Re: [R] Export to .txt

Oh, Im sorry. My file isnt a function but script 'script.R' which looks something like that: cat('Instruction no 1', '\n') browser() # place for fulfilling it cat('Instruction no 2', '\n') browser() # place for fulfilling it etc. I am running it by sink(file='output.txt')

[R] where to get chr_rpts file for dbSNP human 36.3 assembly

Dear list, In terms of dbSNP database in NCBI, I can get the chr_rpts files for the most recent 37.3 assembly from the following FTP site, ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ My question is how/where I can get these chr_rpts files based on the 36.3 assembly Thanks,

Re: [R] Removing or ignoring package version for generic function in locked environment

Interesting. I have a few (untested) thoughts. Before I get into those though, this seem to me like a case where contacting either the maintainer of epicalc or of the functions not under your control that give warnings. I think either would be appropriate because if the default method works

Re: [R] 'tcltk' does not have a name space

It also have this problem when I install qvalue package ... -- View this message in context: http://r.789695.n4.nabble.com/tcltk-does-not-have-a-name-space-tp3020504p3971898.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] 'tcltk' does not have a name space

Please quote the original message you are replying to and read the posting guide! Please update your version of R to R-2.14.0. Looks like the package assumes a more recent version of R without declaring the dependency. You may want to inform the package maintainer. Uwe Ligges On

Re: [R] I really need help to merge two data frames

On 02.11.2011 01:32, Tony wrote: Hello, I need help getting two data sets to merge. The structure of my two data sets are: str(bcusip) 'data.frame': 1391 obs. of 3 variables: $ bond_id : Factor w/ 1391 levels AAGH,AAGI,..: 1 2 3 4 5 6 $ Freq: num 41361 4126 5206 10125 45536 ...

[R] RC33 8th Int Conf on Social Science Methodology -- The R System ...

I wish to draw attention to an R-related session that is planned for the RC33 Eighth International Conference on Social Science Methodology, to be held over July 9 - July 13 2012, at the University of Sydney. The focus of the conference is on innovations and current best practice in all

[R] Size of windows graphics device

R for Windows 2.14.0 Is there a function reporting the size of the current windows device after it has been resized manually? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] How to interpret Spearman Correlation

Hi David, This is not private tutoring, just someone trying to help, and I'm sorry for my distraction. On Tue, Nov 1, 2011 at 10:34 PM, David Winsemius dwinsem...@comcast.netwrote: Shahab; You would be well advised not to seek private tutoring from someone on the Internet who tells you that

Re: [R] triangles point left, filled?

On 11/01/2011 08:05 PM, Martin Ivanov wrote: Dear R users, I want to plot not only triangles point up and triangles point down, which is easy using the pch argument to points. I want to plot left and right pointing triangles as well. They must be fillable with colour. I browsed a little in

Re: [R] why the a[-indx] does not work?

-Original Message- From:Alaios Sent: 30 October 2011 21:09 To: William Dunlap; andrija djurovic Cc: R-help@r-project.org Subject: Re: [R] why the a[-indx] does not work? What is the difference between though !numericVector==0 and -numericVector==0 Er... you need to be (a

Re: [R] Size of windows graphics device

par(fin) : The figure region dimensions, |(width,height)|, in inches. par(din) : the device dimensions, |(width,height)|, in inches. On 2011-11-2 18:50, Erich Neuwirth wrote: R for Windows 2.14.0 Is there a function reporting the size of the current windows device after it has been resized

Re: [R] Size of windows graphics device

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dejian Zhao Sent: 02 November 2011 12:01 To: r-help@r-project.org Subject: Re: [R] Size of windows graphics device par(fin) : The figure region dimensions,

Re: [R] How to interpret Spearman Correlation

What David was getting at is that you interpreted the P-value as one minus the P-value, not a safe practice. There is also some question about whether it would have been better to recommend a good book or course. Frank Raphael Saldanha wrote: Hi David, This is not private tutoring, just

[R] Generate a sequence of vectors of different length

Hi everyone After the following setup sector=2 # Define Number of Sectors sectors=LETTERS[seq( from = 1, to = sector )] # Name sectors No_ent=round(3/runif(sector)) # Number of entities per sector #Tot_No_ent=sum(No_ent) Goal is to get a List like (A1, A2, A3, B1, B2, B3, B4) where A is

Re: [R] Generate a sequence of vectors of different length

One approach is: sectors - 2 namSec - LETTERS[seq_len(sectors)] nSec - round(3 / runif(sectors)) mapply(paste, namSec, sapply(nSec, seq_len), MoreArgs = list(sep = )) I hope it helps. Best, Dimitris On 11/2/2011 2:56 PM, Christian Langkamp wrote: Hi everyone After the following setup

Re: [R] Imputing Missing Data: A Good Starting Point?

You might look at Allison's short book for a quick introduction to the issues: Paul D. Allison. 2002. Missing Data. Sage Quantitative Applications in the Social Sciences No. 136. Online there is http://www.multiple-imputation.com/ which provides a bibliography (with links to articles that are

Re: [R] Export to .txt

So playing around with it quickly, it seems that print() works with sink but cat() doesn't unless you put the sink call in the script at which point it does as you would expect. Does that help? Michael On Wed, Nov 2, 2011 at 2:14 AM, stat.kk stat...@gmail.com wrote: Oh, Im sorry. My file isnt

[R] Proper Syntax for Logical Subset in Subset()

I have measured values for 47 chemicals in a stream. After processing the original data frame through reshape2, the recast data frame has this structure: 'data.frame': 256 obs. of 47 variables: $ site : Factor w/ 143 levels BC-0.5,BC-1,..: 1 1 1 2 2 2 2 2 2 2 ... $ sampdate : Date,

Re: [R] Proper Syntax for Logical Subset in Subset()

On Wed, 2 Nov 2011, Rich Shepard wrote: I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na, SO4, and TDS. I should have also written that what I ultimately want is to create a box-and-whisker plot for these 7 chemicals in a single panel. If that can be done directly from

Re: [R] Proper Syntax for Logical Subset in Subset()

I have measured values for 47 chemicals in a stream. After processing the original data frame through reshape2, the recast data frame has this structure: 'data.frame': 256 obs. of 47 variables: $ site : Factor w/ 143 levels BC-0.5,BC-1,..: 1 1 1 2 2 2 2 2 2 2... $ sampdate :

Re: [R] Proper Syntax for Logical Subset in Subset()

To make such a plot, I would have thought your want your data structure to be: yourdat: Column A: Date Column B; Chemical Column C: Result After subsetting this to the chemicals you want or doing the subsetting in your plot command, something like (base R) boxplot(Result ~ Chemical,

Re: [R] Proper Syntax for Logical Subset in Subset()

Of course I left out the data argument: boxplot(Result ~ Chemical, data= yourdat,subset=yourdat$Chemical %in% c(Ca,Cl, Cond,Mg,Na,SO2,TDS)) -- Bert On Wed, Nov 2, 2011 at 10:08 AM, Bert Gunter bgun...@gene.com wrote: To make such a plot, I would have thought your want your data structure to

[R] how to count number of occurrences

Dear R users, I have this data frame, y samp 8 0.03060419X 18 0.06120838Y 10 0.23588374X 3 0.32809965X 1 0.36007100X 7 0.36730571X 20 0.47176748Y 13 0.65619929Y 11 0.72014201Y 17 0.73461142Y 6 0.76221313X 2 0.77005691X 4 0.92477243

[R] 2nd parameter Power Curves/ANCOVAs

Hi, I am trying to compare the slopes and y-intercepts of the power curves between two plant species to see if they follow similar trends (photosynthesis y-axis, stomatal conductance x-axis). I can fit linear regression lines to the data and run the stats using an ANCOVA, but the specific

Re: [R] does there any function like sumif in excel?

I have a similar problem I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the AreaProtected if it is the same CELLCD in another column :

[R] mapping bathymetries and species abundances

Dear all, I am new to R and even newer to mapping with R. I have installed PBSMapping, maptools and maps, and I am struggling to produce a map of fish abundance in the Grand Banks. I have tried several approaches to plot the bathymetry in my study area: 1) download the data from

[R] Creating deciles on data using one variable

I need to deciles data containing more than one variables using any one variable. I am using script below : id -c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20) tot -c(1230, 1230, 2345, 3456, 456, 4356, 123, 124, 987, 785, 5646, 345, 2345, 3456, 456, 4356, 123, 124, 987, 785) data -

[R] nproc parameter in efpFunctional

Hello all, could anyone explain the exact meaning of parameter nproc? Why different values of nproc give so different critical values, i.e. meanL2BB$computeCritval(0.05,nproc=3) [1] 0.9984853 meanL2BB$computeCritval(0.05,nproc=1) [1] 0.4594827 The strucchange-package description gives integer

[R] Sum with condition

I guess my problem is simple for most of you but I am new with R and I need some help, I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the

[R] overloading + operator for chars

Hello,   I would like to overload the + operator so that it can be used to concatenate two strings, e.g John + Doe = JohnDoe. How can I 'unseal' the + method? setMethod(+, signature(e1=character, e2=character), function(e1, e2) paste(e1, e2, sep=) ) Error in setMethod(+, signature(e1 =

Re: [R] Creating deciles on data using one variable

I need to deciles data containing more than one variables using any one variable. I am using script below : id -c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20) tot -c(1230, 1230, 2345, 3456, 456, 4356, 123, 124, 987, 785, 5646, 345, 2345, 3456, 456, 4356, 123, 124, 987, 785) data -

[R] Multiple comparison test about whole population, not about mean

Multiple comparison tests are usually used to compare groups based on the confidence region about the mean. Some great packages, like agricolae, proposes grouping information based on statistical tests. I am looking for a way to perform such a test, but based on the confidence region about the

[R] difference between foo$a[2] - 1 and foo[2,a] - 1

Hallo Can anyone tell me the difference between foo$a[2] - 1 and foo[2,a] - 1 ? I thought that both expressions are equivalent, but when I run the following example, there is obviously a difference. foo - data.frame(a=NA,b=NA) foo a b 1 NA NA foo$a[1] - 1 foo$b[1] - 2 foo$a[2] - 1

Re: [R] Sum with condition

Hi, On Wed, Nov 2, 2011 at 8:44 AM, Celine bellard.cel...@gmail.com wrote: CELLCD AreaProtected   8928      52.39389   8928      41.91511   8929      21.21975   8929      63.65925   8930      26.08547   8930      14.04602 You'll need to figure out how you want it to be combined with the

[R] array manipulation

Hello, I'm at the very beginning of the learning process of this language. Sorry in advance for the (possible but plausible) stupidity of my question. I would like to find a way to permute the DIMENSIONS of an array. Something that sounds like the function permute() in matlab. Given an array C

Re: [R] how to count number of occurrences

Is the following what you want? It should give the number of Xs immediately preceding each Y. samp - c(X, Y, X, X, X, X, Y, Y, Y, Y, X, X, X, X, X, Y, Y, Y, Y, Y) diff((seq_along(samp) - cumsum(samp==Y))[samp==Y]) [1] 4 0 0 0 5 0 0 0 0 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com

[R] Time Series w/ daily or stochastic observation prediction

Hi, I've got two different types of behaviors for which I have to predict the future development. One is a set of historical data with daily observations and which are following some kind of a seasonal pattern, the second one a set of historical data (measure points), with two observation

Re: [R] how to count number of occurrences

On Nov 2, 2011, at 12:54 PM, Sl K wrote: Dear R users, I have this data frame, y samp 8 0.03060419X 18 0.06120838Y 10 0.23588374X 3 0.32809965X 1 0.36007100X 7 0.36730571X 20 0.47176748Y 13 0.65619929Y 11 0.72014201Y 17 0.73461142Y 6

Re: [R] how to count number of occurrences

Hi, On Wed, Nov 2, 2011 at 12:54 PM, Sl K s.ka...@gmail.com wrote: Dear R users, I have this data frame,           y samp 8 0.03060419    X 18 0.06120838    Y 10 0.23588374    X 3 0.32809965    X 1  0.36007100    X 7 0.36730571    X 20 0.47176748    Y 13 0.65619929    Y 11

Re: [R] Proper Syntax for Logical Subset in Subset()

On Wed, 2 Nov 2011, Bert Gunter wrote: To make such a plot, I would have thought your want your data structure to be: Column A: Date Column B; Chemical Column C: Result Thanks, Bert. I have a data frame in that format. After subsetting this to the chemicals you want or doing the

Re: [R] nproc parameter in efpFunctional

On Wed, 2 Nov 2011, bonda wrote: Hello all, could anyone explain the exact meaning of parameter nproc? Why different values of nproc give so different critical values, i.e. meanL2BB$computeCritval(0.05,nproc=3) [1] 0.9984853 meanL2BB$computeCritval(0.05,nproc=1) [1] 0.4594827 The

Re: [R] Multiple comparison test about whole population, not about mean

1. I found the post incoherent. 2. This appears to have nothing to do with R -- post elsewhere, e.g. http://stats.stackexchange.com/ -- Bert On Wed, Nov 2, 2011 at 10:47 AM, Serge-Étienne Parent separ...@yahoo.comwrote: Multiple comparison tests are usually used to compare groups based on the

Re: [R] does there any function like sumif in excel?

On Nov 2, 2011, at 9:06 AM, Celine wrote: I have a similar problem I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the AreaProtected if it is the same

Re: [R] Sum with condition

On Nov 2, 2011, at 2:11 PM, Sarah Goslee wrote: Hi, On Wed, Nov 2, 2011 at 8:44 AM, Celine bellard.cel...@gmail.com wrote: Celine. Please stop posting duplicates. CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547

Re: [R] array manipulation

On Nov 2, 2011, at 12:16 PM, Simone Salvadei wrote: Hello, I'm at the very beginning of the learning process of this language. Sorry in advance for the (possible but plausible) stupidity of my question. I would like to find a way to permute the DIMENSIONS of an array. Something that sounds

Re: [R] Sum with condition

If you used aggregate() on the data frame you would have a new data frame containing the sum of all AreaProtected for each CELLCD. For your mini-example, using d as your data frame, d2-aggregate(d[,2], by=list(CELLCD=d$CELLCD),sum) d2 # CELLCDx # 1 8928 94.30900 # 2 8929

[R] heteroscedastic bivariate distribution with linear regression - prediction interval

Dear forum, which is the most suitable method to get the prediction interval of a bivariate normal distribution which is consistent with a linear model y = ax + b? I assume it is gls + predict. Am I correct? I'm rather new to R. Is there some reliable sample code for that problem? Thank you

[R] HOW TO REMOVE MTEXT FROM PLOT, plotting changing populations with titles in loop

is there a way to hide/undraw mtext (or lines etc.) in a loop like plot(runif(10)) iterCol - rainbowPalette(10) for(i in 1:10){ mtext(paste(this is iteration , i, sep=)) points(runif(10),col=iterCol[i]) Sys.sleep(1) ## UNDRAW/HIDE the text so that it does not mess up the plot in the next

Re: [R] HOW TO REMOVE MTEXT FROM PLOT, plotting changing populations with titles in loop

It's not perfect, but you could use: mtext(paste(this is iteration , i, sep=), col=white) to overwrite it, or polygon() to draw a white rectangle over the text each time. Sarah On Wed, Nov 2, 2011 at 3:15 PM, prinzOfNorway torgrim...@gmail.com wrote: is there a way to hide/undraw mtext (or

Re: [R] overloading + operator for chars

On 11/02/2011 06:52 AM, Albert-Jan Roskam wrote: Hello, I would like to overload the + operator so that it can be used to concatenate two strings, e.g John + Doe = JohnDoe. How can I 'unseal' the + method? setMethod(+, signature(e1=character, e2=character), function(e1, e2) paste(e1, e2,

[R] Help with curr directory in R

Hello All Thanks for all responses in advance, I am invoking R from command line from C:\TEMP as C:\Program Files\R\R-2.9.1\bin\R.exe --vanilla -f C:\temp\test.R On two different machines The test.R looks like: --SNIP- print(c(CurrDir=, getwd())) proc.time() warnings() --SNIP- On one machine

[R] palettes for the color-blind

Everyone, I'm working with scatter plots with different colored symbols (via lattice). I'm currently using these colors for points and lines: col1 - c(rgb(1, 0, 0), rgb(0, 0, 1), rgb(0, 1, 0), rgb(0.55482458, 0.40350876, 0.0416), rgb(0, 0, 0)) plot(seq(along =

Re: [R] palettes for the color-blind

Hi, Try the dichromat package (also dichromat_pal in the scales package). HTH, baptiste On 3 November 2011 10:26, Max Kuhn mxk...@gmail.com wrote: Everyone, I'm working with scatter plots with different colored symbols (via lattice). I'm currently using these colors for points and lines:

Re: [R] palettes for the color-blind

On Thu, Nov 3, 2011 at 10:26 AM, Max Kuhn mxk...@gmail.com wrote: First, can anyone verify that these the colors in col2 are differentiable to someone who is color blind? Second, are there any other specific palettes that can be recommended? How do the RColorBrewer palettes rate in this

Re: [R] difference between foo$a[2] - 1 and foo[2,a] - 1

Columns in data frames must all have the same number of elements. Your first example attempts to violate that, because it works with a single column. The second example works on the entire data frame, so it is able to lengthen the other column to match.

Re: [R] palettes for the color-blind

Before you pick out a palette: you are aware that their are several different types of color-blindness, aren't you? http://en.wikipedia.org/wiki/Color_blind -- Sent from my Cray XK6 Pendeo-navem mei anguillae plena est. __ R-help@r-project.org

Re: [R] Help with curr directory in R

I think I have solved this problem The issue was: some user had changed the registry entry for HKEY_CURRENT_USER\Software\Microsoft\Command Processor (added Autorun and set it to C:\) So the current dir was always pointing to C:\ I deleted that and everything works. Thanks Shank -Original

[R] Error: serialization is too large to store in a raw vector

Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw vector Is it possible to ask from R to extend the Error messages with more details? I would like to see where this problem exists. B.R Alex

Re: [R] palettes for the color-blind

On Thu, Nov 3, 2011 at 11:04 AM, Carl Witthoft c...@witthoft.com wrote: Before you pick out a palette:  you are aware that their are several different types of color-blindness, aren't you? Yes, but to first approximation there are only two, and they have broadly similar, though not identical

Re: [R] Error: serialization is too large to store in a raw vector

?traceback ?options ## especially _recover_ for the error option. -- Bert On Wed, Nov 2, 2011 at 3:37 PM, Alaios ala...@yahoo.com wrote: Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw

[R] mysterious warning message regarding bytecode...

While running a long script which source()s other scripts I get the following warning: Warning message: In t(object$S[[1]]) : bytecode version mismatch; using eval I cannot replicate it if I run the sourced files line by line though... What is that error? And do I care about it? It doesn't

[R] StatET: Commands are not submitted to the console

Hello! I am working for quite a while now with the Eclipse/StatET approach and it always worked very well until I updated to the 2.0 version of StatET. After the official release the RJ console did not start. After they released another update a couple of days later it worked fine again. I

[R] Lattice plots and missing x-axis labels on second page

Hello, I'm trying to make a lattice plot (using xyplot()). I have included a layout=c(3,4) statement, giving me 12 plots per page and an as.table=TRUE statement, directing the way the plots are laid out. I have 18 plots altogether and so 6 of them end up on the second page. Everything looks fine

[R] R 2.14.0 installation problem (?)

Hi all, I downloaded R-2.14.0.tar.gz, unpacked, ran configure with --with-blas=-lgoto2, built, then issued make install rhome=/usr/local/lib/R-2.14.0-goto This produced the following error: [lots of output deleted] make[3]: Entering directory

[R] Kolmogorov-Smirnov-Test on binned data, I guess gumbel-distributed data

Hi R-Users, I read some texts related to KS-tests. Most of those authors stated, that KS-Tests are not suitable for binned data, but some of them refer to 'other' authors who are claiming that KS-Tests are okay for binned data. I searched for sources and can't find examples which approve that

Re: [R] Lattice plots and missing x-axis labels on second page

I should say I'm using Windows-7, R version 2.13.0 and lattice version 0.19-33. I've pared down my code to this : pdat = read.table(RGRAPHSDGE.csv,header=T,sep=,,fill=T) print(xyplot(pdat$NITRATE~pdat$DATEYR|pdat$WELL, as.table=TRUE, layout=c(3,4), xlab=Year, ylab=Nitrate mg / litre, strip=FALSE

[R] anova or liklihood ratio test from biglm output

(Sorry if this is a repost, I got a bounce reply from the r-help server) Hi, I’m using the biglm() function to create some linear models for a very large data set than lm() can’t fit due to memory issues (the problem is with the number of interactions, I can fit the main effects model) I

Re: [R] Error: serialization is too large to store in a raw vector

On Nov 2, 2011, at 6:37 PM, Alaios ala...@yahoo.com wrote: Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw vector Is it possible to ask from R to extend the Error messages with more

Re: [R] palettes for the color-blind

Yes, I was aware of the different type and their respective prevalences. The dichromat package helped me find what I needed. Thanks, Max On Wed, Nov 2, 2011 at 6:38 PM, Thomas Lumley tlum...@uw.edu wrote: On Thu, Nov 3, 2011 at 11:04 AM, Carl Witthoft c...@witthoft.com wrote: Before you