Re: [R] kalaii...@gmail.com

2009-11-04 Thread Uwe Ligges
Please report it with a reproducible example to the package maintainer. Uwe Ligges kalaii...@gmail.com wrote: i am using R, haplo.stats package. i am working in liux, redhat 5. I run this many times, but suddenly its showing 0xf42418, cause 'memory not mapped'. i run again again its showing

Re: [R] [BioC] MatLab SimBiology

2009-11-04 Thread Dr. Sanjay Bhatikar
The differential equations solvers (LSODA, etc.) used in Matlab are all available in R. You may need to set-up the equations yourself, from a format such as SBML. The capability is all there in R - maybe just not as nicely packaged and pre-digested as Matlab. If you access to programming

[R] read.table (again)

2009-11-04 Thread Sybille Wendel (Udata)
Dear R commnuity, Thanks a lot for your help. I want to read in tables, the problem is that the table is composed in a difficult way. In ariginal it looks like this: 669 736 842101610481029114711811166124312081128117611221026 9581024 992 685 720 829 925 995

Re: [R] read.table (again)

2009-11-04 Thread Uwe Ligges
See ?read.fwf Uwe Ligges Sybille Wendel (Udata) wrote: Dear R commnuity, Thanks a lot for your help. I want to read in tables, the problem is that the table is composed in a difficult way. In ariginal it looks like this: 669 736 842101610481029114711811166124312081128117611221026 9581024

[R] Odp: read.table (again)

2009-11-04 Thread Petr PIKAL
Hi try to look at read.fwf. Regards Petr r-help-boun...@r-project.org napsal dne 04.11.2009 11:03:06: Dear R commnuity, Thanks a lot for your help. I want to read in tables, the problem is that the table is composed in a difficult way. In ariginal it looks like this: 669 736

Re: [R] Plotting an interaction with error bars

2009-11-04 Thread Jim Lemon
On 11/04/2009 06:36 PM, Dror D Lev wrote: Thank you Jim. brkdn.plot() seems to be just the function I need. Still, I wonder if there are lists of labels of the different measures of central tendency (mct argument) and measures of dispersion (md)? Hi Dror, With brkdn.plot (and several

Re: [R] read.table (again)

2009-11-04 Thread Chuck Cleland
On 11/4/2009 5:03 AM, Sybille Wendel (Udata) wrote: Dear R commnuity, Thanks a lot for your help. I want to read in tables, the problem is that the table is composed in a difficult way. In ariginal it looks like this: 669 736 842101610481029114711811166124312081128117611221026 9581024 992

Re: [R] Join points with arrows based a TIME variable

2009-11-04 Thread Uwe Ligges
zhijie zhang wrote: Hi, I have a data set with three variables,X Y and Time. X and Y are the coordinates of points, i want to join these points according to the Time sequence using arrows? Demo Example data: x-c(1:6) y-c(1:6) time-c(6:1) data-cbind(x,y,time) data x y time [1,] 1 16

[R] Patterned shading in ggplot

2009-11-04 Thread Paul Chatfield
Am trying to produce a graph which prints out well in black and white using ggplot2. I have the following example set up nicely, but want to shade the red bars in one pattern and the blue in another so they print out clearly. I tried changing colours to 1 light, 1 dark, but then the overlapping

Re: [R] Plotting an interaction with error bars

2009-11-04 Thread Dror D Lev
Indeed, that seems very convenient. Thanks for your work and for the help. dror - On Wed, Nov 4, 2009 at 12:17 PM, Jim Lemon j...@bitwrit.com.au wrote: On 11/04/2009 06:36 PM, Dror D Lev wrote: Thank you Jim. brkdn.plot() seems to be just the function I need.

Re: [R] Can't pass file name as parameter to Corpus function

2009-11-04 Thread Uwe Ligges
The function Corpus seems to be in some contributed package. If you think you found a bug in a contributed package, please contact the package maintainer. Best wishes, Uwe Ligges renjl0810 wrote: I'm working on a small project to extract high-frequency terms from a document and then

Re: [R] one long column of data - three small columns

2009-11-04 Thread MORNEAU François
Hello ?, Have a look at ?matrix matrix(c(2, 3, 4, 2, 1, 6, 6, 4, 7), ncol = 3) François -Message d'origine- De : r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] De la part de frenchcr Envoyé : mardi 3 novembre 2009 20:06 À : r-help@r-project.org Objet : [R] one

Re: [R] read.table (again)

2009-11-04 Thread Jim Lemon
On 11/04/2009 09:03 PM, Sybille Wendel (Udata) wrote: ... That is, that every 4 digits there is a new number, but when the number is 999, R thinks of course that the number consists of more than 4 digits. So, R can't read in the table. Is there a way I can tell R, that every 4 digits, a new

Re: [R] Help with RGDAL

2009-11-04 Thread Michael Denslow
Hi Charlie! On Fri, Oct 30, 2009 at 5:16 PM, cls59 ch...@sharpsteen.net wrote: Pablo Alvarez-2 wrote: Hello, We (two mac users) have been attempting to install rgdal from http://www.kyngchaos.com/software:frameworks;, given that it is not available as a binary on the CRAN (binaries) of

[R] PCA with tow response variables

2009-11-04 Thread Joel Fürstenberg-Hägg
Hi all, I'm new to PCA in R, so this might be a basical thing, but I cannot find anything on the net about it. I need to make a PCA plot with two response variables (df$resp1 and df$resp2) against eight metabolites (df$met1, df$met2, ...) and I don't have a clue how to do... and I've only

[R] finding an observation with similar characteristics

2009-11-04 Thread slurpy
Hi. I have a data frame with 2 variables (x y). For each row(i) I need to find an alternate row(j) with similar x y by sub-setting such that 0.5x[i] = x(j) = 1.5x[i], and then choosing the minimum y[i]-y[j] from that subset. I am currently implementing this using a for loop:

Re: [R] What happen for Negative binomial link in Lmer

2009-11-04 Thread Patrick Giraudoux
Seems the message below and the thread have reveived no attention/answer. The output presented is quite tricky. Looks like if lmer (lme4 0.9975-10) has accepted a negative binomial link with reasonable estimates, although it was not designed for... What can one think about result validity ?

Re: [R] mac question

2009-11-04 Thread Antje
Hi Steve, Steve Lianoglou wrote: Hi, On Nov 3, 2009, at 2:41 AM, Antje wrote: Hi there, currently, I've updated R on my Mac (OS X) to version 2.10. I was wondering if I have to install all additional packages again??? In Windows, I just needed to copy the library folder of the old

Re: [R] fitting a confined mixture model

2009-11-04 Thread Giovanni Luca Ciampaglia
Any idea anybody? cheers Giovanni Giovanni Luca Ciampaglia ha scritto: Hello all, I would like to fit a mixture model whose components are normal distributions confined in a closed interval. Since there are already several packages for EM, I would like to extend one of these instead of

[R] compute maximum likelihood estimator for a multinomial function

2009-11-04 Thread Benedikt Gehr
Hi there I am trying to learn how to compute mle in R for a multinomial negative log likelihood function. I am using for this the book by B. Bolker Ecological models and data in R, chapter 6: Likelihood an all that. But he has no example for multinomial functions. What I did is the

[R] solving a linear equation

2009-11-04 Thread maram salem
Hi all, I've a linear equation of the form: 0.95=2 ( [3+ln(x/3)]^-13  + 4 [3+2ln(x/3)]^-13  + [3+4ln(x/3)]^-13 ) and I want to solve it for x, can I do this using R? Thanks in advance. Maram. [[alternative HTML version deleted]] __

[R] Fw: solving a linear equation

2009-11-04 Thread maram salem
Sorry, I didn't mean a linear equation, of course this equation is not linear, I meant an equation in one unknown. Hi all, I've a linear equation of the form: 0.95=2 ( [3+ln(x/3)]^-13  + 4 [3+2ln(x/3)]^-13  + [3+4ln(x/3)]^-13 ) and I want to solve it for x, can I do this using R? Thanks in

Re: [R] Conditional read-in of data

2009-11-04 Thread jim holtman
That does not seem like a large data set. How are you reading it? How many columns does it have? What is a lot of time by your definition? You have provided minimal data for obtaining help. I common read in files with 300K rows in under 30 seconds. Maybe you need to consider a relational

Re: [R] solving a linear equation

2009-11-04 Thread Karl Ove Hufthammer
On Wed, 4 Nov 2009 04:34:36 -0800 (PST) maram salem marammagdysa...@yahoo.com wrote: I've a linear equation of the form: 0.95=2 ( [3+ln(x/3)]^-13  + 4 [3+2ln(x/3)]^-13  + [3+4ln(x/3)]^-13 ) and I want to solve it for x, can I do this using R? Yup. Use the 'uniroot' function (assuming that

[R] turn off function output

2009-11-04 Thread Ning Ma
Hi, everybody Is there any way to turn off the output message of a function, maybe a result of cat() or print() command in that function. I only expected it to be executed quite and return a value. Any intermediate messages can be omitted. Thanks! Ma

Re: [R] solving a linear equation

2009-11-04 Thread Berend Hasselman
maram salem wrote: Hi all, I've a linear equation of the form: 0.95=2 ( [3+ln(x/3)]^-13  + 4 [3+2ln(x/3)]^-13  + [3+4ln(x/3)]^-13 ) and I want to solve it for x, can I do this using R? The equation is (highly) nonlinear. Use uniroot. Do plot your function for several different

Re: [R] compute maximum likelihood estimator for a multinomial function

2009-11-04 Thread Ben Bolker
Benedikt Gehr wrote: Hi there I am trying to learn how to compute mle in R for a multinomial negative log likelihood function. I am using for this the book by B. Bolker Ecological models and data in R, chapter 6: Likelihood an all that. But he has no example for multinomial

Re: [R] Conditional read-in of data

2009-11-04 Thread Gabor Grothendieck
1. You can pipe your data through gawk (or other scripting language) process as in: http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2129.html 2. read.csv.sql in the sqldf package on CRAN will set up a database for you, read the file into the database automatically defining the layout of the

[R] unexpected results in comparison (x == y)

2009-11-04 Thread Peter Tillmann
Dear readers of the list, I have a problem a comparison of two data from a vector. The comparison yields FALSE but should be TRUE. I have checked for mode(), length() and attributes(). See the following code (R2.10.0): --- # data vector of 66 double

[R] variable selectin---reduce the numbers of initial variable

2009-11-04 Thread bbslover
hello, my problem is like this: now after processing the varibles, the remaining 160 varibles(independent) and a dependent y. when I used PLS method, with 10 components, the good r2 can be obtained. but I donot know how can I express my equation with the less varibles and the y. It is better to

Re: [R] Fw: solving a linear equation

2009-11-04 Thread David Winsemius
On Nov 4, 2009, at 7:39 AM, maram salem wrote: Sorry, I didn't mean a linear equation, of course this equation is not linear, I meant an equation in one unknown. Hi all, I've a linear equation of the form: 0.95=2 ( [3+ln(x/3)]^-13 + 4 [3+2ln(x/3)]^-13 + [3+4ln(x/3)]^-13 ) and I want to

Re: [R] creating mulptiple new variables from one data.frame according to columns and rows in that frame

2009-11-04 Thread Hayes, Daniel
Jim Holtman, Thank you for your reply. Your script is very concise and I think it could help me. However when I run it on my real data object (musigma.lat.m) the age range from 5-50 skips certain full years (see script below). Am not sure why that is and no error is given. Hoping you can help.

[R] Fw: ROC

2009-11-04 Thread carol white
if nobody knows the answer to my question on time-dependent ROC (see below), does any body know how TP and FP are related to classes and samples (orders) in non-time dependent ROC? Any reference? Thanks --- On Tue, 11/3/09, carol white wht_...@yahoo.com wrote: From: carol white

Re: [R] unexpected results in comparison (x == y)

2009-11-04 Thread David Winsemius
I'm guessing that it's in the FAQ, although I have not committed its number to memory. Try using all.equal() instead of == -- David On Nov 4, 2009, at 7:49 AM, Peter Tillmann wrote: Dear readers of the list, I have a problem a comparison of two data from a vector. The comparison

Re: [R] unexpected results in comparison (x == y)

2009-11-04 Thread Meyners, Michael, LAUSANNE, AppliedMathematics
FAQ 7.31: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-the se-numbers-are-equal_003f -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Peter Tillmann Sent: Mittwoch, 4. November 2009 13:50 To:

[R] vglm(), t values and p values

2009-11-04 Thread Federico Calboli
Hi All, I'm fitting an proportional odds model using vglm() from VGAM. My response variable is the severity of diseases, going from 0 to 5 (the severity is actually an ordered factor). The independent variables are: 1 genetic marker, time of medical observation, age, sex. What I *need* is a

Re: [R] Patterned shading in ggplot

2009-11-04 Thread hadley wickham
Hi Paul, You might want to try the gray colour scale - scale_fill_grey() Unfortunately grid (the underlying graphics library that ggplot2 uses) does not currently support patterns. Hadley On Wed, Nov 4, 2009 at 4:17 AM, Paul Chatfield p.s.chatfi...@rdg.ac.uk wrote: Am trying to produce a

Re: [R] RPostgreSQL: unable to load shared library

2009-11-04 Thread stephenb
I am trying the same as the post above and the actual error is: the ordinal 284 could not be located in the dynamic link library SSLEAY32.dll I searched for that dll and it is not to be found. windows forums provide vague directions to reinstall Windows, which I cannot do because this is a

Re: [R] creating mulptiple new variables from one data.frame according to columns and rows in that frame

2009-11-04 Thread jim holtman
My guess is that we are being affected by FAQ 7.31 (good old floating point numbers). The test 'age %in% 5:50' might be affected by round off. Something like the following might be better: age 5 | (abs(age - round(age)) 0.001) This should give TRUE for all ages that are 'close' to the year.

Re: [R] multivariate numerical integration.

2009-11-04 Thread Ravi Varadhan
I am not sure why it was removed from CRAN repository. You can get it from the archives: http://cran.r-project.org/src/contrib/Archive/adapt/ Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on

[R] Maximum Likelihood Estimation

2009-11-04 Thread Prof. John C Nash
What do you mean by the estimates were very bad? In nearly 40 years of working with optimization, I've seen badly set-up functions cause troubles, I've seen multiple minima situations, I've seen comparisons of results from one data set to the estimates for another, and I've seen optimization

Re: [R] turn off function output

2009-11-04 Thread Paul Hiemstra
Ning Ma wrote: Hi, everybody Is there any way to turn off the output message of a function, maybe a result of cat() or print() command in that function. I only expected it to be executed quite and return a value. Any intermediate messages can be omitted. Thanks! Ma

Re: [R] RandomForest PMML

2009-11-04 Thread NCS
Thanks for the feedback. In the meantime, is there any other way to utilize the model outside of R, even if it is a little more complicated? - Original Message From: Graham Williams graham.willi...@togaware.com To: NCS nc1...@yahoo.com Cc: r-help@r-project.org Sent: Tue, November 3,

Re: [R] R and Python

2009-11-04 Thread Gabor Grothendieck
As far as I know the latest versions of neither RSpython nor rpy2 support Windows. For accessing SymPy (which is a python computer algebra system) from R rSymPy went with jython. Its slower than cpython, particularly the startup, but it should work on all platforms. See

Re: [R] R and Python

2009-11-04 Thread Doran, Harold
I use both python and R, but decided not to mix the two. I'd rather work directly in R for statistics, visual displays, etc. I really like python for pre-processing data, some preliminary data organization, and XML capes. -Original Message- From: r-help-boun...@r-project.org

Re: [R] PCA with tow response variables

2009-11-04 Thread Kevin Wright
After an off-list email exchange, it sounds like the pls package and Partial Least Squares are appropriate for this analysis. Kevin Wright 2009/11/4 Joel Fürstenberg-Hägg joel_furstenberg_h...@hotmail.com Hi all, I'm new to PCA in R, so this might be a basical thing, but I cannot find

[R] Variable selection in NLME or LME4

2009-11-04 Thread Peter Flom
Good morning I am learning about NLME and LME4, using Pinheiro and Bates and other materials from Douglas Bates, but I have not seen anything on how to do variable selection sensibly in this type of model. In OLS regression, I frequently use the lasso, but googling did not reveal a method for

Re: [R] What happen for Negative binomial link in Lmer

2009-11-04 Thread Ben Bolker
Patrick Giraudoux wrote: Seems the message below and the thread have reveived no attention/answer. The output presented is quite tricky. Looks like if lmer (lme4 0.9975-10) has accepted a negative binomial link with reasonable estimates, although it was not designed for... What can

[R] Weird errors with R CMD check/ggplot2 in examples: how to debug?

2009-11-04 Thread Michael Friendly
[Environment: WinXp, R 2.9.2, all packages up to date; building under (StatET 0.8, eclipse 3.5.1) or from a batch file] I'm in the process of creating a package, HistData, on R-forge, containing interesting data sets from the history of statistics and data visualization. It contains several

[R] Output

2009-11-04 Thread Val
Hi all, I fitted a model say with five xc-lm( y~x1,x2,x3,x4,x5) I want to plot the residuals for each factor and I used this, plot(xc,residuals=TRUE,se=TRUE,pch=.) I only get the plot of the last factor (i.e., x5). I think it is overwriting. How can I send the five plots into a file? I

Re: [R] FW: making a plot in xyplot

2009-11-04 Thread Ordaz, Sarah
Thank you! Sarah Ordaz Laboratory of Neurocognitive Development University of Pittsburgh ord...@upmc.edu -Original Message- From: Deepayan Sarkar [mailto:deepayan.sar...@gmail.com] Sent: Friday, October 30, 2009 2:44 AM To: Ordaz, Sarah Cc: r-help@r-project.org;

Re: [R] Conditional read-in of data

2009-11-04 Thread mnstn
Hello Jim and Gabor, Thanks for your inputs. The lines: a-as.matrix(read.table(pipe(awk -f cut.awk Data.file))) cut.awk{for(i = 1; i = NF; i=i+10) print $i,} solved my problem. I know that 40k lines is not a large data set. I have about 150 files each of which has 40k rows and in each file I

Re: [R] Help with RGDAL

2009-11-04 Thread cls59
Michael D. wrote: Hi Charlie! Sorry to jump in here so late but I just gave this a try. I usually install rgdal from CRAN on windows or download the binary from http://www.kyngchaos.com for Mac. I wanted to try your method from building from source since the directions were so clear

Re: [R] variable selectin---reduce the numbers of initial variable

2009-11-04 Thread Ricardo Gonçalves Silva
Hi, Nowdays there's a lot o new variable selection methods, specially using the Bayes Paradigm. For your problem, I think you could try the Bayesian Model Average BMA package. Or, you can reduce your data dimension by PCA, which also permits you see the weight of each variable in the PC.

Re: [R] R and Python

2009-11-04 Thread stephenb
Not only RSPython does not support Windows, but it won't compile on most Unix platforms and fixing it may be more time than writing a package on your own. Like the other post, I use Python for pre-processing and then load into R. If you need text processing with line by line access you can also

Re: [R] R and Python

2009-11-04 Thread baptiste auguie
Hi, It looks like SAGE might be another option, http://www.sagemath.org/index.html though I never tried it. HTH, baptiste __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Graph to show that very few classes has maximum best performers

2009-11-04 Thread Sunita22
Hello I need help for the following: my data is class no. best performers 101 10 102 21 103 1 104 3 105 5 106190 ...... ...... ...... ...... I want to plot a graph using R, to show that very few classes has maximum best performers. can someone

Re: [R] creating mulptiple new variables from one data.frame according to columns and rows in that frame

2009-11-04 Thread Hayes, Daniel
YES, that does the trick. Glad to have your help for I had no idea of the existence of FAQ 7.31 nor for that matter do I completely understand what floating point number are (but that is another story :P)) Think I am all set. Cheers again for your time and energy. Daniel -Original

[R] Convert H:MM:SS PM /AM into 24 HR syntax

2009-11-04 Thread Jason Rupert
I've got an array of times in H:MM:SS PM/AM format, e.g. 5:27:15 PM (no leading zero), and I would like to convert them over to 24 HR syntax, e.g. HH:MM:SS. If it matters, the times are from the Central Time zone. Is there a command to convert the time to a 24HR format? I tried the

Re: [R] Convert H:MM:SS PM /AM into 24 HR syntax

2009-11-04 Thread Henrique Dallazuanna
Try this: strptime(5:27:15 PM, %I:%M:%S %p) On Wed, Nov 4, 2009 at 3:19 PM, Jason Rupert jasonkrup...@yahoo.com wrote: I've got an array of times in H:MM:SS PM/AM format, e.g. 5:27:15 PM (no leading zero), and I would like to convert them over to 24 HR syntax, e.g. HH:MM:SS. If it

Re: [R] Help with RGDAL

2009-11-04 Thread Don MacQueen
I did this recently with a kyngchaos binary build of rgdal, rgdal_0.6-12.tgz and R 2.9.2. I'll assume you have current rgdal binary package file in a directory somewhere. (looks like 0.6-18 is current) Here is what I did (with version 0.6-12). Note that I work from the command line, not from

Re: [R] Join points with arrows based a TIME variable

2009-11-04 Thread zhijie zhang
Hi Uwe, It works. Why does the following argument generate different results? with(data, arrows(x[-length(x)], y[-length(x)], x[-1], y[-1])) #correct,multiple joins with(data, arrows(x[1], y[1], x[length(x)], y[length(x)])) #wrong,seems to be only one join From the ?arrows, the second

Re: [R] Join points with arrows based a TIME variable

2009-11-04 Thread Uwe Ligges
zhijie zhang wrote: Hi Uwe, It works. Why does the following argument generate different results? with(data, arrows(x[-length(x)], y[-length(x)], x[-1], y[-1])) #correct,multiple joins In the former you select all elements of the vectors except the first or last one, respectively. In

Re: [R] Join points with arrows based a TIME variable

2009-11-04 Thread zhijie zhang
Hi Uwe, I mistook the arguments for the function of arrows. I understand now. Thanks again. 2009/11/5 Uwe Ligges lig...@statistik.tu-dortmund.de zhijie zhang wrote: Hi Uwe, It works. Why does the following argument generate different results? with(data, arrows(x[-length(x)],

[R] Correlation of ranks of labels?

2009-11-04 Thread S. Nunes
Hi, I have two ranks of labels (strings) representing user preferences of colors. For instance, here is a simple example with 4 preferences for each user: rank1 [1] red blue green black rank2 [1] white gray black blue How can I compute Kendall's Tau for this scenario? Thanks in advance,

[R] Building from source under Windows 7

2009-11-04 Thread rkevinburton
I have downloaded all of the tools and read the readme's that I know about but I am still getting the following error when I try to build from source: C:\Program Files (x86)\R\R-2.9.2\src\gnuwin32make all recommended make[1]: `Rpwd.exe' is up to date. cp -p etc/Makeconf etc/Rcmd_environ

Re: [R] simulated data

2009-11-04 Thread Gavin Simpson
On Tue, 2009-11-03 at 23:25 -0800, assaedi76 assaedi76 wrote: R users. Thanks in advance. I would be glad if someonecouldtell me how toget a simulated data from AR(1), MA(1) See ?arima.sim HTH G My email is : assaed...@yahoo.com Thanks [[alternative HTML version

Re: [R] Error in segmented() output from segmented package

2009-11-04 Thread Jens Oldeland
__ 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 code.

Re: [R] Building from source under Windows 7

2009-11-04 Thread Joshua Wiley
Hello Kevin, It is possible you took care of this by giving yourself permission, but when I used Vista and now 7 x64; it was easier for me to install in a directory other than program files. For example just installing to a new folder on the C: (or whatever is your primary) drive. I am using

Re: [R] vglm(), t values and p values

2009-11-04 Thread Gavin Simpson
On Wed, 2009-11-04 at 14:00 +, Federico Calboli wrote: Hi All, I can't answer your questions myself - try Thomas Yee, the author and maintainer of the VGAM package - but: I'm fitting an proportional odds model using vglm() from VGAM. Is there a particular reason for choosing a VGLM here?

Re: [R] vglm(), t values and p values

2009-11-04 Thread Federico Calboli
On 4 Nov 2009, at 18:11, Gavin Simpson wrote: Is there a particular reason for choosing a VGLM here? My reading of your post suggests the response is an univariate, ordered factor and VGLMs are especially for multivariate responses. In which case, can you not use polr() in package MASS that

[R] Error invoking R2.10.0

2009-11-04 Thread Enayet Talukder
I just installed R2.10.0. When I tried to activate or invoke R by clicking the shortcut R2.10.0 on my desktop, it is giving an error message on a new window Error in loadNamcespace(name) : there is no package called 'ggplot2' . The program quits when clicked on 'OK. Thanks, Enayet

Re: [R] vglm(), t values and p values

2009-11-04 Thread Gavin Simpson
On Wed, 2009-11-04 at 18:19 +, Federico Calboli wrote: On 4 Nov 2009, at 18:11, Gavin Simpson wrote: Is there a particular reason for choosing a VGLM here? My reading of your post suggests the response is an univariate, ordered factor and VGLMs are especially for multivariate responses.

Re: [R] vglm(), t values and p values

2009-11-04 Thread Federico Calboli
On 4 Nov 2009, at 18:40, Gavin Simpson wrote: Additionally, while extracting the t value is a piece of cake with polr(), the p-value I get a nowhere close to a null distribution. Yes - I see that polr() also doesn't produce p-values in the output from summary. You can use it to get a

Re: [R] Error invoking R2.10.0

2009-11-04 Thread Duncan Murdoch
On 11/4/2009 1:41 PM, Enayet Talukder wrote: I just installed R2.10.0. When I tried to activate or invoke R by clicking the shortcut R2.10.0 on my desktop, it is giving an error message on a new window Error in loadNamcespace(name) : there is no package called 'ggplot2' . The program quits when

[R] (no subject)

2009-11-04 Thread steve . miller
Steve Miller OpenBI 847.778.1145 __ 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,

[R] enter missing into missing fields

2009-11-04 Thread frenchcr
if ive got an incomplete data set thats got thousands of rows and 80 columns with random missing fields...like this say... 3 b 3 41 1 x 2 ? how do i turn it into 3b 3 4 missing 1 1x 2 ...i.e., i want to insert a line of text like..missing... into the empty fields

[R] exclusive access to graphic device

2009-11-04 Thread whizvast
Hi, useR- I want to create a graphic device - e.g., windows() - that only specific function(s) have control over. For example, suppose you run the following code: windows() dv = dev.cur() dv dv is the index for the graphic device. By passing dv value into a new function, I can control the

[R] pb with optimimization and fitdistr

2009-11-04 Thread Nicolas Turenne
Hello i try to fit a data series (N below) with a model consisting of a mixture of two beta distributions for that i am using fitdistr of package MASS as follows library(MASS) N=c(796,3586,4089,3364,2745,1992,1120,432,99,10,0,0) d2 = (N-min(N)+0.01)/(max(N)-min(N)+0.002) mixtBeta -

Re: [R] odfweave table styles

2009-11-04 Thread Colin Robertson
Thanks! The formattingOut.odt document had exactly what I needed. The style highlight wasnt defined in my environment. Cheers, Colin On Wed, Nov 4, 2009 at 4:59 AM, Max Kuhn mxk...@gmail.com wrote: It's hard to say without a reproducible example or the output form sessionInfo(). Before

Re: [R] underflow of fisher.test result

2009-11-04 Thread Ted Harding
On 01-Nov-09 20:23:30, Peng Yu wrote: On Tue, Oct 20, 2009 at 8:14 AM, Ted Harding ted.hard...@manchester.ac.uk wrote: On 20-Oct-09 13:34:49, Peng Yu wrote: fisher.test() gives a very small p-value, which is underflow on my machine. However, the log of it should not be underflow. I'm

[R] Help with a Loop in function

2009-11-04 Thread Ricardo Gonçalves Silva
Dear Users, I follow Andreas idea to simulate an ar(1) model with a new kind of innovation process. The new argument rand.gen, for the arima.sim function, I'm trying to generate as: tGarchGen - function(a, b, c) { # must return a vector of random deviates (eta(t)) for (t in 1:100){

[R] splitting scientific names into genus, species, and subspecies

2009-11-04 Thread Mark W. Miller
I have a list of scientific names in a data set. I would like to split the names into genus, species and subspecies. Not all names include a subspecies. Could someone show me how to do this? My example code is: a - matrix(c('genusA speciesA', 10, 'genusB speciesAA', 20,

Re: [R] enter missing into missing fields

2009-11-04 Thread Bert Gunter
?NA ?read.table (note the na.strings argument) You would have to handle character fields/columns (which would by default be converted to factors)specially to convert blanks to missing within R. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From:

Re: [R] Help with RGDAL

2009-11-04 Thread Michael Denslow
Hi Charlie and Don! On Wed, Nov 4, 2009 at 11:19 AM, cls59 ch...@sharpsteen.net wrote: Michael D. wrote: Hi Charlie! Sorry to jump in here so late but I just gave this a try. I usually install rgdal from CRAN on windows or download the binary from http://www.kyngchaos.com for Mac. I

Re: [R] splitting scientific names into genus, species, and sub

2009-11-04 Thread Ted Harding
On 04-Nov-09 21:09:42, Mark W. Miller wrote: I have a list of scientific names in a data set. I would like to split the names into genus, species and subspecies. Not all names include a subspecies. Could someone show me how to do this? My example code is: a - matrix(c('genusA speciesA',

Re: [R] pb with optimimization and fitdistr

2009-11-04 Thread Ravi Varadhan
I think the problem lies in the mixture model. First, why do you have two free parameters p and q. Shouldn’t that be p and (1-p)? Secondly, I am not sure that your data, d2, is compatible with a binary mixture model. It seems like a sensible binary mixture model cannot be fitted for your data.

Re: [R] splitting scientific names into genus, species, and sub

2009-11-04 Thread Ted Harding
OOPS! Sorry, I made an oversight in the code I posted just now (and I didn't check the result carefullt enough ... ). The line which was A$Count - as.numeric(A$Count) should have been A$Count - as.numeric(levels(A$Count)) (i.e. I overlooked that A$Count as first constructed is a *factor*)! So

[R] spliting a word into letters

2009-11-04 Thread mirauta
Hello, Is there any function to split a word into letters? (eg: AAACC into A,A,A,AC,C ) I need to load some ADN sequences and ussualy these are writen in words without spaces between letters. Thanks, Bogdan -- View this message in context:

Re: [R] fill map with gradient: package?

2009-11-04 Thread Paul Murrell
Hi Thomas Steiner wrote: Hi, I'd like to fill an existing svg (or png) map with gradient colors. In detail: The file http://commons.wikimedia.org/wiki/File:Karte_%C3%96sterreich_Bundesl%C3%A4nder.svg should be filled with the population density data from this table:

Re: [R] spliting a word into letters

2009-11-04 Thread Remko Duursma
strsplit(hello,)[[1]] r - Remko Duursma Post-Doctoral Fellow Centre for Plants and the Environment University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia

Re: [R] Convert H:MM:SS PM /AM into 24 HR syntax

2009-11-04 Thread Jason Rupert
This is exactly what I needed.  Thanks again for all your help. - Original Message From: Henrique Dallazuanna www...@gmail.com To: Jason Rupert jasonkrup...@yahoo.com Cc: R-help@r-project.org Sent: Wed, November 4, 2009 11:22:52 AM Subject: Re: [R] Convert H:MM:SS PM /AM into 24 HR

Re: [R] splitting scientific names into genus, species, and sub

2009-11-04 Thread Ted Harding
OPPS^2!! Did it again. The version given below now does seem to work properly: last line now changed (yet again) to A$Count - as.numeric(levels(A$Count)[unclass(A$Count)]) On 04-Nov-09 21:47:32, Ted Harding wrote: OOPS! Sorry, I made an oversight in the code I posted just now (and I didn't

Re: [R] splitting scientific names into genus, species, and subspecies

2009-11-04 Thread Chris Stubben
Mark W. Miller wrote: I have a list of scientific names in a data set. I would like to split the names into genus, species and subspecies. Not all names include a subspecies. Could someone show me how to do this? strsplit should work for your example... data.frame(

Re: [R] Search values and create a new matrix

2009-11-04 Thread David Winsemius
On Nov 4, 2009, at 4:45 PM, Jose Narillos de Santos wrote: Hi You wrotte me in R help and I´m very gratefull. I couldn´t reply because an illness. I writte this to see if you can help to solve. I´m a begginer (I´m 20 years old ) but I´m trying to learn more about this program also I´m

[R] Activating html help in R 2.10

2009-11-04 Thread Frank E Harrell Jr
After reading the news about the release of R 2.10 I expected that typing for example ?cut would automatically open a web browser. But I don't see any difference in how help is displayed under Ubuntu Linux (karmic). How does one activate the new dynamic html help? Thanks Frank platform

[R] Constrained Optimization

2009-11-04 Thread s t
Hi All, I'm trying to do the following constrained optimization example. Maximize x1*(1-x1) + x2*(1-x2) + x3*(1-x3) s.t. x1 + x2 + x3 = 1 x1 = 0 and x1 = 1 x2 = 0 and x2 = 1 x3 = 0 and x3 = 1 which are the constraints. I'm expecting the answer x1=x2=x3 = 1/3. I tried the constrOptim function in R

Re: [R] Activating html help in R 2.10

2009-11-04 Thread Marc Schwartz
On Nov 4, 2009, at 4:39 PM, Frank E Harrell Jr wrote: After reading the news about the release of R 2.10 I expected that typing for example ?cut would automatically open a web browser. But I don't see any difference in how help is displayed under Ubuntu Linux (karmic). How does one

Re: [R] spliting a word into letters

2009-11-04 Thread Bert Gunter
?strsplit e.g. strsplit(vectorofstrings,split=) Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of mirauta Sent: Wednesday, November 04, 2009 1:07 PM To: r-help@r-project.org

Re: [R] Constrained Optimization

2009-11-04 Thread Ravi Varadhan
Your initial value is indeed infeasible, as the error message says. Your x[1] is 1.4, which is not in the interval [0,1]. To incorporate both equalities and inequalities (linear or nonlinear), you could try my function `constrOptim.nl'. Contact me off the list if you are interested. Ravi.

  1   2   >