R CMD CHECK run configure?

2011-07-28 Thread Alexander James Rickett
I'm trying to get ready to submit a package to CRAN, but in order for the package to install on OS X, I need to temporarily set an environment variable. I put this in the 'configure' script, and 'R CMD INSTALL MyPackage' works fine, but when I do 'R CMD CHECK MyPackage', and it tests installat

Re: [R] grey colored lines and overwriting labels i qqplot2

2011-07-28 Thread Brian Diggs
On 7/25/2011 8:27 PM, Sigrid wrote: Thank you Brian. Sorry for being such a noob. I am not a programmer and just learning R by myself. This is was I typed, but ended up with a couple error messages. df<-structure(list(year = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, + 1L, 1L, 1L, 1L, 1L, 1L,

Re: [R] Data aggregation question

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 4:24 PM, David Warren wrote: Hi all, I'm working with a sizable dataset that I'd like to summarize, but I can't find a tool or function that will do quite what I'd like. Basically, I'd like to summarize the data by fully crossing three variables and getting a co

Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread Rolf Turner
On 29/07/11 09:51, selwyn quan wrote: On Thu, 28 Jul 2011, Duncan Murdoch wrote: On 11-07-28 1:22 PM, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q

[R] Reading name-value data

2011-07-28 Thread Stavros Macrakis
I have a file of data where each line is a series of name-value pairs, but where the names are not necessarily the same from line to line, e.g. a=1,b=2,d=5 b=4,c=3,e=3 a=5,d=1 I would like to create a data frame which lines up the data in the corresponding columns. In this case, this wo

[R] Fwd: Ploting gradient

2011-07-28 Thread Fernando Andreacci
I could not get Jim code to work (can't install colors in R 2.13). However Alexander code seems what I want. Just a litle detail, I need all bars with same size, the only difference between they are the colors. On Thu, Jul 28, 2011 at 6:11 AM, Jim Lemon wrote: > On 07/28/2011 11:25 AM, Fernand

Re: [R] Data aggregation question

2011-07-28 Thread William Dunlap
Have you tried using table()? E.g., > df <- data.frame(x=c("A","A","B","C"), y=c("ii","ii","i","ii"), Age=2^(1:4)) > tab <- do.call("table", df[c("x","y")]) > tab y x i ii A 0 2 B 1 0 C 0 1 > as.data.frame(tab) x y Freq 1 A i0 2 B i1 3 C i0 4 A ii2 5 B ii0 6

Re: [R] Data aggregation question

2011-07-28 Thread Sarah Goslee
You don't offer a reproducible example, but what do you need that table() doesn't provide? testdata <- data.frame(A=factor(sample(1:3, 20)), B=factor(sample(1:3, 20)), C=factor(sample(1:3, 20))) table(testdata) Sarah On Thu, Jul 28, 2011 at 4:24 PM, David Warren wrote: > Hi all, > >     I'm wor

[R] Can R (without GUI) be compiled with static linking?

2011-07-28 Thread Jonathan Callahan
I have a potential client that is considering R for data analysis and visualization modules within a larger framework. The host systems run either Solaris or a version of Linux. One of their requirements (hard or soft?) is that each module in the framework be compiled with statically linked librar

Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread selwyn quan
On Thu, 28 Jul 2011, Duncan Murdoch wrote: On 11-07-28 1:22 PM, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q" in the PDF. dev.copy2eps produces th

Re: [R] smooth scatterplot and geo map

2011-07-28 Thread marco
thanks a lot!! -- View this message in context: http://r.789695.n4.nabble.com/smooth-scatterplot-and-geo-map-tp3702374p3702424.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mail

[R] Data aggregation question

2011-07-28 Thread David Warren
Hi all, I'm working with a sizable dataset that I'd like to summarize, but I can't find a tool or function that will do quite what I'd like. Basically, I'd like to summarize the data by fully crossing three variables and getting a count of the number of observations for every level of that 3

Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread Duncan Murdoch
On 11-07-28 1:22 PM, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q" in the PDF. dev.copy2eps produces the correct results as does cairo_pdf. Other symbo

Re: [R] bug in dev.copy2pdf output?

2011-07-28 Thread Rolf Turner
On 29/07/11 05:22, selwyn quan wrote: Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q" in the PDF. dev.copy2eps produces the correct results as does cairo_pdf. Other symb

Re: [R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread Simon Kiss
Dear John, The Command Tab does not work for me, but I have been able to get expose to work. I.e. it does bring up all windows, including the x11 terminal. It will take a little getting used to, but it is functional. I apologize for cluttering the list with minutiae Thank you! Yours S. On 2011-0

Re: [R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread John Fox
Dear Simon, I'm sitting in front of a MacBook Pro and Command-tab works perfectly fine for me: Selecting X11 brings the R Commander Window to the front, and selecting R brings the Quartz graphics window to the front. I must admit that my habit in classroom demonstrations on a Mac is to use Expo

Re: [R] Help Non-sequential ANOVAs

2011-07-28 Thread John Fox
Dear Ariane, You must be referring to the Anova() function in the car package. The function doesn't have an appropriate method for gls objects. The error was produced by the default method, which is inappropriate for gls objects, as you discovered. I agree that it would be nice for Anova() to h

Re: [R] Animated gif or something similar in R?

2011-07-28 Thread Jean V Adams
Dale, I do not have the same color problem when I run your code on my PC. The colors in both devices look the same. I'm running R version 2.13.0 on Windows. I am not familiar with the rgl package, but I found a function that might be helpful to you when I searched for "gif" in the package re

Re: [R] Animated gif or something similar in R?

2011-07-28 Thread Gene Leynes
It seems like you have two questions, one about color rendering, and another about making animations. For the second question : I've found the animation package useful in similar situations, where I want to share results with non-R users who want a static visualization. By using animation you ca

Re: [R] Data frame to list

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 4:14 PM, Jonathan Greenberg wrote: I'm hoping this is an easy problem that I'm missing something obvious. Given: x=c(1,1,1,2,2,3,3,3) y=c(1:length(x)) dataframe=data.frame(x,y) I would like to convert this to a list for use with certain functions, where each entry of th

Re: [R] Data frame to list

2011-07-28 Thread Jonathan Greenberg
Yep, my R-gut was right! Thanks Jean and Greg! --j On Thu, Jul 28, 2011 at 1:29 PM, Jean V Adams wrote: > > Try this: > > split(dataframe, dataframe$x) > > Jean > > > `·.,, ><(((º> `·.,, ><(((º> `·.,, ><(((º> > > Jean V. Adams > Statistician > U.S. Geological Survey > Great Lakes Scienc

Re: [R] Unable to install packages on Mac OS X

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 3:08 PM, Miguel Leal wrote: I'm having problems installing packages. I'm working on the R version 2.13.1 in a Mac OS X version 10.6.8. I'm not able to search or install packages. For instance, I have the following error message: install.packages("lattice") Warning: u

Re: [R] Data frame to list

2011-07-28 Thread Jean V Adams
Try this: split(dataframe, dataframe$x) Jean `·.,, ><(((º> `·.,, ><(((º> `·.,, ><(((º> Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA From: Jonathan Greenberg To: r-help Date: 07/28/2011 03:22 PM Subject: [

Re: [R] Data frame to list

2011-07-28 Thread Greg Snow
?split -- 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-bounces@r- > project.org] On Behalf Of Jonathan Greenberg > Sent: Thursday, July 28, 2011 2:1

Re: [R] smooth scatterplot and geo map

2011-07-28 Thread Greg Snow
The usual smoothed scatterplot assumes that the x variable (longitude) is fixed and that the y-variable (latitude) is observed with error, and that the mapping is 1 to 1 or 1 to many in that for each value of x you can have at most one y value. These assumptions don't seem to make much sense wi

Re: [R] apply is making me crazy...

2011-07-28 Thread Gene Leynes
Yes, I meant to say drop=FALSE Also, I made a mistake in my "desired answer" structure example, sorry for that confusion. The apply results when margin=1 are very unintuitive. That transposition issue has caused me numerous headaches. I think it's a design error, but that changing it would be a

[R] Data frame to list

2011-07-28 Thread Jonathan Greenberg
I'm hoping this is an easy problem that I'm missing something obvious. Given: x=c(1,1,1,2,2,3,3,3) y=c(1:length(x)) dataframe=data.frame(x,y) I would like to convert this to a list for use with certain functions, where each entry of the list is a subsetted dataframe based on dataframe$x I can d

[R] Animated gif or something similar in R?

2011-07-28 Thread Dale Coons
I'm have a (minor) problem and a question. Problem: The following code creates 5 clusters of dots of different colors. However, I need the second call outside the data.frame call to get the colors to change for some reason. I assume there's an error in the data.frame() call, but I don't know

Re: [R] help with rpart

2011-07-28 Thread Sarah Goslee
Why repost after receiving a reply? Reposting is unnecessary. If the first reply was unsatisfactory, why? More detail in your question leads to a more useful and informative reply. Just in case you didn't get it: On Thu, Jul 28, 2011 at 11:52 AM, wrote: > 1. How can I plot the entire tree produ

[R] smooth scatterplot and geo map

2011-07-28 Thread marco
Hello everybody, I'm trying to understand how to draw a smoothed scatterplot on a geographic map with R. Have a dataframe with point locations (long, lat) and was able to simply plot these points on a shp map by using the maptools package. However, instead of having simply the raw points on the map

Re: [R] Executing for loop by grouping variable within dataframe

2011-07-28 Thread ssobek
Dear Dennis, Thank you very much for your quick response! Your code does indeed solve my problem. I figured I would have to define a function somehow to use anything like ddply or similar, but couldn't wrap my head around how to set it up properly. I only started using R for anything more sophist

[R] bug in dev.copy2pdf output?

2011-07-28 Thread selwyn quan
Hi, Am using R 2.13.1 on Linux (Fedora). Is anybody else having problems with dev.copy2pdf xyplot output with the pch=1 (open circle) symbol? The symbols come out as "q" in the PDF. dev.copy2eps produces the correct results as does cairo_pdf. Other symbols produced with dev.copy2pdf seem ok

Re: [R] Life Cycle Assessment with R.

2011-07-28 Thread mason.earles
Hi there-- To avoid duplication, I would recommend looking at the OpenLCA efforts--see http://www.openlca.org/index.html http://www.openlca.org/index.html . One of the limitations of this OpenLCA software, however, is a lack of statistical tools with which to analyze the results. Perhaps an R mod

Re: [R] Python difflib R equivalent?

2011-07-28 Thread Spencer Graves
There is a package "rJython", which claims to provide an "R interface to Python via Jython". I haven't used it, but the lead author, Gabor Grothendieck, is well known in the R community. Spencer On 7/28/2011 9:15 AM, Prof Brian Ripley wrote: On Thu, 28 Jul 2011, Bert Gunter wrote: Paul:

[R] ggplot2 help/suggestions needed

2011-07-28 Thread Bruce Rex
Hello, I have written a version of the Kohenen Self Organizing Map (in R) and wish to use ggplot2 for the visualization. My results are RGB values in a matrix [x,y,1:3] where x and y comprise the first two dimensions and the third dimension is the RGB vector. I am not sure whether to use geom_ti

Re: [R] apply is making me crazy...

2011-07-28 Thread Gene Leynes
Dennis, ninety Thanks, I did try almost exactly the same thing. I decided it was too complicated, especially since I have a whole mess of functions I want to use this way. You see, I usually work with lists of lists of matrices that are dimensioned by simulations X time, so there's usually a one

[R] R: Re: Problem with anova.lmRob() "robust" package

2011-07-28 Thread m.fen...@libero.it
I'm sorry, maybe the question was bad posed. Ista has well described my problem. Thanks Massimo >Messaggio originale >Da: iz...@psych.rochester.edu >Data: 28/07/2011 17.52 >A: "David Winsemius" >Cc: "m.fen...@libero.it", >Ogg: Re: [R] Problem with anova.lmRob() "robust" package >

[R] help with rpart

2011-07-28 Thread mark
1. How can I plot the entire tree produced by rpart? 2. How can I submit a vector of values to a tree produced by rpart and have it make an assignment? Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do re

[R] Unable to install packages on Mac OS X

2011-07-28 Thread Miguel Leal
I'm having problems installing packages. I'm working on the R version 2.13.1 in a Mac OS X version 10.6.8. I'm not able to search or install packages. For instance, I have the following error message: > install.packages("lattice") Warning: unable to access index for repository http://cran.pt.r

[R] Help Non-sequential ANOVAs

2011-07-28 Thread Ariane Charaoui
Hello, I have data on the maturity of two morphs of fish. I want to test whether their maturity is evolving differently or not on a temporal scale (month). The maturity variable (independent variable) is continuous and the morph and month variables (dependant variables) are categorical. Becaus

Re: [R] filterMicroRna function: Sample replicates in preprocessing Agilent miRNA dataset

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 3:33 PM, Vickie S wrote: Hi, I have a question about filterMicroRna in AgiMicroRna package function for filtering probes in Agilent microRNA dataset. ddPROC = filterMicroRna(ddNORM.micro, dd, control = TRUE, IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetect

Re: [R] apply is making me crazy...

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 3:13 PM, Gene Leynes wrote: Very clever (as usual)… It works, but since I wanted to switch the rows and columns, which would require this: answer.slightly.clumsy = lapply(exampBad, function(x) matrix(apply(x ,1, cumsum), ncol=nrow(x))) However, with a slight m

Re: [R] Tools for professional R developers

2011-07-28 Thread Michael Karol
Hi Uwe: You might want to take a look at RStudio (http://rstudio.org/). Regards,  Michael -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Bert Gunter Sent: Thursday, July 28, 2011 3:24 PM To: Uwe Ligges Cc: r-help@r-project.or

[R] filterMicroRna function: Sample replicates in preprocessing Agilent miRNA dataset

2011-07-28 Thread Vickie S
Hi, I have a question about filterMicroRna in AgiMicroRna package function for filtering probes in Agilent microRNA dataset. >ddPROC = filterMicroRna(ddNORM.micro, dd, control = TRUE, IsGeneDetected = >TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 75, limNEG = 25, makePLOT = >TRUE, target.mi

Re: [R] Tools for professional R developers

2011-07-28 Thread Bert Gunter
+ ESS or some other reasonably capable text editor? -- Bert On Thu, Jul 28, 2011 at 12:14 PM, Uwe Ligges wrote: > > > On 28.07.2011 21:04, Mark Alen wrote: >> >> Hi everyone, >> >> I was wondering what tools professional R users use so I went and posted >> this question on stack overflow. I appr

Re: [R] Tools for professional R developers

2011-07-28 Thread Steve Lianoglou
On Thu, Jul 28, 2011 at 3:14 PM, Uwe Ligges wrote: > > > On 28.07.2011 21:04, Mark Alen wrote: >> >> Hi everyone, >> >> I was wondering what tools professional R users use so I went and posted >> this question on stack overflow. I appreciate if you would please answer >> this question too (either

Re: [R] apply is making me crazy...

2011-07-28 Thread Gene Leynes
Very clever (as usual)… It works, but since I wanted to switch the rows and columns, which would require this: answer.slightly.clumsy = lapply(exampBad, function(x) matrix(apply(x ,1, cumsum), ncol=nrow(x))) However, with a slight modification of your code I can use a wrapper function f

Re: [R] Tools for professional R developers

2011-07-28 Thread Uwe Ligges
On 28.07.2011 21:04, Mark Alen wrote: Hi everyone, I was wondering what tools professional R users use so I went and posted this question on stack overflow. I appreciate if you would please answer this question too (either here or on stackoverflow) My preferred tool is R. If you ask me to

[R] Tools for professional R developers

2011-07-28 Thread Mark Alen
Hi everyone, I was wondering what tools professional R users use so I went and posted this question on stack overflow. I appreciate if you would please answer this question too (either here or on stackoverflow) Here is the link to the question http://stackoverflow.com/questions/6796490/tools-fo

Re: [R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 1:51 PM, Ista Zahn wrote: Hi Simon On Thu, Jul 28, 2011 at 1:40 PM, Simon Kiss wrote: Dear Colleagues, I have recently installed R Commander on my Mac OS 10.6.8. I'd like to use it for an undergraduate class this year. Everything appears to be working fine, except for o

Re: [R] fitting a sinus curve

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 1:07 PM, Hans W Borchers wrote: maaariiianne ec.europa.eu> writes: Dear R community! I am new to R and would be very grateful for any kind of help. I am a PhD student and need to fit a model to an electricity load profile of a household (curve with two peaks). I was th

Re: [R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread Ista Zahn
Hi Simon On Thu, Jul 28, 2011 at 1:40 PM, Simon Kiss wrote: > Dear Colleagues, > I have recently installed R Commander on my Mac OS 10.6.8. I'd like to use it > for an undergraduate class this year. > Everything appears to be working fine, except for one thing.  I cannot use > Command-tab to cy

[R] cycling from x11 window in RCommander to graphics device window: Mac Os 10.6.8

2011-07-28 Thread Simon Kiss
Dear Colleagues, I have recently installed R Commander on my Mac OS 10.6.8. I'd like to use it for an undergraduate class this year. Everything appears to be working fine, except for one thing. I cannot use Command-tab to cycle from the X11 window in which RCommander is running to any other wi

Re: [R] fitting a sinus curve

2011-07-28 Thread Hans W Borchers
maaariiianne ec.europa.eu> writes: > Dear R community! > I am new to R and would be very grateful for any kind of help. I am a PhD > student and need to fit a model to an electricity load profile of a > household (curve with two peaks). I was thinking of looking if a polynomial > of 4th order,

Re: [R] apply is making me crazy...

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 12:31 PM, Gene Leynes wrote: (As I mentioned in my other reply to Dennis, I think I'll stick with for loops, but I wanted to respond.) By "almost does it" I meant that using as.matrix helps because it puts the vector into a column, that "almost does it” because half t

Re: [R] Extend my code to run several data at once.

2011-07-28 Thread Daniel Malter
No, I may not. If you want somebody to check out your code, please adhere to the posting guide (which you should in all your posts), which requires you to provide minimally self-contained code (i.e., an example that we can directly copy-paste to R-prompt). But I will give you an example: Your llik

Re: [R] apply is making me crazy...

2011-07-28 Thread Gene Leynes
(As I mentioned in my other reply to Dennis, I think I'll stick with for loops, but I wanted to respond.) By "almost does it" I meant that using as.matrix helps because it puts the vector into a column, that "almost does it” because half the problem is that the output is a non dimensional vector

Re: [R] Python difflib R equivalent?

2011-07-28 Thread Prof Brian Ripley
On Thu, 28 Jul 2011, Bert Gunter wrote: Paul: 1. I do not know if any such library exists. Not to my knowledge, and we have contemplated providing such functions. But for files see e.g. tools::Rdiff, and generally R will not be a good way to do this sort of thing on files (since the flexi

Re: [R] R

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 11:35 AM, Bert Gunter wrote: Homework? We try not to do homework on this list. -- Bert On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira wrote: Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have

Re: [R] Calculating difference in variable values (e.g. elapsed time) in data frame

2011-07-28 Thread Sarah Goslee
Hi, On Thu, Jul 28, 2011 at 11:38 AM, Philippe Hensel wrote: > Hello, > > I have a data frame containing time (e.g. GMT), and I would like to > create/add a new variable that would be the computation of the elapsed time > since the first observation.  Does anyone have a suggestion for an easy way

Re: [R] Help with R

2011-07-28 Thread Sarah Goslee
Hi Mark, On Thu, Jul 28, 2011 at 10:44 AM, wrote: > >   1.  How can I plot the entire tree produced by rpart? What does plot() not do that you are expecting? >   2.  How can I submit a vector of values to a tree produced by rpart and have >   it make an assignment? What does predict() not do

Re: [R] R

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 11:54 AM, David Winsemius wrote: On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira wrote: Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwi

Re: [R] Problem with anova.lmRob() "robust" package

2011-07-28 Thread Ista Zahn
I found the question really confusing as well, but see below. On Thu, Jul 28, 2011 at 11:42 AM, David Winsemius wrote: > > On Jul 28, 2011, at 9:13 AM, m.fen...@libero.it wrote: > >> >> Dear R users, >> I'd like to known your opinion about a problem with anova.lmRob() of >> "Robust" package that

Re: [R] Fixed effects using Within transformation in PLM package

2011-07-28 Thread Peter Ehlers
On 2011-07-28 06:21, Luca Deckert wrote: Dear R community, I am trying to do my own fixed effects regression using the Within function in PLM. I apply the Within function to all my pseries and then run OLS on the transformed vectors using lm(). When I compare the results to those obtained via p

Re: [R] create a index.date column

2011-07-28 Thread jose Bartolomei
Dear Dennis, I appreciate your time. I studied and implemented your recommendation and is exactly what I needed. I was in an unproductive loop in this. Thank you very much, Jose > Date: Wed, 27 Jul 2011 14:28:51 -0700 > Subject: Re: [R] create a index.date column > From: djmu...@gmail.com > T

Re: [R] construct a data set

2011-07-28 Thread nandan amar
Dear Michael and Vettorazzi, Thanks. It was really helpful. I got the desired answer . Actually I had some weekly data and i wanted to put in ts class for some time series related test. Thanks a lot :) On Thu, Jul 28, 2011 at 8:20 PM, Eik Vettorazzi wrote: > Hi Amar, > you might have a look at ?t

Re: [R] Problem with anova.lmRob() "robust" package

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 9:13 AM, m.fen...@libero.it wrote: Dear R users, I'd like to known your opinion about a problem with anova.lmRob() of "Robust" package that occurs when I run a lmRob() regression on my dataset. I check my univariate model by single object anova as anova(lmRob(y~x)). I

[R] Calculating difference in variable values (e.g. elapsed time) in data frame

2011-07-28 Thread Philippe Hensel
Hello, I have a data frame containing time (e.g. GMT), and I would like to create/add a new variable that would be the computation of the elapsed time since the first observation. Does anyone have a suggestion for an easy way to do this? I am having trouble creating a new variable that woul

Re: [R] R

2011-07-28 Thread Bert Gunter
Homework? We try not to do homework on this list. -- Bert On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira wrote: > Good afternoon. > > I am a master student in University of Porto in Portugal. At this moment I’m > starting to use R, so I have some doubts. > > The aim of my analysis is:  calculate

[R] Help with modFit of FME package

2011-07-28 Thread Paola Lecca
Dear R users, I'm trying to fit a set an ODE to an experimental time series. In the attachment you find the R code I wrote using modFit and modCost of FME package and the file of the time series. When I run summary(Fit) I obtain this error message, and the values of the parameters are equal to

[R] R

2011-07-28 Thread Rui Oliveira
Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape p

[R] Help with modFit of FME package

2011-07-28 Thread Paola Lecca
Dear R users, I’m trying to fit a set an ODE to an experimental time series. In the attachment you find the R code I wrote using modFit and modCost of FME package and the file of the time series. When I run summary(Fit) I obtain this error message, and the values of the parameters are equal t

[R] Help with R

2011-07-28 Thread mark
1. How can I plot the entire tree produced by rpart? 2. How can I submit a vector of values to a tree produced by rpart and have it make an assignment? Mark References Visible links Hidden links: 1. mailto:r-help@r-project.org ___

Re: [R] color of math annotation in legend

2011-07-28 Thread Peter Ehlers
On 2011-07-28 01:11, Zhongyi Yuan wrote: Thank you Tyler. I thought the problem was due to the use of expression(...). Also note that you can simplify your legend text: c(expression(alpha == 1), expression(alpha == 2)) In general, I find that paste() is overused in plotmath. Peter Ehlers

Re: [R] Python difflib R equivalent? -- Correction

2011-07-28 Thread Bert Gunter
Item 1 below should be changed to: 1. I do not know if any such PACKAGE exists. (A "library" in R is a file directory where R packages are stored) -- Bert On Thu, Jul 28, 2011 at 8:05 AM, Bert Gunter wrote: > Paul: > > 1. I do not know if any such library exists. > > 2. However, if I understa

Re: [R] Python difflib R equivalent?

2011-07-28 Thread Bert Gunter
Paul: 1. I do not know if any such library exists. 2. However, if I understand correctly, one usually does this sort of thing in R with functions like ?match (or ?"%in%") and logical comparison operations like ?"==" . Of course, for numeric comparisons, you need to be aware of R FAQ 7.31 If you

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