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 I

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 -

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

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 problems. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

Re: [R] problem in reading a sequence file

? 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 Freising, Germany http://webclu.bio.wzw.tum.de

Re: [R] problem in reading a sequence file

[, 'Sequence'] [1] NNATTAAAGGGC str(dat) 'data.frame': 1 obs. of 1 variable: $ Sequence: chr NNATTAAAGGGC cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http

Re: [R] (no subject)

. 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.wzw.tum.de/~pagel

Re: [R] Shrink file size of pdf graphics

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 Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de

Re: [R] TR: Simulate keyboard

/expect4win/ 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/ __ R

Re: [R] TR: Simulate keyboard

than you will care for. 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] 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 Genomorientierte

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 list and there is no .Machine

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

need to let us know where your Hist() function came from. hist() from package graphics does not have a scale parameter and honours ylim without a problem. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum

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

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 available on Windows for this. cu Philipp -- Dr. Philipp Pagel

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

, 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. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik

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

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 Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum

Re: [R] Simple Missing cases Function

: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 Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

Re: [R] Simple Missing cases Function

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 Lehrstuhl für Genomorientierte Bioinformatik

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. Philipp Pagel Lehrstuhl für

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

. 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 http://webclu.bio.wzw.tum.de/~pagel

Re: [R] Hash table...

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 Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische

Re: [R] for loop performance

-- 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 mailing

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

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: Philipp Pagel p.pa...@wzw.tum.de

Re: [R] for loop performance

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-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de

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

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.bio.wzw.tum.de/~pagel

Re: [R] xyplot, groups and colors

$group2)) Perfect! Using the levels directly had not occured to me. Thanks! cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

Re: [R] list to data frame

the list of elements of ineffFilesList? as.data.frame(ineffFilesList) 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] xyplot, groups and colors

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 Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3

Re: [R] force output dimension of table function

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

Re: [R] function order

,]123 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] Saving console and graph output to same file

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 Universität München Wissenschaftszentrum Weihenstephan Maximus-von

Re: [R] one question about bioconductor

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 Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum

Re: [R] read password-protected files

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 Wissenschaftszentrum Weihenstephan

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

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=). cu Philipp -- Dr. Philipp Pagel Lehrstuhl für

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

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 3 85354 Freising, Germany http

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

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.wzw.tum.de/~pagel

Re: [R] Reversing order of vector

-- 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 mailing list

Re: [R] producing histogram-like plot

- 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 Philipp -- Dr. Philipp Pagel Lehrstuhl für

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

won't have to do it again if I need to produce another revision of the figure - all it takes is anoother run of my script. And I can re-use good solutions in the future. Any manual touch-ups have to be done manually every single time = not my idea of efficiency. cu Philipp -- Dr. Philipp

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

) dat2 - as.data.frame(t(dat)) If the comlumns are of differnt types (e.g. some numeric, some factors) I don't think you can do this at all, because columns of a data.frame represent vectors, i.e. all value sin a column need to be of the same type. cu Philipp -- Dr. Philipp Pagel Lehrstuhl

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

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://webclu.bio.wzw.tum.de/~pagel

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

names rownames(frame) = frame[,1] # remove the old name column frame - frame[,2:ncol(frame)] cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

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

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-von-Imhof-Forum 3 85354 Freising, Germany http

Re: [R] Magic Number Error Message

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

Re: [R] Bar Chart

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 Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

Re: [R] graph lines don;t appear

(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 simply don't see your data... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

Re: [R] beamer overlays with Sweave?

) dev.off() cat(\\only, slidenum, {\includegraphics{, plotfilename ,}}\n ,sep=) @ If you want toget really fancy, you could wrap most of this in a conveniance function... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

Re: [R] beamer overlays with Sweave?

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

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

Re: [R] How two compare two matrixes

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 Freising, Germany http

Re: [R] How two compare two matrixes

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 für Genomorientierte Bioinformatik Technische Universität

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 München

Re: [R] read.table

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

Re: [R] qbeta

/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/ __ R-help

Re: [R] fitting logit to data

() 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, Germany http://webclu.bio.wzw.tum.de/~pagel

Re: [R] Matrix in R

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 Freising, Germany http

Re: [R] saving plots

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. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik

Re: [R] as.Date

at the manual page confirms that Epi's version does not have an origin option. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

Re: [R] as.Date

...): 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 fixed issue? cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte

Re: [R] Average of several line plots

not 100% sure, but if I understand your problem correctly, loess() may be applicable. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

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

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://webclu.bio.wzw.tum.de/~pagel

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. Philipp Pagel Lehrstuhl für

Re: [R] 300 dpi and eps:

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 Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische

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

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.org mailing list

Re: [R] 300 dpi and eps:

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 Bioinformatik Technische Universität

Re: [R] evaluating NAs in a dataframe

cases which, at least in my opinion, is the correct value. 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] How to save a data set as .txt on fly?

like write.table may be of interest to you. Load and save are meant for use in R, only. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

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

, 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, not file names!) that happen to live in your workspace before the load command. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für

Re: [R] shifting down ylab in a plot

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 Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München

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

. 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 mailing list https

Re: [R] Help with 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 Universität München Wissenschaftszentrum

Re: [R] Scripting help

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 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel

[R] lattice: layout and number of pages

(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 Universität München

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

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 Freising, Germany http

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

, 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/~pagel

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

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 -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München

[R] predict.loess and NA/NaN values

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 Genomorientierte Bioinformatik

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 Technische

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

in *.eps; do convert -density 600 $file `basename $file .eps`.png; done cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

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

. 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 mailing list https

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

and it is not a very good idea to use function names as variable names. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http

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

concept that I am missing here... I'm confused - what result where you expecting? p.adjust will need to know the number of test you are trying to adjust for - either by giving explicitly giving the number or by handing a vector of p-values to the function. cu Philipp -- Dr. Philipp

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

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-Forum 3 85354 Freising, Germany http

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

. [...] 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/ __ R-help@r

Re: [R] How to apply apply?!

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 Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität

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

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 vectors. cu Philipp -- Dr. Philipp Pagel Lehrstuhl

Re: [R] Converting dataframe to matrix

(determinant) : no applicable method for determinant det(as.matrix(foo)) [1] -0.1092489 So probably your problem is somewhere else. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Freising

Re: [R] Converting dataframe to matrix

cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.org mailing list https

Re: [R] two graphs 1 x-axis

(mrfow=c(2,1)) plot(d$a, d$b, col=red) plot(d$a, d$c, col=red, pch=|) As both plots use the same data for X you are set. If you need to force 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

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

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://webclu.bio.wzw.tum.de/~pagel

Re: [R] strange split behavior?

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.org mailing list https

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

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: int 1 2 3 4 $ B: num 12300 256001 900 80 cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte

Re: [R] Datetime conversion

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 Genomorientierte Bioinformatik Technische Universität

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 removed. cu Philipp

Re: [R] Datetime conversion

- sorry you are right. There is a Problem with inserting the object. Try this instead: dt$date - as.Date(dt$datetime, %d%b%Y) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising

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

... 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 Weihenstephan 85350 Freising, Germany http

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 that I want to generate tables automatically - and I can't use

Re: [R] Data separated by spaces, getting data into R using field lengths

the impression that your data file uses a mixture of separation characters and fixed-width formatting. Maybe I misinterpreted your example. Have a look at read.fwf() an if that does not solve your problem maybe explain the Structure and expected result a little further. cu Philipp -- Dr. Philipp

Re: [R] Data separated by spaces, getting data into R using field lengths

hard to parse the data - and it may even be impossible depending on what characters are allowed in your free-text fields. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany

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