Re: [R] Generating Patient Data

Hi David, I was thinking something like this: ID Disease 1 A 2 B 3 A 1C 2D 5A 4B 3D 2A .... How can this be done? On Wed, Jun 25, 2014 at 11:34 AM, David Winsemius wrote: > > On Jun 24, 2014, at 10:14 PM, Abhinaba Roy wrote: > > > Dear R helpers, > >

Re: [R] Generating Patient Data

On Jun 24, 2014, at 10:14 PM, Abhinaba Roy wrote: > Dear R helpers, > > I want to generate data for say 1000 patients (i.e., 1000 unique IDs) > having suffered from various diseases in the past (say diseases > A,B,C,D,E,F). The only condition imposed is that each patient should've > suffered fro

[R] Assigning document id to each document containing in the Document Term Matrix (R Package "tm")

Dear All, When I do "DocumentTermMatrix" analysis, can I assign a document id to the document (i.e., the row in the attached matrix marked in red)? Here is my code: tdm=DocumentTermMatrix(corpus,control) inspect (tdm2[5:20,9:14]) Terms Docs 002089 002223 002236 002268 002415 002439 5

Re: [R] converting a list with named member to a vector maintaining original names

To get the vector setNames(stack(test)[,1],stack(test)[,2]) #ABCC2 ABCC5 ABCC5 #37280 12268 13308 #or setNames(unlist(test),stack(test)[,2]) #ABCC2 ABCC5 ABCC5 #37280 12268 13308 A.K. On , arun wrote: You could do: stack(test)[,2:1] #    ind values #1 ABCC2  37280 #2 ABCC5  12268 #3 AB

[R] Generating Patient Data

Dear R helpers, I want to generate data for say 1000 patients (i.e., 1000 unique IDs) having suffered from various diseases in the past (say diseases A,B,C,D,E,F). The only condition imposed is that each patient should've suffered from *atleast* two diseases. So my data frame will have two columns

Re: [R] rfImpute

Ideas: Read the Posting Guide (http://www.R-project.org/posting-guide.html) for this mailing list (one of the gems in there warns you to not post using HTML email) Provide a reproducible example (e.g. per [1]) that includes the library/require statements that load your packages Consider subscr

Re: [R] saving a 'get' object in R

The main reason to avoid assign/get is that there are better ways. You can use a list or environment more directly without using assign/get. Also the main reason to use assign/get is to work with global variables which are frowned on in general programming (and prone to hard to find bugs). Consid

Re: [R] saving a 'get' object in R

Have you read "An Introduction to R" (ships with R) or other online R tutorial (there are many good ones). Looks to me like you haven't these are pretty basic R basics. But maybe I misinterpret... Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not inf

Re: [R] saving a 'get' object in R

Thanks to all for the replies. I tried all three and they work great. I was misinterpreting the list = parameter in save(...) and I get your point about overwriting existing objects. I've heard about not using assign/get before. Can anyone point me to why and what alternatives there are? Reg

Re: [R] Sample all possible contingency tables both margin fixed

Hi, Thank you all! Best regards, Tahira On Tue, Jun 24, 2014 at 9:07 PM, David L Carlson wrote: > Michael is correct. I answered too quickly. This will correct the original > suggestion: > > > M <- c(15, 5, 15, 5) # New example where M[2] and M[4] are smaller > > M[1]+M[2] == M[3]+M[4] > [1]

Re: [R] saving a 'get' object in R

I recommend to use saveRDS()/readRDS() instead. More convenient and avoids the risk that load() has of overwriting existing variables with the same name. /Henrik On Tue, Jun 24, 2014 at 1:45 PM, Greg Snow <538...@gmail.com> wrote: > I think that you are looking for the `list` argument in `save`.

[R] Biplot interpretation

Dear all; I did biplot in R. How can I interpret them in order that i can create two or more groups in each biplot. I wanna determine the variables that have the same origin. please help me. many thanks. -- Best Regards Javad Bayat M.Sc. Environment Engineering Shahid Beheshti (National)

[R] force dialog window to front?

Howdy - I'm wondering if there is a way to force an R dialog window to "the front" in a Windows OS.  In particular, I defined a .Last function in my Rprofile.site file that consists only of the updateR() function so as to check for R updates on close.  However, the dialog window for this pops u

Re: [R] saving a 'get' object in R

I think that you are looking for the `list` argument in `save`. save( list=foo, file=paste0(foo, '.Rdata') ) In general it is best to avoid using the assign function (and get when possible). Usually there are better alternatives. On Tue, Jun 24, 2014 at 2:35 PM, David Stevens wrote: > R commun

Re: [R] saving a 'get' object in R

You can use the following command: tmp <- get(foo) save(tmp,file=paste(foo,'.rData',sep='')) Best, Mike 2014-06-24 15:35 GMT-05:00 David Stevens : > R community, > > Apologies if this has been answered. The concept I'm looking for is to > save() an object retrieved using get() for an object >

[R] saving a 'get' object in R

R community, Apologies if this has been answered. The concept I'm looking for is to save() an object retrieved using get() for an object that resulted from using assign. Something like save(get(foo),file=paste(foo,'rData',sep='')) where assign(foo,obj) creates an object named foo with the con

Re: [R] converting a list with named member to a vector maintaining original names

You're amazing. Thanks so much! That's exactly what I am looking for. > From: istaz...@gmail.com > Date: Tue, 24 Jun 2014 14:32:27 -0400 > Subject: Re: [R] converting a list with named member to a vector maintaining > original names > To: bac...@hotmail.co

[R] Fortune nomination; was Re: (no subject)

On Jun 24, 2014, at 7:52 AM, Jeff Newmiller wrote: Jeff Newmiller's rhelp/ggplot strategy checklist: > Reproducibility == good (except for mixing in invalid code and failing to set > RNG seed) > HTML email == bad > Missing subject == bad > Using matrices with ggplot == pushing a rope > Using fo

Re: [R] Sample all possible contingency tables both margin fixed

Michael is correct. I answered too quickly. This will correct the original suggestion: > M <- c(15, 5, 15, 5) # New example where M[2] and M[4] are smaller > M[1]+M[2] == M[3]+M[4] [1] TRUE > upper <- min(M[c(1,3)]) > lower <- 0 > if (min(M) < upper) lower <- upper - min(M) > all.2x2s <- t(sapply

Re: [R] Sample all possible contingency tables both margin fixed

David gave a great solution. I think it is better to start from 0 to min(M) instead of from min(M[c(1,3)]) to avoid negative values in the table. If the minimum is in M[1] or M[3], a = 1:min(M). Otherwise, d=1:min(M). Best, Gang 2014-06-24 13:18 GMT-05:00 David L Carlson : > Since a 2x2 table w

Re: [R] converting a list with named member to a vector maintaining original names

How about x <- unlist(test) (names(x) <- rep(names(test), times = sapply(test, length))) ? See also unlist2 from http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html Best, Ista On Tue, Jun 24, 2014 at 12:56 PM, C Lin wrote: > Dear R users, > > I have a list that I'd like

Re: [R] Query

Have you installed it, perhaps with install.packages("ltm") ??? If you have, and it installed correctly, then we'll need the information on your system requested in the posting guide linked at the end of this message. Sarah On Tue, Jun 24, 2014 at 1:49 PM, Anchal wrote: > Dear Sir, > > I wis

Re: [R] Sample all possible contingency tables both margin fixed

Since a 2x2 table with fixed row and column margins has only one degree of freedom, it is pretty easy to enumerate them: AB A acM[3] B bdM[4] M[1] M[2] N Create a vector of the margins: M <- c(a+b, c+d, a+c, b+d) The number of possible tables is min(M[c(1, 3)])+1

[R] Query

Dear Sir, I wish to use the ltm package but it gives the following error Error in library("ltm") : there is no package called ‘ltm’ How to resolve this issue in R Looking forward to your reply. Thanks & Regards anchal [[alternative HTML version deleted]] _

[R] converting a list with named member to a vector maintaining original names

Dear R users, I have a list that I'd like to convert to a vector while preserving the original names. For example: test <- list(ABCC2=37280,ABCC5=c(12268,13308)); If I do unlist, it automatically renamed the ABCC5 to ABCC51 and ABCC52 > unlist(test)  ABCC2 ABCC51 ABCC52   37280  12268  13308 

Re: [R] non-interactive error in .First function

(a) Sorry, that was my first post.  I'll be sure to plain text from here on. (b) Hmm.  "It is not intended that there be interaction with the user during startup code.  Attempting to do so can crash the R process, especially so prior to R 3.0.2."  I had been using this with <3.0.1. with no probl

Re: [R] Sample all possible contingency tables both margin fixed

On 24 Jun 2014, at 16:41 , Tahira Jamil wrote: > Hi, > > I am interested in generating all possible contingency table (2 by 2) with > fixed row margins and column margins. Can anyone help me. > It's pretty easy, just find one compatible solution and add or subtract 1 -1 -1 1 until one o

Re: [R] Sample all possible contingency tables both margin fixed

On Tue, Jun 24, 2014 at 10:41 AM, Tahira Jamil wrote: > Hi, > > I am interested in generating all possible contingency table (2 by 2) with > fixed row margins and column margins. Can anyone help me. > If the reason you want this is to sample them then r2dtable can do that directly.

[R] ASA Conf. on Stats Practice - deadline THURSDAY

R users, Abstracts are now being accepted for the 2015 ASA Conference on Statistical Practice, February 19-21, New Orleans, Louisiana, USA. Each presentation will have a 45-minute time slot. If you are interested, you may submit your abstract on the website, http://www.amstat.org/meetings/c

[R] Sample all possible contingency tables both margin fixed

Hi, I am interested in generating all possible contingency table (2 by 2) with fixed row margins and column margins. Can anyone help me. Best regards, Tahira [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://s

Re: [R] rfImpute

I am having the same problem trainImp <- rfImpute(train[,!colnames(train)=="score"],train$score) yields Error in randomForest.default(xf, y, ntree = ntree, ..., do.trace = ntree, : NA not permitted in predictors any ideas? -- View this message in context: http://r.789695.n4.nabble.com/r

[R] Need help to understand ecdf (empirical cumulative distribution function)

Hi, I m a new user of R. I need to plot distribution of some computed centrality metrics of my network. I used ecdf to compute the cumulative distribution of degrees and then plotted the resultat. However, i got a different distribution from the one computed using the degree.distribution function

Re: [R] Dead link in the help page of as.Date()

Fortunately we have the wayback machine: https://web.archive.org/web/20120425004417/http://www.mathworks.com/help/techdoc/matlab_prog/bspgcx2-1.html Best, Ista On Tue, Jun 24, 2014 at 8:53 AM, Prof Brian Ripley wrote: > On 23/06/2014 20:41, Christofer Bogaso wrote: >> >> Hi, >> >> I was reading

Re: [R] c() with POSIXlt objects and their timezone is lost

This is a rope. Don't push it. Been there, been swatted. The current structure of R cannot support vectors of POSIXt timestamps that have different tzones in different elements. You can keep a parallel vector of tzones separately and manage environment variable TZ as needed if you really must

Re: [R] non-interactive error in .First function

Suggestions: a) Don't post in HTML format... your code appears corrupt. b) Don't do this. Read the Note in ?.First On Tue, 24 Jun 2014, Brian Chalfant wrote: Hi all - Long-time user, first-time poster. I added a .First function to my Rprofile.site file to check for updates, clean the console

Re: [R] (no subject)

Reproducibility == good (except for mixing in invalid code and failing to set RNG seed) HTML email == bad Missing subject == bad Using matrices with ggplot == pushing a rope Using for loops to build a ggplot == missing the point Using wide-form data with ggplot == pushing a rope Study the follow

Re: [R] (no subject)

the loop is 1 thru 9 but the manual is just 1, 2, 3, 4? change the loop from 1:dim(mydata)[2] to 1:4 and it works :) On Tue, Jun 24, 2014 at 9:43 AM, Zayd Farah wrote: > I hope the following script is reproducible enough to highlight my issue, > which is to automatically (in this case by loop

[R] (no subject)

I hope the following script is reproducible enough to highlight my issue, which is to automatically (in this case by loop, but it does not necessarily have to be by a loop) add geom_line layers for each column of mydata to the ggplot variable p1. for some reason doing this only works by manually ad

[R] Retaining the original document id in #topicmodels in R

Hi all, I am currently using package "topicmodels" to find the topics of a given text. The dataset contains 8523 documents. I would like to see which documents belong to which topic. Here is my code: get the documentTermMatrix# tdm=DocumentTermMatrix(corpus,control)

[R] non-interactive error in .First function

Hi all - Long-time user, first-time poster. I added a .First function to my Rprofile.site file to check for updates, clean the console, and put some fun quotes on startup.  This used to work without error.  I hadn't used R (which I usually play with in RStudio) in a few weeks, but when I start

[R] Retaining the original document id in #topicmodels in R

Hi all, I am currently using package "topicmodels" to find the topics of a given text. The dataset contains 8523 documents. I would like to see which documents belong to which topic. Here is my code: get the documentTermMatrix# tdm=DocumentTermMatrix(corpus,control)

Re: [R] Making several plots using a loop function

Well you can use the main argument of the plot function together with a call to sprintf(). Like this: main = sprintf("Plot %s", i) Best regards Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: li li Dato:24/06/2014 15.19 (GMT+01:00) Til: r-help Emne: [R] Making sev

Re: [R] help plsr function

Ok, yes, I can match them now. Thank you very much! On Tue, Jun 24, 2014 at 3:58 AM, Bjørn-Helge Mevik wrote: > annie Zhang writes: > > > ## the predicted scores from the model > > (pred <- predict(data.cpls,n.comp=1:2,newdata=x.new,type="score")) > > ## the predicted scores using x%*%projec

Re: [R] Making several plots using a loop function

What about title(paste("plot", i)) ? Sarah On Tue, Jun 24, 2014 at 9:17 AM, li li wrote: > Hi all, >When making a bunch of plots using a loop function, how to add title to > reflect different plots. > Specifically, for the code below, I generated 9 plots. I would like to add > a title to

Re: [R] Making several plots using a loop function

Hi, try something like main=paste("plot",i) in the plot command. HTH, kd Feladó: r-help-boun...@r-project.org [r-help-boun...@r-project.org] ; meghatalmazó: li li [hannah@gmail.com] Küldve: 2014. június 24. 15:17 To: r-help Tárgy: [R] Making severa

[R] Making several plots using a loop function

Hi all, When making a bunch of plots using a loop function, how to add title to reflect different plots. Specifically, for the code below, I generated 9 plots. I would like to add a title to each plot. For example, the titles will be respectively, plot1, plot 2, … plot 9. Thank you very much!

[R] Problem with "nlm" function to minimize the negative log likelihood

This is almost always "user error" in setting up the problem, but without a reproducible example, you won't get any real help on this list. JN On 14-06-24 06:00 AM, r-help-requ...@r-project.org wrote: > Message: 11 > Date: Mon, 23 Jun 2014 09:14:23 -0700 > From: Ferra Xu > To: "r-sig-...@r-proje

Re: [R] Dead link in the help page of as.Date()

On 23/06/2014 20:41, Christofer Bogaso wrote: Hi, I was reading the help page for as.Date() function for some reason, and noticed a Matlab link: http://www.mathworks.com/help/techdoc/matlab_prog/bspgcx2-1.html It looks like this link is dead. So may be it would be better to put a correct link

[R] matrix built by diagonal matrices with a given structure

Dear R-users, I have a matrix with a series of "not-overlapping in a row dimension" vectors in a given structure. Something like: |a1, 0, 0, 0| | 0, a2, a3, 0| |a4, 0, 0, a5| where "ai" are column-vectors of the equal length, m. My aim is to construct a new matrix formed by diagona

Re: [R] Custom sampling method in R XXXX

Hi Daniel, Great! Many thanks! Dan On Mon, Jun 23, 2014 at 8:23 PM, Daniel Nordlund wrote: > Something like this could work > > > x <- 0.250 > new_sample <- function(xx) { > j<-c(0.000,0.125,0.250,0.375,0.500,0.625,0.750,0.875,1.000) > probs<-c(0.02307692,0.20769231,0.53846154,0.20769231,0

Re: [R] Help partimat()

On 23.06.2014 19:28, daniel_st...@operamail.com wrote: I am a bit late for this discussion but hope that I might still get an answer. I tried to follow your advice and had a look at "drawparti" but could not find the relevant section about how to plot specific pairs of variables I am trying to

Re: [R] help plsr function

annie Zhang writes: > ## the predicted scores from the model > (pred <- predict(data.cpls,n.comp=1:2,newdata=x.new,type="score")) > ## the predicted scores using x%*%projection > cbind(x.new.centered%*%data.cpls$projection[,1],x.new.centered%*%data.cpls$projection[,2]) > > Can someone please tell