Re: [R] Performance (speed) of ggplot

2014-09-26 Thread Jeff Newmiller
You are asked in the Posting Guide to provide a small, reproducible example. Your function is Byzantine, and depends on who knows what, and I can't even see what your end product is intended to be. I will say that I think you have missed the point with your approach to using ggplot... you

Re: [R] error in rownames

2014-09-26 Thread PIKAL Petr
Hi. Partly. You got response from David regarding HTML formating. I polished scrammbled text but I got AsciiGridImpute(type.rf, xfile, outfile) Error in file(xfiles[[i]], open = rt) : cannot open the connection In addition: Warning message: In file(xfiles[[i]], open = rt) : cannot open file

Re: [R] Median of streaming data

2014-09-26 Thread Martin Maechler
Rolf Turner r.tur...@auckland.ac.nz on Thu, 25 Sep 2014 11:44:38 +1200 writes: On 24/09/14 20:16, Martin Maechler wrote: SNIP 1) has your proposal ever been provided in R? I'd be happy to add it to the robustX (http://cran.ch.r-project.org/web/packages/robustX) or

Re: [R] Performance (speed) of ggplot

2014-09-26 Thread PIKAL Petr
Hi I will second Jeff. If you want several plots on one page it could be more convenient to use standard plot. see ?layout or ?split.screen for complex figures or ?par mfrow for simple layout. In all cases it is difficult to combine base and grid graphics though. Regards Petr

Re: [R] Performance (speed) of ggplot

2014-09-26 Thread ONKELINX, Thierry
You are using ggplot2 very inefficiently. Many geom's plot only one data point. You can combine several of them in a single geom. Have a look at this gridExtra package which has some useful functions like grid.arrange and tableGrob. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en

Re: [R] Can't seem to get lapply to work.

2014-09-26 Thread Keith S Weintraub
Jeff, Of course a data.frame is a list of columns. Duh! Sorry about that. Was working about 10 hours straight. Also sorry about the excess attributes. They were created by via expand.grid. Here is my current solution which seems to be working: lapply(1:nrow(tstSet), function(x, y, z)

[R] Help with conversion of variable labels (Hmisc and Epicalc)

2014-09-26 Thread Otto Pichlhöfer
For my epidemiological analysis I use the packages Epicalc and Hmisc – among others. Both packages allow to assign variable labels that will appear in the output of the respective packages’ own functions. The modes of storage of the labels in a dataframe are very different. I am wonderiung if

[R] Savitzky-Golay Smoother

2014-09-26 Thread Erick Okuto
Dear Paul and Henrik, I have a time series with some missing data points that i need smoothed using Savitzky-Golay filter. Related question was asked here http://thr3ads.net/r-help/2012/11/2121748-Savitzky-Golay-filtering-with-missing-data but no straight forward answer was posted. However,

[R] [rJava] RJavaClassLoader and system classloader

2014-09-26 Thread Benoît Thiébault
Hi everyone, I want to call a Java application from R and have encountered some problems with the way rJava deals with the system class loader. To run my application, I use the following R script: library(rJava) .jinit() .jaddClassPath(myApp.jar) rWrapper - .jnew(org/test/RWrapper)

Re: [R] Help with conversion of variable labels (Hmisc and Epicalc)

2014-09-26 Thread David Winsemius
On Sep 26, 2014, at 3:21 AM, Otto Pichlhöfer wrote: For my epidemiological analysis I use the packages Epicalc and Hmisc – among others. Both packages allow to assign variable labels that will appear in the output of the respective packages’ own functions. The modes of storage of the

[R] package loadable in R 3.1.1 Rterm but not in emacs/ESS

2014-09-26 Thread Christopher W Ryan
I'm running R on Windows 7. Clean install on a brand new computer yesterday. I installed Protext then R then Vincent Goulet's emacs with ESS, in that order. I then installed some R packages, in the R terminal window. Among them was car Today I opened emacs, hit M-x R to start an R session, and

[R] question regarding pcalg package

2014-09-26 Thread Jack Luo
Hi, I am trying to use the pcalg package to do some causal inference on some high dimensional omics data (~ 30k variables). It takes forever to run and my machine get stuck. I just realized that conditional independence test can be calculated without using the correlation matrix (I think it's

Re: [R] Savitzky-Golay Smoother

2014-09-26 Thread Paul Kienzle
You can perform the equivalent filtering by hand using something like: k = (window_length - 1) / 2 for i in k to len(x) - k xh,yh = x[points-k:points+k], y[points-k:points+k] idx = isfinite(xh) and isfinite(yh) xh,yh = xh[idx],yh[idx] p = polyfit(xh,yh,

[R] Histogram from a single column of a data frame

2014-09-26 Thread Richard Lerner
Column 7 of oded is Breed. If I enter summary(Breed) I get the counts of the numbers in each breed. However, if I enter I have tried hist($Breed) Error: unexpected '$' in hist($ hist(Breed) Error in hist(Breed) : object 'Breed' not found hist(Breed) Error in hist.default(Breed) : 'x' must

Re: [R] Help with conversion of variable labels (Hmisc and Epicalc)

2014-09-26 Thread David Winsemius
On Sep 26, 2014, at 4:21 AM, Otto Pichlhöfer wrote: For my epidemiological analysis I use the packages Epicalc and Hmisc – among others. Both packages allow to assign variable labels that will appear in the output of the respective packages’ own functions. The modes of storage of the labels

Re: [R] Histogram from a single column of a data frame

2014-09-26 Thread William Dunlap
Try hist(oded$Breed) (I suspect that summary(Breed) does not work in your current session either - perhaps you had a dataset named just Breed or had attached the data.frame oded in the session where summary(Breed) works.) Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Sep 26, 2014 at

Re: [R] Histogram from a single column of a data frame

2014-09-26 Thread Rolf Turner
On 27/09/14 05:57, Richard Lerner wrote: Column 7 of oded is Breed. If I enter summary(Breed) I get the counts of the numbers in each breed. However, if I enter I have tried hist($Breed) Error: unexpected '$' in hist($ hist(Breed) Error in hist(Breed) : object 'Breed' not found

Re: [R] Median of streaming data

2014-09-26 Thread Rolf Turner
On 26/09/14 21:48, Martin Maechler wrote: Rolf Turner r.tur...@auckland.ac.nz SNIP I have coded up the algorithm from the Cameron and Turner paper. Dunno if it gives exactly the same results as my (Splus?) code from lo these many years ago (the code that is lost in

Re: [R] Savitzky-Golay Smoother

2014-09-26 Thread Gabor Grothendieck
On Fri, Sep 26, 2014 at 3:32 AM, Erick Okuto erickok...@gmail.com wrote: Dear Paul and Henrik, I have a time series with some missing data points that i need smoothed using Savitzky-Golay filter. Related question was asked here

[R] quadprog::solve.QP sometimes returns NaNs

2014-09-26 Thread Benjamin Tyner
Hello, Here is an example; hopefully it is reproducible on others' platform: library(quadprog) n - 66L set.seed(6860) X - matrix(1e-20, n, n) diag(X) - 1 Dmat - crossprod(X) y - seq_len(n) dvec - crossprod(X, y) Amat - diag(n) bvec - y + runif(n)