[R] ECCB 2014

We are pleased to invite you to the 13th European Conference on Computational Biology ! ECCB 2014 will take place in Strasbourg, France, september 7 - 10. Website : http://www.eccb14.org Area topics : A. Sequencing and sequence analysis for genomics B. Gene expression C: Pathways and molecular

Re: [R] HAC standard errors

On Mon, 2 Jun 2014, Nick Pretnar wrote: Hello, I am having a great amount of difficulty running a simple linear regression model with entity and time fixed effects and HAC standard errors. I have a data set with 3 million observations and 30 variables. My data is structured as follows:

[R] Change the raster data extent

Hi, I’m trying to check if several raster data stored in temp.data have the same extent of target raster. I guarantee that all data in temp.data overlap the target and they have the same resolution and crs. The conditional test is ok, because the “OK! ” is printed. But the algorithm return:

Re: [R] Descriptive Stat

HI Farnoosh, May be this helps: set.seed(497) dat - data.frame(Unit=sample(10, 200,replace=TRUE), MD= sample(5,200,replace=TRUE), Response=sample(3, 200, replace=TRUE)) library(reshape2) res - dcast(dat, Unit+MD~Response, value.var=Response, length)  res[,-(1:2)] -

[R] plot in package psych with function error.bars.by

Hi, I have a problem with the function error.bars.by in package psych. This is the code for example of a graph: keys.list=list(Agree=c(-1,2:5),Conscientious=c(6:8,-9,-10),Extraversion=c(-11,-12,13:15),Neuroticism=c(16:20),Openness = c(21,-22,23,24,-25)) keys =

[R] tkbind (callback)

Hello, I've migrated an ADMB application with a user dialog from S to R. The script below will produce a dialog in R, and don't need data to address this issue. It works in terms of capturing user inputs to pass along, no problem running the ADMB program. However some of the options have

[R] Code for generating states and observations for HMM

Dear R buddies, Sorry for this silly question but am new to R. I am trying to generate states and observations to be use for Bayesian Hidden Markov Models analysis where i intend using mixture of Poisson and Negative binomial as emulsion. I use the code below to generate states and

Re: [R] Time Series

I know essentially nothing about plotting time series so so I just let it pass hoping someone with knowledge of time series would help What were you expecting to get? Just plotting the time series without labels etc, since I am getting some weird error messages about pch having a “unexpected

Re: [R] Time Series

It would be great to get a detailed question. As far as I understood you wanted to plot your series in a single frame. There are plenty examples in the help of plot.ts and plot.zoo for that. I prefer working with time series be using the zoo package. But most things can also be done within ts.

[R] control for repeated observations in a simple correlation design

Dear all I want to correlate 2 variables (EEG and Motorperformance) for 18 observations. However, these variables consist of only 6 subjects that were measured 3 times (leading to 18 observations). How can I calculate the correlation coefficient and p-value and control for this repeated

[R] control for repeated observations in a simple correlation design

Dear all I want to correlate 2 variables (EEG and Motorperformance) for 18 observations. However, these variables consist of only 6 subjects that were measured 3 times (leading to 18 observations). How can I calculate the correlation coefficient and p-value and control for this repeated

Re: [R] Question about setdiff()

There are two kinds of set difference: the usual set difference https://en.wikipedia.org/wiki/Set_difference#Relative_complement, also called the asymmetric difference or relative complement, and the symmetric difference https://en.wikipedia.org/wiki/Symmetric_difference. In R, setdiff(a,b) is

Re: [R] Time Series

Not sure where things are up to in the thread but this may illuminate things Using the test data.frame from an old thread I was just looking at https://stat.ethz.ch/pipermail/r-help/2007-May/133033.html ylabGrob - function(...) { # ...is lab1, lab2, etc labs - lapply(list(...), textGrob, rot =

[R] Online, automatic evaluation of class assessment R scripts

Dear R group, I will be giving a course on R in a bit of time. I am very intrigued by the way R coding assessments are done in several courses on Coursera and would like to figure out whether I am capable of setting up such a system for my course. On Coursera, R scripts are submitted online and

[R] R-memory: clearing memory within a function?

Dear R-users, I'm working on a project in which many simulations have to be performed within functions. The simulations are quite time consuming. I thought that in general an empty memory is better for speed performance than a full memory. If I call a function which performs simulations

Re: [R] Time Series

Hi Wayne, As John mentioned, it is not clear about your expectations.  May be this helps: library(xts) x2New - xts(test[,-1], order.by=test[,1]) library(xtsExtra) plot(x2New,screens=1,auto.legend=TRUE) A.K. On Tuesday, June 3, 2014 9:29 AM, John Kane jrkrid...@inbox.com wrote: I know

[R] Yield Curve Package Svensson

Hi, thank you for your rapid answer. The problem is solved. My second and last question is as follows: I use the yield curve package and I want to calculate the fitted yields via the Svensson approach. The I have already calculated the six required parameters. At first I read them in from

Re: [R] Prediction interval with GAM?

I apologize in advance for my very basic question. I would like to plot prediction intervals for my GAM model, however, instead of using a Gamma GAM, I assumed a Gaussian distribution (I standardized my response variable, which resulted in negative values). To create the prediction interval

Re: [R] tkbind (callback)

I think the problem is that the tkbind function is expecting the 3rd argument to be a function and the arguments of functions passed to tkbind need to have specific names. In your call when you do the binding the OtoFanCallback function is called at that time (hence the initial print) and its

[R] detect escape character

Dear All, I should be knowing this, but not get it right... For a string like this: Man\Woman I would like to detect the escape character \ and replace it with /. Tried various ways using gsub(), but don't get it right yet. Any suggestion would be highly welcomed... Thank you, Adrian --

Re: [R] detect escape character

Hi, R uses \ as a metacharacter, so you need a non-intuitive number of \: mystring - Man\\Woman # \\ is a metacharacter and a \, so it's equivalent to \ in normal text sub(, /, mystring) Sarah On Tue, Jun 3, 2014 at 2:03 PM, Adrian Dușa dusa.adr...@unibuc.ro wrote: Dear All, I should

Re: [R] detect escape character

Hmmmmm. mystring - Man\\Woman cat(mystring) Man\Woman mystring - Man\Woman Fejl: '\W' is an unrecognized escape in character string starting Man\W So was the OP asking about? We need some more information, thank you!. Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen

Re: [R] detect escape character

On Tue, Jun 3, 2014 at 2:29 PM, Frede Aakmann Tøgersen fr...@vestas.com wrote: Hmmmmm. mystring - Man\\Woman cat(mystring) Man\Woman mystring - Man\Woman Fejl: '\W' is an unrecognized escape in character string starting Man\W Right. As the comment in my code indicated, \ is a

Re: [R] detect escape character

With the right mental model, though, it can become intuitive. That is, keep in mind that the R interpreter uses \ as a metacharacter, and so does the regex library. You want to search for a \, which regex thinks is special, so you have to escape it for regex functions (\\). Then, because R

[R] Star schema

Are there any libraries for R that would enable the import of data stored in star schema? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Star schema

On Tue, Jun 3, 2014 at 2:31 PM, kyle polich kylepol...@gmail.com wrote: Are there any libraries for R that would enable the import of data stored in star schema? As I understand it star schema is an organizational concept, not a file format. How are the data actually stored? In a RDBMS? As csv

Re: [R] ICL for betamix()

I found a way to manually calculate the ICL for a betamix() result, using the entropy.empirical() command from the 'entropy' package. Here is the code: model=betamix(y~x) BIC(model)+entropy.empirical(posterior(model)) Cheers, Chris -- View this message in context:

Re: [R] plot in package psych with function error.bars.by

On Mon, 2 Jun 2014 11:28:19 PM Tham Tran wrote: Hi, I have a problem with the function error.bars.by in package psych. This is the code for example of a graph: keys.list=list(Agree=c(-1,2:5),Conscientious=c(6:8,-9,-10),Extraversion=c(-1 1,-12,13:15),Neuroticism=c(16:20),Openness =

[R] Multiplicative Heterogeneous DIFFusion (mhdiff) models in R

Hi, I am looking for a port of the SAS mhdiff macro ( http://www.soc.cornell.edu/faculty/strang/mhdiff/mhdiff_b.sas) to R, to estimate multiplicative heterogeneous diffusion models (see http://www.soc.cornell.edu/faculty/strang/mhdiff/mhdiff_b.pdf or http://www.jstor.org/stable/2781285) Thanks

Re: [R] Code for generating states and observations for HMM

You might find it helpful to look at the sim.hmm() function in the hmm.discnp package, or the simHMM() function in the HMM package. cheers, Rolf Turner On 03/06/14 21:17, Bukar Alhaji wrote: Dear R buddies, Sorry for this silly question but am new to R. I am trying to generate states and

[R] tab auto-fill and arrow keys are not working in R on a linux cluster

Hi List, We have R 3.1.0 installed on the head node of our linux cluster, but the tab auto-complete and the arrow keys are not working.  When I was trying to use the up/down arrow key to scroll through the old command history I got something like this.  Any ideas on what's going on here? Many

Re: [R] tab auto-fill and arrow keys are not working in R on a linux cluster

FAQ 7.20 --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#..

Re: [R] R-memory: clearing memory within a function?

Hi Frank, I don't think it is possible to state a general rule about which will be faster. For example this system.time({ for(i in 1:1) { x - matrix(rnorm(10), ncol = 10) y - mean(x) #rm(x) z - matrix(runif(10), ncol = 100) #rm(z) } }) gets a

Re: [R] detect escape character

On Jun 3, 2014, at 11:03 AM, Adrian Dușa wrote: Dear All, I should be knowing this, but not get it right... I'm a little surprised to see you ask this, too, but we each have lacunae in our R knowledge, so I hope this helps: s - scan(what=) # Assuming you were asking about items coming

Re: [R] R-memory: clearing memory within a function?

See blog post 'Speed trick: Assigning large object NULL is much faster than using rm()!': http://www.jottr.org/2013/05/speed-trick-assigning-large-object-null.html /Henrik On Tue, Jun 3, 2014 at 5:35 PM, Ista Zahn istaz...@gmail.com wrote: Hi Frank, I don't think it is possible to state a

Re: [R] Plotting issues with -par(mfrow=c(r,c))- after -boot-

On 1 June 2014 22:07, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Read ?plot.boot, in particular the Side Effects section. Not a very friendly function... you will have to modify it if you wish to proceed. I guess you were expecting me to come back at some stage to say that I'd figured out

Re: [R] Plotting issues with -par(mfrow=c(r,c))- after -boot-

No, because I have never used Boot, or tried to use plot.boot... I just know that there are three main styles of plotting in R and the manual pages are usually informative on which is in use. I am glad you figured out a better solution though, and thanks for reporting back.

[R] as.character.call?

How can I get a call object as a character string? Example: cl - quote(round(10.5)) str(cl) language round(10.5) as.character(cl) [1] round 10.5 How can I get round(10.5)? I can get this answer for this toy problem with paste0(paste(as.character(cl), collapse='('),

Re: [R] as.character.call?

cl - quote(round(10.5)) deparse(cl) [1] round(10.5) /Henrik On Tue, Jun 3, 2014 at 8:07 PM, Spencer Graves spencer.gra...@structuremonitoring.com wrote: How can I get a call object as a character string? Example: cl - quote(round(10.5)) str(cl) language round(10.5)

Re: [R] as.character.call?

Hi, Henrik: Thanks. I should probably know that by now ... but it didn't come to mind just now. Thanks again. Spencer. On 6/3/2014 8:13 PM, Henrik Bengtsson wrote: cl - quote(round(10.5)) deparse(cl) [1] round(10.5) /Henrik On Tue, Jun 3, 2014 at 8:07 PM, Spencer Graves

[R] Extraction of forecats from VAR prediction

Hi, my question is the following one: predict(VAR(y,p=1,type=none),n.ahead=500) How can I extract the forecasts of this prediction? y is a dataset of four parameters with 500 values each.One parameter for instance is lambda the head looks like this: $lambda fcst lower

Re: [R] R-memory: clearing memory within a function?

On 04/06/2014 01:35, Ista Zahn wrote: Hi Frank, I don't think it is possible to state a general rule about which will be faster. For example this system.time({ for(i in 1:1) { x - matrix(rnorm(10), ncol = 10) y - mean(x) #rm(x) z - matrix(runif(10),