Re: [R] list of valid R encodings.in source(...,encoding=)

2014-07-11 Thread Hadley Wickham
It's documented in the Encodings section of ?file: "As from R 3.0.0 the encoding "UTF-8-BOM" is accepted for reading and will remove a Byte Order Mark if present (which it often is for files and webpages generated by Microsoft applications). If it is required (it is not recommended) when writing i

Re: [R] Cutting hierarchical cluster tree at specific height fails

2014-07-11 Thread Johannes Radinger
Hi, @David: Thanks for the explanation why this does not work. This of course makes theoretically sense. However in a recent discussion ( http://stats.stackexchange.com/questions/107448/spatial-distance-between-cluster-means ) it was stated that "the 'reversals problem' of centroid method is not

Re: [R] Installing RMySQL on Debian

2014-07-11 Thread Federico Razzoli
> I'm wondering if you understand the RMySQL is only an interface to the > MySQL package, and it needs to be installed separately for your OS. > > -- > David Hi David. As I wrote in my first mail, MySQL (MariaDB) is installed from the tar file. Please, if you want to help me, re-read my first mai

Re: [R] Paper on Analytics using R

2014-07-11 Thread Timothy W. Cook
A quick Google Scholar search turned up the (below paper. It has been cited 38 times so that should give you plenty of references. More than likely you are looking for use cases in your own context; correct? http://goo.gl/Vcx4j1 On Fri, Jul 11, 2014 at 3:17 AM, Katherine Gobin wrote: > Dear

Re: [R] Median expected survival

2014-07-11 Thread Andrews, Chris
Hi Lars, Graph it: plot(pred_leuk) will show that some of the survival curves do not reach 0.5 before you run out of data. Thus the median is not estimated and you get NA. Chris -Original Message- From: Lars Bishop [mailto:lars...@gmail.com] Sent: Thursday, July 10, 2014 6:23 AM To:

[R] Grouped Boxplot

2014-07-11 Thread anupam sinha
Dear all, I need some help with plotting boxplots in groups. I have a file of the following format: - POS DISONODE_CAT -- A20Hubs C30Nonhubs B50

Re: [R] Grouped Boxplot

2014-07-11 Thread Jorge I Velez
Dear Anupam, Try boxplot(DISO ~ POS * NODE_CAT, data = yourdata) Another option would be the last example in ?boxplot HTH, Jorge.- On Fri, Jul 11, 2014 at 4:38 PM, anupam sinha wrote: > Dear all, > I need some help with plotting boxplots in groups. I have a > file of the followin

Re: [R] Cutting hierarchical cluster tree at specific height fails

2014-07-11 Thread David L Carlson
The easiest workaround is the one you included in your original posting. Specify k= and not h=. Examine the dendrogram and decide how many clusters are at the level you want. You could add guidelines to the dendrogram with abline() to make it easier to see the number of clusters at various heigh

Re: [R] Cansisc: Error in eigen(eHe, symmetric = TRUE)

2014-07-11 Thread John Fox
Dear Judith, Michael and David's suggestion (and my earlier suggestion) that you use a method appropriate to the distribution of your data is no doubt good advice, but it remains to be explained why candisc() produced an error. If you do the following, you'll see that many of your variables are i

[R] Merge rows

2014-07-11 Thread Ryan de Vera
Hello all, I have a data frame filled with senders and recipients. Some of the senders have multiple rows with different recipients and I want to merge those rows. For example I have a...@email.com b...@email.com a...@email.com c...@email.com d...@email.com r...@email.com f...@em

Re: [R] Merge rows

2014-07-11 Thread Sarah Goslee
Hi Ryan, We can't tell from your example what structure your original data are in, nor what your output is intended to look like, or for that matter how you got from one to the other. Please don't post in HTML because it gets mangled! Using dput() to provide your example data is the best thing, b

Re: [R] Information about font

2014-07-11 Thread Sébastien Bihorel
If I may ask, how can I know the path to the font file(s) used by R when it generates the png files with the Helvetica font? Thanks On Thu, Jul 10, 2014 at 12:21 AM, David Winsemius wrote: > > On Jul 9, 2014, at 7:47 PM, Sébastien Bihorel wrote: > > > Hi, > > > > I have this set of R scripts

[R] CI for nlme predictions

2014-07-11 Thread Robert Lynch
I am running a mixed effects model with random intercepts fit.courseCross <- lme(fixed= zGrade ~ Rep + ISE +P7APrior+Female+White+HSGPA+MATH+Years+Course+Course*P7APrior , random= ~1|SID, data = Master.complete[Master.complete$Course != "P7A",]) where all varia

[R] (no subject)

2014-07-11 Thread Millo Giovanni
Dear Katie, the code looks all right. On a standard example, everything works fine, e.g.: # example(plm) # coefs<-names(coef(zz)) # lht(zz, coefs) # lht(zz, coefs, vcov=vcovHC) # "arellano" is the default HC method anyway As the error message says, your case is somehow ill-conditioned and the vc

[R] Problems with read.table and data structure

2014-07-11 Thread Tim Richter-Heitmann
Hi there! I have huge datafile of 600 columns 360 samples: data <- read.table("small.txt", header = TRUE, sep = "\t", dec = ".", row.names=1) The txt.file (compiled with excel) is showing me only numbers, however R gives me the structure of ANY column as "factor". When i try "stringsAsFactors

Re: [R] Problems with read.table and data structure

2014-07-11 Thread Marc Schwartz
On Jul 11, 2014, at 9:15 AM, Tim Richter-Heitmann wrote: > Hi there! > > I have huge datafile of 600 columns 360 samples: > > data <- read.table("small.txt", header = TRUE, sep = "\t", dec = ".", > row.names=1) > > The txt.file (compiled with excel) is showing me only numbers, however R >

Re: [R] Problems with read.table and data structure

2014-07-11 Thread Marc Schwartz
On Jul 11, 2014, at 2:36 PM, Marc Schwartz wrote: > > On Jul 11, 2014, at 9:15 AM, Tim Richter-Heitmann > wrote: > >> Hi there! >> >> I have huge datafile of 600 columns 360 samples: >> >> data <- read.table("small.txt", header = TRUE, sep = "\t", dec = ".", >> row.names=1) >> >> The txt

Re: [R] Merge rows

2014-07-11 Thread Sarah Goslee
Hi John, I don't think your x2 is right, but who knows? One possible approach would be: R> lapply(split(x2$recipients, unique(x2$sender)), paste, collapse=", ") $`a...@email.com` [1] "b...@email.com, f...@email.com" $`r...@email.com` [1] "c(\"c...@email.com\", \"d...@email.com\"), h...@email.co

Re: [R] Problems with read.table and data structure

2014-07-11 Thread David L Carlson
It is hard to diagnose without looking at the file. For example readLines("small.txt", n=5) would print out the first five lines that might show problems with wrapping the lines. What does dim(data) give you? Are you getting all 360 samples and 600 columns? You could also try using the colClass

Re: [R] Problems with read.table and data structure

2014-07-11 Thread William Dunlap
> data <- read.table("small.txt", header = TRUE, sep = "\t", dec = ".", > row.names=1) > ... > Factor w/ 358 levels "0,123111694",..: 11 14 50 12 38 44 13 76 31 30 It looks like your data file used commas for the decimal point. Is that right? You used dec="." when reading it; does dec="," work b

Re: [R] CI for nlme predictions

2014-07-11 Thread Bert Gunter
Full Disclosure: I am not an expert on this and this requires an expert's answer. But my understanding is that inference in mixed effect models is an entirely nontrivial matter -- i.e. exactly what you want must be clearly defined (what variance components to include) and the distributions of the

[R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

2014-07-11 Thread Megan Bartlett
Hi everyone, Since metafor doesn't have its own list, I hope this is the correct place for this posting- my apologies if there is a more appropriate list. I'm conducting a meta-analysis where I would like to determine the correlation between plasticity in leaf traits and climate. I'm calculating

[R] Finding sparse cuts in a graph

2014-07-11 Thread Anirudh Kondaveeti
Is there an algorithm to find sparse cuts in a graph ? I am looking to find the best cut which minimizes the sparsity of a graph. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-

[R] Zeta-squared transformation use R?

2014-07-11 Thread Miles Yang
Hi R-helpers, Is there any packages can do "*zeta-squared transformation*"? The Zeta-squared transformation comes from the following article: Standardizing Variables in Multiplicative Choice Models Lee G. Cooper and Masao Nakanishi Journal of Consumer Research, Vol. 10, No. 1 (Jun., 1983), pp. 96

Re: [R] Zeta-squared transformation use R?

2014-07-11 Thread Jeff Newmiller
Have you tried RSiteSearch("zeta squared") ? Someone may recognize this, but it never hurts to communicate where you have already looked. --- Jeff NewmillerThe . . Go Live... DCN: