[R] plotting matrix into 2D color plots with rainbow colors

2011-07-28 Thread hitendra padalia
Dear all, Can you pl. help me in plotting a matrix into 2D plot with more color options. I tried to plot with myImagePlot with RGB color ramp but it shows limited variation in color. There is a rainbow plot option also. Can anyone help me. Regards, Hitendra -- Hitendra Padalia, PhD

Re: [R] Ploting gradient

2011-07-28 Thread Alexander Engelhardt
Am 28.07.2011 03:25, schrieb Fernando Andreacci: I have a simple bar chart with annual precipitation (jan to dez). I want to plot, above each bar (on a line), a square wich is color based on a scale (0-100%). With 0 being white and 100 black, like a gradient. Is it possible? How to? Thanks

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-28 Thread Martin Maechler
PM == Paul Menzel paulepan...@users.sourceforge.net on Wed, 27 Jul 2011 23:53:51 +0200 writes: PM Am Mittwoch, den 27.07.2011, 17:21 -0400 schrieb David Winsemius: On Jul 27, 2011, at 4:53 PM, Paul Menzel wrote: Am Mittwoch, den 27.07.2011, 13:26 -0700 schrieb Bert Gunter:

[R] color of math annotation in legend

2011-07-28 Thread Zhongyi Yuan
Dear useRs, Can someone help me to adjust the color of math annotation in a legend? The following code gives me a black alpha = 2. x=y=1:100 z=seq(0.5,50,by=0.5) plot(x,y,type='l',col='black') lines(x,z,col='red') legend('topleft',c(expression(paste(alpha, = , 1)), expression(paste(alpha, = ,

[R] [R-pkgs] CatDyn - Estimation of wild populations abundance

2011-07-28 Thread Rubén Roa
Dear ComRades, Package CatDyn 1.0-3 is now available on CRAN. The package allows the estimation of the absolute abundance of a wild population during a capture season using a nonlinear and recursive discrete-time structural model. The response variable is the catch, assumed a random variable

Re: [R] color of math annotation in legend

2011-07-28 Thread Tyler Rinker
Use the text.col argument as below ?legend x=y=1:100 z=seq(0.5,50,by=0.5) plot(x,y,type='l',col='black') lines(x,z,col='red') legend('topleft',c(expression(paste(alpha, = , 1)), expression(paste(alpha, = , 2))),text.col=c(black,red)) Date: Thu, 28 Jul 2011 02:32:04 -0500 From:

Re: [R] replacing elements of vector through elements of another vector

2011-07-28 Thread Marcus Mund
Dear Marc and David, thank you so much for casting off my blinkers - it works! Marcus Am 27.07.2011 17:52, schrieb David Winsemius: On Jul 27, 2011, at 10:52 AM, Marcus Mund wrote: Hello everybody, I hope this question is not too silly but I'm almost going crazy about that and could not

Re: [R] color of math annotation in legend

2011-07-28 Thread Zhongyi Yuan
Thank you Tyler. I thought the problem was due to the use of expression(...). Best, Zhongyi On Thu, Jul 28, 2011 at 2:49 AM, Tyler Rinker tyler_rin...@hotmail.comwrote: Use the text.col argument as below ?legend x=y=1:100 z=seq(0.5,50,by=0.5) plot(x,y,type='l',col='black')

Re: [R] Hidden Markov Models in R

2011-07-28 Thread Ingmar Visser
Dear Edward, Without knowing what you want exactly, it is basically impossible to help you out. The following code (with simulated data) works just fine. In what sense did you not have success with HMM and/or depmixS4? Best, Ingmar library(HMM) dat -

Re: [R] plotting matrix into 2D color plots with rainbow colors

2011-07-28 Thread Jim Lemon
On 07/28/2011 04:00 PM, hitendra padalia wrote: Dear all, Can you pl. help me in plotting a matrix into 2D plot with more color options. I tried to plot with myImagePlot with RGB color ramp but it shows limited variation in color. There is a rainbow plot option also. Can anyone help me. Hi

Re: [R] Ploting gradient

2011-07-28 Thread Jim Lemon
On 07/28/2011 11:25 AM, Fernando Andreacci wrote: I have a simple bar chart with annual precipitation (jan to dez). I want to plot, above each bar (on a line), a square wich is color based on a scale (0-100%). With 0 being white and 100 black, like a gradient. Is it possible? How to? Hi

[R] construct a data set

2011-07-28 Thread nandan amar
Hi, i want to construct a data set similar to AirPassengers. Its attributes are following. attributes(AirPassengers) $tsp [1] 1949.000 1960.917 12.000 $class [1] ts How Can I construct a data set similar to it having same class and attributes. Thanks -- Amar Kumar Nandan

Re: [R] fitting sine wave

2011-07-28 Thread Rolf Turner
On 28/07/11 02:36, Tonja Krueger wrote: Dear R-helpers I have 7 data points that I want to fit a continuous curve to, that should look similar to a sine wave My data points would mark the local minima and maxima respectively. This is what I’ve got so far. And I would keep doing so, but sadly

Re: [R] _: how to replace values in x by means in subgroups created in ...(not loops)

2011-07-28 Thread Eugeniusz Kałuża
Re:_: how to replace values in x by means in subgroups created in ...(not loops) Thanks, below some code and reply: #_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_# #--- # my slow function with loops: # replace_x_by_locallyMean_x_4_0s_in_y.f(x,y)

[R] Legend in image.plot( )

2011-07-28 Thread Sumukh Sathnur
Hello all, Using image.plot from the fields package, I created a heatmap for a matrix I had saved as a text file. Everything works fine, but my legend goes up to a value of 300 (the maximum value in my matrix) whereas my scale goes up to 20 for assigning colors. Is there any way to truncate

[R] order a data frame after date and hour

2011-07-28 Thread anglor
Hi, I've got a dataframe looking like this: DateHour TcuvInt.A TcuvInt.B TcuvInt.C 1757 2007-03-15 14:00:007.83 NA 1758 2007-03-15 14:30:00 7.42 7.69 NA 1759 2007-03-15 15:00:00 7.53 7.75 NA 1760 2007-03-15 15:30:00 7.65

[R] Fixed effects using Within transformation in PLM package

2011-07-28 Thread Luca Deckert
Hi all, 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 plm (within), the estimates are not always the same.

Re: [R] GLM different results with the same factors

2011-07-28 Thread Mark Difford
On Jul 27, 2011 gaiarrido wrote: I've been reading these days about what you tell me, but i don't understand properly. How could I know, with this tests, which variables are significant?... Mario, You need to get in touch with a statistician at your university. You are fitting quite a

[R] fitting a sinus curve

2011-07-28 Thread maaariiianne
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, a sinus/cosinus combination or a combination of

Re: [R] construct a data set

2011-07-28 Thread R. Michael Weylandt michael.weyla...@gmail.com
Well, depending on how similar you want/need it to be, you could simply make a copy and directly modify it as desired; AP2 - AirPassengers AP2$tsp - c(3,4,5) # or whatever It's quick and dirty but sounds like it works for you. Write back if this isn't clear or if you care to provide more info

Re: [R] 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 j...@bitwrit.com.au wrote: On

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

2011-07-28 Thread Justin
anglor angelica.ekenstam at dpes.gu.se writes: Hi, I've got a dataframe looking like this: DateHour TcuvInt.A TcuvInt.B TcuvInt.C 1757 2007-03-15 14:00:007.83 NA 1758 2007-03-15 14:30:00 7.42 7.69 NA 1759 2007-03-15 15:00:00

[R] how to shift a chron timestamp by 6:30 hours

2011-07-28 Thread Maciej Hoffman-Wecker
Dear help list, I have a timestamp in as a chron object: (x - chron(dates = c(12/02/11, 22/11/11), + times = c(07:30:00, 04:00:00), + format = c(dates = d/m/y, times = h:m:s))) [1] (12/02/11 07:30:00) (22/11/11 04:00:00) Now I want to shift the timestamp by 06:30

Re: [R] how to shift a chron timestamp by 6:30 hours

2011-07-28 Thread Jeff Newmiller
Create a difftime object and subtract it from your chron vector. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer

[R] sorting data from dataframe with oter dataframe

2011-07-28 Thread ראובן אברמוביץ
Hi, the subject isn't define well the problem, so i'll explain it in detail: i've got a csv.file with data on number of factors (every column got the name of the factor as header and the data below). on another csv file, i've got the factors sorted by their type. for example-

[R] Regression with ranges and displaying them in an XY-Plot

2011-07-28 Thread Johannes Radinger
Hello UseRs, I've got 3 variables, the dependent variable Y as well as a max and a min value of the independent variable (Xa and Xb) where in some cases Xa=Xb (so actually a single value for X). First I'd like to perform a regression, but my problem is that my X is a range (acutally a censored

[R] Python difflib R equivalent?

2011-07-28 Thread Paul
Hi, Does anyone know of a R library that is equivalent in functionality to the Python standard libraries' difflib library? The python docs say this about difflib: This module provides classes and functions for comparing sequences. It can be used for example, for comparing files, and can produce

[R] not working yet: Re: lattice overlay

2011-07-28 Thread Ram H. Sharma
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= function(x, y, subscripts) {

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

2011-07-28 Thread m.fen...@libero.it
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)). If I compare my model with the null model (y~1), I must obtain the

[R] Fixed effects using Within transformation in PLM package

2011-07-28 Thread Luca Deckert
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 plm (within), the estimates are not always

Re: [R] construct a data set

2011-07-28 Thread nandan amar
Thanks a lot Michael, I wanted to create similar data set for weekly data, for say 2 weeks data-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14) now i want to put data[ ] in the same structure as AirPassengers i.e. instead of 12x12 matrix AP2 should be a 2x7 matrix and with same attributes as AirPassengers I

Re: [R] how to shift a chron timestamp by 6:30 hours

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 9:37 AM, Maciej Hoffman-Wecker wrote: Dear help list, I have a timestamp in as a chron object: It would have been courteous to put in: library(chron) (x - chron(dates = c(12/02/11, 22/11/11), + times = c(07:30:00, 04:00:00), + format = c(dates

Re: [R] sorting data from dataframe with oter dataframe

2011-07-28 Thread Jean V Adams
Try this c1[, match(c2[, type1], names(c1), nomatch=0)] Jean `·.,, (((? `·.,, (((? `·.,, (((? Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA From: øàåáï àáøîåáéõ gantk...@walla.com To: r-help@r-project.org

Re: [R] construct a data set

2011-07-28 Thread R. Michael Weylandt michael.weyla...@gmail.com
I'm a little confused: what is making data = 1:14 into a 12x12 matrix and how is that related to AirPassengers? Best I understand it, tsp is a little fun and included as an S legacy. If you want to access tsp directly, take a look at the tsp(x) function (and the associated hasTsp(x) function). If

Re: [R] construct a data set

2011-07-28 Thread Eik Vettorazzi
Hi Amar, you might have a look at ?ts, which creates time-series objects (as AirPassengers actually is, see class(AirPassengers)). hth Am 28.07.2011 11:27, schrieb nandan amar: Hi, i want to construct a data set similar to AirPassengers. Its attributes are following.

Re: [R] how to shift a chron timestamp by 6:30 hours

2011-07-28 Thread Gabor Grothendieck
On Thu, Jul 28, 2011 at 9:37 AM, Maciej Hoffman-Wecker maciej.hoffman-wec...@bioskin.de wrote: Dear help list, I have a timestamp in as a chron object: (x - chron(dates = c(12/02/11, 22/11/11), +             times = c(07:30:00, 04:00:00), +             format = c(dates = d/m/y, times =

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

2011-07-28 Thread David Winsemius
On Jul 28, 2011, at 7:50 AM, Ram H. Sharma 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

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

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 bgun...@gene.com wrote: Paul: 1. I do not know if any such library exists. 2. However, if

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

[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

[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

[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

[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

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 rui18oli...@gmail.com 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

[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

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)). If

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 e.vettora...@uke.uni-hamburg.de wrote: Hi

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 To:

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

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 dwinsem...@comcast.net 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

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 rui18oli...@gmail.com 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

Re: [R] Help with R

2011-07-28 Thread Sarah Goslee
Hi Mark, On Thu, Jul 28, 2011 at 10:44 AM, m...@statcourse.com 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

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 philippe.hen...@noaa.gov 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

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 rui18oli...@gmail.com wrote: Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m

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

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] 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

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 the

Re: [R] fitting a sinus curve

2011-07-28 Thread Hans W Borchers
maaariiianne marianne.zeyringer at 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

[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

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 sjk...@gmail.com 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

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 marianne.zeyringer at 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

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 sjk...@gmail.com 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

[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

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

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

Re: [R] Tools for professional R developers

2011-07-28 Thread Steve Lianoglou
On Thu, Jul 28, 2011 at 3:14 PM, Uwe Ligges lig...@statistik.tu-dortmund.de 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

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 lig...@statistik.tu-dortmund.de 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

[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,

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:

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

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,

[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

[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.

[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 Winsemiusdwinsem...@comcast.net Cc: m.fen...@libero.itm.fen...@libero.it, r-help@r-project.org Ogg: Re:

[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] 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

[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

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: 1.

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

[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] 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

[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

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, m...@statcourse.com wrote: 1. How can I plot

[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

[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

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

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

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 2:14

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 j...@illinois.edu To: r-help r-help@r-project.org Date:

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:

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 jvad...@usgs.gov wrote: Try this: split(dataframe, dataframe$x) Jean `·.,, (((º `·.,, (((º `·.,, (((º Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science

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

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

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: [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

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

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

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

  1   2   >