Re: [R] control the conversion of factor to numeric

On Tue, Oct 18, 2011 at 03:40:27PM +0200, Martin Batholdy wrote: > Ok, I think that would work – thanks! > > However, in my case I read a data.frame via read.table(). > So some of the columns get transformed to factors automatically – > I don't > generate the factor-variables as in the example, so

Re: [R] Histogram for each ID value

> where the first column is the chromosome location and the second column is > some value. What I'd like to do is have a histogram created for each chr > location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and > chr22). I am just having a hard time getting everything to work out

Re: [R] Sweave doesn't work

On Sun, Aug 21, 2011 at 09:18:25AM -0700, danielepippo wrote: > Sweave("example.Rtex") in R it seems working [...] > <*> ...le/Desktop/dati/LaTeX1.Rtex* Sounds like you are first running sweave on the file 'example.Rtex' and later LaTex on 'LaTeX1.Rtex' Two points: 1) why do these files have

Re: [R] Is this a bug for my fault?

On Thu, Aug 18, 2011 at 04:52:58PM +0700, Rut S wrote: > I tried to recode some complex multiple variables and run into a problem that > r can change only some column that I want to change. > > I can reproduce the problem with this > > idfortest <- c(6,23,46,63,200,238,297,321,336,364,386,392,414

Re: [R] write merged data frame to a file

the merged data.frame? Are the rows in question really ok in the data frame? If my guess is correct you should be able to fix your problem by including quote="" in both your read.table commands. If it doesn't, also try comment.char="" - another popular source of pro

Re: [R] problem in reading a sequence file

s your header line using the header=TRUE option. Now you can address column 'Sequence' as such. Example: > dat <- read.table('seq.txt', as.is=T, header=TRUE) > dat$Sequence [1] "NNATTAAAGGGC" > dat[, 'Sequence'] [1] "NNATTAAAGG

Re: [R] problem in reading a sequence file

f strings? Something else? Does your file ONLY contain sequences - or are there also identifiers, annotations etc.? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Fr

Re: [R] (no subject)

bout volcano plot. http://lmgtfy.com/?q=r+volcano+plot cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.

Re: [R] Shrink file size of pdf graphics

se there is a limit to how much you can compress a file without resorting to lossy compression. You may have hit that limit. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maxi

Re: [R] TR: Simulate keyboard

x27;windows macro recorder' and you'll get more varieties than you will care for. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85

Re: [R] TR: Simulate keyboard

windows from activestate: http://docs.activestate.com/activetcl/8.5/expect4win/ cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 8535

Re: [R] RV: R question

On Fri, May 06, 2011 at 09:17:11AM -0400, David Winsemius wrote: > > On May 6, 2011, at 4:03 AM, Philipp Pagel wrote: > >The .Machine() command will provide some insight into these matters. > > On my device (and I suspect on all versions of R) .Machine is a > built-in

Re: [R] RV: R question

> which is the maximum large of digits that R has?, because SQL work > with 50 digits I think. and I need a software that work with a lot > of digits. The .Machine() command will provide some insight into these matters. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomor

Re: [R] read.csv fails to read a CSV file from google docs

Warning message: In open.connection(file, "rt") : unsupported URL scheme ?url told me "Note that ‘https://’ connections are not supported." Case closed, problem unsolved... Dirty workaround: use system() and wget or whatever command is

Re: [R] plot several histograms with same y-axes scaling using hist()

ot;Bewertungsfehler"", > ylab=""Haeufigkeit (in %)"", main=""KBV"", border=""white"")" Before anyone can really help you'll need to let us know where your Hist() function came from. hist() from package graphics does not have

Re: [R] bwlpot problems: printing, and tick labels

alues of > x$maxthreads in a single swoop, on a single figure). That's what I was about to suggest. Don't loop over the tasks - use the power of lattice. I think this should be close to what you want: bwplot(factor(maxthreads) ~ time | factor(tasks), x) cu Philipp -- Dr.

[R] read.table: fill=T for header?

e fixed with fill=T I was hoping something like fill.header=T or fill='header' may exist. Did I just not find it or does it not exist? And if it doesn't - does anyone else think it would be a nice item for the wishlist? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für

Re: [R] Simple Missing cases Function

current form it works but is slow because I > have used several loops to achieve this simple task. Oh - and in case you ONLY wnt the number of NAs in each column this should be pretty efficient: lapply(foo, function(x){sum(is.na(x))}) cu Philipp -- Dr. Philipp Pagel Lehrst

Re: [R] Simple Missing cases Function

c Min. :1.000 Min. :4 A :2 1st Qu.:2.000 1st Qu.:5 B :1 Median :3.000 Median :6 NA's:1 Mean :2.667 Mean :6 3rd Qu.:3.500 3rd Qu.:7 Max. :4.000 Max. :8 NA's :1.000 NA's :2 cu Phili

Re: [R] (no subject)

On Mon, Apr 18, 2011 at 04:11:57PM +0530, Ramnath R wrote: > Hai > > From which CRAN mirror can get the package ?LPP2005REC? As the first hit of a google search for "LPP2005REC" told me it is not a package but a dataset in package timeSeries. cu Philipp -- Dr. Phil

Re: [R] for loop performance

n rely on your impression (system.time, Rprof, ...) in order to find out what part of the program is actually eating up the most time. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-v

Re: [R] Clearing Console; of weeks of codes!

saying it gain does not make it less wrong: rm() will delete objects from the workspace but has absolutely no effect on the history. cu Philipp > /...Tanvir Ahamed > > > > ━━━━━━━━━━━ > From:

Re: [R] for loop performance

input data that is slow. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __

Re: [R] Hash table...

he $`12` [1] 3.464102 $`98` [1] 9.899495 Of course this can get you in trouble if y is a floating point number because of the issues with "identity" of such numbers, as discussed in ?all.equal and FAQ 7.31 "Why doesn't R think these numbers are equal?". cu

Re: [R] Clearing Console; of weeks of codes!

can be used to control the size of the history. see ?history for details. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany h

Re: [R] Compatibility with Work Load/Resource Managers

I am not sure what you mean by "integrating with" these systems. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bi

Re: [R] xyplot, groups and colors

x27;, 'blue')) > xyplot(circumference~age, dat, groups=Tree, type='l', > col.line = levels(dat$group2)) Perfect! Using the levels directly had not occured to me. Thanks! cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Tec

Re: [R] list to data frame

ing this such that the computer will do > the work of recurring through the list of elements of > ineffFilesList? as.data.frame(ineffFilesList) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenste

[R] xyplot, groups and colors

at, groups=Tree, type='l') # better, but now each Tree has its own color Of course I can now use the col argument to manually assign the colors by group but is there a more elegant way that I missed? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Tec

Re: [R] force output dimension of table function

Note that this excludes zero, though. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/

Re: [R] function order

] [,3] [1,]231 [2,]652 [3,]12 3 cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Ge

Re: [R] Saving console and graph output to same file

and then > the output from the graph window be appended to the same file? Sweave an odfWeave are very nice methods for generating reports with both text, R code, Results from R and Graphics. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universi

Re: [R] read password-protected files

is such a thing as a password protected csv file. They are just text files, after all. So I guess you have something else. How or what did the presumed pasword protection? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München

Re: [R] one question about bioconductor

spoecific packages you were using. E.g. ReadAffy most certainly requires at least a filename which seems to be missing from your comamnd above. In addition, I recommend to post your question on the bioconductor mailing list. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomori

Re: [R] Using graphics straight from R into published articles

F And don't forget to close the device with dev.off() after the plot. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.

Re: [R] Using graphics straight from R into published articles

noption a high resolution tiff or png is the way out. And of course, I agree that jpeg should never be used for graphs. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum

Re: [R] Not all rows are being read-in

tinely happens in situations like this: ID x description 1 0.4 my first measurement 2 1.6 Normal 5" object 3 0.4 Some measuremetn 4 0.7 A 4" long sample R thinks that the description in row 2 ends in row 4 and you loose data. Try read.delim(..., quote

Re: [R] Using graphics straight from R into published articles

=> not my idea of efficiency. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ ___

Re: [R] producing histogram-like plot

data and then simply use hist: dat <- data.frame(x=c(0,0,0.9,0.73,0.78,1,0.3,0.32), freq=c(14,3,12,15,2,15,2,8)) hist(with(dat, rep(x, times=freq))) My example did not take special binning wishes into account but you can easily customiye that with the breaks argument to hist. cu

Re: [R] Reversing order of vector

> I want to reverse the order of this vector as > > vect2 = c("DEF", "LMN", "XYZ", "ABC") vect2 <- rev(vect1)) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik T

Re: [R] Magic Number Error Message

you want to run a SCRIPT you are probably looking for source(). cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pag

Re: [R] read.xls -> rotate data.frame

tation still only works for columns, of course. Maybe, if you tell us some more about your actual analysis, more help can be provided. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-

Re: [R] read.xls -> rotate data.frame

ould like to address certain rows by name rather than by index. Is that correct? If so you could solve it like this: # assign the desired row names rownames(frame) = frame[,1] # remove the old name column frame <- frame[,2:ncol(frame)] cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Gen

Re: [R] read.xls -> rotate data.frame

an suggest an alternative solution that doesn't require the transposition. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://web

Re: [R] read.xls -> rotate data.frame

a column need to be of the same type. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ _

Re: [R] Bar Chart

7;B', 'B') barplot(v1, names.arg=v2) If v1 is a named vector things are even easier: names(v1) <- v2 barplot(v1) As I said, there are a bunch of other ways - e.g. using the lattice function barchart() which works a bit differently. cu Philipp -- Dr. Philipp

Re: [R] graph lines don;t appear

ny=NULL)) > plot(log(pln[,1]), type="l", ylab="EUR/PLN", xlab=NULL, xlim = c(1993, > 2011), panel.first = grid(equilogs = FALSE)) pln[,1] is just one column, so you are not plotting the values vs the year but vs. their index. As xlim is set to the interval 1993-2011 you si

Re: [R] creating additional column

Hi! max.col does what you want. Example: > dat <- data.frame(a=rnorm(20),b=rnorm(20),c=rnorm(20)) > dat a b c 1 1.17910304 -0.56951219 -0.2243664 2 -1.43840866 -0.99013855 -0.1613536 3 1.08515152 -0.77975274 0.3734530 4 -0.92154605 -0.20318367 0.1

Re: [R] beamer overlays with Sweave?

Oops - have to comment my own answer: > <>= For this to work it needs to be <>= cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freisin

Re: [R] beamer overlays with Sweave?

enum + 1 plotfilename <- paste(plotbasenema, slidenum, ".pdf", sep="") pdf(file=plotfilename) plot(stuff) dev.off() cat("\\only", slidenum, "{\includegraphics{", plotfilename ,"}}\n" ,sep="") @ If yo

Re: [R] overleap an iteration within a for-loop when error message produced

> Assume that the 5th iteration (subject=5) leads to the error > message. How can I tell R to continue with the 6th iteration? try or tryCatch are probably what you want. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität M

Re: [R] How two compare two matrixes

if you're on a laptop... Maybe you could write both matrices to files and compare them in an external viewer (Excel, less, ...). If I remember correctly, the object browser/data viewer of JGR allows editing several objects at once. cu Philipp -- Dr. Philipp Pagel Lehrstuhl

Re: [R] How two compare two matrixes

them. I'm not sure what else you could do if you are not interested in a specific distance emasure etc. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Fre

Re: [R] qbeta

1/src/nmath/qbeta.c cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ _

Re: [R] read.table

igits=7) [1] "20110221" > format(a, digits=20) [1] "20110221.114041" cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.w

Re: [R] fitting logit to data

it in [0,1] before fitting a glm 2) Use nls() to fit whatever function you find suitable cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Ger

Re: [R] Matrix in R

, if you are modelling something that would like to be indexed starting with 1 - just the other way round. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354

Re: [R] saving plots

I am aware that we need to do some thing like this > jpeg('somefilename.jpg') > ... plot... commands... > dev.off() In addition to savePlot, which has already been recommended, you may also want to look at dev.copy2eps and dev.copy2pdf. cu Philipp -- Dr. P

Re: [R] as.Date

ng: > library(Epi) Attaching package: 'Epi' The following object(s) are masked from 'package:base': as.Date.numeric, merge.data.frame A quick look at the manual page confirms that Epi's version does not have an origin option. cu Philipp -- Dr. Philipp

Re: [R] as.Date

correct, too lazy to count leap years...): > as.Date(36525, origin="1900-01-01'") [1] "2000-01-02" At first I thought the excess single quote maight be causingyour problem, but it doesn't for me. Maybe you need to upgrade R? Possibly it's an already

Re: [R] Average of several line plots

values of X (and at different intervals) across the sample. Is my > description any better this time? I am not 100% sure, but if I understand your problem correctly, loess() may be applicable. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technis

Re: [R] pdf greek letter typos

ont substitution in some version of the poppler library which is uses by many LINUX PDF viewers. Try to view the file in acrobat reader and possibly other viewers. Also: the files I had issues with printed correctly. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bio

Re: [R] CSV value not being read as it appears

check if the number of levels of each factor in my data.frame seems to make sense. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://w

Re: [R] Panel title: mfrow() or ?

> par(mfrow=c(3,2)) > > The 6 graphs are coming out quite all right, but now I would like to > put a title on top of the page - i.e. something that is common for > all 6 graphs - how can I do that? title(main="My title", outer=TRUE) cu Philipp -- Dr. Ph

Re: [R] How to save & play back an entire R session?

scripts to begin with. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.

Re: [R] 300 dpi and eps:

rPoint does not support any vector formats except that flaky wms/ems format there is no other choice. So I convert to a e.g. 600dpi png. (Has this changed in recent versions of PowerPoint?) But mind you: I don't do that in R, so I always have a vector format master figure. cu Ph

Re: [R] 300 dpi and eps:

s an eps and thus of essentually infinite resolution for all practial purposes. So your problem is not with the R-generated eps but somewhere downstream from that. Any postprocessing, conversion or editing? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinfo

Re: [R] evaluating NAs in a dataframe

: # make up some data foo <- data.frame(a=sample(1:20, 20, replace=TRUE)) # assign to classes foo$class <- cut(foo$a, breaks=c(-1, 7, 13, 20), labels=c('small', 'medium', 'large')) This also works in the presence of NAs - but of course the class will be NA in those ca

Re: [R] How to save a data set as .txt on fly?

d. R does not care about the file unless you load it and you can pick any filename you like without affecting the name of the object(s). Once loaded, there is no magical link between the two. Of course, when you load objects from a file this will overwrite any objects of the same names (object names,

Re: [R] How to save a data set as .txt on fly?

the .txt file created in this way can't be read with > Notpad and WordPad? It can be read with them - only it does not look the way you expected. If you want to export data for use in other software funcitons like write.table may be of interest to you. Load and save are meant for use i

Re: [R] shifting down ylab in a plot

ot; to shift down my "ylab" ?? There may be a simpler/more elegant way to do it, but this does what you asked for: # plot data omitting the ylab plot(1:10,1:10, ylab='') # add the ylab myself using flushleft (adj=0.0) mtext('foo', side=2, line=3, adj=0.0) cu

Re: [R] Change column of numbers in data frame to days

7;Wed', 'Thu', 'Fri', 'Sat', 'Sun')) foo cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webcl

Re: [R] Help with R

he closes. Re-installation of R will most likely not fix this (unless a change in the format of the .RData files had occurred - but to my knowledge no such thing has happened, recently.) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universi

Re: [R] Scripting help

Oh - and also have a look at the R graph gallery for inspiration: http://addictedtor.free.fr/graphiques/ cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354

Re: [R] Scripting help

- choosing the respective functions depending on the complexity of the task. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Frei

[R] lattice: layout and number of pages

, layout=c(2,1,5)) Did I misinterpret the sentence from the help page or is this a bug? Yes - I know that his works fine: stripplot(yield~year|site, barley, layout=c(2,1)) Just curious... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universit

Re: [R] How to Adaptively Set Up the Coordinate Range of Multiple Graphs in One Figure

d waht exactly you want to get but if you explicitly set the limits that's what R is going to use. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354

Re: [R] predict.loess and NA/NaN values

e wrapper that puts NAs back into results, is not a big deal and in that respect my problem is solved. > Nevertheless, take a look at the version in R-devel (pre-2.12.0) > which give you more options. Thanks for that information - I will definitely have a look at that. cu Philipp

Re: [R] predict.loess and NA/NaN values

he NAs, where I would like to have them. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/

[R] predict.loess and NA/NaN values

thing in the manual page that explains this behaviour or says how to change it. So I'm asking the community: Is there a way to fix this or do I have to code around it? This is in R 2.11.1 (Linux), by the way. Thanks in advance Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientie

Re: [R] Fwd: basic hist() question

> It works fine. > > Could you explain to me why it did not worked for read.table? Because of what Gavin already explaied in his reply: read.table returns a data.frame and hist needs a vector. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik T

Re: [R] which one give clear picture-pdf, jpg or tiff?

turn EPS into PNG at 600dpi convert -density 600 foo.eps foo.png Very conveniant, especially if there are lots of figures to be converted: for file in *.eps; do convert -density 600 $file `basename $file .eps`.png; done cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientier

Re: [R] reading a text file, one line at a time

Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.org mai

Re: [R] Where the data file is stored?

ur current work directory (together with other variables in your workspace). If that is not what you did please give us mre information. BTW: R has a function called data and it is not a very good idea to use function names as variable names. cu Philipp -- Dr. Philipp Pagel Lehrstu

Re: [R] basic question about t-test with adjusted p value

the number or by handing a vector of p-values to the function. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~p

Re: [R] How to apply apply?!

g the command as an argument to the help function - specificly: ?apply help(apply) Especially the example section is useful for a jumpstart. Here is an example of computing row means: apply(foo, 1, mean) Instead of 'mean' you can insert whatever function you'd like to apply. cu

Re: [R] 64-bit R on 64-bit Windows box... Still not enough memory?!

builds of R. [...] cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ _

Re: [R] 64-bit R on 64-bit Windows box... Still not enough memory?!

ou may have to put your data into a database and process it in pieces. Or use sqldf or bigmemory or something like that. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-For

Re: [R] Error: cannot allocate vector of size xxx Mb

lable. What is wrong? > Shouldn't 38 MB be very feasible? >From what I gather fomr ?memory.limit it does not tell you how much memory it currently available. So my guess is that you have som rather large objects in your workspace already and thus there is not enough space left for you v

Re: [R] two graphs 1 x-axis

e two datasets with different x-ranges into the same range, you can use the xlim parameter to define the desired range. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Freising, Germany h

Re: [R] Converting dataframe to matrix

5 18 > apply(matrix(1:9, nrow=1), 1, sum) [1] 45 cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ _

Re: [R] Converting dataframe to matrix

3 332 1.732051 0.6931472 441 2.00 0.000 > det(foo) Error in UseMethod("determinant") : no applicable method for "determinant" > det(as.matrix(foo)) [1] -0.1092489 So probably your problem is somewhere else. cu Philipp -- Dr. Phili

Re: [R] Stretch the x-axis for better alignment comparison

t it. If reading out data from the graph is a concern, you may also want to look at the grid() command. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://web

Re: [R] strange split behavior?

a c d e a c d e Levels: a c d e cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-

Re: [R] Datetime conversion

lt;- as.data.frame(datetime) > > dt$date<-strptime(as.character(dt$datetime),"%d%b%Y") > > and got the following error : > > Error in `$<-.data.frame`(`*tmp*`, "date", value = list(sec = c(0, 0, : > replacement has 9 rows, data has 12. Oops - so

Re: [R] Suppressing script commands in R console when executing long program

On Fri, Sep 18, 2009 at 12:59:16PM +0200, Philipp Pagel wrote: > > foo$B <- as.numeric(sub(',', '', as.character(foo$B))) Thinking about it some more, you should use gsub instead of sub here. Otherwise only the first occurrence of the thousands separator will be

Re: [R] Datetime conversion

inly not from the example used in previous postings, as the data fram eused there has 9 rows, not 14. Without the details (code) on what you did its all guesswork. Perhaps you are mixing two data.frames of differnt shape or ... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorient

Re: [R] Suppressing script commands in R console when executing long program

: Factor w/ 4 levels "12,300","256,001.01",..: 1 2 4 3 > foo$B <- as.numeric(sub(',', '', as.character(foo$B))) > foo AB 1 1 12300.0 2 2 256001.0 3 3900.1 4 4 80.0 > str(foo) 'data.frame': 4 obs. of 2 variables: $ A

Re: [R] latex code in R -> convert to pdf

On Thu, Sep 17, 2009 at 10:08:57AM +0200, Philipp Pagel wrote: > > > > is it possible to convert latex code to pdf in R (like a > > latex-program would do it)? > > Is there a package that comes with this capabilities? > > > > > > My problem is th

Re: [R] latex code in R -> convert to pdf

ter ... > > > Besides latex ... are there good ways to generate tables in R? Have a look at Sweave and xtable - I think that's what you want. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum

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