Re: [R] loop for a large database
On Sun, Feb 26, 2012 at 11:39:01AM -0800, mari681 wrote: SORRY! The data in MyTable are tagsets of photos, like this: V1 V2 V3 V4 V5 V6V7 V8 230green nailpolish barrym 0 00 00 231 ny green brooklyn cleanup clean gowanus volunteer gcc 232green saul lecture 0 00 00 233green colorscores market colores marakesh mercado malu 234 ny green brooklyn cleanup clean gowanus volunteer gcc 235green saul lecture 0 00 00 236 portraitpetwhite green catcanonsquare eos V9 V10 V11 V12 V13 V14 V15 230 0 000 0 0 0 231 gowanuscanalconservancy 000 0 0 0 232 0 000 0 0 0 233 malugreen maroc souk marrocos 0 0 0 234 gowanuscanalconservancy 000 0 0 0 235 0 000 0 0 0 236 is eyes mark taiwan ii mk2 5d while data of MyVector is a list of tags (none of the columns in particular) whose frequency in MyTable has to be computed. Like this: [1] life wood pink house green fall Hi. Just to be sure, in all the previous solutions, malugreen is not an occurence of green. Is this correct? MyTable has 21 millions rows and 15 columns, and the data is character, they are words. Do you use the argument stringsAsFactors=FALSE, when reading the data from a file? Otherwise, character data are converted to a factor. The discussed solutions work in both cases, however, if we try to prepare simplified data for testing efficiency, we should use the same column class as in the real situation. When I tried the loop my computer crashed in the meaning that it freezed (froze?) and didn't allow me to do anything. The morning after I forced it off and rebooted. This does not seem to be a consequence of a too long computation. A possible cause can be too large memory requirements. How large memory the R process uses after loading the data? Try gc() command after loading the data and compare with the amount of memory available. On a Linux machine, it is also possible to see the memory usage with top command in the row, where R is reported. Petr. __ 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.
[R] Bayesian Hidden Markov Models
Dear R buddies, Recently, I attempt to model the US/RMB Exchange rate log-return time series with a *Hidden Markov model (first order Markov Chain mixed Normal distributions). * I have applied the RHmm package to accomplish this task, but the results are not so satisfying. So, I would like to try a *Bayesian method *for the parameter estimation of the Hidden Markov model. Could anyone kindly tell me which R package can perform Bayesian estimation of the model? Many thanks for your help and time. Best Regards, James Allan -- View this message in context: http://r.789695.n4.nabble.com/Bayesian-Hidden-Markov-Models-tp4423946p4423946.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] What is the fastest way to combine all columns of a matrix to one column?
Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? -- View this message in context: http://r.789695.n4.nabble.com/What-is-the-fastest-way-to-combine-all-columns-of-a-matrix-to-one-column-tp4423882p4423882.html Sent from the R help mailing list archive at Nabble.com. __ 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] randomForest2Rules
Hi, The work around this is to use printRandomForests function in Rattle package. It outputs the forest in the form of rules. For ex: #Load libraries library(rattle) library(randomForest) #Load sample data data(iris) #Build a forest iris.rf - randomForest(Species ~ ., data=iris, importance=TRUE,keep.forest=T, ntree=5, do.trace=T) iris.rf #send rules in above forest to a textfile sink(file = rfrules.txt, append = FALSE, type = output) printRandomForests(iris.rf) sink() After getting the rules in to a text file, and because the text is structured, you can use the language of your choice to transform the rules in to a format you need. -- View this message in context: http://r.789695.n4.nabble.com/randomForest2Rules-tp3822530p4423956.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] Need advice on GLM
Dear all, I was trying to fit a GLM on the following data (this data was taken from Agresti): Dat - matrix(c(24, 1355, 35, 603, 21, 192, 30, 224), 4, byrow = TRUE) Here the 1st column denotes the success and the second column is for failure. We have 4 rows represeting the 4 states of some explanatory variable, let say those states are: Scores - c(0, 2, 4, 5) My goal is to estimate the success probabilities for each state. Therefore, I use a simple GLM: p(x) = alpha + beta * x *** My first approach Here I break my sample into sample from Bernoulli distribution and fit glm: YY - c(rep(1, 24), rep(0, 1355), rep(1, 35), rep(0, 603), rep(1, 21), rep(0, 192), rep(1, 30), rep(0, 224)) XX - c(rep(0, 24 + 1355), rep(2, 35 + 603), rep(4, 21 + 192), rep(5, 30 + 224)) summary(glm(YY~XX, binomial(link = identity))) *** My second approach Here I work with the given sample as it is. Hence assuming Binomial distribution as follows: Proportion - apply(Dat, 1, function(x) return(x[1]/(x[1]+x[2]))) summary(glm(Proportion~c(0,2,4,5), binomial(link = identity))) Here I was expecting those 2 approaches should give exactly same result (i.e. same estimates and same SE), which is not the case. Can somebody point me what I am missing here? Thanks and regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop for a large database
Hi SORRY! The data in MyTable are tagsets of photos, like this: V1 V2 V3 V4 V5 V6V7 V8 230green nailpolish barrym 0 00 00 231 ny green brooklyn cleanup clean gowanus volunteer gcc 232green saul lecture 0 00 00 233green colorscores market colores marakesh mercado malu 234 ny green brooklyn cleanup clean gowanus volunteer gcc 235green saul lecture 0 00 00 236 portraitpetwhite green catcanonsquare eos V9 V10 V11 V12 V13 V14 V15 230 0 000 0 0 0 231 gowanuscanalconservancy 000 0 0 0 232 0 000 0 0 0 233 malugreen maroc souk marrocos 0 0 0 234 gowanuscanalconservancy 000 0 0 0 235 0 000 0 0 0 236 is eyes mark taiwan ii mk2 5d while data of MyVector is a list of tags (none of the columns in particular) whose frequency in MyTable has to be computed. Like this: [1] life wood pink house green fall What about changing your data frame to matrix and use table set.seed(111) x-sample(letters, 200, replace=T) y-letters[3:6] dim(x)-c(20,10) dd-data.frame(x) tt-table(as.matrix(dd)) tt[names(tt) %in% y] c d e f 13 5 8 3 Regards Petr Thanks!! Marianna -- View this message in context: http://r.789695.n4.nabble.com/loop-for-a- large-database-tp4422052p4422776.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] What is the fastest way to combine all columns of a matrix to one column?
Hi Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? If mm is your matrix use dim(mm) -NULL Regards Petr -- View this message in context: http://r.789695.n4.nabble.com/What-is-the- fastest-way-to-combine-all-columns-of-a-matrix-to-one-column-tp4423882p4423882.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] tcl tk command function with arguments ??
Hi Elai and Peter, thanks a lot for your suggestions. I am still reading your answers, but I didn't get at the begining the difference between c-NULL for (i in seq(3)) c[[i]]-i c and the exempel with the tcl tk buttons. Now I think, it is clear. Its due to the interaction between R and tcl. The button created by R is executed far later by tcltk and therefore, the button doesn't take the i during its creation, but the last available i of its environment. Do you know any manuals, articles, etc... which describe the interaction between R and tcl. Now I learn only by examples which I find in the web. Alexander -- View this message in context: http://r.789695.n4.nabble.com/tcl-tk-command-function-with-arguments-tp4416470p4423969.html Sent from the R help mailing list archive at Nabble.com. __ 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] Bayesian Hidden Markov Models
Dear James,
Although designed for the analysis of copy number CGH microarrays, RJaCGH
uses a Bayesian HMM model.
Cheers,
Oscar
On 27/2/12 08:32, monkeylan lanjin...@yahoo.com.cn wrote:
Dear R buddies,
Recently, I attempt to model the US/RMB Exchange rate log-return time series
with a *Hidden Markov model (first order Markov Chain mixed Normal
distributions). *
I have applied the RHmm package to accomplish this task, but the results are
not so satisfying.
So, I would like to try a *Bayesian method *for the parameter estimation of
the Hidden Markov model.
Could anyone kindly tell me which R package can perform Bayesian estimation
of the model?
Many thanks for your help and time.
Best Regards,
James Allan
--
View this message in context:
http://r.789695.n4.nabble.com/Bayesian-Hidden-Markov-Models-tp4423946p4423946.
html
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Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
Cancer Research UK Cambridge Research Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
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Re: [R] tm_map help
Le lundi 27 février 2012 à 10:47 +1100, Sachinthaka Abeywardana a écrit : Hi all, I am trying to do some text mining with twitter and I am getting the error: Error in structure(names(sapply(possibleCompletions, [, 1)), names = x) : 'names' attribute [1] must be the same length as the vector [0] When I use tm_map. Has anyone had/seen this error before? The code I have is shown below and this error only occurs with #qantas, hashtags like #asx, #obama work ok. Please try to identify the document and the steps that trigger the problem more precisely. You should come up with the simplest example that reproduces the bug with #qantas, and then remove half the documents of the corpus, retry, and do that until you find the culprit. Then it will be easier to find the cause of the bug. Regards __ 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] What is the fastest way to combine all columns of a matrix to one column?
Hi Hi, Thank you. I actually wanted to reserve the rows, I dont know how to do this with dim(mm) -NULL I do not understand. What does it mean reserve rows. Matrix is a vector with dimension so you can change dimensions freely with dim(mm) - any suitable combination dim(mm) -NULL gives you plain vector dim(mm) - c(rows, columns) gives you now matrix with specified number of rows and columns. You can put columns to 1 and in that case you will get one column matrix. Please provide some toy example what do you really want. Regards Petr thanks again On 2/27/12, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? If mm is your matrix use dim(mm) -NULL Regards Petr -- View this message in context: http://r.789695.n4.nabble.com/What-is-the- fastest-way-to-combine-all-columns-of-a-matrix-to-one-column- tp4423882p4423882.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] Military Time Comparison
what does 'str' of the object show? are the columns factors/characters? does
the comparison have to consider the date?
Sent from my iPad
On Feb 27, 2012, at 0:37, Edgar Alminar eaalmi...@ucsd.edu wrote:
Oh, haha -- sorry for the vagueness:
I was expecting to get the comparison to work. I also didn't mention that the
dataset is much larger; I just wanted to give the first few rows.
So, basically, I have a bunch of times in three columns, and I'm looking to
compare them in which the command works correctly.
Let's say, using the example below, that I want to get:
match2 = subset(match2, AEONTIME INFTIME.x)
Well, with that exact syntax, it's not working because I'm getting back a
dataset in which some AEONTIMEs are actually INFTIME.x.
So, I feel like I'm just missing a piece of the syntax (i.e. as.date,
as.character, but what works for time?)
I hope this helps. :-)
Thanks!
On Feb 26, 2012, at 9:32 PM, David Winsemius wrote:
On Feb 26, 2012, at 10:31 PM, Edgar Alminar wrote:
Hello All,
I have this dataset:
RID VISCODE SCRNO RECNO AEWHEN AEONDATE AEONTIME INFPOINT.x
INFDATE.x INFTIME.x INFPOINT.y INFDATE.y INFTIME.y
1 100 w00 IGI1480069 4 2 09/15/2009 1118 1
09/15/2009 947 14 -4 1117
2 100 w00 IGI1480069 8 2 09/15/2009 1132 1
09/15/2009 947 14 -4 1117
3 100 w00 IGI1480069 5 2 09/15/2009 1125 1
09/15/2009 947 14 -4 1117
I have AEONTIME, INFTIME.x, and INFTIME.y, and they are all military times.
I'm trying to do a comparison like this:
match2 = subset(match2, AEONTIME INFTIME.x)
But it's not working correctly.
Define what you expected. In the sample you offered none of those logical
comparisons would be true so you should get a dataframe with zero rows. (And
since you gave the result the same name, you have basically wiped out
match2.)
How do I do this? :-)
Do what?
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
Edgar Alminar
Clinical Operations
Alzheimer's Disease Cooperative Study
University of California, San Diego
9500 Gilman Drive, MC-0949
La Jolla, CA 92093-0949
Tel: (858) 622-8798
Fax: (858) 622-5876
Email: eaalmi...@ucsd.edu
Confidentiality Notice- This e-mail message from the Alz...{{dropped:11}}
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Re: [R] best option for big 3D arrays?
Steven, sorry for the delay in responding,
I have been investigating this also and here is the way I do it (though
probably not the best way):
# .. define a 3D array
ngen = 904
gratios - ff(NA, dim=rep(ngen,3), vmode=double)
# .. fill the array with standard R functions
ffsave (gratios, file=mydir/myfile)# without extension
finalizer(gratios) - delete
# ..
so, you firstly define the ff object, you put the data inside, and you
ffsave it. The ffsave function will generate two files, with extensions
ffdata and a Rdata. Then you set 'delete' to be the 'finalizer' of the
object; in this way you avoid ff to save it in some tmp dir and occupy disk
space forever. Then, you can access your object in the next R session:
ffload(mydir/myfile)# also without extension
I hope this helped.
Cheers,
djordje
2012/2/23 steven mosher mosherste...@gmail.com
Did you have to use a particular filename? or extension.
I created a similar file but then could not read it back in
Steve
On Mon, Feb 13, 2012 at 6:45 AM, Djordje Bajic je.li@gmail.comwrote:
I've been investigating and I partially respond myself. I tried the
packages 'bigmemory' and 'ff' and for me the latter did the work I need
pretty straightforward. I create the array in filebacked form with the
function ff, and it seems that the usual R indexing works well. I have yet
to see the limitations, but I hope it helps.
a foo example:
myArr - ff(NA, dim=rep(904,3), filename=arr.ffd, vmode=double)
myMat - matrix(1:904^2, ncol=904)
for ( i in 1:904 ) {
myArr[,,i] - myMat
}
Thanks all,
2012/2/11 Duncan Murdoch murdoch.dun...@gmail.com
On 12-02-10 9:12 AM, Djordje Bajic wrote:
Hi all,
I am trying to fill a 904x904x904 array, but at some point of the loop
R
states that the 5.5Gb sized vector is too big to allocate. I have
looked
at
packages such as bigmemory, but I need help to decide which is the
best
way to store such an object. It would be perfect to store it in this
cube
form (for indexing and computation purpouses). If not possible, maybe
the
best is to store the 904 matrices separately and read them individually
when needed?
Never dealed with such a big dataset, so any help will be appreciated
(R+ESS, Debian 64bit, 4Gb RAM, 4core)
I'd really recommend getting more RAM, so you can have the whole thing
loaded in memory. 16 Gb would be nice, but even 8Gb should make a
substantial difference. It's going to be too big to store as an array
since arrays have a limit of 2^31-1 entries, but you could store it as a
list of matrices, e.g.
x - vector(list, 904)
for (i in 1:904)
x[[i]] - matrix(0, 904,904)
and then refer to entry i,j,k as x[[i]][j,k].
Duncan Murdoch
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[R] read.csv converts NA to missing values
Hello, I have a CSV file with region codes listed in a column. E.g. 'AS' for Asia, 'AU' for Australia and 'NA' North America. However, the data frame created using read.csv shows NA where the string variable should have had the value 'NA'. How can I input the value 'NA' present in a column in a CSV file without R changing it to missing? Thanks Nikhil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read.csv converts NA to missing values
I believe read.csv(..., na.strings = ) will do it. Michael On Mon, Feb 27, 2012 at 8:15 AM, nikhil abhyankar nsabhyan...@gmail.com wrote: Hello, I have a CSV file with region codes listed in a column. E.g. 'AS' for Asia, 'AU' for Australia and 'NA' North America. However, the data frame created using read.csv shows NA where the string variable should have had the value 'NA'. How can I input the value 'NA' present in a column in a CSV file without R changing it to missing? Thanks Nikhil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] read.csv converts NA to missing values
On Feb 27, 2012, at 14:15 , nikhil abhyankar wrote: Hello, I have a CSV file with region codes listed in a column. E.g. 'AS' for Asia, 'AU' for Australia and 'NA' North America. However, the data frame created using read.csv shows NA where the string variable should have had the value 'NA'. How can I input the value 'NA' present in a column in a CSV file without R changing it to missing? I'd try na.strings= (or maybe NULL or character(0)) -pd Thanks Nikhil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ 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.
[R] identify and delete in table
Dear all, I want to delete the exact matches in a large dataset based on a smaller dataset. In other words I want to subtract the smaller dataset from the larger one. The smaller dataset is a part of the larger one. The datasets contains hundred of thousands of lines (1 column) and the content on each line differ in length. The data is extracted paths from web logs. On an abstract level I want to subtract dataset2 from dataset1 to get dataset3: dataset1: 1 A 2 B 3 X 4 AA 5 A 6 D 7 XA 8 C dataset2: 1 A 2 X 3 A dataset3: 1 B 2 AA 3 D 4 XA 5 C The final order in dataset3 is not important. Thanks, Jonas Fransson Ph.D.stud. IVA / Det Informationsvidenskabelige Akademi Royal School of Library and Information Science Birketinget 6 DK-2300 Copenhagen S T +45 32 58 60 66 D +45 32 34 15 10 www.iva.dk/jf __ 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.
[R] solnp inconsistent error messages
Dear all, I am tryng to solve a nonlinear optimization probel using the solnp function. I have different datasets. For the smaller I get full solutions, for the bigger I got an error message stating: Iter: 1 fn: 101.8017 Pars: 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 0.21000 solnp-- Solution not reliableProblem Inverting Hessian. Warning messages: 1: In p0 * vscale[(neq + 2):(nc + np + 1)] : longer object length is not a multiple of shorter object length 2: In cbind(temp, funv) : number of rows of result is not a multiple of vector length (arg 1) Anyone knows what may be the reason? Just remembering that the same problem runs OK for smaller datasets. Thanks in advance, Diogo André Portugal __ 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.
[R] Extract data point coordinates from kernel home range estimation
Hello, I'm very new in working on R and maybe that's a simple thing I'm trying to do, but I am really stuck. I have a data point set of animal tracking coordinates and I have implemented a kernel utilization distribution analysis in order to find the home range for 95% of the relocation data. I have used the ud.kde() and hr.kde() functions of the wild1 package, so I have a number of polygons (peaks of kernel density) as an object of the following class: class(homerange) [1] Polygons attr(,package) [1] sp My question is how can I extract the point coordinates within each polygon-circle? Because, the home range coordinates are arbitrary points contouring the real data points. Hope it's clear, Despina -- View this message in context: http://r.789695.n4.nabble.com/Extract-data-point-coordinates-from-kernel-home-range-estimation-tp4424107p4424107.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] General question about GLMM and heterogeneity of variance
My data have heterogeneity of variance (in a categorical variable), do I need to specify a variance structure accounting for this in my model or do GLMMs by their nature account for such heterogeneity (as a result of using deviances rather than variances)? And if I do need to do this, how do I do it (e.g. using something like the VarIdent function in nlme) and in what package? This is my first post so apologies for any breach of etiquette! -- View this message in context: http://r.789695.n4.nabble.com/General-question-about-GLMM-and-heterogeneity-of-variance-tp4424429p4424429.html Sent from the R help mailing list archive at Nabble.com. __ 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] loop for a large database
2012/2/27 Petr Savicky [via R] ml-node+s789695n4423895...@n4.nabble.com On Sun, Feb 26, 2012 at 11:39:01AM -0800, mari681 wrote: SORRY! The data in MyTable are tagsets of photos, like this: V1 V2 V3 V4 V5 V6V7 V8 230green nailpolish barrym 0 00 00 231 ny green brooklyn cleanup clean gowanus volunteer gcc 232green saul lecture 0 00 00 233green colorscores market colores marakesh mercado malu 234 ny green brooklyn cleanup clean gowanus volunteer gcc 235green saul lecture 0 00 00 236 portraitpetwhite green catcanonsquare eos V9 V10 V11 V12 V13 V14 V15 230 0 000 0 0 0 231 gowanuscanalconservancy 000 0 0 0 232 0 000 0 0 0 233 malugreen maroc souk marrocos 0 0 0 234 gowanuscanalconservancy 000 0 0 0 235 0 000 0 0 0 236 is eyes mark taiwan ii mk2 5d while data of MyVector is a list of tags (none of the columns in particular) whose frequency in MyTable has to be computed. Like this: [1] life wood pink house green fall Hi. Just to be sure, in all the previous solutions, malugreen is not an occurence of green. Is this correct? correct!! MyTable has 21 millions rows and 15 columns, and the data is character, they are words. Do you use the argument stringsAsFactors=FALSE, when reading the data from a file? Otherwise, character data are converted to a factor. The discussed solutions work in both cases, however, if we try to prepare simplified data for testing efficiency, we should use the same column class as in the real situation. Ok. Thanks! When I tried the loop my computer crashed in the meaning that it freezed (froze?) and didn't allow me to do anything. The morning after I forced it off and rebooted. This does not seem to be a consequence of a too long computation. A possible cause can be too large memory requirements. How large memory the R process uses after loading the data? Try gc() command after loading the data and compare with the amount of memory available. On a Linux machine, it is also possible to see the memory usage with top command in the row, where R is reported. Petr. I should have tried before with a sample of data, rather than with the whole table. I'll try again with all your suggestions. Thanks!!! marianna __ [hidden email] http://user/SendEmail.jtp?type=nodenode=4423895i=0mailing 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. -- If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/loop-for-a-large-database-tp4422052p4423895.html To unsubscribe from loop for a large database, click herehttp://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4422052code=bWFyaWFubmEuYm9sb2duZXNpQGdtYWlsLmNvbXw0NDIyMDUyfDY2MTc1ODA1OA== . NAMLhttp://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://r.789695.n4.nabble.com/loop-for-a-large-database-tp4422052p4424086.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Loop
I've tried to create a loop for the following code but have failed miserably.
This is what the code is:
pnorm((Normal.Team.LnAveragePPPConceded.LnAveragePPPScores.HA.pred[1,1]
-Normal.Team.LnAveragePPPConceded.LnAveragePPPScores.HA.pred[50,1])/
sqrt(prediction.SE[1]^2 + prediction.SE[50]^2))
I'd like a loop so that it is something like this:
for (i in 1:50) {
pnorm((Normal.Team.LnAveragePPPConceded.LnAveragePPPScores.HA.pred[i,1]
-Normal.Team.LnAveragePPPConceded.LnAveragePPPScores.HA.pred[i+49,1])/
sqrt(prediction.SE[i]^2 + prediction.SE[i+49]^2))
}
Many thanks
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[R] goodness of fit for glms
We are working on trying to find how well glm models fit our set of sports results. We want to consider the following two models and work out which one fits the data better: summary(Tries.Team.Ha.glm) (Dispersion parameter for poisson family taken to be 1) Null deviance: 321.46 on 269 degrees of freedom Residual deviance: 274.15 on 257 degrees of freedom AIC: 879.06 Number of Fisher Scoring iterations: 5 and summary(Tries.Team.Ha.Distance.glm) (Dispersion parameter for poisson family taken to be 1) Null deviance: 321.46 on 269 degrees of freedom Residual deviance: 272.06 on 256 degrees of freedom AIC: 878.97 Number of Fisher Scoring iterations: 5 Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/goodness-of-fit-for-glms-tp4424193p4424193.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] how to read file append at specified positon
i have one file as munnabhai-read.table(hyphen[1],skip=1) munnabhai V1 V2 V3 V4 V5 V6 V7 1 1 12AS_A 4 A0.0 157.8994119 2 2 2 12AS_A 5 Y -41.61818 -56.8011795 1 3 3 12AS_A 6 I -55.47021 -51.1328352 1 4 4 12AS_A 7 A -54.43085 -58.3428366 1 5 5 12AS_A 8 K -54.31525 -39.2709474 1 6 6 12AS_A 9 Q -61.37700 -33.5304490 1 7 7 12AS_A 10 R -86.14173 -32.3448242 1 8 8 12AS_A 11 Q -52.88589 -57.2830246 1 want to read v7 vector add V8, edit it as in the same file V1 V2 V3 V4 V5 V6 V7V8 1 1 12AS_A 4 A0.0 157.8994119 22.3 2 2 12AS_A 5 Y -41.61818 -56.8011795 145.5 3 3 12AS_A 6 I -55.47021 -51.1328352 178.5 4 4 12AS_A 7 A -54.43085 -58.3428366 17.3 5 5 12AS_A 8 K -54.31525 -39.2709474 18.9 6 6 12AS_A 9 Q -61.37700 -33.5304490 14.5 7 7 12AS_A 10 R -86.14173 -32.3448242 17.3 8 8 12AS_A 11 Q -52.88589 -57.2830246 11.0 -- View this message in context: http://r.789695.n4.nabble.com/how-to-read-file-append-at-specified-positon-tp4424227p4424227.html Sent from the R help mailing list archive at Nabble.com. __ 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] strange behaviour of POSIXlt POSIXt object
Hi,
I do not know what part of my code should I post here (I use large size of
data, the loop for contains many lines). The situation is difficult to
post here, but I hope these lines would be useful for help:
hcEndDateTmp = userDateStart
if((hcStartTime=23:59) (hcEndTime = 00:00)){
hcEndDateTmp$mday = userDateStart$mday + 1
}
hcEndDate = strftime(hcEndDateTmp, %Y-%m-%d)
hcStart =
hcEnd = as.POSIXlt(paste(hcEndDate, hcEndTime))
for(rowNum in 1:nbJour){
...
hcStart = as.POSIXlt(ecs$startAt[[rowNum]])
ecsInterval2 =
datePower[(datePower$DateTime=hcStart)(datePower$DateTime=hcEnd), ]
...
hcEnd$mday = hcEnd$mday + 1
cat(DEBUG: rowNum=, rowNum, is.na(hcEnd)=, is.na(hcEnd), \n)
}
the two last lines are very important. It yields:
DEBUG: rowNum= 1 is.na(hcEnd)= FALSE
DEBUG: rowNum= 2 is.na(hcEnd)= FALSE
DEBUG: rowNum= 3 is.na(hcEnd)= FALSE
DEBUG: rowNum= 4 is.na(hcEnd)= FALSE
DEBUG: rowNum= 5 is.na(hcEnd)= FALSE
DEBUG: rowNum= 6 is.na(hcEnd)= FALSE
DEBUG: rowNum= 7 is.na(hcEnd)= TRUE
Browse[1] hcEnd
[1] 2009-03-29 06:30:00
Browse[1] class(hcEnd)
[1] POSIXlt POSIXt
So, At the end of 7th iteration, hcEnd becomes NA (I guess because of
hcEnd$mday = hcEnd$mday + 1 ?!?). But It remains strange because the class
of hcEnd is here POSIXlt POSIXt (it should be logical.!! Am I
wrong???)
Here is the version of R:
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 13.2
year 2011
month 09
day30
svn rev57111
language R
version.string R version 2.13.2 (2011-09-30)
thanks for your help
--
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[R] compare two data frames with same columns names but of different dimensions
Dear List, I want to compare and return the rows which are NOT in the two data frames. Classic methods don't work as the df have NOT the same dimensions. Here are one example of my df: reported - structure(list(Product = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 3L, 4L, 5L, 5L), .Label = c(Cocoa, Coffee C, GC, Sugar No 11, ZS), class = factor), Price = c(2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61L, -61L, 5L, 1L, 40L, 40L, -1L, -1L, -1L, 1L)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1L, 2L, 3L, 4L, 6L, 7L, 5L, 10L, 8L, 9L), class = data.frame) exportfile - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(NA, 9L), class = data.frame) As you can see, they have same column names. My idea was to merge these two df when passing as argument not to take into account duplicate rows, so I will get one df with rows which are not in both df. Is it possible? How to do it? TY for any help. Arnaud Gaboury A2CT2 Ltd. __ 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.
[R] Ubuntu jaunty - R can't be install
Dear helpers, I would like to install R on a computer with Ubuntu Jaunty. Unfortunately, Jaunty does not appear in any CRAN mirror website I have tried (France, Canada, Italy, Germany). Could you give me any mirror website allowing installation on Jaunty?or could you give me a procedure to passby this problem? Thanks for your help, Best regards, Marine Veyssière __ 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] identify and delete in table
Is this what you want: ds1 - read.table(text = 1 A + 2 B + 3 X + 4 AA + 5 A + 6 D + 7 XA + 8 C, as.is = TRUE) ds2 - read.table(text = 1 A + 2 X + 3 A, as.is = TRUE) # find matches ds3 - ds1[!(ds1$V2 %in% ds2$V2), ] ds3 V1 V2 2 2 B 4 4 AA 6 6 D 7 7 XA 8 8 C On Mon, Feb 27, 2012 at 6:17 AM, Jonas Fransson j...@iva.dk wrote: Dear all, I want to delete the exact matches in a large dataset based on a smaller dataset. In other words I want to subtract the smaller dataset from the larger one. The smaller dataset is a part of the larger one. The datasets contains hundred of thousands of lines (1 column) and the content on each line differ in length. The data is extracted paths from web logs. On an abstract level I want to subtract dataset2 from dataset1 to get dataset3: dataset1: 1 A 2 B 3 X 4 AA 5 A 6 D 7 XA 8 C dataset2: 1 A 2 X 3 A dataset3: 1 B 2 AA 3 D 4 XA 5 C The final order in dataset3 is not important. Thanks, Jonas Fransson Ph.D.stud. IVA / Det Informationsvidenskabelige Akademi Royal School of Library and Information Science Birketinget 6 DK-2300 Copenhagen S T +45 32 58 60 66 D +45 32 34 15 10 www.iva.dk/jf __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. __ 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] Ubuntu jaunty - R can't be install
I don't understand where is your problem. Are you looking for jaunty as a package on R Crans?? Are you looking to install R package on your Ubuntu box? As you know, Jaunty is no more supported by Ubuntu, so packets have been moved in Archives. Arnaud Gaboury A2CT2 Ltd. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Veyssière Marine Sent: lundi 27 février 2012 14:50 To: r-help@r-project.org Subject: [R] Ubuntu jaunty - R can't be install Dear helpers, I would like to install R on a computer with Ubuntu Jaunty. Unfortunately, Jaunty does not appear in any CRAN mirror website I have tried (France, Canada, Italy, Germany). Could you give me any mirror website allowing installation on Jaunty?or could you give me a procedure to passby this problem? Thanks for your help, Best regards, Marine Veyssière __ 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. __ 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] Matrix problem to extract animal associations
set.seed(1) (DFid - data.frame( x = sample(1:20,10), y = sample(1:20,10), IDs = sapply(1:10,function(i) paste(ID,i,sep= require(spdep) coordinates(DFid) - ~x+y coords - coordinates(DFid) dnn4 - dnearneigh(DFid,0,4) summary(dnn4) plot(DFid) plot(dnn4,coords,add=T,col=2) nb2mat(dnn4, zero.policy=TRUE) This just one option from the multitude of spatial packages. HTH On Sun, Feb 26, 2012 at 4:55 PM, Ross Dwyer ross.dw...@uq.edu.au wrote: Dear List, I have been trying to extract associations from a matrix whereby individual locations are within a certain distance threshold from one another. I have been able to extract those individuals where there is 'no interaction' (i.e. where these individuals are not within a specified distance threshold from another individual) and give these individuals a unique Group ID containing that one individual. i.e. ID Group 1 ID1 1 2 ID3 2 3 ID4 3 4 ID5 4 5 ID7 5 6 ID8 6 7 ID9 7 What I need assistance with is allocating associations with a unique group id. i.e. If we have interactions between ID2_ID6, ID6_ID2, ID6_ID10, ID10_ID6 as in the example code... ID Group 1 ID1 1 2 ID3 2 3 ID4 3 4 ID5 4 5 ID7 5 6 ID8 6 7 ID9 7 ## 8 ID2 8 9 ID6 8 10 ID10 8 ## The code also needs to robust enough to recognize instances where we have an interaction in a separate group... i.e. ID11_ID12 should be in a separate group (Group 9) as they don't interact with IDs 2, 6, or 10 (not in below code!) 11 ID11 9 12 ID12 9 I've been trying to figure this out but have drawn a blank. My example code can be found below. Very best wishes, Ross Dr Ross Dwyer Postdoctoral Research Fellow University of Queensland ### require(stats) x - sample(1:20,10) y - sample(1:20,10) IDs - sapply(1:10,function(i) paste(ID,i,sep=)) (DFid - data.frame(x,y)) x y 1 7 20 2 5 3 3 12 5 4 3 12 5 18 19 6 2 1 7 19 15 8 20 11 9 13 14 10 1 2 (DMdist - dist(DFid, method = euclidean, + diag = FALSE, upper = TRUE)) 1 2 3 4 5 6 7 8 9 10 1 17.117243 15.811388 8.944272 11.045361 19.646883 13.00 15.811388 8.485281 18.973666 2 17.117243 7.280110 9.219544 20.615528 3.605551 18.439089 17.00 13.601471 4.123106 3 15.811388 7.280110 11.401754 15.231546 10.770330 12.206556 10.00 9.055385 11.401754 4 8.944272 9.219544 11.401754 16.552945 11.045361 16.278821 17.029386 10.198039 10.198039 5 11.045361 20.615528 15.231546 16.552945 24.083189 4.123106 8.246211 7.071068 24.041631 6 19.646883 3.605551 10.770330 11.045361 24.083189 22.022716 20.591260 17.029386 1.414214 7 13.00 18.439089 12.206556 16.278821 4.123106 22.022716 4.123106 6.082763 22.203603 8 15.811388 17.00 10.00 17.029386 8.246211 20.591260 4.123106 7.615773 21.023796 9 8.485281 13.601471 9.055385 10.198039 7.071068 17.029386 6.082763 7.615773 16.970563 10 18.973666 4.123106 11.401754 10.198039 24.041631 1.414214 22.203603 21.023796 16.970563 #Generate True/False matrix on those individuals 4 units apart DMTF - apply(as.matrix(DMdist), c(1,2), function(x) ifelse(x=4,T,F)) diag(DMTF)- NA #replace diagonal with NA dimnames(DMTF) - list(IDs, IDs) #add individual's name to matrix DMTF ID1 ID2 ID3 ID4 ID5 ID6 ID7 ID8 ID9 ID10 ID1 NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ID2 FALSE NA FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE ID3 FALSE FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE ID4 FALSE FALSE FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE ID5 FALSE FALSE FALSE FALSE NA FALSE FALSE FALSE FALSE FALSE ID6 FALSE TRUE FALSE FALSE FALSE NA FALSE FALSE FALSE TRUE ID7 FALSE FALSE FALSE FALSE FALSE FALSE NA FALSE FALSE FALSE ID8 FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA FALSE FALSE ID9 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA FALSE ID10 FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE NA irow - as.character(gl(length(IDs),length(IDs),labels=IDs)) icol -rep(IDs, length(IDs)) AssocMatrix - matrix(data=paste(irow,_,icol,_,sep=), + nrow = length(IDs), ncol = length(IDs), + dimnames= list(IDs, IDs)) AssocMatrix ID1 ID2 ID3 ID4 ID5 ID6 ID7 ID8 ID9 ID10 ID1 ID1_ID1_ ID2_ID1_ ID3_ID1_ ID4_ID1_ ID5_ID1_ ID6_ID1_ ID7_ID1_ ID8_ID1_ ID9_ID1_ ID10_ID1_ ID2 ID1_ID2_ ID2_ID2_ ID3_ID2_ ID4_ID2_ ID5_ID2_ ID6_ID2_ ID7_ID2_ ID8_ID2_ ID9_ID2_ ID10_ID2_ ID3 ID1_ID3_ ID2_ID3_ ID3_ID3_ ID4_ID3_ ID5_ID3_ ID6_ID3_ ID7_ID3_ ID8_ID3_ ID9_ID3_
Re: [R] strange behaviour of POSIXlt POSIXt object
is.na(POSIXltObject) can behave oddly if you manipulate
the fields of the POSIXlt object directly so as to
cause illegal combinations of values. E.g., the 35th
of February, 2009, is not considered an NA but the 36th
and above are:
z - as.POSIXlt(2009-02-25 06:30:00)
for(i in 1:20){ z$mday - z$mday + 1L ; cat(is.na(z), : );print(z)}
FALSE : [1] 2009-02-26 06:30:00
FALSE : [1] 2009-02-27 06:30:00
FALSE : [1] 2009-02-28 06:30:00
FALSE : [1] 2009-03-01 06:30:00
FALSE : [1] 2009-03-02 06:30:00
FALSE : [1] 2009-03-03 06:30:00
FALSE : [1] 2009-03-04 06:30:00
FALSE : [1] 2009-03-05 06:30:00
FALSE : [1] 2009-03-06 06:30:00
FALSE : [1] 2009-03-07 06:30:00
TRUE : [1] 2009-03-08 06:30:00
TRUE : [1] 2009-03-09 06:30:00
TRUE : [1] 2009-03-10 06:30:00
TRUE : [1] 2009-03-11 06:30:00
TRUE : [1] 2009-03-12 06:30:00
TRUE : [1] 2009-03-13 06:30:00
TRUE : [1] 2009-03-14 06:30:00
TRUE : [1] 2009-03-15 06:30:00
TRUE : [1] 2009-03-16 06:30:00
TRUE : [1] 2009-03-17 06:30:00
The print routine does not seem to consult is.na().
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of ikuzar
Sent: Monday, February 27, 2012 2:41 AM
To: r-help@r-project.org
Subject: Re: [R] strange behaviour of POSIXlt POSIXt object
Hi,
I do not know what part of my code should I post here (I use large size of
data, the loop for contains many lines). The situation is difficult to
post here, but I hope these lines would be useful for help:
hcEndDateTmp = userDateStart
if((hcStartTime=23:59) (hcEndTime = 00:00)){
hcEndDateTmp$mday = userDateStart$mday + 1
}
hcEndDate = strftime(hcEndDateTmp, %Y-%m-%d)
hcStart =
hcEnd = as.POSIXlt(paste(hcEndDate, hcEndTime))
for(rowNum in 1:nbJour){
...
hcStart = as.POSIXlt(ecs$startAt[[rowNum]])
ecsInterval2 =
datePower[(datePower$DateTime=hcStart)(datePower$DateTime=hcEnd), ]
...
hcEnd$mday = hcEnd$mday + 1
cat(DEBUG: rowNum=, rowNum, is.na(hcEnd)=, is.na(hcEnd), \n)
}
the two last lines are very important. It yields:
DEBUG: rowNum= 1 is.na(hcEnd)= FALSE
DEBUG: rowNum= 2 is.na(hcEnd)= FALSE
DEBUG: rowNum= 3 is.na(hcEnd)= FALSE
DEBUG: rowNum= 4 is.na(hcEnd)= FALSE
DEBUG: rowNum= 5 is.na(hcEnd)= FALSE
DEBUG: rowNum= 6 is.na(hcEnd)= FALSE
DEBUG: rowNum= 7 is.na(hcEnd)= TRUE
Browse[1] hcEnd
[1] 2009-03-29 06:30:00
Browse[1] class(hcEnd)
[1] POSIXlt POSIXt
So, At the end of 7th iteration, hcEnd becomes NA (I guess because of
hcEnd$mday = hcEnd$mday + 1 ?!?). But It remains strange because the class
of hcEnd is here POSIXlt POSIXt (it should be logical.!! Am I
wrong???)
Here is the version of R:
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 13.2
year 2011
month 09
day30
svn rev57111
language R
version.string R version 2.13.2 (2011-09-30)
thanks for your help
--
View this message in context:
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Re: [R] strange behaviour of POSIXlt POSIXt object
So, how is the correct way to increment the day ? -- View this message in context: http://r.789695.n4.nabble.com/strange-behaviour-of-POSIXlt-POSIXt-object-tp4418115p4425206.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] RStudio: how to change language from fr(french) to eng(english)
Hello, RStudio displays errors in french . I'd like to change it in english Please help, Thanks -- View this message in context: http://r.789695.n4.nabble.com/RStudio-how-to-change-language-from-fr-french-to-eng-english-tp4424972p4424972.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] set heatmap.2 color ranges
Hi all, I have a matrix with values between 0 and 1. I want to plot this matrix on a heat map so anything 0.05 is blue, anything =0.05 and 0.01 is yellow, and anything else is grey. I am using the heatmap.2 function. I searched around but did not find an efficient way to set colour ranges as I described. Could anybody give some hints? Thank you in advance. Wendy -- View this message in context: http://r.789695.n4.nabble.com/set-heatmap-2-color-ranges-tp4425166p4425166.html Sent from the R help mailing list archive at Nabble.com. __ 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] RStudio: how to change language from fr(french) to eng(english)
On 27/02/2012 15:29, ikuzar wrote: Hello, RStudio displays errors in french . I'd like to change it in english See the 'R Installation and Administration' manual. If that does not help, ask RStudio's help (it is not a product supported here). Setting the LANGUAGE environment variable to 'en' should work unless RStudio is itself setting it. Please help, Thanks -- View this message in context: http://r.789695.n4.nabble.com/RStudio-how-to-change-language-from-fr-french-to-eng-english-tp4424972p4424972.html Sent from the R help mailing list archive at Nabble.com. __ 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. PLEASE do: the 'at a minimum' information requested would have been helpful here. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] RStudio: how to change language from fr(french) to eng(english)
Then why don't you ask about it on the RStudio support forum? --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. ikuzar raz...@hotmail.fr wrote: Hello, RStudio displays errors in french . I'd like to change it in english Please help, Thanks -- View this message in context: http://r.789695.n4.nabble.com/RStudio-how-to-change-language-from-fr-french-to-eng-english-tp4424972p4424972.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] best option for big 3D arrays?
Thanks,
That helped. Maybe when I get a chance I will do some blog posts on the
basics of ff
I think some tutorials would be a good idea
Steve
On Mon, Feb 27, 2012 at 3:47 AM, Djordje Bajic je.li@gmail.com wrote:
Steven, sorry for the delay in responding,
I have been investigating this also and here is the way I do it (though
probably not the best way):
# .. define a 3D array
ngen = 904
gratios - ff(NA, dim=rep(ngen,3), vmode=double)
# .. fill the array with standard R functions
ffsave (gratios, file=mydir/myfile)# without extension
finalizer(gratios) - delete
# ..
so, you firstly define the ff object, you put the data inside, and you
ffsave it. The ffsave function will generate two files, with extensions
ffdata and a Rdata. Then you set 'delete' to be the 'finalizer' of the
object; in this way you avoid ff to save it in some tmp dir and occupy disk
space forever. Then, you can access your object in the next R session:
ffload(mydir/myfile)# also without extension
I hope this helped.
Cheers,
djordje
2012/2/23 steven mosher mosherste...@gmail.com
Did you have to use a particular filename? or extension.
I created a similar file but then could not read it back in
Steve
On Mon, Feb 13, 2012 at 6:45 AM, Djordje Bajic je.li@gmail.com
wrote:
I've been investigating and I partially respond myself. I tried the
packages 'bigmemory' and 'ff' and for me the latter did the work I need
pretty straightforward. I create the array in filebacked form with the
function ff, and it seems that the usual R indexing works well. I have
yet
to see the limitations, but I hope it helps.
a foo example:
myArr - ff(NA, dim=rep(904,3), filename=arr.ffd, vmode=double)
myMat - matrix(1:904^2, ncol=904)
for ( i in 1:904 ) {
myArr[,,i] - myMat
}
Thanks all,
2012/2/11 Duncan Murdoch murdoch.dun...@gmail.com
On 12-02-10 9:12 AM, Djordje Bajic wrote:
Hi all,
I am trying to fill a 904x904x904 array, but at some point of the
loop
R
states that the 5.5Gb sized vector is too big to allocate. I have
looked
at
packages such as bigmemory, but I need help to decide which is the
best
way to store such an object. It would be perfect to store it in this
cube
form (for indexing and computation purpouses). If not possible, maybe
the
best is to store the 904 matrices separately and read them
individually
when needed?
Never dealed with such a big dataset, so any help will be appreciated
(R+ESS, Debian 64bit, 4Gb RAM, 4core)
I'd really recommend getting more RAM, so you can have the whole thing
loaded in memory. 16 Gb would be nice, but even 8Gb should make a
substantial difference. It's going to be too big to store as an array
since arrays have a limit of 2^31-1 entries, but you could store it
as a
list of matrices, e.g.
x - vector(list, 904)
for (i in 1:904)
x[[i]] - matrix(0, 904,904)
and then refer to entry i,j,k as x[[i]][j,k].
Duncan Murdoch
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Re: [R] Need advice on GLM
On Mon, Feb 27, 2012 at 1:44 AM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Here I was expecting those 2 approaches should give exactly same result (i.e. same estimates and same SE), which is not the case. Can somebody point me what I am missing here? The vector of weights as described in ?glm which from your example is clear you either didn't look at or completely misinterpreted. summary(glm(YY~XX, binomial(link = identity))) summary(glm(Dat~Scores, binomial(link = identity))) summary(glm(Proportion~Scores, weights=rowSums(Dat),binomial(link = identity))) Thanks and regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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.
[R] compare two data frames of different dimensions and only keep unique rows
Dear list, I am still struggling with something that should be easy: I compare two data frames with a lot of common rows and want to keep only rows that are NOT in both data frames, unique. Here are an example of these data frame. reported - structure(list(Product = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 3L, 4L, 5L, 5L), .Label = c(Cocoa, Coffee C, GC, Sugar No 11, ZS), class = factor), Price = c(2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61L, -61L, 5L, 1L, 40L, 40L, -1L, -1L, -1L, 1L)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1L, 2L, 3L, 4L, 6L, 7L, 5L, 10L, 8L, 9L), class = data.frame) exportfile - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(NA, 9L), class = data.frame) I can rbind() them, thus resulting in one data frame with duplicated row, but I have no idea how to delete duplicated rows. I have tried plyaing with unique(), duplicated with no success v-rbind(exportfile,reported) v - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS, Cocoa, Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25, 2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1, -61, -61, 5, 1, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 31, 41, 61, 71, 51, 10, 81, 91), class = data.frame) TY for your help Arnaud Gaboury A2CT2 Ltd. __ 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.
[R] problem with assign and get
Dear list members,
does anyone have an idea why the following construction does not work
but gives the following error message:
assign('test', array(1:10, dim=c(10,10)))
dimnames(get('test')) - list(1:10,1:10)
Error in dimnames(get(test)) - list(1:10, 1:10) :
target of assignment expands to non-language object
What could be a way to get this to work?
thanks a lot
Jannis
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Re: [R] compare two data frames of different dimensions and only keep unique rows
is this what you want: v - rbind(reported, exportfile) v[!duplicated(v), ] ProductPrice Nbr.Lots 1Cocoa 2331.00 -61 2Cocoa 2356.00 -61 3Cocoa 2440.005 4Cocoa 2450.001 6 Coffee C 204.55 40 7 Coffee C 205.45 40 5 GC 17792.00 -1 10 Sugar No 1124.81 -1 8 ZS 1273.50 -1 9 ZS 1276.251 13 Cocoa 2440.006 On Mon, Feb 27, 2012 at 12:36 PM, Arnaud Gaboury arnaud.gabo...@a2ct2.com wrote: Dear list, I am still struggling with something that should be easy: I compare two data frames with a lot of common rows and want to keep only rows that are NOT in both data frames, unique. Here are an example of these data frame. reported - structure(list(Product = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 3L, 4L, 5L, 5L), .Label = c(Cocoa, Coffee C, GC, Sugar No 11, ZS), class = factor), Price = c(2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61L, -61L, 5L, 1L, 40L, 40L, -1L, -1L, -1L, 1L)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1L, 2L, 3L, 4L, 6L, 7L, 5L, 10L, 8L, 9L), class = data.frame) exportfile - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(NA, 9L), class = data.frame) I can rbind() them, thus resulting in one data frame with duplicated row, but I have no idea how to delete duplicated rows. I have tried plyaing with unique(), duplicated with no success v-rbind(exportfile,reported) v - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS, Cocoa, Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25, 2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1, -61, -61, 5, 1, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 31, 41, 61, 71, 51, 10, 81, 91), class = data.frame) TY for your help Arnaud Gaboury A2CT2 Ltd. __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. __ 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] problem with assign and get
On Mon, Feb 27, 2012 at 9:41 AM, Jannis bt_jan...@yahoo.de wrote:
Dear list members,
does anyone have an idea why the following construction does not work but
gives the following error message:
assign('test', array(1:10, dim=c(10,10)))
dimnames(get('test')) - list(1:10,1:10)
Error in dimnames(get(test)) - list(1:10, 1:10) :
target of assignment expands to non-language object
What could be a way to get this to work?
dimnames(test) - list(1:10,1:10)
Peter
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Re: [R] problem with assign and get
Hi,
On Mon, Feb 27, 2012 at 12:41 PM, Jannis bt_jan...@yahoo.de wrote:
Dear list members,
does anyone have an idea why the following construction does not work but
gives the following error message:
assign('test', array(1:10, dim=c(10,10)))
dimnames(get('test')) - list(1:10,1:10)
Error in dimnames(get(test)) - list(1:10, 1:10) :
target of assignment expands to non-language object
There's no object to assign dimnames to. Think about it
this way - what do you expect the dimnames of to be
changed? test has no dimnames; get(test) would
print the object named test, but how could you change
the dimnames of a displayed object?
If you want to change the dimnames of the object named
test, you first need to use get(test) to assign that object
to a new object, then change the dimnames, then assign
the changed object to the desired name.
myobject - get(test)
dimnames(myobject) - list(1:10, 1:10)
assign(test, myobject)
Note: I'm assuming your small reproducible example (thank
you!) is a surrogate for something more complex, so that
dimnames(test) - list(1:10, 1:10) is not an acceptable
solution. But frequently there are better options than the
use of get/assign for solving particular problems.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [R] compare two data frames of different dimensions and only keep unique rows
No, but I tried your way too. In fact, the only three unique rows are these ones: Product Price Nbr.Lots Cocoa 24405 Cocoa 24501 Cocoa 24406 Here is a dirty working trick I found : df-merge(exportfile,reported,all.y=T) df1-merge(exportfile,reported) dff1-do.call(paste,df) dff-do.call(paste,df) dff1-do.call(paste,df1) df[!dff %in% dff1,] Product Price Nbr.Lots 3 Cocoa 24405 4 Cocoa 24501 My two problems are : I do think it is not so a clean code, then I won't know by advance which of my two df will have the greates dimension (I can add some lines to deal with it, but again, seems very heavy). I hoped I could find a better solution. A2CT2 Ltd. -Original Message- From: jim holtman [mailto:jholt...@gmail.com] Sent: lundi 27 février 2012 18:42 To: Arnaud Gaboury Cc: r-help@r-project.org Subject: Re: [R] compare two data frames of different dimensions and only keep unique rows is this what you want: v - rbind(reported, exportfile) v[!duplicated(v), ] ProductPrice Nbr.Lots 1Cocoa 2331.00 -61 2Cocoa 2356.00 -61 3Cocoa 2440.005 4Cocoa 2450.001 6 Coffee C 204.55 40 7 Coffee C 205.45 40 5 GC 17792.00 -1 10 Sugar No 1124.81 -1 8 ZS 1273.50 -1 9 ZS 1276.251 13 Cocoa 2440.006 On Mon, Feb 27, 2012 at 12:36 PM, Arnaud Gaboury arnaud.gabo...@a2ct2.com wrote: Dear list, I am still struggling with something that should be easy: I compare two data frames with a lot of common rows and want to keep only rows that are NOT in both data frames, unique. Here are an example of these data frame. reported - structure(list(Product = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 3L, 4L, 5L, 5L), .Label = c(Cocoa, Coffee C, GC, Sugar No 11, ZS), class = factor), Price = c(2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61L, -61L, 5L, 1L, 40L, 40L, -1L, -1L, -1L, 1L)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1L, 2L, 3L, 4L, 6L, 7L, 5L, 10L, 8L, 9L), class = data.frame) exportfile - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(NA, 9L), class = data.frame) I can rbind() them, thus resulting in one data frame with duplicated row, but I have no idea how to delete duplicated rows. I have tried plyaing with unique(), duplicated with no success v-rbind(exportfile,reported) v - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS, Cocoa, Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25, 2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1, -61, -61, 5, 1, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 31, 41, 61, 71, 51, 10, 81, 91), class = data.frame) TY for your help Arnaud Gaboury A2CT2 Ltd. __ 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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. __ 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] Virus Infection in colorspace_1.1-1.zip (R x64 2.14.1)
On 24/01/2012 7:44 PM, R. Michael Weylandt wrote: I'm skeptical that CRAN would produce a bug, but it's not unheard of for anti-viruses to not like its compiled code. Are you able to compile locally? That might make it more comfortable -- if you do so, you could also white list those files (since you made them) Not a perfect workaround, but AV tends not to like OSS stuff for whatever reason... AVG contacted me about colorspace.dll. They tracked down the false positive and have corrected it. For future problems like this, they said: In the future if any part of the R Project software is being detected by AVG Anti-Virus software, please submit them to our Virus Labs at http://www.avg.com/us-en/whitelist. Could you help me with forwarding this information to your public forums? Duncan Murdoch __ 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] problem with assign and get
Sarah Gosless said
But frequently there are better options than the
use of get/assign for solving particular problems.
I tend to be more extreme say recommend that you forget
you ever heard of the get and assign functions.
First, out-of-the-local-evaluation-environment assignments
make for confusing code. You can usually do what you
need to do by having functions that return values.
Replacement functions, defined with
`something-` - function(x, ..., value) { x$something-value; x }
and used as
something(x) - newSomething
can be used to alter an existing object.
Second, if you decide that you need to do an assignment
outside of the current evironment, you ought to know which
environment you want to use. It is often .GlobalEnv.
Then you can use
yourEnvironment[[itemName]]
instead of
get(itemName, envir=yourEnvironment)
and
yourEnvironment[[itemName]] - itemValue
instead of
assign(itemName, itemValue, envir=yourEnvironment)
The advantages of the [[ syntax are (a) it forces you
to decide where the data should be and (b) it lets you
use natural R syntax to modify objects. E.g.,
rownames(yourEnvironment[[itemName]]) - c(R1,R2)
will change the rownames of itemName in the environment
called yourEnvironment.
At somepoint you may decide to use a list instead of
an environment to hold your objects, in which case the
[[ syntax still works without any changes.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Sarah Goslee
Sent: Monday, February 27, 2012 9:58 AM
To: Jannis
Cc: r-help@r-project.org
Subject: Re: [R] problem with assign and get
Hi,
On Mon, Feb 27, 2012 at 12:41 PM, Jannis bt_jan...@yahoo.de wrote:
Dear list members,
does anyone have an idea why the following construction does not work but
gives the following error message:
assign('test', array(1:10, dim=c(10,10)))
dimnames(get('test')) - list(1:10,1:10)
Error in dimnames(get(test)) - list(1:10, 1:10) :
target of assignment expands to non-language object
There's no object to assign dimnames to. Think about it
this way - what do you expect the dimnames of to be
changed? test has no dimnames; get(test) would
print the object named test, but how could you change
the dimnames of a displayed object?
If you want to change the dimnames of the object named
test, you first need to use get(test) to assign that object
to a new object, then change the dimnames, then assign
the changed object to the desired name.
myobject - get(test)
dimnames(myobject) - list(1:10, 1:10)
assign(test, myobject)
Note: I'm assuming your small reproducible example (thank
you!) is a surrogate for something more complex, so that
dimnames(test) - list(1:10, 1:10) is not an acceptable
solution. But frequently there are better options than the
use of get/assign for solving particular problems.
Sarah
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Re: [R] set heatmap.2 color ranges
On Feb 27, 2012, at 11:26 AM, Wendy wrote: 0.05 is blue, anything =0.05 and 0.01 is yellow, and anything else is grey No data structures offered, but this may be a useful example: col= c(grey, yellow, blue)[findInterval(X, c(-.01, 0.01, 0.05, 1.1))] -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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.
[R] How can the citation to be included in the manual for a package?
Hi All, I have a CITATION file in inst for my package, however I would like to have our relevant paper to show up in the package documentation file as well. I tried to put the paper in the Description field but that does not seem to allow formatting (like a new line before the reference) it is a single paragraph only What is the R way of doing this? Thanks! -Matyas [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing package QRMlib
Hi, I am having real problems downloading the package 'QRMlib'. The tar.gz file is shown here: http://cran.r-project.org/src/contrib/Archive/QRMlib/ I have downloaded this to my local folder and entered the following command: nstall.packages(myLocalFolder/QRMlib_1.4.5.1.tar.gz, repos = NULL) but I am getting the following error message Installing package(s) into ‘C:/Program Files/R/R-2.14.1/library’ (as ‘lib’ is unspecified) Warning in install.packages : error 1 in extracting from zip file Warning in install.packages : cannot open compressed file 'QRMlib_1.4.5.1.tar.gz/DESCRIPTION', probable reason 'No such file or directory' Error in install.packages : cannot open the connection What am I doing wrong?? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Installing-package-QRMlib-tp4425269p4425269.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] macro function
hi,
I know how to use the for loop function like:
for(i in 1:ncol(mat)){
mat[i]-b[i,2]
}
but, in this case
r1-b[1,1]
r2-b[2,1]
r3-b[3,1]
r4-b[4,1]
*
*
*
r3002-b[3002,1]
r3003-b[3003,1]
- must make vectors
how should I make a efficient code for that?
Is there anything in R like SAS MACRO function?
Please help me.
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Re: [R] compare two data frames of different dimensions and only keep unique rows
Hello, In fact, the only three unique rows are these ones: Product Price Nbr.Lots Cocoa 24405 Cocoa 24501 Cocoa 24406 The code below doesn't give the three in one step. (ixmat - apply(reported, 1, function(x) apply(exportfile, 1, function(y) any(x != y reported[apply(ixmat, 2, all), ] exportfile[apply(ixmat, 1, all), ] But it does give all three. Problem: it's inefficient. If n1 - nrow(reported) and n2 - nrow(exportfile), to form the index matrix alone it will make ncol times n1*n2 comparisons. And the matrix dims are n1, n2 ... Anyway, I hope it gives ideas, Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/compare-two-data-frames-of-different-dimensions-and-only-keep-unique-rows-tp4425379p4425605.html Sent from the R help mailing list archive at Nabble.com. __ 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] set heatmap.2 color ranges
On Feb 27, 2012, at 1:32 PM, David Winsemius wrote: On Feb 27, 2012, at 11:26 AM, Wendy wrote: 0.05 is blue, anything =0.05 and 0.01 is yellow, and anything else is grey No data structures offered, but this may be a useful example: col= c(grey, yellow, blue)[findInterval(X, c(-.01, 0.01, 0.05, 1.1))] Except you would want to have matching '''s col= c(grey, yellow, blue)[findInterval(X, c(-.01, 0.01, 0.05, 1.1))] Why are these things easier to see when they show in Received? -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] macro function
On Mon, Feb 27, 2012 at 9:56 AM, mrzung mrzun...@gmail.com wrote:
hi,
I know how to use the for loop function like:
for(i in 1:ncol(mat)){
mat[i]-b[i,2]
}
but, in this case
r1-b[1,1]
r2-b[2,1]
r3-b[3,1]
r4-b[4,1]
*
*
*
r3002-b[3002,1]
r3003-b[3003,1]
- must make vectors
how should I make a efficient code for that?
You shouldn't. There is no reason to do this.
Is there anything in R like SAS MACRO function?
No! -- Thank goodness! R is a programming language to begin with. Have
you read An Intro to R?' If not, why not? There are numerous
resources available on CRAN to help you. Use them.
Please help me.
Please first make an effort to help yourself.
-- Bert
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Re: [R] compare two data frames of different dimensions and only keep unique rows
On Mon, Feb 27, 2012 at 07:10:57PM +0100, Arnaud Gaboury wrote:
No, but I tried your way too.
In fact, the only three unique rows are these ones:
Product Price Nbr.Lots
Cocoa 24405
Cocoa 24501
Cocoa 24406
Here is a dirty working trick I found :
df-merge(exportfile,reported,all.y=T)
df1-merge(exportfile,reported)
dff1-do.call(paste,df)
dff-do.call(paste,df)
dff1-do.call(paste,df1)
df[!dff %in% dff1,]
Product Price Nbr.Lots
3 Cocoa 24405
4 Cocoa 24501
My two problems are : I do think it is not so a clean code, then I won't know
by advance which of my two df will have the greates dimension (I can add some
lines to deal with it, but again, seems very heavy).
Hi.
Try the following.
setdiffDF - function(A, B)
{
A[!duplicated(rbind(B, A))[nrow(B) + 1:nrow(A)], ]
}
df1 - setdiffDF(reported, exportfile)
df2 - setdiffDF(exportfile, reported)
rbind(df1, df2)
I obtained
Product Price Nbr.Lots
3Cocoa 24405
4Cocoa 24501
31 Cocoa 24406
Is this correct? I see the row
Cocoa 2440.006
only in exportfile and not in reported.
The trick with paste() is not a bad idea. A variant of
it is used also in the base function duplicated.matrix(),
since it contains
apply(x, MARGIN, function(x) paste(x, collapse = \r))
If speed is critical, then possibly the paste() trick
written for the whole columns, for example
paste(df[[1]], df[[2]], df[[3]], sep=\r)
and then setdiff() can be better.
Hope this helps.
Petr Savicky.
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Re: [R] strange behaviour of POSIXlt POSIXt object
Hadley's lubridate package might be of some help to you. Michael On Mon, Feb 27, 2012 at 11:40 AM, ikuzar raz...@hotmail.fr wrote: So, how is the correct way to increment the day ? -- View this message in context: http://r.789695.n4.nabble.com/strange-behaviour-of-POSIXlt-POSIXt-object-tp4418115p4425206.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] Installing package QRMlib
Do you perhaps need to add install.packages(..., type=src)? Just a (untested) guess... Michael On Mon, Feb 27, 2012 at 12:07 PM, DT54321 deepan.tailo...@gmail.com wrote: Hi, I am having real problems downloading the package 'QRMlib'. The tar.gz file is shown here: http://cran.r-project.org/src/contrib/Archive/QRMlib/ I have downloaded this to my local folder and entered the following command: nstall.packages(myLocalFolder/QRMlib_1.4.5.1.tar.gz, repos = NULL) but I am getting the following error message Installing package(s) into ‘C:/Program Files/R/R-2.14.1/library’ (as ‘lib’ is unspecified) Warning in install.packages : error 1 in extracting from zip file Warning in install.packages : cannot open compressed file 'QRMlib_1.4.5.1.tar.gz/DESCRIPTION', probable reason 'No such file or directory' Error in install.packages : cannot open the connection What am I doing wrong?? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Installing-package-QRMlib-tp4425269p4425269.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] Installing package QRMlib
On 27/02/2012 3:01 PM, R. Michael Weylandt wrote: Do you perhaps need to add install.packages(..., type=src)? Just a (untested) guess... That should be type=source, and that should solve the problem, assuming Deepan has the necessary tools installed. If not, he can get them from CRAN in the bin/windows/Rtools directory. Duncan Murdoch Michael On Mon, Feb 27, 2012 at 12:07 PM, DT54321deepan.tailo...@gmail.com wrote: Hi, I am having real problems downloading the package 'QRMlib'. The tar.gz file is shown here: http://cran.r-project.org/src/contrib/Archive/QRMlib/ I have downloaded this to my local folder and entered the following command: nstall.packages(myLocalFolder/QRMlib_1.4.5.1.tar.gz, repos = NULL) but I am getting the following error message Installing package(s) into ‘C:/Program Files/R/R-2.14.1/library’ (as ‘lib’ is unspecified) Warning in install.packages : error 1 in extracting from zip file Warning in install.packages : cannot open compressed file 'QRMlib_1.4.5.1.tar.gz/DESCRIPTION', probable reason 'No such file or directory' Error in install.packages : cannot open the connection What am I doing wrong?? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Installing-package-QRMlib-tp4425269p4425269.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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. __ 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.
[R] Principal Components for matrices with NA
Hello, I have a matrix with 267 columns, all rows of which have at least one column missing (NA). All three methods i've tried (pcs, princomp, and prcomp) fail with either Error in svd(zsmall) : infinite or missing values in 'x' (latter two) or Error in cov.wt(z) : 'x' must contain finite values only The last one happens because of the check if (!all(is.finite(x))) in cov.wt Q: is there a way to do princomp or another method where every row has at least one missing column? I guess if missing values are thrown out, that leaves me with a zero row matrix. I could find the maximal set of columns such that there exists a subset of rows with non NA values for every column in the set - what is an efficient way to do that? Kind Regards JS [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to incorporate interaction terms in MRM function of ecodist library?
Hi, I'm interested in incorporating some interaction terms between my explanatory variables (distance matrices in this case) when I'm using the function MRM of the package ecodist. The function is doing a multiple regression on distance matrices. I can get the function to work perfectly on my explanatory matrices by adding a (+) sign as known. However, when I try to use the (*) sign or (:) between two terms that I'd like to check the interaction for, I get same results as with just additive model. Is there something that I do wrong? Thanks, *For example: * mrm.S10z_A- MRM(Adis ~ S10z.st+Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.06 S10z.st -0.002587542 0.86 Distance.st 0.028866573 0.07 $r.squared R2pval 0.004180399 0.06000 $F.test F F.pval 4.634535 0.06 mrm.S10z_A- MRM(Adis ~ S10z.st*Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.05 S10z.st -0.002587542 0.80 Distance.st 0.028866573 0.07 $r.squared R2pval 0.004180399 0.05000 $F.test F F.pval 4.634535 0.05 mrm.S10z_A- MRM(Adis ~ S10z.st:Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.05 S10z.st -0.002587542 0.81 Distance.st 0.028866573 0.11 $r.squared R2pval 0.004180399 0.05000 $F.test F F.pval 4.634535 0.05 -- View this message in context: http://r.789695.n4.nabble.com/How-to-incorporate-interaction-terms-in-MRM-function-of-ecodist-library-tp4425767p4425767.html Sent from the R help mailing list archive at Nabble.com. __ 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] How to incorporate interaction terms in MRM function of ecodist library?
Hi, On Mon, Feb 27, 2012 at 2:28 PM, Hossm_R hossamesap...@gmail.com wrote: Hi, I'm interested in incorporating some interaction terms between my explanatory variables (distance matrices in this case) when I'm using the function MRM of the package ecodist. The function is doing a multiple regression on distance matrices. MRM() will not process interaction terms. You can use R's regular regression methods to get estimates of the coefficients, but statistical significance from those methods is unusable in this case. I can get the function to work perfectly on my explanatory matrices by adding a (+) sign as known. However, when I try to use the (*) sign or (:) between two terms that I'd like to check the interaction for, I get same results as with just additive model. Is there something that I do wrong? Thanks, *For example: * mrm.S10z_A- MRM(Adis ~ S10z.st+Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.06 S10z.st -0.002587542 0.86 Distance.st 0.028866573 0.07 $r.squared R2 pval 0.004180399 0.06000 $F.test F F.pval 4.634535 0.06 mrm.S10z_A- MRM(Adis ~ S10z.st*Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.05 S10z.st -0.002587542 0.80 Distance.st 0.028866573 0.07 $r.squared R2 pval 0.004180399 0.05000 $F.test F F.pval 4.634535 0.05 mrm.S10z_A- MRM(Adis ~ S10z.st:Distance.st, nperm=100) mrm.S10z_A $coef Adis pval Int 0.553605282 0.05 S10z.st -0.002587542 0.81 Distance.st 0.028866573 0.11 $r.squared R2 pval 0.004180399 0.05000 $F.test F F.pval 4.634535 0.05 -- Sarah Goslee http://www.functionaldiversity.org __ 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.
[R] Help with rJava
I am trying to invoke an in house developed java program from R and am
running into some confusing issues.
I've written this function:
DoNormalSkew - function() {
.jaddClassPath(U:/development/software/untilities/ELVeSkew/dist/ELVeSkew.jar)
.jpackage(U:/development/software/utilities/ELVeS/dist/ELVeSkew.jar)
.jcall(java/lang/System, V, method=Main.main(),
U:/development/software/utilities/ELVeSkew/test/csv,
U:/development/software/utilities/ELVeSkew/test/out.csv
}
When I run this the function returns the following:
Error in .jcall(java/lang/System, V, method=Main.main(),
U:/development/software/utilities/ELVeSkew/test/csv, :
could not find function Main.man
I have searched on line for examples and have not found any that can
explain this process clearly.
1.) Do I need each of the statements for .jaddClassPath and .jpackage ?
2.) Can you help me understand the .jcall statement better, am I at least
on the right track?
3.) The java program arguments include an input file and output file, these
are given in the last 2 lines of the function.
I'm working on a Windows XP machine, R version 2.14.1
packages updated today 2/27/2012
Your help is greatly appreciated.
Thanks
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
steve_fried...@nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
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Re: [R] What is the fastest way to combine all columns of a matrix to one column?
On 27/02/12 20:57, ali_protocol wrote: Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? What (on earth!) do you mean by ``combine''? *You* understand what you mean; I doubt that anyone else does. For Pete's sake, if you are going to ask a question, make it clear what the expletive deleted you are asking! A self-contained reproducible example always helps. cheers, Rolf Turner __ 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] Bootstrapping
Hi, I am doing some bootstrap. This the is the method I am procceding: I select a value of sigma and set the sharp ratio = 4. From this I can compute the mean mu. For a set sample size say n = 11, I generate 999 samples of size 11 with the sigma and mean above. This is a 11 x 999 matrix. Now, I repeat this process times. so I have a list of (11 x 999) matrices. For each of the matrices, I compute the sharp ratio for each of the 999 columns. The means of these 999 srs are taken and put in a column. These are the point estimates of the sharp ratios. I create a 0.025 and 0.975 quantile and store these in a matrix. SO I have a x 2 matrix with these confidence intrevcals. I want to do the following: (1) Compute the coverage probability (2) The coverage error (3) The length pf the interval (4)The loeft bias (5) The right bias (6) The relative bias. Any help with the code is greatly appreciated. -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Principal Components for matrices with NA
Hello,
I could find the maximal set of columns such that there exists a subset of
rows with non NA values for every column in the set - what is an
efficient
way to do that?
Try 'na.exclude' on the transpose matrix.
Example:
set.seed(1)
x - matrix(1:200, ncol=25)
f - function(x){x[sample(length(x), 1)] - NA; x}
x - t(apply(x, 1, f))
x
x.without.NA - t(na.exclude(t(x)))
Hope this helps,
Rui Barradas
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[R] Non linear regression with complex equation
Hi all, Is it possible to model a function where the unknown parameter appears both in the fitted equation AND in the determination of other parameters? E.g. y = a^2 + b/2 + k where a = 2/k and b = k^2 and the model needs to determine k? I know this is a very simple equation (its just an example), the one I am modelling is much more complicated! k appears in the equation which the n.l.r model fits, but it also affects other parameters in the equation. Please let me know if you know a way of achieving this. I realise it is possible to set up a loop where the modelled value for k is fed back in to a and b, and the model is run again - but it seems like there should be a more elegant way within one run of the model. Thanks, Jeff -- View this message in context: http://r.789695.n4.nabble.com/Non-linear-regression-with-complex-equation-tp4425942p4425942.html Sent from the R help mailing list archive at Nabble.com. __ 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] compare two data frames with same columns names but of different dimensions
m - rbind(reported, exportfile) m1 - m[duplicated(m),] m[is.na(match(m$key, m1$key)),] On Mon, Feb 27, 2012 at 9:46 AM, Arnaud Gaboury arnaud.gabo...@a2ct2.com wrote: Dear List, I want to compare and return the rows which are NOT in the two data frames. Classic methods don't work as the df have NOT the same dimensions. Here are one example of my df: reported - structure(list(Product = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 3L, 4L, 5L, 5L), .Label = c(Cocoa, Coffee C, GC, Sugar No 11, ZS), class = factor), Price = c(2331, 2356, 2440, 2450, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61L, -61L, 5L, 1L, 40L, 40L, -1L, -1L, -1L, 1L)), .Names = c(Product, Price, Nbr.Lots), row.names = c(1L, 2L, 3L, 4L, 6L, 7L, 5L, 10L, 8L, 9L), class = data.frame) exportfile - structure(list(Product = c(Cocoa, Cocoa, Cocoa, Coffee C, Coffee C, GC, Sugar No 11, ZS, ZS), Price = c(2331, 2356, 2440, 204.55, 205.45, 17792, 24.81, 1273.5, 1276.25), Nbr.Lots = c(-61, -61, 6, 40, 40, -1, -1, -1, 1)), .Names = c(Product, Price, Nbr.Lots), row.names = c(NA, 9L), class = data.frame) As you can see, they have same column names. My idea was to merge these two df when passing as argument not to take into account duplicate rows, so I will get one df with rows which are not in both df. Is it possible? How to do it? TY for any help. Arnaud Gaboury A2CT2 Ltd. __ 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. __ 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.
[R] export 3D array to .txt file
Hey, I have an array with the dimensions 200x6x200 and I want to save it in a textfile. I want to be able to reload the text file to get the same array again: new.array-load(mytextfile.txt) or something similar. I was not able to figure out a way to do that with write.table without having to save 200 text files. Is there another way? Thank you! Frauke -- View this message in context: http://r.789695.n4.nabble.com/export-3D-array-to-txt-file-tp4426005p4426005.html Sent from the R help mailing list archive at Nabble.com. __ 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] memory management
It appears that the intermediate data in functions is never GCed even after the return from the function call. R's RSS is 4 Gb (after a gc()) and sum(unlist(lapply(lapply(ls(),get),object.size))) [1] 1009496520 (less than 1 GB) how do I figure out where the 3GB of uncollected garbage is hiding? -- Sam Steingold (http://sds.podval.org/) on Ubuntu 11.10 (oneiric) X 11.0.11004000 http://www.childpsy.net/ http://camera.org http://truepeace.org http://www.PetitionOnline.com/tap12009/ http://thereligionofpeace.com Modern man is the missing link between apes and human beings. __ 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.
[R] asking for a script
Dear who may concern, I am sending you this email to ask if I could have someone help me to write this script I am interested in. I am requesting the script for performing variance-stabilizing normalizations on the R language. Could you please help me on that? If I am asking a wrong person, could you please tell me the right email address I should contact? Appreciated! Thanks! Regards Ruijuan Luo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Note: no visible binding for global variable 'Dimnames'
I get this (twice): Note: no visible binding for global variable 'Dimnames' Note: no visible binding for global variable 'Dimnames' on the __first__ invocation of a function which does this: sm - sparseMatrix(i = ..., j = ..., x = ...) for (i in 1:length(mynames)) usr[[mynames[i]]] - sm[,i] the Notes are printed when the usr-sm assignment is evaluated for i==1. (but not for any subsequent i's of subsequent calls to the function). I seem to be getting the right results, so I have been ignoring these messages, but I was wondering if I was doing something wrong. (needless to say that I do not have the word Dimnames anywhere in my code) -- Sam Steingold (http://sds.podval.org/) on Ubuntu 11.10 (oneiric) X 11.0.11004000 http://www.childpsy.net/ http://dhimmi.com http://americancensorship.org http://iris.org.il http://www.memritv.org http://jihadwatch.org Stupidity, like virtue, is its own reward. __ 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] export 3D array to .txt file
You can save it directly as an R object with save() and load with load() -- that's probably easiest. It should be portable between R platforms and sesions, but won't be easily accessible to other programs. Michael On Mon, Feb 27, 2012 at 3:45 PM, frauke fh...@andrew.cmu.edu wrote: Hey, I have an array with the dimensions 200x6x200 and I want to save it in a textfile. I want to be able to reload the text file to get the same array again: new.array-load(mytextfile.txt) or something similar. I was not able to figure out a way to do that with write.table without having to save 200 text files. Is there another way? Thank you! Frauke -- View this message in context: http://r.789695.n4.nabble.com/export-3D-array-to-txt-file-tp4426005p4426005.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] export 3D array to .txt file
why a text file? are you going to pass it to another program? 'load'/'save' has already been suggested. if you really want text, try 'dump'. Sent from my iPad On Feb 27, 2012, at 15:45, frauke fh...@andrew.cmu.edu wrote: Hey, I have an array with the dimensions 200x6x200 and I want to save it in a textfile. I want to be able to reload the text file to get the same array again: new.array-load(mytextfile.txt) or something similar. I was not able to figure out a way to do that with write.table without having to save 200 text files. Is there another way? Thank you! Frauke -- View this message in context: http://r.789695.n4.nabble.com/export-3D-array-to-txt-file-tp4426005p4426005.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] What is the fastest way to combine all columns of a matrix to one column?
Mod Rolf's question, the answer probably is: do nothing -- it already **is** a single column. If you read the section on arrays and matrices in An Intro to R *carefully* (this is part of every standard R distro) you will be enlightened. Have you read it? If not, why not? If mat is your matrix, c(mat) may also be enlightening. -- Bert On Mon, Feb 27, 2012 at 1:42 PM, Rolf Turner rolf.tur...@xtra.co.nz wrote: On 27/02/12 20:57, ali_protocol wrote: Dear all, Newbie: What is the fastest way to combine all columns of a matrix to one column? What (on earth!) do you mean by ``combine''? *You* understand what you mean; I doubt that anyone else does. For Pete's sake, if you are going to ask a question, make it clear what the expletive deleted you are asking! A self-contained reproducible example always helps. cheers, Rolf Turner __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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.
[R] from data.frame to Venn diagram
Hello All,
I have a data.frame with this structure:
m - matrix(sample(c(rep('yes', 10, replace = TRUE), rep('no', 10,
replace = TRUE), NA), 500, replace = TRUE), nrow = 100, ncol = 5)
colnames(m) - colnames(m, do.NULL = FALSE, prefix = col)
m - as.data.frame(m)
I need to generate a Venn diagram from this data.frame, displaying the
various intersections of 'yes' for the different columns. Ideally, the
circle for each column should be proportional to the number of non-NA
entries.
The package VennDiagram (described here:
http://www.biomedcentral.com/1471-2105/12/35) can do all this.
However, I have not been able to figure out how to transform the
data.frame into the required list format.
Any suggestions on how to do this?
Many thanks,
Lara
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] from data.frame to Venn diagram
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Lara Poplarski
Sent: Monday, February 27, 2012 5:24 PM
To: r-help@r-project.org
Subject: [R] from data.frame to Venn diagram
Hello All,
I have a data.frame with this structure:
m - matrix(sample(c(rep('yes', 10, replace = TRUE), rep('no', 10,
replace = TRUE), NA), 500, replace = TRUE), nrow = 100, ncol = 5)
colnames(m) - colnames(m, do.NULL = FALSE, prefix = col)
m - as.data.frame(m)
I need to generate a Venn diagram from this data.frame, displaying the
various intersections of 'yes' for the different columns. Ideally, the
circle for each column should be proportional to the number of non-NA
entries.
The package VennDiagram (described here:
http://www.biomedcentral.com/1471-2105/12/35) can do all this.
However, I have not been able to figure out how to transform the
data.frame into the required list format.
Any suggestions on how to do this?
Many thanks,
Lara
Lara,
I assume you wish to look at which people answered yes on col1 and which
answered yes for col2 and the overlap. So, something like this might help get
you started
C1 - which(m$col1 == 'yes')
C2 - which(m$col2 == 'yes')
venn.diagram(list(C1=C1, C2=C2), c:/tmp/Venn_2set_simple.tiff)
If that is not what you want, then you will need to provide an example of what
you want your output to be.
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
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Re: [R] Non linear regression with complex equation
Your question is (completely) ill-posed. What is your actual model? What you have said makes no sense at all as it stands. (Minimal self-contained example .) cheers, Rolf Turner On 28/02/12 09:25, jeff_hawkes wrote: Hi all, Is it possible to model a function where the unknown parameter appears both in the fitted equation AND in the determination of other parameters? E.g. y = a^2 + b/2 + k where a = 2/k and b = k^2 and the model needs to determine k? I know this is a very simple equation (its just an example), the one I am modelling is much more complicated! k appears in the equation which the n.l.r model fits, but it also affects other parameters in the equation. Please let me know if you know a way of achieving this. I realise it is possible to set up a loop where the modelled value for k is fed back in to a and b, and the model is run again - but it seems like there should be a more elegant way within one run of the model. __ 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.
[R] Packages/functions for competing risk analysis
Hi Rs, I am analyzing a time to event dataset with several competing risks. 0 = Active by end of study 1 = Stopped treatment to start another treatment 2 = Lost 3 = Dead My event of interest in Lost to Followup but starting a different treatment and dying are competing risks. All 1,2,3 events are events of exiting the study, but it's only 2-LTFU that we are concerned with (I know I am repeating myself, sorry). I can't seem to find a package or function that can handle 2 competing risks for the main event. I realize I may be using the well-known ones, timereg and cmprisk, wrong. And if I am, then I'd appreciate a correction. Here's the model I tried (and it crashes) comp.risk(Surv(futime, retention==2) ~ sex, data=dta, dta$retention, causeS=c(1,3), resample.iid=1, n.sim=100) I apologize, but I am cannot create the example dataset using code. I am not able. The data, though is one to one. ID retention sex futime 1 0 1 524.3 etc. Thank you, in advance, if you can help me. Best, Jen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] General question about GLMM and heterogeneity of variance
GibsonR rachel.gibson at bristol.ac.uk writes: My data have heterogeneity of variance (in a categorical variable), do I need to specify a variance structure accounting for this in my model or do GLMMs by their nature account for such heterogeneity (as a result of using deviances rather than variances)? And if I do need to do this, how do I do it (e.g. using something like the VarIdent function in nlme) and in what package? We need a little more information. Also, it might be better to send follow-ups to r-sig-mixed-models at r-project.org . Is your a categorical variable a predictor (independent) or response (dependent) variable? If it's a predictor, then the details of its distribution are not important for the validity of the analysis. It it's a response, then you need to be doing a multinomial or ordinal response model. GLMs and GLMMs do account for some forms of heterogeneity in variance. You probably need to tell us more about what you tried to do and how you concluded that heteroscedasticity was a problem. __ 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] Principal Components for matrices with NA
Hello again, Q: is there a way to do princomp or another method where every row has at least one missing column? See also package 'psych', function 'principal'. You can impute mean or median to NAs. Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/Principal-Components-for-matrices-with-NA-tp4425930p4426284.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] row names of a heatmap on left hand side
Hello R Gurus, I have a matrix for which I am doing a heatmap using heatmap.2. I want to put the rownames on the lefthand side instead of the right side of the heatmap. how can i put the rownames on left hand side: I have already tried axis but could not make it work ccc-structure(c(1, 0.283300333755851, 0.237863231117007, 0.0148696794159253, -0.0780756406815149, -0.106161465097659, -0.0756387578559718, -0.0331407390639047, -0.0707492640028071, -0.0613323523367336, 0.160614869977481, 0.163220169151304, -0.00799405273310068, 0.0702415660531524, -0.00269044770795431, 0.022118567043969, 0.0620175783757948, 0.071884246401891, -0.0469804302975448, 0.0261500962333625, 0.126816435101853, 0.135887180731395, 0.0110308674727327, 0.0805731314652419, -0.147245436227401, NA, 1, 0.756696630102848, -0.0253573545151531, -0.0436449174849985, -0.0681193805838121, -0.125651668003682, -0.132100479190945, -0.0672954083207475, -0.230426861035276, -0.000418410746782722, 0.0769862111911649, -0.0335582429785183, -0.0842411971843023, -0.122530783393992, -0.0649446178327085, -0.077787483725924, -0.0351869234224504, -0.083404295266297, -0.0381865040141299, 0.106839122670871, 0.110275858855431, 0.0863464084194804, 0.153158957903198, -0.0240563780789799, NA, NA, 1, -0.0581824191662743, -0.0577752089674947, -0.0732098989298006, -0.128791472234673, -0.0988078828924034, -0.0679818896618525, -0.17312177564727, 0.012457362675565, 0.0592327855817399, -0.0666240794205135, -0.0715883024096398, -0.0922611542475004, -0.0690818250876944, -0.0580129934906561, -0.0172677939384777, -0.107766765710368, 0.00520294080324943, 0.0784863927912482, 0.102062918116874, 0.0571392089924128, 0.122231446563675, -0.037588761722365, NA, NA, NA, 1, 0.525472699159769, 0.514041356697963, 0.561064373161352, 0.431210983834436, 0.452619063041757, 0.147444937649346, 0.0499871095691751, 0.101711708044079, 0.313069848945963, 0.173478908711319, 0.234099595958429, 0.442444172603688, 0.271047417517104, 0.271574694324702, 0.335146377247985, 0.261796658619168, 0.20615917507402, 0.179710108054483, 0.00693091170071528, 0.0572351824096096, 0.0421931015525606, NA, NA, NA, NA, 1, 0.500262732680092, 0.575331145231366, 0.535966575237105, 0.588011751256699, 0.209316134244339, 0.178306362315634, 0.144372963193607, 0.449164822440907, 0.311585643277039, 0.373916415586687, 0.42342063290168, 0.257074092743689, 0.235277302551095, 0.349938957503695, 0.330125591891904, 0.343804820698451, 0.273320029845419, -0.00571265033987237, 0.0226529101519386, 0.0133821821423264, NA, NA, NA, NA, NA, 1, 0.783943436792447, 0.738881212745611, 0.74753358245511, 0.154011088987657, -0.0345413593712036, 0.0774290165561568, 0.270530619110383, 0.197653878154696, 0.175622464937608, 0.494122861400667, 0.205654982662595, 0.262435922111394, 0.336248481780927, 0.2457208720417, 0.225645535832965, 0.166011304030232, -0.000628760762335414, -0.0498164098632905, 0.0504668500594617, NA, NA, NA, NA, NA, NA, 1, 0.694267683304991, 0.665025879567406, 0.202215608856743, 0.0242420445336668, 0.115486719828318, 0.327074561287353, 0.232316609009873, 0.252557073368415, 0.528071198751934, 0.271456859045674, 0.308461563380474, 0.430695444971444, 0.343610015300747, 0.270906939265836, 0.233818502929012, 0.0267752322720164, 0.0263022347486687, 0.0451312848263739, NA, NA, NA, NA, NA, NA, NA, 1, 0.776593952305343, 0.264441281328401, 0.18148880771864, 0.123206249983537, 0.298515458147549, 0.325676094897333, 0.269563532182944, 0.500437079037779, 0.315922872681825, 0.320594404612037, 0.342087722381524, 0.234383707828859, 0.333287400951434, 0.218902122287433, 0.0369772789625516, 0.0129942406701288, 0.0489108090105715, NA, NA, NA, NA, NA, NA, NA, NA, 1, 0.162583487686877, 0.195970937901678, 0.120763943840432, 0.436732203917893, 0.466737746485222, 0.37904462705, 0.512555709916608, 0.242432982203289, 0.253876944460396, 0.309350372966892, 0.251258196675636, 0.230011894342281, 0.127848664881258, -0.0115057022105185, -0.00311190058097034, 0.0549673967736474, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 0.245845410111639, 0.244681678373053, 0.345224517493842, 0.231228340394969, 0.375331818652881, 0.279222931694161, 0.449497588453708, 0.381759655904665, 0.125594966938876, 0.123732822791146, 0.242643089641339, 0.213713940442987, -0.0464978734739873, -0.0530884098109049, 0.00741507616587697, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 0.257637258425107, 0.266404784079116, 0.418770493609101, 0.380954319800656, 0.225911833064407, 0.239940125963318, 0.166185116079108, 0.0545692769866459, 0.104587370234936, 0.157906865871569, 0.153607122076791, -0.0654111656429167, -0.00340208731802426, -0.0629540855938132, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1, 0.302626240633324, 0.314160256475753, 0.36659577440935, 0.283381437378777, 0.356824428698387, 0.458399544248849, 0.0513918399545163, 0.175229426288891, 0.219315198173476, 0.379344376229316, 0.0380837761734483, 0.052844098764557,
[R] kmeans: how to retrieve clusters
Hello, I'd like to classify data with kmeans algorithm. In my case, I should get 2 clusters in output. Here is my data colCandInd colCandMed 1 822950.5 2 83 1831.5 3 1192 2899.0 4 1193 2103.5 The first cluster is the two first lines the 2nd cluster is the two last lines Here is the code: x = colCandList$colCandInd y = colCandList$colCandMed m = matrix(c(x, y), nrow = length(colCandList$colCandInd), ncol=2) kres = kmeans(m, 2) Is there a way to retrieve both clusters in output of the algorithm in order to process in each cluster ? (I am looking for smthing like kres$clustList ... where I can process each cluster) kres$cluster did not yield what I expected ... thanks for your help -- View this message in context: http://r.789695.n4.nabble.com/kmeans-how-to-retrieve-clusters-tp4426427p4426427.html Sent from the R help mailing list archive at Nabble.com. __ 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] memory management
This appears to be the sort of query that (with apologies to other R gurus) only Brian Ripley or Luke Tierney could figure out. R generally passes by value into function calls (but not *always*), so often multiple copies of objects are made during the course of calls. I would speculate that this is what might be going on below -- maybe even that's what you meant. Just a guess on my part, of course, so treat accordingly. -- Bert On Mon, Feb 27, 2012 at 1:03 PM, Sam Steingold s...@gnu.org wrote: It appears that the intermediate data in functions is never GCed even after the return from the function call. R's RSS is 4 Gb (after a gc()) and sum(unlist(lapply(lapply(ls(),get),object.size))) [1] 1009496520 (less than 1 GB) how do I figure out where the 3GB of uncollected garbage is hiding? -- Sam Steingold (http://sds.podval.org/) on Ubuntu 11.10 (oneiric) X 11.0.11004000 http://www.childpsy.net/ http://camera.org http://truepeace.org http://www.PetitionOnline.com/tap12009/ http://thereligionofpeace.com Modern man is the missing link between apes and human beings. __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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] Bayesian Hidden Markov Models
Dear Oscar,
Â
I really appreciate your help for my problem. I have taken a look at the R
package RJaCGH you mentioned roughly, but I am really a little confused by the
CGH microarrays background of the package. Actually, I am a graduate student,
majoring Mathematical Statistics. So, I know nothing about the CGH microarrays.
Â
Have you ever used the RJaCGH package before? If so, could you please briefly
tell me how to use RJaCGH to implement a Bayesian Hidden Markov Models for my
univariate time series?
Â
Thanks again for your patience and time.
Â
Best Regards,
Â
James Allan
Â
--- 12å¹´2æ27æ¥ï¼å¨ä¸, Oscar Rueda [via R]
ml-node+s789695n4424152...@n4.nabble.com åéï¼
å件人: Oscar Rueda [via R] ml-node+s789695n4424152...@n4.nabble.com
主é¢: Re: Bayesian Hidden Markov Models
æ¶ä»¶äºº: monkeylan lanjin...@yahoo.com.cn
æ¥æ: 2012å¹´2æ27æ¥,å¨ä¸,ä¸å6:05
Dear James,
Although designed for the analysis of copy number CGH microarrays, RJaCGH
uses a Bayesian HMM model.
Cheers,
Oscar
On 27/2/12 08:32, monkeylan [hidden email] wrote:
Dear R buddies,
Recently, I attempt to model the US/RMB Exchange rate log-return time series
with a *Hidden Markov model (first order Markov Chain mixed Normal
distributions). *
I have applied the RHmm package to accomplish this task, but the results are
not so satisfying.
So, I would like to try a *Bayesian method *for the parameter estimation of
the Hidden Markov model.
Could anyone kindly tell me which R package can perform Bayesian estimation
of the model?
Many thanks for your help and time.
Best Regards,
James Allan
--
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and provide commented, minimal, self-contained, reproducible code.
Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
Cancer Research UK Cambridge Research Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
NOTICE AND DISCLAIMER
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[R] R for Mac - editor's pick on Download Typhoon
Dear R Development Core Team R for Mac has been reviewed by Download Typhoon and got Editor's Pick award: http://www.downloadtyphoon.com/r-for-mac/infoyvnppyhf Please publish Download Typhoon Editor's Pick award on your website by adding the following HTML code: 160 x 80: a href=http://www.downloadtyphoon.com/; target=_blankimg src=http://www.downloadtyphoon.com/templates/downty/images/award_pick.gif; alt=Download Typhoon - Editor's Pick border=0//a 120 x 60: a href=http://www.downloadtyphoon.com/; target=_blankimg src=http://www.downloadtyphoon.com/templates/downty/images/award_120x60_pick.gif; alt=Download Typhoon - Editor's Pick border=0//a Text link: a href=http://www.downloadtyphoon.com/; target=_blankEditor's Pick on Download Typhoon/a Here are more images and options how link to us: http://www.downloadtyphoon.com/linktous.html We're looking forward for further co-operation. Best regards, Download Typhoon http://www.downloadtyphoon.com/ __ 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] compare two data frames of different dimensions and only keep unique rows
Hello,
I've made Petr's solution a bit more general
Petr Savicky wrote
On Mon, Feb 27, 2012 at 07:10:57PM +0100, Arnaud Gaboury wrote:
No, but I tried your way too.
In fact, the only three unique rows are these ones:
Product Price Nbr.Lots
Cocoa 24405
Cocoa 24501
Cocoa 24406
Here is a dirty working trick I found :
df-merge(exportfile,reported,all.y=T)
df1-merge(exportfile,reported)
dff1-do.call(paste,df)
dff-do.call(paste,df)
dff1-do.call(paste,df1)
df[!dff %in% dff1,]
Product Price Nbr.Lots
3 Cocoa 24405
4 Cocoa 24501
My two problems are : I do think it is not so a clean code, then I won't
know by advance which of my two df will have the greates dimension (I can
add some lines to deal with it, but again, seems very heavy).
Hi.
Try the following.
setdiffDF - function(A, B)
{
A[!duplicated(rbind(B, A))[nrow(B) + 1:nrow(A)], ]
}
df1 - setdiffDF(reported, exportfile)
df2 - setdiffDF(exportfile, reported)
rbind(df1, df2)
I obtained
Product Price Nbr.Lots
3Cocoa 24405
4Cocoa 24501
31 Cocoa 24406
Is this correct? I see the row
Cocoa 2440.006
only in exportfile and not in reported.
The trick with paste() is not a bad idea. A variant of
it is used also in the base function duplicated.matrix(),
since it contains
apply(x, MARGIN, function(x) paste(x, collapse = \r))
If speed is critical, then possibly the paste() trick
written for the whole columns, for example
paste(df[[1]], df[[2]], df[[3]], sep=\r)
and then setdiff() can be better.
Hope this helps.
Petr Savicky.
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It produces the symmetric difference for vectors, matrices, data.frames and
(so-so tested) lists.
#-
# First the set difference
`%-%` - function(x, y) UseMethod(%-%)
`%-%.default` - function(x, y){
f - function(A, B)
!duplicated(c(B, A))[length(B) + 1:length(A)]
ix - f(x, y)
x[ix]
}
`%-%.matrix` - `%-%.data.frame` - function(x, y){
f - function(A, B)
!duplicated(rbind(B, A))[nrow(B) + 1:nrow(A)]
ix - f(x, y)
x[ix, ]
}
`%-%.list` - function(x, y){
f - function(A, B)
if(class(A) == class(B)) A %-% B
lapply(y, function(Y) lapply(x, f, Y))
}
# Then the set symmetric difference
symdiff - function(x, y) UseMethod(symdiff)
symdiff.default - function(x, y)
c(x %-% y, y %-% x)
symdiff.matrix - symdiff.data.frame - function(x, y){
xclass - class(x)
res - rbind(x %-% y, y %-% x)
class(res) - xclass
res
}
symdiff.list - function(x, y){
f - function(A, B)
if(class(A) == class(B)) symdiff(A, B)
lapply(y, function(Y) lapply(x, f, Y))
}
# Test it with data.frames first (the OP data)
reported %-% exportfile
exportfile %-% reported
symdiff(reported, exportfile)
symdiff(exportfile, reported)
#-
# And some other data types
x - 1:5
y - 3:8
x %-% y
y %-% x
symdiff(x, y)
symdiff(y, x)
X - list(a=x, rp=reported)
Y - list(b=y, ef=exportfile)
X %-% Y
Y %-% X
symdiff(X, Y)
symdiff(Y, X)
P.S. This question seems to pop-up repeatedly
Rui Barradas
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Re: [R] Bayesian Hidden Markov Models
Dear Doctor Oscar,
Â
Sorry for not noticing that you are the author of the RJaCGH package.
But I noticed that hidden Markov model in your package is with non-homogeneous
transition probabilities. Here in my work, the HMM is just a first-order
homogeneous Markov chain, i.e. the transition matrix is constant.
Â
So, Could you please tell me how can I adjust the R functions in your package
to implement my analysis?
Â
Best Regards,
Â
James Allan
--- 12å¹´2æ27æ¥ï¼å¨ä¸, Oscar Rueda [via R]
ml-node+s789695n4424152...@n4.nabble.com åéï¼
å件人: Oscar Rueda [via R] ml-node+s789695n4424152...@n4.nabble.com
主é¢: Re: Bayesian Hidden Markov Models
æ¶ä»¶äºº: monkeylan lanjin...@yahoo.com.cn
æ¥æ: 2012å¹´2æ27æ¥,å¨ä¸,ä¸å6:05
Dear James,
Although designed for the analysis of copy number CGH microarrays, RJaCGH
uses a Bayesian HMM model.
Cheers,
Oscar
On 27/2/12 08:32, monkeylan [hidden email] wrote:
Dear R buddies,
Recently, I attempt to model the US/RMB Exchange rate log-return time series
with a *Hidden Markov model (first order Markov Chain mixed Normal
distributions). *
I have applied the RHmm package to accomplish this task, but the results are
not so satisfying.
So, I would like to try a *Bayesian method *for the parameter estimation of
the Hidden Markov model.
Could anyone kindly tell me which R package can perform Bayesian estimation
of the model?
Many thanks for your help and time.
Best Regards,
James Allan
--
View this message in context:
http://r.789695.n4.nabble.com/Bayesian-Hidden-Markov-Models-tp4423946p4423946.
html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
Cancer Research UK Cambridge Research Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for ...{{dropped:16}}
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[R] aggregating specific parts in zoo index column to perform sliding average
Here's my code: http://pastebin.com/0yRxEVtm The important parts are uncommented and should be easy to find using the link above. For the following line of code, I plan on looking for a way to offset it up 7 rows so that the 15 minute timestamp would be considered the median of the subset being averaged to find the mean: avgCool = aggregate(intCool, trunc(time(intCool), times(00:15:00)), mean) Currently the issue is that, with the truncate function, it truncates but really rounds down the time series values to the 15 minute time stamp earlier in the series. For example, let's say we have one minute intervals 0:00, 0:01, 0:02,,0:37. It takes 0:00 - 0:14 and replaces that with 0:00. Then it sees 0:15, and changes values from 0:15 - 0:29 to 0:15. In effect, aggregating the values and creating subsets. What I want to do here is change 0:00 - 0:07 to 0:00, change 0:08 - 0:22 to 0:15, and change 0:23 - 0:37 to 0:30 in which 0:15 and 0:30 are the medians of each subset. Anyway, I hope that makes sense. Any ideas on which function will make this an easy job? Much thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/aggregating-specific-parts-in-zoo-index-column-to-perform-sliding-average-tp4426798p4426798.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] having this error below.
hi. can anybody help me to resolve this problem i am facing? Warning in odbcDriverConnect(con, tabQuote = c([, ]), ...) : [RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified Warning in odbcDriverConnect(con, tabQuote = c([, ]), ...) : ODBC connection failed Error in sqlTables(channel) : first argument is not an open RODBC channel -- View this message in context: http://r.789695.n4.nabble.com/having-this-error-below-tp4427054p4427054.html Sent from the R help mailing list archive at Nabble.com. __ 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] from data.frame to Venn diagram
Hello,
Lara Poplarski wrote
Hello All,
I have a data.frame with this structure:
m - matrix(sample(c(rep('yes', 10, replace = TRUE), rep('no', 10,
replace = TRUE), NA), 500, replace = TRUE), nrow = 100, ncol = 5)
colnames(m) - colnames(m, do.NULL = FALSE, prefix = col)
m - as.data.frame(m)
I need to generate a Venn diagram from this data.frame, displaying the
various intersections of 'yes' for the different columns. Ideally, the
circle for each column should be proportional to the number of non-NA
entries.
The package VennDiagram (described here:
http://www.biomedcentral.com/1471-2105/12/35) can do all this.
However, I have not been able to figure out how to transform the
data.frame into the required list format.
Any suggestions on how to do this?
Many thanks,
Lara
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Try this:
# First make a list of where there are 'yes' values in 'm'
mvenn - lapply(m, function(x) which(x == yes))
mvenn
venn.diagram(
x = mvenn[-5], # exclude a list element (the 5th)
filename = vd_without_5th.tiff,
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0
)
# Doesn't work or I'm missing something
venn.diagram(
x = mm,
filename=vd_all.tiff,
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0
)
Error: Incorrect number of elements.
It seems to have a limit...
Hope this helps,
Rui Barradas
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Re: [R] having this error below.
Quite possibly, after you read the posting guide and provide a complete example of code that is causing the problem. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. wilson_peter88 weele...@hotmail.com wrote: hi. can anybody help me to resolve this problem i am facing? Warning in odbcDriverConnect(con, tabQuote = c([, ]), ...) : [RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified Warning in odbcDriverConnect(con, tabQuote = c([, ]), ...) : ODBC connection failed Error in sqlTables(channel) : first argument is not an open RODBC channel -- View this message in context: http://r.789695.n4.nabble.com/having-this-error-below-tp4427054p4427054.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] R for Mac - editor's pick on Download Typhoon
Thanks for taking the time to really kick the tires on R for mac and providing a great service to the community. The screen shots[1] you chose to use in order to really highlight R for mac as well as ensuring that you are reviewing the latest and greatest[2] really says volumes about the wonderfully thorough job you folks are doing over there at downloadtyphoon. Keep up the good work! Also, nice ads! -steve [1] I see some X windows manager all the way down [2] The version you are using is ~ 1 year old On Mon, Feb 27, 2012 at 4:35 PM, Download Typhoon awa...@downloadtyphoon.com wrote: Dear R Development Core Team R for Mac has been reviewed by Download Typhoon and got Editor's Pick award: http://www.downloadtyphoon.com/r-for-mac/infoyvnppyhf Please publish Download Typhoon Editor's Pick award on your website by adding the following HTML code: 160 x 80: a href=http://www.downloadtyphoon.com/; target=_blankimg src=http://www.downloadtyphoon.com/templates/downty/images/award_pick.gif; alt=Download Typhoon - Editor's Pick border=0//a 120 x 60: a href=http://www.downloadtyphoon.com/; target=_blankimg src=http://www.downloadtyphoon.com/templates/downty/images/award_120x60_pick.gif; alt=Download Typhoon - Editor's Pick border=0//a Text link: a href=http://www.downloadtyphoon.com/; target=_blankEditor's Pick on Download Typhoon/a Here are more images and options how link to us: http://www.downloadtyphoon.com/linktous.html We're looking forward for further co-operation. Best regards, Download Typhoon http://www.downloadtyphoon.com/ __ 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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] To define a function which includes two functions as arguments such as plot and text
Hi Mr. Uwe Ligges,
I really thankful for the reply. I even tried the same,
means writing the new function. But the result is same as the last. Here is
the picture below,
Telco.Rpart.PLOT.TEXT.Functn -
function(Telco.Rpart.METHOD.CLASS)
{
Telco.Rpart.PLOT -
plot(Telco.Rpart.METHOD.CLASS,compress=FALSE,uniform=TRUE)
Telco.Rpart.TEXT -
text(Telco.Rpart.METHOD.CLASS,use.n = TRUE, cex = .75)
}
Telco.Rpart.PLOT.TEXT -
Telco.Rpart.PLOT.TEXT.Functn(Telco.Rpart.METHOD.CLASS)
Telco.Rpart.PLOT.TEXT
Again if I solely run the command Telco.Rpart.PLOT.TEXT, the output it is
displaying as NULL. Please help me finding out the desired result ASAP.
Regards,
Yashwanth M.R
From: Uwe Ligges-3 [via R] [mailto:ml-node+s789695n4417618...@n4.nabble.com]
Sent: Friday, February 24, 2012 9:16 PM
To: Yashwanth M.R
Subject: Re: To define a function which includes two functions as arguments
such as plot and text
On 24.02.2012 12:22, Yashwanth M.R wrote:
Here is the two functions which I have used during my practice.
*plot(Telco.rpart.METHOD.CLASS,compress=FALSE,uniform=TRUE)
text(Telco.rpart.METHOD.CLASS,use.n = TRUE, cex = .75))*
Telco.rpart.METHOD.CLASS is my rpart object of the method class.
If I run this,
*Telco.Rpart.PLOT.TEXT-
c(plot(Telco.rpart.METHOD.CLASS,compress=FALSE,uniform=TRUE),
text(Telco.rpart.METHOD.CLASS,use.n = TRUE, cex =
.75))
c() concatenates the returned values of the two functions. If you want
to define a sequence of function calls, define them within your own
function, calling that new function will produce your desired results,
as far as I understand.
Uwe Ligges
http://r.789695.n4.nabble.com/file/n4416881/Rpart.gif
the output is getting generated as shown in the figure. But if I solely
run
the same command Telco.Rpart.PLOT.TEXT right after the above, the output
is as below,
/$x
[1] 4.035156 1.00 7.070312 3.015625 2.00 4.031250
[7] 3.00 5.062500 4.00 6.125000 5.00 7.25
[13] 6.50 6.00 7.00 8.00 11.125000 10.25
[19] 9.50 9.00 10.00 11.00 12.00
$y
[1] 1.125 1.000 1.000 0.875 0.750 0.750 0.625 0.625 0.500 0.500 0.375
[12] 0.375 0.250 0.125 0.125 0.250 0.875 0.750 0.625 0.500 0.500 0.625
[23] 0.750
/
Please help me in getting the output which is there is the Image..
Regards,
Yashwanth M,R
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Re: [R] kmeans: how to retrieve clusters
On Mon, Feb 27, 2012 at 3:18 PM, ikuzar raz...@hotmail.fr wrote: Hello, I'd like to classify data with kmeans algorithm. In my case, I should get 2 clusters in output. Here is my data colCandInd colCandMed 1 82 2950.5 2 83 1831.5 3 1192 2899.0 4 1193 2103.5 The first cluster is the two first lines the 2nd cluster is the two last lines Here is the code: x = colCandList$colCandInd y = colCandList$colCandMed m = matrix(c(x, y), nrow = length(colCandList$colCandInd), ncol=2) kres = kmeans(m, 2) Is there a way to retrieve both clusters in output of the algorithm in order to process in each cluster ? (I am looking for smthing like kres$clustList ... where I can process each cluster) kres$cluster did not yield what I expected ... Not sure what you mean by process each cluster and why kres$cluster is not what you expected. kres$cluster will tell you which cluster each point (row of your matrix) belongs to. The result depends on how you initialize the kmeans since the inter-point distances are quite similar to one another. For example, I get set.seed(10) kres = kmeans(m, 2) kres$cluster [1] 2 2 1 1 set.seed(1) kres = kmeans(m, 2) kres$cluster [1] 1 1 2 2 set.seed(200) kres = kmeans(m, 2) kres$cluster [1] 2 2 1 1 kres = kmeans(m, 2) kres$cluster [1] 1 2 1 2 So 3 times out of 4 I get the result you expect, and once a different one. If you need the result in a different format, that should be no problem. __ 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.
[R] e1071 : class.weights
Dear R-society,
I know this is probably a question to LibSVM, but I have not found a
LibSVM mailing list, so I would be really grateful if someone from this
list helped me.
In the LibSVM documentation I have found a passage about dealing with
unbalanced sets, that says that in this case one sets two different
regularization parameters C^{-} and C^{+}. However I am not sure about how
this corresponds to the parameters in the svm function. There I find C and
class.weights. So am I right supposing that
C^{-} = class.weights[1]*C and C^{+} = class.weights[2]*C ?
--
Sincerely yours,
Yulia Matveyeva,
Department of Statistical Modelling,
Faculty of Mathematics and Mechanics,
St Petersburg State University, Russia
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