[R] Major discrepancy between R and Stata for ARIMA

Hi all, I've been looking through documentation to try to understand why Stata and R occasionally come up with very different parameter estimates for ARIMA, and am stumped. Existing discussion on this question, including code, can be found here: https://stackoverflow.com/questions/22443395/major-d

Re: [R] Polychoric Principal Component Analysis (pPCA)

Peter, I am not sure if anyone answered your question about doing biplots using polychoric output and PCA. The biplot.psych example # 3 shows how to do this library(psych) > responses <- table2df(bock.table[,2:6],count=bock.table[,7], > labs= paste ("lsat6.",1:5,sep="”)) > W <-

Re: [R] Issues with fa() function in "psych"

Thanks a lot Bill and Revelle for your helpful response. It would have been great if I could know when we can expect the release of the edited version 1.4.4. Sagnik On Wed, Apr 9, 2014 at 8:05 PM, William Revelle wrote: > Sagnik raises the question as to why the psych package does not offer th

Re: [R] simulation data

On 10/04/14 09:28, thanoon younis wrote: hi i want to simulate multivariate dichotomous data matrix with categories (0,1) and n=1000 and p=10. Nobody's stopping you! :-) cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] ggplot / ggmap: fixing geom_point size to break bins

Hello, I'm been playing around trying to get some maps working in ggplot & ggmap. I have a series of maps I'm trying to make and I want to fix the bubble area size of banana catches to the specified breaks. I.e so banana catches of 2 will always be a specified size so when I make the next map, b

Re: [R] Fractional multinomial logit model or similar in R for analysis of behavior?

On Apr 9, 2014, at 10:25 AM, Brian Battaile wrote: > I'm looking for a method to analyse behavior data that can be assigned to > multiple categories > as a proportion with all the categories adding to 1 and some explanatory > variables and repeated measures on some individuals. Maybe expanding y

Re: [R] Label axis tick marks with a simple function of axis value

On Apr 9, 2014, at 6:17 PM, Hurr wrote: > What we've covered so far is of great value. > For a neater plot, > the next step will be to learn how to put > numbers with units at each tick mark. > I suppose I can form the number-unit string myself in > separate code and put the tickmark in a place t

Re: [R] Generate Crosstab in R

Hi, Suppose your data is similar to below: dat <- structure(list(Custom = c("Judi", "Judi", "Ben", "Tom", "Tom", "Bill", "Lindy", "Shary", "Judu", "Judu", "Billy", "Tommy", "Tommy", "Benjum", "Linda", "Shiry", "Shiry", "Shiry", "Judu", "Billy", "Tommy", "Lindy"), Gender = c("Female", "Female", "

[R] simulation data

hi i want to simulate multivariate dichotomous data matrix with categories (0,1) and n=1000 and p=10. thanks alot in advance [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Label axis tick marks with a simple function of axis value

What we've covered so far is of great value. For a neater plot, the next step will be to learn how to put numbers with units at each tick mark. I suppose I can form the number-unit string myself in separate code and put the tickmark in a place that I calculate in separate code. But I need to learn

Re: [R] Memory allocation using .C interface

Cassiano dos Santos gmail.com> writes: > I am testing a call to a C function from R, using .C interface. The test > consists in passing a numeric vector to the C function with no entries, > dynamically allocates n positions, makes attributions and return the > vector to R. Asking on StackOverflo

Re: [R] Memory allocation using .C interface

On Wed, Apr 9, 2014 at 11:27 AM, Cassiano dos Santos wrote: > I am testing a call to a C function from R, using .C interface. The test > consists in passing a numeric vector to the C function with no entries, > dynamically allocates n positions, makes attributions and return the vector > to R. Wh

Re: [R] How to implement a recurring "check for updates" for R and packages?

Thank you very much for the reply Henrik, you gave great pointers for me to look at. I am now curious about R.cache (although I am not sure it will help in my case, I'll need to look at it further). Also, I was debating if to use R-help or R-devel for this, since I was not sure from the descripti

Re: [R] Generate Binary Matrix

You could randomly assign 1 to a single column in each row and then use binomial draws on the remaining 0's: > set.seed(42) > dimMat <- matrix(0, 1000, 4) > dimMat[cbind(1:1000, sample.int(4, 1000, replace=TRUE))] <- 1 > dimMat[dimMat<1] <- sample(0:1, 3000, replace=TRUE, prob=c(.6, .4)) > table(r

Re: [R] Generate Binary Matrix

A bit kludgey but how about: dimMat <- matrix(0, 1000, 4) for(i in 1:1000){ while(sum(dimMat[i, ] <- sample(c(0,1), 4, replace = TRUE, prob = c(.3, .7)))==0) dimMat[i, ] <- sample(c(0,1), 4, replace = TRUE, prob = c(.3, .7)) } table(rowSums(dimMat)) Clint BowmanINTERNET:

Re: [R] getting arg names in function calls?

Thanks very much to both Bill Dunlap and Hadley Wickham. Per Bill's second suggestion, "match.call(eval(bo[[1]]), bo)" returned the desired "plot(x = 0, y = 1)" [with bo <- body(function()plot(0, 1)]. Hadley's "standardise_call(bo)" [from library(pryr)] is much simpler.

Re: [R] Generate Binary Matrix

Doran, Harold air.org> writes: > I am trying to generate a binary matrix where row in the matrix is guaranteed to have at least one 1. > Ideally, I would like most rowSums to be equal 2 or 3 with some 1s and some 4s. But, rowSums cannot be equal > to 0. > > I can tinker with the vector o

[R] Generate Binary Matrix

I am trying to generate a binary matrix where every row in the matrix is guaranteed to have at least one 1. Ideally, I would like most rowSums to be equal to 2 or 3 with some 1s and some 4s. But, rowSums cannot be equal to 0. I can tinker with the vector of probability weights, but in doing so

Re: [R] Summing up realizations

You might be thinking of bootstrap analysis. Note that measures are often correlated, so beware of just introducing randomness one measure at a time. Discussions about background theory are not really R-specific, so further chatter about this would not be on topic here, but the term "bootstrap"

[R] illumina probeID to entrezID

Hi, how do you convert the illumina ProbeID to entrezID? I've used LIMMA to identify top genes but i'm not sure how to apply illuminaHumanv4.db to get the EntrezID. Thanks in advance, .kripa [[alternative HTML version deleted]] _

[R] Memory allocation using .C interface

I am testing a call to a C function from R, using .C interface. The test consists in passing a numeric vector to the C function with no entries, dynamically allocates n positions, makes attributions and return the vector to R. I'm using Calloc from R.h. The prototype of the function is type* Call

[R] Fractional multinomial logit model or similar in R for analysis of behavior?

I'm looking for a method to analyse behavior data that can be assigned to multiple categories as a proportion with all the categories adding to 1 and some explanatory variables and repeated measures on some individuals. Data would look something like this AnimalID Behavior1 Behavior2 Behavior3 Co

Re: [R] Generate Crosstab in R

Hi, Try: datNew <- read.csv("customer_samples.csv",stringsAsFactors=FALSE) #I could reproduce similar error message with: dat[] <- lapply(dat,as.factor)  dat1 <- within(dat, Categ <- ave(Product, Custom, FUN= function(x) if(length(x)>1) "A and B" else x)) #Warning messages: 1: In `[<-.facto

Re: [R] Summing up realizations

Have you read "An Introduction to R" (or a web tutorial) to learn R? This looks straightforward, if I understand you correctly. ?sample and indexing operations might be all you need. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Informatio

[R] logistical indexing in R

Dear mates, I am bit of stuck with a coding, all I have to do is to clean and tranform the missing data "-97" of the attribute "ej" into a normal number value in a range from 0 to 22. My steps are : 1) first return the subsets, as check, they do sum to original 2) manipulate the attribute "ej

[R] Summing up realizations

Due in large part to my nonexistent statistics vocabulary, I'm not sure what the name is for the type of analysis I'm trying to do. I have, however, started to cobble something together (below) that is undoubtedly reinventing the wheel (i.e., someone has probably already written something to do th

Re: [R] Meta-analysis of prevalence at the country level with mgcv/gamm4

At 09:31 08/04/2014, Julien Riou wrote: Dear R community, Comments in line below I'm working on a meta-analysis of prevalence data. The aim is to get estimates of prevalence at the country level. The main issue is that the disease is highly correlated with age, and the sample ages of included

Re: [R] flowDensity package

On 04/09/2014 07:23 AM, Raghu wrote: I am unable to install flowDensity package from bioconductor in R version 3.0 or 3.1. did anyone have the same problems with this. Please ask questions about Bioconductor packages on the Bioconductor mailing list http://bioconductor.org/help/mailing-list

Re: [R] How to implement a recurring "check for updates" for R and packages?

[Sounds like a question for R-devel] On Wed, Apr 9, 2014 at 5:02 AM, Tal Galili wrote: > Hello all, > > > I wish to add to the > installrpackage the > ability to check for new versions of R once every X units of > time (maybe once every two weeks)

[R] glmulti wrapper for lmer does not produce results

I posted this on SO, got no response. Sorry about cross-posting, but atleast I would like to know if I am understading something totally wrong I am using a `glmulti` wrapper for glmer (binomial) and the `summary` is: `This is glmulti 1.0.7, Apr. 2013. Length Class Mode 0 NULL NULL`

[R] flowDensity package

I am unable to install flowDensity package from bioconductor in R version 3.0 or 3.1. did anyone have the same problems with this. Thanks, Raghu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posti

Re: [R] Ignore escape characters in a string...

Thanks all, I'll try some of these suggestions out but it seems like a raw string ability could come in helpful -- there aren't any packages out there that have this capability? --j On Tue, Apr 8, 2014 at 1:23 PM, Jeff Newmiller wrote: > What is wrong with > > winpath <- readLines("clipboard ")

[R] Error object .Source not found when using package tm.plugin.webmining

I don't understand this error or how to resolve it. Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object '.Source' not found Using R version 3.1.0 beta (2014-03-28 r65330) -- "Spring Dance" # output from console ## > library(quantmod) Loading required package: Defau

Re: [R] Generate Crosstab in R

Hi, Try: dat <- structure(list(Custom = c("Judi", "Judi", "Ben", "Tom", "Tom", "Bill", "Lindy", "Shary", "Judu", "Judu", "Billy", "Tommy", "Tommy", "Benjum", "Linda", "Shiry"), Gender = c("Female", "Female", "Male", "Male", "Male", "Male", "Female", "Female", "Female", "Female", "Male", "Male"

Re: [R] Issues with fa() function in "psych"

Sagnik raises the question as to why the psych package does not offer the ‘equamax’ rotation. It is because all rotations are handled through the GPArotation package which does not offer equamax. Sagnik also points out that if the requested rotation is not available, fa defaults to rotate=“none

Re: [R] Not able to convert data.frame to numeric properly

I would suggest that unlist(lapply(... should always be preferable to sapply(lapply... if you want to convert data in a data frame to a vector. I can't see any reason to run the same loop twice. But check timings -- maybe I'm overly sensitive to unimportant aesthetics. Cheers, Bert Bert Gunter Ge

[R] How to implement a recurring "check for updates" for R and packages?

Hello all, I wish to add to the installrpackage the ability to check for new versions of R once every X units of time (maybe once every two weeks). I would like to keep a time stamp somewhere, that would stay persistent across R sessions (i.e.: t

[R] Fw: Re: Splitting columns and forming new data files in R

On Wednesday, April 9, 2014 1:26 AM, arun wrote: Hi Atem, If you change colnames(mat1)[-(2:3)] <- ' ' in 'lst1New' lst1New <- lapply(lst1,function(x) {lst2 <- setNames(lapply(x,function(y) {dat <- read.table(y,sep=" ",header=TRUE, stringsAsFactors=FALSE); dat[,1:104]} ), names1); dat2 <-

Re: [R] Label axis tick marks with a simple function of axis value

On 04/09/2014 06:17 PM, Hurr wrote: Thanks Jim, Labels for the following are at 0,2,4,6,8,10,12, not data, good. and omitted where lack of room. h=c(1.2,2.4,3.1,4.7,5.3,6.2,7.6,8.8,9.7) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n',xlim=c(-1,13)) x<-c(1.6,2.6,6.6,9.6,12.9) axis_labels<-1/pretty(x) ax

Re: [R] Label axis tick marks with a simple function of axis value

Thanks Jim, Labels for the following are at 0,2,4,6,8,10,12, not data, good. and omitted where lack of room. h=c(1.2,2.4,3.1,4.7,5.3,6.2,7.6,8.8,9.7) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n',xlim=c(-1,13)) x<-c(1.6,2.6,6.6,9.6,12.9) axis_labels<-1/pretty(x) axis(1,at=pretty(x),labels=axis_labels)

Re: [R] Label axis tick marks with a simple function of axis value

On 04/09/2014 01:12 PM, Hurr wrote: This still puts tick marks at data points: h=c(1,2,3,4,5,6,7,8,9) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n') x<-c(1.6,2.6,6.6,9.6,12.9) axis_labels<-1/pretty(x) axis(1,at=pretty(x),labels=axis_labels) How do I get the axis to approx 13 ? plot(x,xaxt="n",xlim

Re: [R] Not able to convert data.frame to numeric properly

Hi, Try: min(sapply(lapply(a,as.character),as.numeric))  #[1] 2.2194 A.K. On Wednesday, April 9, 2014 2:27 AM, Sachinthaka Abeywardana wrote: a is ofcourse a subset of data.frame, a ROW of the original table specifically. > str(a) 'data.frame': 1 obs. of  4 variables: $ GHP: Factor w/ 51 le

Re: [R] Replacement Value

Hi Dila, If 'dat' is the dataset: dat$C[dat$B==0] <- 0  A.K. On Wednesday, April 9, 2014 1:30 AM, dila radi wrote: Dear arun Yes indeed..if the value in B is O..next value in the same row also 0.. other value than 0 remains unchanged. On Apr 9, 2014 12:48 PM, "arun" wrote: Dear Dila, > >What