Re: [R] covariance estimate in function sem (Lavaan)

2012-08-10 Thread yrosseel
On 07/30/2012 11:00 PM, Luna wrote: Dear R users, I have a hard time interpreting the covariances in the parameter estimates output (standardized), even in the example documented (PoliticalDemocracy). Can anyone tell me if the estimated covariances are residual covariances (unexplained by the mod

[R] device "mismatch", coordinates trouble with X11 and pdf devices

2012-08-10 Thread Paul Johnson
Greetings. I'm trying to understand a problem on a Dell Laptop. Details below, also uploaded the R working example that I pasted below. http://pj.freefaculty.org/scraps/testSymbols.R > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_U

Re: [R] How to add values on bar of grouped bar plot using mtext?

2012-08-10 Thread arun
Hello, I hope this helps. p1<-barplot(counts, main="Car  Distribution by Gears and VS",xlab="Number of Gears",  col=c("darkblue","red"),legend = rownames(counts), beside=TRUE, horiz=TRUE) mtext(text=counts,las=1,side=2,outer=FALSE,at=p1) A.K. - Original Message - From: Manish Gupta

Re: [R] How to add values on bar of grouped bar plot using mtext?

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 7:55 PM, Manish Gupta wrote: How to write values on bars using mtext? Grouped Bar Plot counts <- table(mtcars$vs, mtcars$gear) barplot(counts, main="Car Distribution by Gears and VS",xlab="Number of Gears", col=c("darkblue","red"),legend = rownames(counts), beside=TRUE, h

[R] stopping rule in hierarchical Clustering

2012-08-10 Thread eliza botto
Dear R users, Is there a way to apply a “stopping rule” in hierarchical Clustering? I have a data and I want to find the optimal number of clusters while doing hierarchical clustering. I would be deeply obliged if someone, whoever applied stopping rule, could send me the scripts. thanks in adva

[R] How to add values on bar of grouped bar plot using mtext?

2012-08-10 Thread Manish Gupta
How to write values on bars using mtext? Grouped Bar Plot counts <- table(mtcars$vs, mtcars$gear) barplot(counts, main="Car Distribution by Gears and VS",xlab="Number of Gears", col=c("darkblue","red"),legend = rownames(counts), beside=TRUE, horiz=TRUE) mtext(counts ) # But poistion is not at eac

[R] How to add values on bar of groouped bar plot using mtext?

2012-08-10 Thread Manish Gupta
How to write values on bars using mtext? Grouped Bar Plot counts <- table(mtcars$vs, mtcars$gear) barplot(counts, main="Car Distribution by Gears and VS",xlab="Number of Gears", col=c("darkblue","red"),legend = rownames(counts), beside=TRUE, horiz=TRUE) mtext(counts ) # But poistion is not at eac

Re: [R] Align columns in data frame write.table

2012-08-10 Thread arun
HI, Not sure how you want to align the columns. If you want to write the columns in fixed width format, you can use, write.fwf() from library(gdata). A.K. - Original Message - From: sharx To: r-help@r-project.org Cc: Sent: Friday, August 10, 2012 9:39 PM Subject: [R] Align columns i

Re: [R] vectorization condition counting

2012-08-10 Thread arun
HI, This may also help: someTags <- data.frame(tag_id = c(1, 2, 2, 3, 4, 5, 6, 6), lgth = 50*(1:8), stage=factor(rep(".",8), levels=c(".","J"))) f2<-function(x){   needsChanging<-with(someTags,is.na(match(tag_id,tag_id[duplicated(tag_id)]))&lgth<300)  x$stage[needsChanging]<-"J"  x  }  f2(some

Re: [R] using eval to handle column names in function calling scatterplot graph function

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 6:23 PM, Elaine Jones wrote: I am running R version 2.15.1 in Windows XP I am having problems with a function I'm trying to create to: 1. subset a data.frame based on function arguments (colname & parmname) 2. rename the PARMVALUE column in the data.frame based on

Re: [R] Align columns in data frame write.table

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 6:39 PM, sharx wrote: Does anyone know of a way to specify the alignment of individual columns in a data frame so that after using write.table the columns are aligned in the file? Do you mean by padding with spaces? set numzer.pad to the desired width and then perhap

Re: [R] Align columns in data frame write.table

2012-08-10 Thread Joshua Wiley
I do not know of any option in write.table() that would allow a variable spacer, such as padding with spaces to make columns centered or right aligned. Everything is just separated somehow. You could look at ?format or ?sprintf which have padding/alignment options. Once you had properly padded ch

[R] Align columns in data frame write.table

2012-08-10 Thread sharx
Does anyone know of a way to specify the alignment of individual columns in a data frame so that after using write.table the columns are aligned in the file? -- View this message in context: http://r.789695.n4.nabble.com/Align-columns-in-data-frame-write-table-tp4640007.html Sent from the R hel

Re: [R] How do I find the apparent magnitude of a galaxy from a FITS file?

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 4:06 PM, andrej wrote: I put "sos::findFn('fits')" into the search engine and it returned 0 results, so how are you finding this? 'sos' is an R package. I'm guessing you did not install and load 'sos' before typing that command at the console. (You might be able to ge

[R] using eval to handle column names in function calling scatterplot graph function

2012-08-10 Thread Elaine Jones
I am running R version 2.15.1 in Windows XP I am having problems with a function I'm trying to create to: 1. subset a data.frame based on function arguments (colname & parmname) 2. rename the PARMVALUE column in the data.frame based on function argument (xvar) 3. generate charts p

Re: [R] summarize a vector

2012-08-10 Thread arun
HI, Same result, with data.frame: dat1<-data.frame(V1=v[1:3],V2=v[4:6],V3=v[7:9],V4=c(v[10],rep(0,2))) sapply(dat1,cumsum)[3,] V1 V2 V3 V4  6 15 24 10  sapply(dat1,sum) V1 V2 V3 V4  6 15 24 10 A.K. - Original Message - From: David Winsemius To: Michael Weylandt Cc: "r-help@r-proj

Re: [R] How do I find the apparent magnitude of a galaxy from a FITS file?

2012-08-10 Thread andrej
I put "sos::findFn('fits')" into the search engine and it returned 0 results, so how are you finding this? Also: Why was my mailing list message rejected as a duplicate? I don't even understand how these underground subscriptions work, am I off the mailing list because it's a duplicate? -- View

Re: [R] Parsing large XML documents in R - how to optimize the speed?

2012-08-10 Thread Martin Morgan
On 08/10/2012 03:46 PM, Frederic Fournier wrote: Hello everyone, I would like to parse very large xml files from MS/MS experiments and create R objects from their content. (By very large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) I'm not 100% sure of i

Re: [R] vectorization condition counting

2012-08-10 Thread William Dunlap
Your sum(tag_id==tag_id[i])==1, meaning tag_id[i] is the only entry with its value, may be vectorized by the sneaky idiom !(duplicated(tag_id,fromLast=FALSE) | duplicated(tag_id,fromLast=TRUE) Hence f0() (with your code in a loop) and f1() are equivalent: f0 <- function (tags) { for (i in s

Re: [R] Function definition: where is the error in the "for" loop?

2012-08-10 Thread Rui Barradas
Hello, Generally those error messages refer to something that preceeds them. This is the current case: the parser is expecting a function's argument. The function name is 'For' with uppercase 'F'. The first argument is 'i', then there should be a comma before a second argument. The solution

Re: [R] Analyzing Poor Performance Using naiveBayes()

2012-08-10 Thread Kirk Fleming
As some additional information, I re-ran the model across the range of n = 50 to 150 (n being the 'top n' parameters returned by chi.squared), and this time used a completed different subset of the data for both training and test. Nearly identical results, with the typical train AUC about 0.98 and

[R] Function definition: where is the error in the "for" loop?

2012-08-10 Thread Dr. Holger van Lishaut
Dear all, The following function code fails with errors (see below): RegPlots <- function (data, ContrVar, RespVar){ intNmbrRows<-length(RespVar);intNmbrCols<-lenght(ContrVar) par(mfrow=c(intNmbrRows,intNmbrCols)) For(i in 1:intNmbrRows){ For (j in 1:intNmbrCols){

Re: [R] summarize a vector

2012-08-10 Thread Bert Gunter
Certainly ... but this is of course limited to the few C coded functions available. Back to apply-type stuff for, say, median as a summary statistic. -- Bert On Fri, Aug 10, 2012 at 3:58 PM, David Winsemius wrote: > > On Aug 10, 2012, at 3:42 PM, Michael Weylandt wrote: > >> I wouldn't be surpri

[R] Kfn for 1D data?

2012-08-10 Thread redrascal
Is it possible to adapt the 'spatial' function Kfn to analyze the correlation between two 1D point processes? It's not obvious to me from the documentation; maybe a pointer to an example would help me get started. Thanks in advance. Red __ R-help@r

[R] vectorization condition counting

2012-08-10 Thread Guillaume2883
Hi all, I am working on a really big dataset and I would like to vectorize a condition in a if loop to improve speed. the original loop with the condition is currently writen as follow: if(sum(as.integer(tags$tag_id==tags$tag_id[i]))==1&tags$lgth[i]<300){ tags$stage[i]<-"J" }

Re: [R] summarize a vector

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 3:42 PM, Michael Weylandt wrote: I wouldn't be surprised if one couldn't get an *apply-free solution by using diff(), cumsum() and selective indexing as well. What about colSums on a matrix extended with the right number of zeros. > colSums(matrix (c(v, rep(0, 3- length(

Re: [R] How do I find the apparent magnitude of a galaxy from a FITS file?

2012-08-10 Thread Rui Barradas
Hello, A search using sos::findFn('fits') returned package FITSio as number three. It would enable you to read FITS files. As for the question, how do you do what you want to do, I don't know. Hope this helps, Rui Barradas Em 10-08-2012 15:50, andrej escreveu: Greetings! I am still new to R

[R] Parsing large XML documents in R - how to optimize the speed?

2012-08-10 Thread Frederic Fournier
Hello everyone, I would like to parse very large xml files from MS/MS experiments and create R objects from their content. (By very large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) My first attempt at parsing the 40M file, using the XML package, took more

Re: [R] summarize a vector

2012-08-10 Thread Michael Weylandt
I wouldn't be surprised if one couldn't get an *apply-free solution by using diff(), cumsum() and selective indexing as well. Cheers, Michael On Aug 10, 2012, at 5:07 PM, David Winsemius wrote: > > On Aug 10, 2012, at 12:57 PM, Bert Gunter wrote: > >> ... or perhaps even simpler: >> >>> sz

Re: [R] summarize a vector

2012-08-10 Thread Bert Gunter
Oh yes, I stand corrected. I didn't look at your code carefully enough. -- Bert On Fri, Aug 10, 2012 at 3:07 PM, David Winsemius wrote: > > On Aug 10, 2012, at 12:57 PM, Bert Gunter wrote: > >> ... or perhaps even simpler: >> >>> sz <- function(x,k)tapply(x,(seq_along(x)-1)%/%k, sum) >>> sz(1:10

Re: [R] export table in separate file

2012-08-10 Thread Duncan Mackay
Hi Here is some code I used to produce an html table file within my Sweave chunk . I needed to produce html tables to go into word as well as producing a pdf file.create(fhtml) # file name # open to append ff <- file(fhtml, "a+") # Table fchars <- c('\n', '\n',

Re: [R] summarize a vector

2012-08-10 Thread Bert Gunter
Oh yes, I stand corrected. I didn't look at your code carefully enough. -- Bert On Fri, Aug 10, 2012 at 3:07 PM, David Winsemius wrote: > > On Aug 10, 2012, at 12:57 PM, Bert Gunter wrote: > >> ... or perhaps even simpler: >> >>> sz <- function(x,k)tapply(x,(seq_along(x)-1)%/%k, sum) >>> sz(1:10

Re: [R] summarize a vector

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 12:57 PM, Bert Gunter wrote: ... or perhaps even simpler: sz <- function(x,k)tapply(x,(seq_along(x)-1)%/%k, sum) sz(1:10,3) 0 1 2 3 6 15 24 10 Note that this works for k>n, where the previous solution does not. sz(1:10,15) 0 55 I agree that it is more elegant, but

Re: [R] Batch Mode for Windows

2012-08-10 Thread Duncan Mackay
Hi Here is a script I have used sometime ago to do a job i cannot remember what Windows OS it was. the first line is the general form # R CMD BATCH [options] infile [outfile] c:\rw\bin\R CMD BATCH --no-restore --no-save D:/Feh/R/FEH_Index_in.R D:/Feh/R/FEH_Batch.txt the FEH_Batch.txt is

Re: [R] question about windows Rgui.exe startup

2012-08-10 Thread Bert Gunter
Read ?Startup _carefully_ (it's pretty dense!). Does the .First file on the search path give you the functionality you seek? -- Bert On Fri, Aug 10, 2012 at 12:34 PM, Ryan Rene wrote: > > Hi all, > > I had a specific question about the loading of objects > into R. I apologize in advance if I ha

Re: [R] summarize a vector

2012-08-10 Thread Sam Steingold
Thanks David & Bert. It turned out that what I actually wanted was much simpler. my vector's elements are 0&1 and the right way to "summarize" it is hist(which(v==1)) however, your replies were quire educational! Thanks again, Sam. > * Bert Gunter [2012-08-10 12:57:40 -0700]: > >> sz <- function(

[R] Batch Mode for Windows

2012-08-10 Thread sharx
Hi, I have researched batch mode for windows and could not find anything that worked. I know the code should be $ R CMD BATCH inputfile.R outputfile.Rout or R outputfile.Rout I tried these without success. I need detailed, step by step instructions on how to do this. I have tried typing C:\R\bi

Re: [R] debug vs regular mode

2012-08-10 Thread Zhang, Peng
If you read my bug report, I just ran the same thing on both regular mode and debug mode. That is why I think it is related with R base, though there might be some other bugs related with glmulti or rJava. Peng On 08/10/2012 04:03 PM, peter dalgaard wrote: > On Aug 10, 2012, at 21:23 , Zhang, P

[R] question about windows Rgui.exe startup

2012-08-10 Thread Ryan Rene
Hi all, I had a specific question about the loading of objects into R. I apologize in advance if I have overlooked anything in the manual but as far as I can tell I have yet to find a solution to my problem. I am on a Windows platform. So what I am trying to do is have R read in a binary fi

Re: [R] debug vs regular mode

2012-08-10 Thread Zhang, Peng
Ok. I will stop here. I have just created a bug report. https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15013 If anyone is interested, please see if you can reproduce it. Thanks, Peng On 08/10/2012 03:04 PM, peter dalgaard wrote: > Not to spoil your fun, but this is getting a bit off-topic

[R] Interper output from cajorls and VECM

2012-08-10 Thread Rmillan
Hi all R users, I'm finding it a bit hard to interpret the output from the cajorls and VECM function. I'm trying to model a VECM model with cointegration rank of 6, and therefore I get the varibles ECT1, ECT2... ECT6 in my output. Are these representing the estimates for my loading matrix or also

Re: [R] Analyzing Poor Performance Using naiveBayes()

2012-08-10 Thread Kirk Fleming
Per your suggestion I ran chi.squared() against my training data and to my delight, found just 50 parameters that were non-zero influencers. I built the model through several iterations and found n = 12 to be the optimum for the training data. However, results still no so good for the test data. H

Re: [R] Lavaan: Immediate non-positive definite matrix

2012-08-10 Thread Joshua Wiley
Dear Andrew, Maximum likelihood estimation with missing data typically makes some rather strong assumptions. If I am not mistaken, the default covariance coverage in Mplus is .05, the fact that you need to set it lower suggests you have some combinations of variables with less than 5% jointly pre

Re: [R] debug vs regular mode

2012-08-10 Thread peter dalgaard
On Aug 10, 2012, at 21:23 , Zhang, Peng wrote: > Ok. I will stop here. I have just created a bug report. > > https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15013 ...which is exactly what you should NOT do, if the bug is likely to live in a contributed package!! -pd > > If anyone is i

Re: [R] summarize a vector

2012-08-10 Thread Bert Gunter
... or perhaps even simpler: > sz <- function(x,k)tapply(x,(seq_along(x)-1)%/%k, sum) > sz(1:10,3) 0 1 2 3 6 15 24 10 Note that this works for k>n, where the previous solution does not. > sz(1:10,15) 0 55 -- Bert On Fri, Aug 10, 2012 at 12:37 PM, David Winsemius wrote: > > On Aug 10, 201

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread Fred G
Thanks Bill! Works great! Thanks again guys! On Fri, Aug 10, 2012 at 2:43 PM, William Dunlap wrote: > If you think about this as a runs problem you can get a loopless solution > that I think is easier to read (once the requisite functions are defined). > > First define the function to canonicali

Re: [R] Alternating between "for loops"

2012-08-10 Thread Claudia Penaloza
This is what my code looks like now. However, there is one thing I can't/don't know how to fix. I can't get it to be "once dead always dead", i.e., in any given row, after a "D" or a "d" there should be only zeros. I've tried applying a flag to break the loop if dead but I can't get it to work. Cou

Re: [R] summarize a vector

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 12:20 PM, Sam Steingold wrote: I have a long numeric vector v (length N) and I want create a shorter vector of length N/k consisting of sums of k-subsequences of v: v <- c(1,2,3,4,5,6,7,8,9,10) N=10, k=3 ===> [6,15,24,10] I can, of course, iterate: w <- vector(mode="num

[R] summarize a vector

2012-08-10 Thread Sam Steingold
I have a long numeric vector v (length N) and I want create a shorter vector of length N/k consisting of sums of k-subsequences of v: v <- c(1,2,3,4,5,6,7,8,9,10) N=10, k=3 ===> [6,15,24,10] I can, of course, iterate: > w <- vector(mode="numeric",length=ceiling(N/k)) > for (i in 1:length(w)) w

[R] Lavaan: Immediate non-positive definite matrix

2012-08-10 Thread Andrew Miles
Hi, I recently tried to estimate a linear unconditional latent growth curve on 7 repeated measures using lavaan (most recent version): modspec=' alpha =~ 1*read_g0 + 1*read_g1 + 1*read_g2 + 1*read_g3 + 1*read_g4 + 1*read_g5 + 1*read_g6 beta =~ 0*read_g0 + 1*read_g1 + 2*read_g2 + 3*read_g3 + 4*r

Re: [R] debug vs regular mode

2012-08-10 Thread peter dalgaard
Not to spoil your fun, but this is getting a bit off-topic for R-help. If you wish to continue the debugging process in public, I think you should move to R-devel. Also, it sounds like the problem is in the glmulti package, so you might want to involve its maintainer at some point. -pd On A

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread William Dunlap
If you think about this as a runs problem you can get a loopless solution that I think is easier to read (once the requisite functions are defined). First define the function to canonicalize the name nickname <- function(x) sub(" .*", "", x) then define some handy runs functions isFirstInRun

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread Fred G
Thanks so much, and thanks for the clarification. "New York" ---> "New" should not match "Other New" because "New" is not the first. Thanks so much, testing it on my data now. On Fri, Aug 10, 2012 at 2:35 PM, Rui Barradas wrote: > Hello, > > My code doesn't predict a point you've made clear in

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread Rui Barradas
Hello, My code doesn't predict a point you've made clear in this post. Inline. Em 10-08-2012 19:05, Fred G escreveu: Thanks Arun. The only issue is that I need the code to be very generalizable, such that the grep() really has to be if the first string up to the whitespace in a row (ie "New", "B

Re: [R] debug vs regular mode

2012-08-10 Thread Zhang, Peng
Thanks! It is interesting that Windows has pointed the problem to Java. So it is probable that how I did my debug led me to the wrong direction. Since I was unsure how to debug S4 class, I copied the source implement R function from glmulti package into my testing program. The segmentation faul

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread arun
Hi, Try this: dat1<-read.table(text=" ID,    NAME,    YEAR,    SOURCE 1,    New York Mets,    1900,    ESPN 2,    New York Yankees,    1920,    Cooperstown 3,    Boston Redsox,    1918,    ESPN 4,    Washington Nationals,    2010,    ESPN 5,    Detroit Tigers,    1990,    ESPN ",sep=",",header=T

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread Rui Barradas
Hello, Try the following. d <- read.table(textConnection(" ID NAME YEAR SOURCE 1 'New York Mets' 1900 ESPN 2 'New York Yankees' 1920 Cooperstown 3 'Boston Redsox' 1918 ESPN 4 'Washington Nationals' 2010

Re: [R] help error histograma

2012-08-10 Thread John Kane
Oh, okay. I just missed it completely since your data didn't have any missing data so I could not visualise why it was there. I assume -999.9 was in older data. John Kane Kingston ON Canada > -Original Message- > From: aprendizprog...@hotmail.com > Sent: Fri, 10 Aug 2012 20:51:48 +0

[R] samr package: missing values in RNAseq data

2012-08-10 Thread Vickie S
Hi All, As mentioned in the manual of SAMseq function of samr package,  missing values in the data are allowed in the input data matrix. "x-- Feature matrix: p (number of features) by n (number of samples), one observation per column (missing values allowed)" When I try a matrix with missing

Re: [R] Regular Expressions + Matrices

2012-08-10 Thread Fred G
Thanks Arun. The only issue is that I need the code to be very generalizable, such that the grep() really has to be if the first string up to the whitespace in a row (ie "New", "Boston", "Washington", "Detroit below) is the same as the first string up to the whitespace in the row directly below it,

[R] Direct Method Age-Adjustment to Complex Survey Data

2012-08-10 Thread Anthony Damico
Hi everyone, my apologies in advance if I'm overlooking something simple in this question. I am trying to use R's survey package to make a direct method age-adjustment to some complex survey data. I have played with postStratify, calibrate, rake, and simply multiplying the base weights by the cor

Re: [R] help error histograma

2012-08-10 Thread aprendiz programa
Hi, The problem solved! thank you very much !!! Kane, the command > is.na(dados) <- dados == -999.9,substituting missing values ​​(-999.9) for NA > From: dcarl...@tamu.edu > To: jrkrid...@inbox.com; aprendizprog...@hotmail.com; r-help@r-project.org > Subject: RE: [R] help error histo

[R] Regular Expressions + Matrices

2012-08-10 Thread Fred G
Hi all, My code looks like the following: inname = read.csv("ID_error_checker.csv", as.is=TRUE) outname = read.csv("output.csv", as.is=TRUE) #My algorithm is the following: #for line in inname #if first string up to whitespace in row in inname$name = first string up to whitespace in row + 1 in in

[R] plotting profile likelihood curves

2012-08-10 Thread adw adwadw
Hello, I am trying to figure out how to plot the profile likelihood curve of a GLM parameter with 95% pCI's on the same plot. The example I have been trying with is below. The plots I am getting are not the likelihood curves that I was expecting. The y-axis of the plots is tau and I would like

Re: [R] subsetting levels of a vector

2012-08-10 Thread arun
Hi, Try this: dat <- read.table(text=" ParticipID    ERP  Electrode 1    s1  0.0370  FP1 2    s2 35.0654  FP2 3    s3 -3.3852    F4 4    s4  2.6119    P3 5    s5  0.1224    P4 6    s6 -5.3153    O1 7    s7 -3.88  F4 8    s8  -4.988   

Re: [R] basehaz() in package 'Survival' and warnings() with coxph

2012-08-10 Thread hazbro
Okay the data sets dat1 and dat 2 are the same dat1 just has fewer covariates. David, I understand your concern with the number of events and number of variables I am using however. 611 is only the unique times at which the events occur where as there are 6987 events in my data of 77272 observatio

Re: [R] debug vs regular mode

2012-08-10 Thread Henric (Nilsson) Winell
On 2012-08-10 15:42, Zhang, Peng wrote: You are right. I am running Arch Linux. However, I obtained a segmentation directly, so didn't know where to find the bug?? > library("glmulti") Loading required package: rJava > testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol =

[R] How do I find the apparent magnitude of a galaxy from a FITS file?

2012-08-10 Thread andrej
Greetings! I am still new to R but have been asked to look at doing astronomy with R. I have a FITS file which contains an optical telescope image (it can be viewed in SAOimageDS9). I need to estimate the magnitude of a galaxy... and eventually other optical sources. How do I find the apparent mag

Re: [R] translating HTML character entities to accented characters

2012-08-10 Thread Michael Friendly
Thanks, David I need an all-R solution for this, because the author.csv file is exported from a database that enforces the HTML encoding and the import into R may have to be repeated several times as the database is updated. -Michael On 8/10/2012 12:40 PM, David L Carlson wrote: It's not qu

Re: [R] Simple question about formulae in R!?

2012-08-10 Thread Joshua Wiley
On Fri, Aug 10, 2012 at 9:16 AM, S Ellison wrote: >> > R in general tries hard to prohibit this behavior (i.e., including an >> > interaction but not the main effect). When removing a main effect and >> > leaving the interaction, the number of parameters is not reduced by >> > one (as would be ex

Re: [R] translating HTML character entities to accented characters

2012-08-10 Thread David L Carlson
It's not quite an R solution, but I just pasted your examples into a script window in R and saved it as chars.html. Then I opened it in Firefox and pasted the results here (with returns inserted to match your original). > grep("&", author$lname, value=TRUE) [1] "Frère de Montizon" "Lumière" [3]

[R] export table in separate file

2012-08-10 Thread Alexander Shenkin
Hi Folks, I'm using Sweave to generate png & pdf graphics that I then "Import & Link" in a Word document. This let's me create sharable and editable dynamic documents. They are dynamic in that I can regenerate figures when the data changes, and have those figures automatically updated in my Word

Re: [R] Simple question about formulae in R!?

2012-08-10 Thread Bert Gunter
Sheesh! Yes. ... and in the case where B is a factor with k levels and x is continuous, the model ~B:x yields k+1 parameters, which in default contrasts would be a constant term, x, and k-1 interactions between x and the corresponding k-1 "contrasts"(which they aren't really) for B. ~B*x would add

Re: [R] significance of character (Anova)

2012-08-10 Thread peter dalgaard
On Aug 10, 2012, at 15:47 , Jennifer Kaiser wrote: > > Model: poisson, link: log > > Response: sb_ek_ber > > Terms added sequentially (first to last) > > > Df Deviance Resid. Df Resid. Dev Pr(>Chi) > NULL 1237837 4.4998e+10 > ABWHALT_C 2 244

Re: [R] image.plot side effects

2012-08-10 Thread Uwe Ligges
On 10.08.2012 11:52, baschti wrote: Hi r-users, i have a problem with image.plot. When i add two image.plots with the add function, the second is out of border. http://r.789695.n4.nabble.com/file/n4639881/test.png In r helps are the hint to use the par function with plt, but it did not work.

Re: [R] help error histograma

2012-08-10 Thread David L Carlson
Now that John has put your data into a readable format, there are a number of issues with your histogram that don't make much sense. You have enlarged the text of the labels and greatly enlarged the size of the title, but then printed no title (you have cex.main=6 and main="") and you have set p

Re: [R] Simple question about formulae in R!?

2012-08-10 Thread S Ellison
> > R in general tries hard to prohibit this behavior (i.e., including an > > interaction but not the main effect). When removing a main effect and > > leaving the interaction, the number of parameters is not reduced by > > one (as would be expected) but stays the same, at least > > when using

[R] translating HTML character entities to accented characters

2012-08-10 Thread Michael Friendly
I've imported a .csv file where character strings that contained accented characters were written as HTML character entities. Is there a function that works on a vector to translate them back to accented (latin1) characters? Some examples: > grep("&", author$lname, value=TRUE) [1] "Frère de M

Re: [R] Running odfWeave on its own examples.odt

2012-08-10 Thread John C Nash
WinXP says OS reports request to set locale to "en_US.UTF-8" cannot be honored. Sigh. JN On 08/10/2012 11:40 AM, Frans Marcelissen wrote: > Hi, > I had the same problem unde linux. My friend Albert Jan Roskam knew the > solution: add > Sys.setlocale(category = "LC_ALL", locale = "en_US.UTF-8"

Re: [R] Simple question about formulae in R!?

2012-08-10 Thread David Winsemius
On Aug 10, 2012, at 8:09 AM, Joshua Wiley wrote: On Fri, Aug 10, 2012 at 7:39 AM, Henrik Singmann wrote: Dear Michael and list, R in general tries hard to prohibit this behavior (i.e., including an interaction but not the main effect). When removing a main effect and leaving the interaction,

[R] Does A Choice-Based Conjoint Study Have To Be Full Profile?

2012-08-10 Thread Vik Rubenfeld
In a Conjoint study, it's difficult for respondents to evaluate more than 6 product attributes at a time. Some studies require more attributes. Often this is solved via the use of Adaptive Conjoint Analysis (ACA), in which the questionnaire is modified for each individual respondent as the surv

Re: [R] Running odfWeave on its own examples.odt

2012-08-10 Thread Frans Marcelissen
Hi, I had the same problem unde linux. My friend Albert Jan Roskam knew the solution: add Sys.setlocale(category = "LC_ALL", locale = "en_US.UTF-8") I suppose this also works under windows. Frans -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.

Re: [R] Simple question about formulae in R!?

2012-08-10 Thread Joshua Wiley
On Fri, Aug 10, 2012 at 7:39 AM, Henrik Singmann wrote: > Dear Michael and list, > > R in general tries hard to prohibit this behavior (i.e., including an > interaction but not the main effect). When removing a main effect and > leaving the interaction, the number of parameters is not reduced by o

Re: [R] help error histograma

2012-08-10 Thread S Ellison
> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of aprendiz programa > Sent: 10 August 2012 01:37 > To: r-help@r-project.org > Subject: [R] help error histograma > > > Hi, > My error isErro em hist.default(dados[[1]], freq =

Re: [R] R versus SAS

2012-08-10 Thread S Ellison
> > Thanks to R, the internet and pretentious, semi-literate public > > servants around the world, there probably is now. > > > Wait a minute now. Perhaps it's some recursive compensation scheme/ > Indeed, perhaps the general remark might be reconsidered. As jane Austen said, "Where any one

Re: [R] subsetting levels of a vector

2012-08-10 Thread Marc Schwartz
On Aug 10, 2012, at 4:07 AM, simona mancini wrote: > Hi, > > > I need to subset different levels of vector in a dataset to create a new > dataframe that contains only these. These observations are not numerical, so > I can't use the subset() function (at least this is the response I get from

Re: [R] help error histograma

2012-08-10 Thread John Kane
Thank you but it is not a good idea to send attachments. I received them because the email came directly to me butw probablyw others did not because the R-list usually removes them to protect against viruses. It is better to put everything in the email. I have included your code

Re: [R] subsetting levels of a vector

2012-08-10 Thread John Kane
subset should work fine. My guess would be that Electrode is a character or factor variable. Use str() to see what kind of variables you have in the data set. If we call the data set dat1 this works. subset(dat1, dat1$Electrode =="FP1" | dat1$Electrode =="FP2" | dat1$Electrode == "F4")

Re: [R] subsetting levels of a vector

2012-08-10 Thread Rui Barradas
Hello, I don't see the problem. d <- read.table(text=" ParticipIDERP Electrode 1 s1 0.0370 FP1 2 s2 35.0654 FP2 3 s3 -3.3852F4 4 s4 2.6119P3 5 s5 0.1224P4 6 s6 -5.3153O1 ", header=TRUE) str(d) w

[R] replacing a character string

2012-08-10 Thread toehanus
I am working on modifying a REDCap survey. The data dictionary column for the response field has the following value. 1, Strongly disagree | 2, Disagree | 3, Agree | 4, Strongly Agree | 5, Don't Know | 6, Refuse to Answer | 7, Not Applicable I am wanting to convert this so that it looks as follo

Re: [R] creating a contingency table from a data.frame automatically (NOT BY HAND)

2012-08-10 Thread arun
HI, Try this: n<-100 dat1<-data.frame(hunting.prev=sample(c("success","fail"),n, replace=TRUE),groupsize=sample(c("small","large"),n,replace=TRUE),dogs=sample(c("yes","no"),n,replace=TRUE), guns=sample(c("yes","no"),n,replace=TRUE)) mytable<-xtabs(~hunting.prev+groupsize+dogs+guns,data=dat1)  ft

[R] significance of character (Anova)

2012-08-10 Thread Jennifer Kaiser
Hi,  I have a problem with the output of my anova. > Tabelle2 <- data.frame(sb_ek_ber, JE, ABWHALT_C, ALLEINF, > Alter_Ältester_inklVN_C, Alter_Jüngster_C_inkl_AlterNutz, ALTERKAU_C, > Wuerfel, BEGKUNDE_C, Geoscore_C, GESCHL_VN, +  NUTZART, NUTZKREIS, NICHTK_C_korrigiert, TARIFDAT_C, TARIFG

Re: [R] debug vs regular mode

2012-08-10 Thread Zhang, Peng
You are right. I am running Arch Linux. However, I obtained a segmentation directly, so didn't know where to find the bug?? > library("glmulti") Loading required package: rJava > testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50))) > glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8

[R] error applying user-defined link function to lmer

2012-08-10 Thread Kathleen Vancleef
Dear R users, I'm struggling with applying a user-defined link function in lmer. For analyzing data of a 2AFC psychophysical experiment, I would like to model my binary data with a logistic function with a lower limit at 0.5 instead of 0. In a previous question this has been described as a half

Re: [R] debug vs regular mode

2012-08-10 Thread Henric (Nilsson) Winell
On 2012-08-10 06:10, Zhang, Peng wrote: Thanks to both for your reply. library(glmulti) testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50))) glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, data = testdata, level = 2) This is reproducible to get a seg

[R] Solving binary integer optimization problem

2012-08-10 Thread aajit75
Hi, I am new to R for solving optimization problems, I have set of communication channels with limited capacity with two types of costs, fixed and variable cost. Each channel has expected gain for a single communication. I want to determine optimal number of communications for each channel maximiz

Re: [R] Zoo object problem: Find the column name of a univariate zoo object

2012-08-10 Thread arun
HI, I guess names() work if the zoo object has columns. (https://stat.ethz.ch/pipermail/r-help/2006-November/117448.html) x <- sin(1:4) library(zoo)  x2<-zoo(as.matrix(x)) names(x2)<-"test"  names(x2) #[1] "test"  x2     test 1  0.8414710 2  0.9092974 3  0.1411200 4 -0.7568025 x3<-zoo(x)  na

[R] odfWeave , UTF-8 locale and posix

2012-08-10 Thread Frans Marcelissen
Hello, I have a serious problem with odfWeave. I use odfWeave to produce on-line reports on a webserver. When the template file contains trema's (ë) or accents (é), odfWeave breaks with the unfamous error "Unable to convert h.odt to the current locale. You may need to process this file in a UTF

Re: [R] how to read .bam file

2012-08-10 Thread mengxin
Yes,it's genomic alignment files. Thanks for your help. At 2012-08-10 18:10:02,"peter dalgaard" wrote: > >On Aug 10, 2012, at 08:24 , mengxin wrote: > >> Hi all: >> I've got a data of ".bam" which is created from my partner under linux >> sysyem. >> My system is window xp, and I wanna kn

Re: [R] Olympics: 200m Men Final

2012-08-10 Thread Daróczi Gergely
On Fri, Aug 10, 2012 at 10:23 AM, Rui Barradas wrote: > Hello, > > The main critique, I think, is that we assume a certain type of model > where the times can decrease until zero. And that they can do so linearly. > I believe that records can allways be beaten but 40-50 years ago times were > mea

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