Re: [R] simulated correlated vectors
On Thu, 12 Nov 2009 08:10:12 -0800 (PST) carol white wht_...@yahoo.com wrote: Having a vector x of float type without any assumption of its distribution (mean, variance etc), how to generate another vector that is correlated with x? Define an arbitrary function 'f', where 'f' may have a random component, and calculate f(x). Extensibility: how to simulate more than two correlated vectors (again float type and no preference for their distribution and without having vector x)? Repeat step 1 several times. If you don't have 'x', define an arbitrary vector 'x' first ... HTH. HAND. -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] survreg function in survival package
Hi, Is it normal to get intercept in the list of covariates in the output of survreg function with standard error, z, p.value etc? Does it mean that intercept was fitted with the covariates? Does Value column represent coefficients or some thing else? Regards, - tmp = survreg(Surv(futime, fustat) ~ ecog.ps + rx, ovarian, dist='weibull',scale=1) summary(tmp) Call: survreg(formula = Surv(futime, fustat) ~ ecog.ps + rx, data = ovarian, dist = weibull, scale = 1) Value Std. Error zp (Intercept) 6.962 1.322 5.267 1.39e-07 ecog.ps -0.433 0.587 -0.738 4.61e-01 rx 0.582 0.587 0.991 3.22e-01 Scale fixed at 1 Weibull distribution Loglik(model)= -97.2 Loglik(intercept only)= -98 Chisq= 1.67 on 2 degrees of freedom, p= 0.43 Number of Newton-Raphson Iterations: 4 n= 26 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting Histogram using histogram() and for loop and I want to save the histogram individually ... HELP
On Thu, 12 Nov 2009 19:10:52 -0800 (PST) ychu066 ychu066 @aucklanduni.ac.nz wrote: And I also want to save each histogram in each separate pdf file using the following codes ?. png(hist.png[i]) dev.off() Try png(paste(hist,i,.png,sep=) instead. -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem building R 2.10.0 - Matrix package
Thank you, Russ,
but ...
RPH == R P Herrold herr...@owlriver.com
on Thu, 12 Nov 2009 14:13:26 -0500 (EST) writes:
TA == Thomas Adams thomas.ad...@noaa.gov
TA Attached is the output file from building R 2.10.0 on RedHat Linux. I
TA have never previously experienced any problems when building R from
TA source with new releases. But, now I get a compile error with the Matrix
TA package:
[...]
RPH The Raw Hide packaging of R 2.10.0 has Matrix in it as a
RPH new addition ...
RPH [herr...@centos-5 monit]$ rpm -qf /usr/lib64/R/library/Matrix
RPH R-core-2.10.0-2orc
RPH ... whose packaging of such a build of R are you using, that
RPH you need to package /Matrix separately?
No, we were talking about building R from the sources.
That should still be pretty easily possible on any Linux system
{which has compilers/perl/latex/tcltk/ and a couple of libraries}.
Martin
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Re: [R] XML: Reading transition matrices into R
Thank you so much
You really helped me a lot!
Best from R'dam,
Stefan
On Fri, Nov 13, 2009 at 2:14 AM, Duncan Temple Lang
dun...@wald.ucdavis.edu wrote:
stefan.d...@gmail.com wrote:
Hello,
thanks a lot. This is a form which I can work with in R.
Another question, which I hope is not a bridge too far: Can I write
the R matrix which your code created back into the xml format (i.e.
with the same tags and structure) from which it came and hence feed it
back to the original software?
trans = apply(xx, 1, function(x) {
tr = newXMLNode(transition)
mapply(newXMLNode, names(x), x, MoreArgs = list(parent
= tr))
tr
})
top = newXMLNode(transitionmatrix, .children = trans)
saveXML(top, newTransition.xml)
Best,
Stefan
On Thu, Nov 12, 2009 at 3:17 PM, Duncan Temple Lang
dun...@wald.ucdavis.edu wrote:
stefan.d...@gmail.com wrote:
Hello,
from a software I have the following output in xml (see below):
It is a series of matrices, for each age one. I have 3 categories
(might vary in the application), hence, 3x3 matrices where each
element gives the probability of transition from i to j. I would like
read this data into R (preferably in a list, where each list element
is one of the age specific matrices) and - after altering the values
in R - write it back into the file. I know that there is an xml
package in R with which I have already struggled, but I have to admit
my understanding is too limited. Maybe somebody had a similar problem
or know the code of the top of his or her head.
Hi Stefan
There are many approaches for handling this. I assume that the primary
obstacle you are facing is extracting the values from the XML. The
following
will do that for you.
We start with the content in transition.xml (or in a string in R).
Since the XML is very shallow, i.e. not very hierarchical, and all
the information is in the transition nodes under the root, we can
use xmlToList().
This returns a list with an element for each transition
element, and such elements are character vectors containing the
values from age, sex, from, to, and percent.
So I've put these into a matrix and you are now back entirely
within R and can group the values by age and arrange them into
the individual transition matrices.
doc = xmlParse(transition.xml)
matrix(as.numeric(unlist(xmlToList(doc))), , 5, byrow = TRUE,
dimnames = list(NULL, names(xmlRoot(doc)[[1]])))
D.
Any help appreciated.
Thanks and best,
Stefan
?xml version=1.0 encoding=UTF-8 standalone=no?transitionmatrix
transitionage0/agesex0/sexfrom1/fromto1/topercent99.9/percent/transitiontransitionage0/agesex0/sexfrom1/fromto2/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom1/fromto3/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom2/fromto1/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom2/fromto2/topercent99.85/percent/transitiontransitionage0/agesex0/sexfrom2/fromto3/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom3/fromto1/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom3/fromto2/topercent0.0/percent/transitiontransitionage0/agesex0/sexfrom3/fromto3/topercent99.85/percent/transitiontransitionage0/agesex1/sexfrom1/fromto1/topercent100.0/percent/transitiontransitionage
0
/!
agesex1/sexfrom1/fromto2/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom1/fromto3/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom2/fromto1/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom2/fromto2/topercent100.0/percent/transitiontransitionage0/agesex1/sexfrom2/fromto3/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom3/fromto1/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom3/fromto2/topercent0.0/percent/transitiontransitionage0/agesex1/sexfrom3/fromto3/topercent100.0/percent/transitiontransitionage1/agesex0/sexfrom1/fromto1/topercent99.9/percent/transitiontransitionage1/agesex0/sexfrom1/fromto2/topercent0.0/percent/transitiontransitionage1/agesex0/sexfrom1/f
ro
m!
to3/topercent0.0/percent/transitiontransitionage1/age
sex0/sexfrom2/fromto1/topercent0.0/percent/transitiontransitionage1/agesex0/sexfrom2/fromto2/topercent99.85/percent/transitiontransitionage1/agesex0/sexfrom2/fromto3/topercent0.0/percent/transitiontransitionage1/agesex0/sexfrom3/fromto1/topercent0.0/percent/transitiontransitionage1/agesex0/sexfrom3/fromto2/topercent0.0/percent/transitiontransitionage1/agesex0/sexfrom3/fromto3/topercent99.85/percent/transitiontransitionage1/agesex1/sexfrom1/fromto1/topercent100.0/percent/transitiontransitionage1/agesex1/sexfrom1/fromto2/topercent0.0/percent/transitiontransitionage1/agesex1/sexfrom1/fromto3/topercent0.0/percent/transitiontransitionage1/agesex1/sexfrom2/fromto1/topercent0.0/percent/transitiontransitionage1/agesex1/sexfrom2/f
ro
m!
[R] All combination
Please consider the following : expand.grid(rep(list(c(1:3)), 3)) Var1 Var2 Var3 1 111 2 211 3 311 4 121 5 221 6 321 7 131 8 231 9 331 10112 11212 12312 13122 14222 15322 16132 17232 18332 19113 20213 21313 22123 23223 24323 25133 26233 27333 Now I want to remove the rows which has any repetition of number. For example I want to remove row 1-5 but not 6 and so on Is there any easy way to do that? Thanks, -- View this message in context: http://old.nabble.com/All-combination-tp2648p2648.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] All combination
have a look at function permutations from package 'e1071', e.g., library(e1071) permutations(3) I hope it helps. Best, Dimitris RON70 wrote: Please consider the following : expand.grid(rep(list(c(1:3)), 3)) Var1 Var2 Var3 1 111 2 211 3 311 4 121 5 221 6 321 7 131 8 231 9 331 10112 11212 12312 13122 14222 15322 16132 17232 18332 19113 20213 21313 22123 23223 24323 25133 26233 27333 Now I want to remove the rows which has any repetition of number. For example I want to remove row 1-5 but not 6 and so on Is there any easy way to do that? Thanks, -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dfbetas vs dfbeta
alphaace wrote:
Hi, I've looked around but can't find a clear answer to the difference for
these two? Any help?
Thanks!
One is a scaled version of the other, at least for lm objects:
stats:::dfbetas.lm
function (model, infl = lm.influence(model, do.coef = TRUE),
...)
{
xxi - chol2inv(model$qr$qr, model$qr$rank)
dfbeta(model, infl)/outer(infl$sigma, sqrt(diag(xxi)))
}
so it is essentially dividing by s.e.(beta), except that it uses
infl$sigma which AFAICS is the leave-one-out residual sd.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
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Re: [R] R package for reading / writing 3D file (. PLY)
Duncan Murdoch-2 wrote: On 11/12/2009 11:37 AM, kvarpun wrote: Duncan Murdoch-2 wrote: On 11/12/2009 4:56 AM, kvarpun wrote: Hi, Is there an R package that reads and writes 3D images having the extension PLY (PLY images of Stanford University)? Currently, I installed the package misc3d. This package displays these images PLY, but it can neither read nor write PLY images. This doesn't make sense. How can it display PLY images if it can't read them? Could you give an example? Duncan Murdoch Thank you to tell me the name of a package that will read and write such images. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thank you for quick answer. I have to inform you that the only available functions in the package misc3d are: contour3d Draw an Isosurface, a Three Dimension Contour Plot drawSceneRendering of Triangular Mesh Surface Data image3dDraw Points on a 3D Grid kde3dCompute a Three Dimension Kernel Density Estimate makeTriangles Triangle Mesh Functions parametric3d Draw a 3D Parametric Plot perspLighting Lighting Functions phongLighting Lighting Functions pointsTetrahedra Create a Set of Tetrahetra Centered at Data Points scaleTriangles Triangle Mesh Functions slices3d Interactive Image Slices of 3D or 4D Volume Data surfaceTriangles Create a Triangle Mesh Representing a Surface teapotUtah Teapot translateTriangles Triangle Mesh Functions updateTriangles Triangle Mesh Functions None of them does read/write a PLY file. You will find below a simple code for drawing a 3D image. The displayed image is stored in the package misc3d (not read from a file). library(misc3d) data(teapot) haveRGL - suppressWarnings(require(rgl,quietly=TRUE)) ttri - makeTriangles(teapot$vertices, teapot$edges, color = red, color2 = green) ## draw the teapot drawScene(ttri,screen=list(y=-30,x=40), scale = FALSE) str(teapot) # str(teapot) # List of 2 # $ vertices: num [1:3, 1:1976] -3,00 1,65 0,00 -2,99 1,65 ... # $ edges : int [1:3, 1:3751] 1455 1469 1459 1449 1455 1459 1462 1449 1459 1469 ... # My images (PLY images) have vertices and edges like the teapot image in the example. If PLY images are read by R, I will be able to manipulate them. Okay, I understand now. Yes, R can display 3D images based on lines and polygons using the rgl package or scatterplot3d or grid graphics, but those have nothing to do with PLY files. As far as I know there is no existing code to read or write a PLY file, but from the look of it, it's a simple format and it wouldn't be hard to write input/output routines. The likely problems are: - it's an open ended format, with each application allowed to define its own record types. If your files come from an application that did that you may have trouble working out what was intended and reading it in. - some of the recommended elements are not supported in rgl or other 3D renderers in R. In particular, polygons with more than 4 vertices need to be decomposed into triangles or quads, and rgl knows nothing about refraction index: you'd probably need a ray-tracing renderer for that. - rgl scenes contain text, and as far as I can see, there's no way to include that in a standard PLY file, so you'd need to invent your own record type for it. Text is always hard to describe graphically, so this wouldn't be easy. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thank you for all these precisions. I guess developping an R package for reading/writing PLY files is required. Have a nice day. -- View this message in context: http://old.nabble.com/R-package-for-reading---writing-3D-file-%28.-PLY%29-tp26315292p26333989.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] starting html help for a package?
On 11/12/09, Duncan Murdoch murd...@stats.uwo.ca wrote: help(package=boot, help_type = html) The page displayed there was never an HTML page. In the future it probably should be, but it hasn't been implemented yet. At the moment is there a way to call the html help for a package, that is starting in a browser the text displayed by help(package=boot)? It's in the tools package, which you probably hadn't attached. If you followed the advice and used ??, you would have got it. Indeed. I assumed that with 2.10 this was deprecated, but I was wrong. Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why the same values cannot be judged to be the same in R
I think you want to use '%in%' instead of '=='. Try debugging (or understanding) what is happening by evaluating the subexpressions of the compares you have in your original posting. Also take a look at the 'recycling' of arguments and then you may understand what is happening: data2[(data2$x1 %in% data_1$x1) (data2$y1 %in% data_1$y1) (data2$tag == 0),] areaid x1 y1 tag 2 1 1.53 2.34 0 4 1 1.52 2.35 0 On Thu, Nov 12, 2009 at 10:04 PM, rusers.sh rusers...@gmail.com wrote: Hi Rusers, I found sometimes that the same values cannot be judged to be the same in R. Anybody knows the probelm? I think i ignored some minor detail. Thanks. Here is the example. data1-matrix(data=c(1,1.2,1.3,3/23/2004,1,1.5,2.3,3/22/2004,2,0.2,3.3,4/23/2004,3,1.5,1.3,5/22/2004),nrow=4,ncol=4,byrow=TRUE) data1-data.frame(data1);names(data1)-c(areaid,x,y,date) data2-matrix(data=c(1,1.22,1.32,1, 1.53, 2.34,1, 1.21, 1.37,1, 1.52, 2.35,2, 0.21, 3.33,2, 0.23, 3.35,3, 1.57, 1.31,3, 1.59, 1.33),nrow=8,ncol=3,byrow=TRUE) data2-data.frame(data2);names(data2)-c(areaid,x1,y1) data2$tag-0 data1_1-data1[1,] data2_1-data2[data2$areaid==data1_1$areaid data2$tag==0,] ran_1-sample(c(1:length(data2_1)),2, replace = FALSE) data2_1-data2_1[ran_1,] data_1-merge(data1_1,data2_1) #data_1 # areaid x y date x1 y1 tag # 1 1 1.2 1.3 3/23/2004 1.52 2.35 0 # 2 1 1.2 1.3 3/23/2004 1.53 2.34 0 data2[data_1$x1==data2$x1 data_1$y1==data2$y1 data2$tag==0,] #data2[c(data_1$x1==data2$x1 data_1$y1==data2$y1 data2$tag==0),] # areaid x1 y1 tag #2 1 1.53 2.34 0 There should be two same observations between data_1 and data2, but here only one was identified. Thanks a lot. -- - Jane Chang Queen's [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] processing log file
Dear all, I'm trying to process a log file which logs the date, the username and the computer number accessed. The table looks like this: table.users Date UserName Machine 1 2008-11-25 John 641 2 2008-11-25 Clive 611 3 2008-11-25 Jeremy 641 4 2008-11-25 Walt 722 5 2008-11-25 Tony 645 6 2008-11-26 Tony 645 7 2008-11-26 Tony 641 8 2008-11-26 Tony 641 9 2008-11-26 Walt 641 10 2008-11-26 Walt 645 11 2008-11-30 John 641 12 2008-11-30 Clive 611 13 2008-11-30 Tony 641 14 2008-11-30 John 641 15 2008-11-30 John 641 ..etc What I want to do is to find out how many unique users logged on each day, and how many individual machines where accessed per day. In the above example, therefore on 2008-11-25 there were 5 separate users accessing 4 machines, on 2008-11-26 there were 2 unique users who used 2 machines (although both logged on more than once). I've got as far as apply(table.users, 2, FUN=table) which gives me an output of date, or username or machine and how many times they were accessed, but not really what I want. Any help appreciated Jabez [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R, NIH and FDA
Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] z-test with NAs
Dear all I am learning R I am doing Z-test with package 'BSDA' here is my syntax and result: sdgr.ztest-z.test(growth[type=='SD' from_treeline=='above'], + growth[type=='SD' from_treeline=='below'],alternative = two.sided, + mu = 0, sigma.x =(sd(growth[type=='SD' from_treeline=='above'],na.rm = T)), + sigma.y =(sd(growth[type=='SD' from_treeline=='below'],na.rm = T)), conf.level = 0.95) sdgr.ztest # Z-test for Seedling Growth above and below treeline Two-sample z-Test data: growth[type == SD from_treeline == above] and growth[type == SD from_treeline == below] z = NA, p-value = NAalternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: NA NA sample estimates:mean of x mean of yNANA I don't understand where my syntax went wrong. Similar syntax works for sapling case, but not for seedling case. is it due to the NAs in my data set for seedlings?, as the package says, NAs are allowed but will be removed during analysis, i don't think it is the problem. i am attaching the data file too. and one more information, I am using MS Windows 2003 OS. Please guide me, how can i go ahead. Thanking you in anticipation Warm regard MS Madan _ Bing brings you maps, menus, and reviews organized in one place. a=TEXT_MFESRP_Local_MapsMenu_Resturants_1x1id,code,growth,from_treeline,type 1,SD1,1.73,below,SD 2,SD2,1.12,above,SD 3,SD3,1.6,above,SD 4,SD4,1.66,above,SD 5,SD5,1.65,below,SD 6,SD6,1.43,above,SD 7,SD7,,above,SD 9,SD9,1.1,below,SD 10,SD10,1.44,above,SD 11,SD11,1.48,above,SD 12,SD12,2.25,above,SD 13,SD13,,above,SD 14,SD14,1.5,above,SD 15,SD15,,above,SD 16,SD16,1.06,above,SD 17,SD17,1.5,above,SD 18,SD18,4.17,below,SD 19,SD19,2.02,below,SD 20,SD20,1.38,above,SD 21,SD21,2,below,SD 22,SD22,1.41,above,SD 23,SD23,1.9,above,SD 24,SD24,1.7,above,SD 25,SD25,2.08,above,SD 26,SD26,1.92,below,SD 27,SD27,1.55,below,SD 28,SD28,1.48,below,SD 29,SD29,1.33,below,SD 30,SD30,1.5,above,SD 31,SD31,1.6,below,SD 32,SD32,1.24,below,SD 33,SD33,1.56,above,SD 34,SD34,1.58,below,SD 35,SD35,1.43,above,SD 36,SD36,1.3,above,SD 37,SD37,2.12,below,SD 38,SD38,1.63,below,SD 39,SD39,1.3,above,SD 40,SD40,1.16,below,SD 41,SD41,1.13,below,SD 42,SD42,1.43,below,SD 43,SD43,1.07,below,SD 44,SD44,1.25,below,SD 45,SD45,1.18,below,SD 46,SD46,1.17,above,SD 47,SD47,1,below,SD 48,SD48,1.43,above,SD 49,SD49,1.18,above,SD 50,SD50,1.17,below,SD 51,SD51,1.78,below,SD 52,SD52,1.67,above,SD 53,SD53,1,above,SD 54,SD54,1.8,below,SD 55,SD55,0.8,above,SD 56,SD56,0.95,above,SD 57,SD57,1.8,below,SD 58,SD58,,above,SD 59,SD59,,below,SD 60,SD60,,below,SD 61,SD61,,below,SD 62,SD62,,below,SD 63,SD63,,below,SD 64,SD64,,below,SD 65,SD65,0.93,below,SD 66,SD66,1.35,below,SD 67,SD67,1.33,below,SD 68,SD68,1.09,below,SD 69,SD69,1.41,below,SD 70,SD70,1.3,below,SD 71,SD71,1.2,below,SD 72,SD72,1.27,above,SD 73,SD73,0.7,below,SD 74,SD74,1.05,below,SD 75,SD75,1.68,below,SD 76,SD76,1.57,below,SD 77,SD77,1.22,above,SD 78,SD78,1.46,below,SD 79,SD79,2.32,below,SD 80,SD80,2.7,below,SD 81,SD81,1.57,above,SD 82,SD82,1.53,below,SD 83,SD83,1.63,below,SD 84,SD84,1.23,above,SD 85,SD85,1.77,below,SD 86,SD86,1.53,below,SD 87,SD87,1.39,below,SD 88,SD88,1.18,above,SD 89,SD89,1.85,below,SD 90,SD90,1.82,below,SD 91,SD91,,below,SD 92,SD92,1.74,below,SD 93,SD93,1.76,below,SD 94,SD94,1.16,below,SD 95,SD95,,below,SD 96,SD96,1.2,below,SD 97,SD97,1.42,below,SD 98,SD98,0.95,below,SD 99,SD99,2.43,below,SD 100,SD100,,below,SD 101,SD101,1.48,below,SD 102,SD102,1.33,below,SD 103,SD103,,below,SD 104,SD104,0.94,below,SD 105,SD105,,below,SD 106,SD106,1.15,below,SD 107,SD107,,below,SD 108,SD108,1.87,below,SD 109,SD109,1.23,below,SD 110,SD110,1.83,below,SD 111,SD111,1.47,below,SD 112,SD112,,below,SD 113,SD113,1.28,below,SD 114,SD114,,below,SD 115,SD115,1.57,below,SD 116,SD116,,below,SD 117,SD117,1.75,below,SD 118,SD118,1.8,below,SD 119,SD119,1.49,below,SD 120,SD120,1.54,below,SD 1,SPB1,2.19,above,SPB 2,SPB2,1.66,above,SPB 3,SPB3,1.78,above,SPB 4,SPB4,1.73,above,SPB 5,SPB5,8.63,above,SPB 6,SPB6,1.96,below,SPB 7,SPB7,5.17,above,SPB 8,SPB8,3.5,above,SPB 9,SPB9,2.78,above,SPB 10,SPB10,5.5,above,SPB 11,SPB11,2.75,below,SPB 12,SPB12,3,above,SPB 13,SPB13,4.71,above,SPB 14,SPB14,4.86,above,SPB 15,SPB15,4.63,below,SPB 16,SPB16,1.92,below,SPB 17,SPB17,3,below,SPB 18,SPB18,1.48,below,SPB 19,SPB19,2.35,below,SPB 20,SPB20,2.9,below,SPB 21,SPB21,2.35,below,SPB 22,SPB22,2.11,above,SPB 23,SPB23,1.92,below,SPB 24,SPB24,19.38,below,SPB 25,SPB25,2.33,above,SPB 27,SPB27,3.17,below,SPB 28,SPB28,1.73,below,SPB 29,SPB29,2.31,below,SPB 30,SPB30,1.9,below,SPB 31,SPB31,2.23,below,SPB 32,SPB32,2.04,below,SPB 33,SPB33,2.38,above,SPB 34,SPB34,4.9,above,SPB 35,SPB35,5.96,below,SPB 36,SPB36,1.77,below,SPB 37,SPB37,2.64,above,SPB 38,SPB38,4.01,above,SPB 39,SPB39,1.94,below,SPB 40,SPB40,1.8,above,SPB 41,SPB41,14.14,below,SPB 42,SPB42,6.5,above,SPB
Re: [R] starting html help for a package?
Liviu Andronic wrote: On 11/12/09, Duncan Murdoch murd...@stats.uwo.ca wrote: help(package=boot, help_type = html) The page displayed there was never an HTML page. In the future it probably should be, but it hasn't been implemented yet. At the moment is there a way to call the html help for a package, that is starting in a browser the text displayed by help(package=boot)? If you look at the index page, and if the package author created a package man page, you'll find it. That would give you the same thing as package?foo, not the same thing you asked for, which always generates package info, never looks it up. At some point in the future the package?info page will be able to be generated automatically, and I imagine it will end up containing the package info you saw. It would make sense for help(package=boot, help_type = html) to give the same result. Duncan Murdoch It's in the tools package, which you probably hadn't attached. If you followed the advice and used ??, you would have got it. Indeed. I assumed that with 2.10 this was deprecated, but I was wrong. Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to pass matrices from C to R effectively
Hao Cen wrote:
Hi Duncan,
Thanks for your reply. I am not sure what you meant by tell your C
function to use the memory that R sent to it. What R can pass to C is a
pointer to an array and the array size, assuming we are taking about the
.C mechanism. Did you mean my C function takes that array pointer and
generate the required matrix along the length of the array? If this is not
what you meant, would you please give me a small example?
Yes, that is what I meant.
Duncan Murdoch
Jeff
On Thu, November 12, 2009 6:53 pm, Duncan Murdoch wrote:
On 12/11/2009 6:45 PM, Hao Cen wrote:
Hi,
I have C code to produce a lot of matrices to be analyzed. As these
matrices are large ( 1000*1) and are a lot ( 1000), I am thinking
about how to pass them from C to R effectively.
Would you think about the following solution? In R, I create a wrapper
function
passDataFromCToR = function(row, col) { mat = matrix(0, row, col)
.C(passDataFromCToR,mat)[[1]]
That .C call doesn't match the header of the function below: you didn't
pass row and col.
}
It wraps the following C function
void passDataFromCToR (double *m, int *row, int* col){ mymat = f() // my
c function to produce a matrix // then I copy mymat to m element by
element via a loop
}
Then to use these functions, I would write in R
mat = passDataFromCToR(1000, 1)
Two issues with this approach are that 1) I have to copy the data once
and 2)to the worse, in R I have to know the dimension of the matrices to
be passed from C. This information is not always available.
Why would you have to copy the data? Just tell your C function to use
the memory that R sent to it, instead of copying entries into it. (R may
be doing a copy when you extract the results, though.)
If your C code can't use memory provided to it, then there are no simple
ways to avoid copying. The complicated way is to use the .Call interface
instead of .C. There are examples in Writing R Extensions. They *will*
require modifications to your code if it can't take a pointer to the
memory to use.
For the question of the dimensions being unknown in advance: Just write
two functions. The first does the calculations up to the point where it
needs the memory, the second works on an appropriately sized array, that
your R code allocated based on the first result. Or use the .Call()
interface.
Duncan Murdoch
I would appreciate if you share with me your thoughts on how to solve
this problem better.
thanks
Jeff
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Re: [R] processing log file
On Nov 13, 2009, at 6:03 AM, Jabez Wilson wrote: Dear all, I'm trying to process a log file which logs the date, the username and the computer number accessed. The table looks like this: table.users Date UserName Machine 1 2008-11-25 John 641 2 2008-11-25Clive 611 3 2008-11-25 Jeremy 641 4 2008-11-25 Walt 722 5 2008-11-25 Tony 645 6 2008-11-26 Tony 645 7 2008-11-26 Tony 641 8 2008-11-26 Tony 641 9 2008-11-26 Walt 641 10 2008-11-26 Walt 645 11 2008-11-30 John 641 12 2008-11-30Clive 611 13 2008-11-30 Tony 641 14 2008-11-30 John 641 15 2008-11-30 John 641 ..etc What I want to do is to find out how many unique users logged on each day, and how many individual machines where accessed per day. In the above example, therefore on 2008-11-25 there were 5 separate users accessing 4 machines, on 2008-11-26 there were 2 unique users who used 2 machines (although both logged on more than once). I've got as far as apply(table.users, 2, FUN=table) which gives me an output of date, or username or machine and how many times they were accessed, but not really what I want. Any help appreciated You were almost there. Just use lapply on the list object you produced: lapply(apply(table.users, 2, FUN=table), length) $Date [1] 3 $UserName [1] 5 $Machine [1] 4 Or if you want the individual items that you requested: lapply(apply(table.users, 2, FUN=table), length)$UserName [1] 5 lapply(apply(table.users, 2, FUN=table), length)$Machine [1] 4 -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splus
ozgur gultekin wrote: I am modelling oil price data in s plus, but I have some problem in my code, especially while I am estimating my model (ARMA GARCH) and also I have some question too, anyone can help me about S-plus? I think it has same syntax with R You should call their tech support, or use their mailing list. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data frame subsets?
On Nov 12, 2009, at 10:57 PM, Douglas M. Hultstrand wrote: Hello, I am trying to create data frame subsets based on binned temperature data. I have code working to create the bins (d.1 and d.2), but it takes two steps, I was wondering if I could merge into one step. See Below d n year mo da hr t td tw rh kPa 1 1 1945 3 1 0 1.1 0.0 0.6 92 101.7 2 2 1945 3 1 1 2.8 -1.1 1.1 76 101.8 3 3 1945 3 1 2 2.2 -1.7 0.6 75 101.9 4 4 1945 3 1 3 1.7 -1.1 0.6 82 102.0 5 5 1945 3 1 4 1.7 -2.8 0.0 72 102.1 6 6 1945 3 1 5 1.7 -1.7 0.0 78 102.2 7 7 1945 3 1 6 1.1 -2.8 0.0 75 102.2 8 8 1945 3 1 7 1.1 -1.7 0.0 82 102.4 9 9 1945 3 1 8 1.7 -1.1 0.6 82 102.5 10 10 1945 3 1 9 2.8 -3.3 0.6 64 102.6 d.1 - d[d$t = 1.0,] d.2 - d.1[d.1$t 2.0,] How can I make d.1 and d.2 into one step? I have tried several different methods such as example below. d.1 - d[d$t = 1.0, d$t 2.0,] Instead of using , use . It is the vectorized version of the AND operation. only operated on the first two elements and returned a scalar rather than the vector you needed. -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] survreg function in survival package
On Nov 13, 2009, at 3:17 AM, carol white wrote: Hi, Is it normal to get intercept in the list of covariates in the output of survreg function with standard error, z, p.value etc? Does it mean that intercept was fitted with the covariates? Does Value column represent coefficients or some thing else? Don't you need a baseline scale parameter for the Weibull function? You didn't offer the structure of your dataframe, but if it is the standard ovarian set, then the rx coef is just the difference between the scale parameter of rx=2 from that of rx=1, and similarly for ecog.ps. You would not have an estimate for rx=1 and ecog.ps=1 if you were not given the Intercept coef. In the future it would be good manners to indicate what grad school you are taking classes at. -- David Regards, - tmp = survreg(Surv(futime, fustat) ~ ecog.ps + rx, ovarian, dist='weibull',scale=1) summary(tmp) Call: survreg(formula = Surv(futime, fustat) ~ ecog.ps + rx, data = ovarian, dist = weibull, scale = 1) Value Std. Error zp (Intercept) 6.962 1.322 5.267 1.39e-07 ecog.ps -0.433 0.587 -0.738 4.61e-01 rx 0.582 0.587 0.991 3.22e-01 Scale fixed at 1 Weibull distribution Loglik(model)= -97.2 Loglik(intercept only)= -98 Chisq= 1.67 on 2 degrees of freedom, p= 0.43 Number of Newton-Raphson Iterations: 4 n= 26 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] starting pdf help for a package? (was starting html help for a package?)
Dear all A sequel to my previous post. On Fri, Nov 13, 2009 at 11:33 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: At some point in the future the package?info page will be able to be generated automatically, and I imagine it will end up containing the package info you saw. It would make sense for help(package=boot, help_type = html) to give the same result. Alternatively, I was also experimenting with help(package=boot, help_type = pdf) to call a formatted help of a package, but this too fell back to text, although I would have expected it to pop up [1]. Would it make sense to make the command do so in the future? Thank you Liviu [1] http://cran.r-project.org/web/packages/boot/boot.pdf __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R, NIH and FDA
On 13 Nov 2009, at 12:25, Barry Rowlingson wrote: Working with is different to Working for. Assuming they want to work with you then they want you for your abilities and skills, and if those skills are with R then you go ahead and use R. You don't employ a bricklayer to build a wall and then tell them you want it made from reinforced concrete. While I agree in principle I am not high enough in the food chain to avoid substantial pressure, unless using R is already established. Plus I'm working 'with' people who are either working 'for' or are just a step removed from doing so. F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] processing log file
On Fri, 13 Nov 2009 11:03:31 + (GMT) Jabez Wilson jabez...@yahoo.co.uk wrote: What I want to do is to find out how many unique users logged on each day, and how many individual machines where accessed per day. Use the 'plyr' package: library(plyr) ddply(table.users, .(Date), summarise, users=length(unique(Username)), machines=length(unique(Machine))) -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R, NIH and FDA
On Fri, Nov 13, 2009 at 11:21 AM, Federico Calboli f.calb...@imperial.ac.uk wrote: Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Working with is different to Working for. Assuming they want to work with you then they want you for your abilities and skills, and if those skills are with R then you go ahead and use R. You don't employ a bricklayer to build a wall and then tell them you want it made from reinforced concrete. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rarefaction Curve by Individuals not Sites - vegan (specaccum)
Hi List, Im using the vegan function specaccum to produce a rarefaction curve. In the functions help it says: Function specaccum finds species accumulation curves or the number of species for a certain number of sampled sites or individuals. Well, I would like to finds this curve for individuals, but when I compute it the function (using the rarefaction method) gives me Sites, Richness and Standand Deviation as values. When I plot it, y axis is the richness (ok with that) and x axis is Sites (here is the question), how could I make it calculate and plot the accumulating individuals number? Well, one problem may be the fact that my data frame has species as columns and Sites as rows (and abundance data frame) May you help me? Ps.: The rarefaction method option brings this details: All these methods are based on sampling sites without replacement. In contrast, the method = rarefaction finds the expected species richness and its standard deviation by sampling individuals instead of sites. Exactly what I really want, but not what I get! Here is the command line used. plot(specaccum(Spp[,-227],'rarefaction'),col='black',lwd=2,ci.lty=0,ci.type= 'poly',ci.col='lightgray',ylab='Riqueza',ylim=c(0,250),yaxp=c(0,250,10),bty= 'n',main='Fauna Viva - Bacia de Campos - Março 2009') Thank you very much. Regards. - MSc. mailto:r.alui...@gmail.com Rodrigo Aluizio Centro de Estudos do Mar/UFPR Laboratório de Micropaleontologia Avenida Beira Mar s/n - CEP 83255-000 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] speech spectogram
Le Mon, 19 Oct 2009 12:00:16 +0530, rajesh j a écrit : Hi, I need to plot a spectogram for a speech signal. Is there a package that can do this? Late answer, but you should have a look at seewave package on CRAN. The function spectro() is what you need. Olivier. -- Olivier Crouzet, PhD Laboratoire de Linguistique -- EA3827 Département de Sciences du Langage UFR Lettres et Langages Université de Nantes Chemin de la Censive du Tertre - BP 81227 44312 Nantes cedex 3 France phone:(+33) 02 40 14 14 05 (lab.) (+33) 02 40 14 14 36 (office) fax: (+33) 02 40 14 13 27 e-mail: olivier.crou...@univ-nantes.fr http://www.lling.fr/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] p-value 1
Dear all, I am trying to use SAMr-library(samr), it gives me p-value = 1.001, any idea why? Many thanks, Amor __ z gegen Massenmails. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R, NIH and FDA
Federico Calboli wrote: Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Cheers, Federico There are many R users are FDA, NIH, CDC, and other federal agencies. IT support tends to be a problem. Some agencies are using R 2.7, and getting packages installed in a timely manner may be difficult. Frank -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R, NIH and FDA
On Fri, 13 Nov 2009 11:21:30 + Federico Calboli f.calb...@imperial.ac.uk wrote: I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? You will (hopefully) be able to use R. See this document: http://www.r-project.org/doc/R-FDA.pdf -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem building R 2.10.0 - Matrix package
Martin,
That's exactly right. I'm simply building R from source, downloaded from
CRAN, and doing exactly what I have easily been able to do previously. I
think I first encountered this problem with version 2.9.2 (if memory
serves…).
Tom
Martin Maechler wrote:
Thank you, Russ,
but ...
RPH == R P Herrold herr...@owlriver.com
on Thu, 12 Nov 2009 14:13:26 -0500 (EST) writes:
TA == Thomas Adams thomas.ad...@noaa.gov
TA Attached is the output file from building R 2.10.0 on RedHat Linux. I
TA have never previously experienced any problems when building R from
TA source with new releases. But, now I get a compile error with the Matrix
TA package:
[...]
RPH The Raw Hide packaging of R 2.10.0 has Matrix in it as a
RPH new addition ...
RPH [herr...@centos-5 monit]$ rpm -qf /usr/lib64/R/library/Matrix
RPH R-core-2.10.0-2orc
RPH ... whose packaging of such a build of R are you using, that
RPH you need to package /Matrix separately?
No, we were talking about building R from the sources.
That should still be pretty easily possible on any Linux system
{which has compilers/perl/latex/tcltk/ and a couple of libraries}.
Martin
--
Thomas E Adams
National Weather Service
Ohio River Forecast Center
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Re: [R] Escaping regular expressions
Try the fixed argument: grep(.$^, c(Test.$^, Test), fixed = TRUE) On Fri, Nov 13, 2009 at 11:33 AM, Hadley Wickham had...@rice.edu wrote: Hi all, Is there a method for escaping strings to be used regular expressions? i.e. if I have a user supplied string that I'd like to use as a fixed component is there a method that will turn (e.g.) .$^ into \\.\\$\\^ ? Thanks, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Escaping regular expressions
Hi all, Is there a method for escaping strings to be used regular expressions? i.e. if I have a user supplied string that I'd like to use as a fixed component is there a method that will turn (e.g.) .$^ into \\.\\$\\^ ? Thanks, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with complicated regular expression
Colleagues, I am using R (2.9.2, all platforms) to search for a complicated text string using regular expressions. I would appreciate any help you can provide. The string consists of the following elements: SOMEWORDWITHNOSPACES any number of spaces and/or tabs ( any number of spaces and/or tabs integer any number of spaces and/or tabs ) Examples include: WORD ( 123) WORD(1 ) WORD\t ( 21\t) WORD \t ( 1 \t ) etc. I don't need to substitute anything, only to identify if such a string exists. Any help with regular expressions would be appreciated. Thanks. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with complicated regular expression
One of these should be a start. If there can be no extra text at the beginning or end, start with ^ and end with $. x - c(WORD ( 123), WORD(1 ), WORD\t ( 21\t), WORD \t ( 1 \t ), decoy((2)), more words in front(2)) grep([[:alpha:]]+[ \t]*\\([ \t]*[0-9]+[ \t]*\\), x) [1] 1 2 3 4 6 grep(^[[:alpha:]]+[ \t]*\\([ \t]*[0-9]+[ \t]*\\), x) [1] 1 2 3 4 -- Tony Plate Dennis Fisher wrote: Colleagues, I am using R (2.9.2, all platforms) to search for a complicated text string using regular expressions. I would appreciate any help you can provide. The string consists of the following elements: SOMEWORDWITHNOSPACES any number of spaces and/or tabs ( any number of spaces and/or tabs integer any number of spaces and/or tabs ) Examples include: WORD ( 123) WORD(1 ) WORD\t ( 21\t) WORD \t ( 1 \t ) etc. I don't need to substitute anything, only to identify if such a string exists. Any help with regular expressions would be appreciated. Thanks. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with complicated regular expression
On Nov 13, 2009, at 8:12 AM, Dennis Fisher wrote: Colleagues, I am using R (2.9.2, all platforms) to search for a complicated text string using regular expressions. I would appreciate any help you can provide. The string consists of the following elements: SOMEWORDWITHNOSPACES any number of spaces and/or tabs ( any number of spaces and/or tabs integer any number of spaces and/or tabs ) Examples include: WORD ( 123) WORD(1 ) WORD\t ( 21\t) WORD \t ( 1 \t ) etc. I don't need to substitute anything, only to identify if such a string exists. Any help with regular expressions would be appreciated. Thanks. Dennis How about this: Lines - c(WORD ( 123),WORD(1), WORD\t ( 21\t) , WORD\t ( 21\t) ) Lines [1] WORD ( 123) WORD(1) WORD\t ( 21\t) [4] WORD\t ( 21\t) grep(^[A-Za-z]+.*\\(.*[0-9]+.*\\), Lines) [1] 1 2 3 4 You should test it on some real data to see if it works or needs to be tweaked further. ^[A-Za-z]+ finds one or more characters at the beginning of the line .* finds zero or more characters after the word \\( finds an open paren .* finds zero or more characters after the open paren [0-9]+ finds one or more digits .* finds zero or more characters after the digits \\) finds the close paren HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with complicated regular expression
try this:
x - c('WORD(12 )', 'WORD[123)', 'WORD ( 123 )', WORD(xx), WORD(1))
grep([[:alnum:]]+[[:space:]]*\\([[:space:]]*[[:digit:]]+[[:space:]]*\\), x)
[1] 1 3 5
On Fri, Nov 13, 2009 at 9:12 AM, Dennis Fisher fis...@plessthan.com wrote:
Colleagues,
I am using R (2.9.2, all platforms) to search for a complicated text string
using regular expressions. I would appreciate any help you can provide.
The string consists of the following elements:
SOMEWORDWITHNOSPACES
any number of spaces and/or tabs
(
any number of spaces and/or tabs
integer
any number of spaces and/or tabs
)
Examples include:
WORD ( 123 )
WORD(1 )
WORD\t ( 21\t)
WORD \t ( 1 \t )
etc.
I don't need to substitute anything, only to identify if such a string
exists.
Any help with regular expressions would be appreciated.
Thanks.
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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[R] Change working directory
Hello, I am using setwd() to change the working directory but I have to enter it everytime I open R, is there a way to set this permanently as a working directory? Thanx =^D -- View this message in context: http://old.nabble.com/Change-working-directory-tp26337486p26337486.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] LINEAR MIXED EFFECT
Douglas Bates-2 wrote: On Thu, Nov 12, 2009 at 10:14 AM, milton ruser milton.ru...@gmail.com wrote: Hi Ana, I am not quite sure if it is the problem, but if you call your data.frame as exp, you will crash exp() function... try use another name for your data.frame. By the way, I suggest you not use attach(). Try something like model-lme(weight~date*diet, data=yourdataframe) good luck and include the random specification in the call to lme, not as a separate assignment. milton On Thu, Nov 12, 2009 at 5:43 AM, ANARPCG a.gouvei...@imperial.ac.uk wrote: Milton's point is dead-on, and I would highly encourage you to give the posting guide a look. That said... you might try na.action = na.omit in your call to... actually, we don't know what function you are using (see first point). Regardless, sounds like you have missing data and na.action is set to na.fail (ie, fail if any missing data). cheers, Dave milton ruser wrote: Dear Ana Golveia, It is completelly impossible someone realise what kind or help you need or what is happening. I suggest you give a look on the posting guide, mainly that part about a minimum reproducible code with self explaining information, etc. Cheers milton On Wed, Nov 11, 2009 at 7:22 AM, ANARPCG a.gouvei...@imperial.ac.uk wrote: CAN ANYONE PLEASE HELP ME WITH THIS i HAVE TO DO A MIXED EFFECT LINEAR MODEL WITH MY DATA DUE TO THE FACT THAT I have pseudoreplication! Although after reading and trying it for several times can get around due to Error in na.fail.default(list(date = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, : missing values in object I uploaded my data file Thank you so much Kind regards AG http://old.nabble.com/file/p26300394/rawoctobercalciumexperiment2.txt rawoctobercalciumexperiment2.txt -- View this message in context: http://old.nabble.com/LINEAR-MIXED-EFFECT-tp26300394p26300394.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. sorry I am new on this things the point is after trying to run the model all that happens is: exp-read.table(file=file.choose(),header=T) attach(exp) names(exp) [1] group date diet weight thickness length [7] width liplength lipwidth exp$diet=factor(exp$diet,levels=c(zeropercent,tenpercent,twentypercent,thirtypercent,fortypercent,cuttleprecent)) exp=na.omit(exp) library(nlme) random=~date model-lme(weight~date*diet) Error in na.fail.default(list(date = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, : missing values in object I have pseudoreplications due to the fact that the measurements of the replicates have different starting points so I was advised to do lme. I never used it before and I cant get arround with it! the help I wanted from you is to help me to understand how to do a runable model! http://old.nabble.com/file/p26315302/rawoctobercalciumexperiment2.txt rawoctobercalciumexperiment2.txt -- View this message in context: http://old.nabble.com/LINEAR-MIXED-EFFECT-tp26300394p26315302.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. :handshake:it did work finally thk for the help it went like this data-read.table(H:\\5.11.09\\rawoctobercalciumexperiment2.txt,header=T) names(data)
Re: [R] Escaping regular expressions
I want the user supplied string to be used as a component of a regular expression that I build up from other pieces that need actual regular expressions. Hadley On Fri, Nov 13, 2009 at 7:41 AM, Henrique Dallazuanna www...@gmail.com wrote: Try the fixed argument: grep(.$^, c(Test.$^, Test), fixed = TRUE) On Fri, Nov 13, 2009 at 11:33 AM, Hadley Wickham had...@rice.edu wrote: Hi all, Is there a method for escaping strings to be used regular expressions? i.e. if I have a user supplied string that I'd like to use as a fixed component is there a method that will turn (e.g.) .$^ into \\.\\$\\^ ? Thanks, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Change working directory
.Rprofile is executed everytime you start up R On Fri, Nov 13, 2009 at 8:34 AM, anna_l lippelann...@hotmail.com wrote: Hello, I am using setwd() to change the working directory but I have to enter it everytime I open R, is there a way to set this permanently as a working directory? Thanx =^D -- View this message in context: http://old.nabble.com/Change-working-directory-tp26337486p26337486.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] p-value 1
amor Gandhi wrote: Dear all, I am trying to use SAMr-library(samr), it gives me p-value = 1.001, any idea why? Well, the package maintainer might be a better place to ask. (Bring an example if you do.) However, as a generic matter, the result is obviously nonsensical, and could be due to a sloppy approximation of a distribution function, or maybe it is a (say) Bonferroni-adjusted p-value which is really an upper bound for the correct p-value. Notice, though, that you should only very rarely care about the exact p-value. As soon as it is above 0.1, the message is just that you have not proven that there is an effect. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with complicated regular expression
Hello, The function you are looking for is grepl. Something like this perhaps: words - c(WORD ( 123),WORD(1), WORD\t ( 21\t) , WORD\t ( 21\t) ) grepl( [[:space:]]*[(][[:space:]]*[0-9]+[[:space:]]*[)], words ) [1] TRUE TRUE TRUE TRUE [[:space:]]* : any number of spaces or tabs (including 0 times) [(] : a ( [0-9]+ : any number of digits, but at least one [)] : a ) Romain On 11/13/2009 03:12 PM, Dennis Fisher wrote: Colleagues, I am using R (2.9.2, all platforms) to search for a complicated text string using regular expressions. I would appreciate any help you can provide. The string consists of the following elements: SOMEWORDWITHNOSPACES any number of spaces and/or tabs ( any number of spaces and/or tabs integer any number of spaces and/or tabs ) Examples include: WORD ( 123 ) WORD(1 ) WORD\t ( 21\t) WORD \t ( 1 \t ) etc. I don't need to substitute anything, only to identify if such a string exists. Any help with regular expressions would be appreciated. Thanks. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/EAD5 : LondonR slides |- http://tr.im/BcPw : celebrating R commit #5 `- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Escaping regular expressions
This is not minimal (it will escape every non-word character) but is short and the needlessly escaped ones should do no harm (though you might want to double check that assumption on a few examples): gsub((\\W), \\1, x) On Fri, Nov 13, 2009 at 8:33 AM, Hadley Wickham had...@rice.edu wrote: Hi all, Is there a method for escaping strings to be used regular expressions? i.e. if I have a user supplied string that I'd like to use as a fixed component is there a method that will turn (e.g.) .$^ into \\.\\$\\^ ? Thanks, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with complicated regular expression
\w+ will match one or more word characters and \s* will match 0 or more spacing characters so if this must the described text must be the complete expression then: grepl(^\\w+\\s*\\(\\s*\\w+\\s*\\)$, x) or if its ok for other text to appear before and after as long as the indicated text is among it then remove the ^ and $. The above gives a logical vector as a result or if we use grep rather than grepl we can get a vector of indexes. On Fri, Nov 13, 2009 at 9:12 AM, Dennis Fisher fis...@plessthan.com wrote: Colleagues, I am using R (2.9.2, all platforms) to search for a complicated text string using regular expressions. I would appreciate any help you can provide. The string consists of the following elements: SOMEWORDWITHNOSPACES any number of spaces and/or tabs ( any number of spaces and/or tabs integer any number of spaces and/or tabs ) Examples include: WORD ( 123 ) WORD(1 ) WORD\t ( 21\t) WORD \t ( 1 \t ) etc. I don't need to substitute anything, only to identify if such a string exists. Any help with regular expressions would be appreciated. Thanks. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] format help()
Hi everybody, probably a really stupid question. I updated to 2.10 recently and was surprised that the help function comes in a different format, i.e. in the old-style as single pages for each function. I know I can use the html format in a browser, but would prefer the in-between format with the list of all functions (in a specific package) on the left, and browsable content on the right... How do I get it back? Thanks, Gabriel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] replace a whole word with sub()
Dear all, I cannot figure out how to solve a small problem (well, not for me), surely somebody can help me in few seconds. I have a series of strings in a vector X of the type xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa. I want to substitute every ENTIRE string beginning with Ig with 0. So, I'd like to have xxx, yyy, zzz, 0, 0, kkk, 0, aaa. I can easily identify these strings with grep(^Ig, X), but if I use this criterion in the sub() function (sub(^Ig, 0, X) I obviously get 0A, 0G etc. I didn't expect to do it in this way and I tried with metacharacters and regexps in order to grep and substitute the whole word (\b \, $). I don't post here my tryings, because they were obviously wrong. Please can you help me? Giulio _ Carica e scarica in un clic. Fino a 25 GB su SkyDrive [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replace a whole word with sub()
On Nov 13, 2009, at 9:13 AM, Giulio Di Giovanni wrote: Dear all, I cannot figure out how to solve a small problem (well, not for me), surely somebody can help me in few seconds. I have a series of strings in a vector X of the type xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa. I want to substitute every ENTIRE string beginning with Ig with 0. So, I'd like to have xxx, yyy, zzz, 0, 0, kkk, 0, aaa. I can easily identify these strings with grep(^Ig, X), but if I use this criterion in the sub() function (sub(^Ig, 0, X) I obviously get 0A, 0G etc. I didn't expect to do it in this way and I tried with metacharacters and regexps in order to grep and substitute the whole word (\b \, $). I don't post here my tryings, because they were obviously wrong. Please can you help me? x - c(xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa) sub(^Ig.*$, 0, x) [1] xxx yyy zzz 0 0 kkk 0 aaa You need to have the search regex include the entire element and not just the first couple of characters in order to replace the entire element. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replace a whole word with sub()
Here are two ways: s - c(xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa) sub(^Ig.*, 0, s) [1] xxx yyy zzz 0 0 kkk 0 aaa replace(s, grepl(^Ig, s), 0) [1] xxx yyy zzz 0 0 kkk 0 aaa On Fri, Nov 13, 2009 at 10:13 AM, Giulio Di Giovanni perimessagg...@hotmail.com wrote: Dear all, I cannot figure out how to solve a small problem (well, not for me), surely somebody can help me in few seconds. I have a series of strings in a vector X of the type xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa. I want to substitute every ENTIRE string beginning with Ig with 0. So, I'd like to have xxx, yyy, zzz, 0, 0, kkk, 0, aaa. I can easily identify these strings with grep(^Ig, X), but if I use this criterion in the sub() function (sub(^Ig, 0, X) I obviously get 0A, 0G etc. I didn't expect to do it in this way and I tried with metacharacters and regexps in order to grep and substitute the whole word (\b \, $). I don't post here my tryings, because they were obviously wrong. Please can you help me? Giulio _ Carica e scarica in un clic. Fino a 25 GB su SkyDrive [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replace a whole word with sub()
Isn't this more straightforward? w - grep(^Ig, vec) vec[w] - 0 Regards, Adai Giulio Di Giovanni wrote: Dear all, I cannot figure out how to solve a small problem (well, not for me), surely somebody can help me in few seconds. I have a series of strings in a vector X of the type xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa. I want to substitute every ENTIRE string beginning with Ig with 0. So, I'd like to have xxx, yyy, zzz, 0, 0, kkk, 0, aaa. I can easily identify these strings with grep(^Ig, X), but if I use this criterion in the sub() function (sub(^Ig, 0, X) I obviously get 0A, 0G etc. I didn't expect to do it in this way and I tried with metacharacters and regexps in order to grep and substitute the whole word (\b \, $). I don't post here my tryings, because they were obviously wrong. Please can you help me? Giulio _ Carica e scarica in un clic. Fino a 25 GB su SkyDrive [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How can this code be improved?
Jim, Dennis,
Once again, thanks for all your suggestions. After developing a more R-like
version of the script I terminated the running one after 976 (of 1697) reports
had been processed. At that point, the script had been running for approx.
33.5 hours! Here is the new version:
library(filehash)
db - dbInit(/Volumes/Work on RDR Test Documents/R Databases/DB_TXT, type =
RDS)
dbLoad(db)
dba - dbInit(/Volumes/Work on RDR Test Documents/R Databases/DB_Aux, type =
RDS)
dbLoad(dba)
tokens - sentences.all.tokenized
stopwords - stopwords.pubmed
# Convert to lowercase, remove beginning and end punctuation, tabulate
my.func - function(sent, stop, ...){
list(
freq.table = (temp.table - table(
sub(
[[:punct:]]*$, , sub(
^[[:punct:]]*, , tolower(sent)
)
)
)),
stopword.matches = (temp.matches - match(names(temp.table),
stop)),
stopword.summary = array(tapply(temp.table,
!is.na(temp.matches), sum), dim
= 2, dimnames = list(c(no.non.stopwords, no.stopwords)))
)
}
cat(Beginning at , date(), .\n, sep = )
token.tables -
lapply(1:length(tokens),
function(i.d, doc, stop, func, ...){
if ((i.d - 1) %% 10 == 0) cat((i.d - 1), report(s)
completed at ,
date(), .\n, sep = )
lapply(1:length(doc[[i.d]]),
function(i.s, sent, stop, func, ...){
func(sent[[i.s]], stop, ...)
}
, sent = doc[[i.d]], stop = stop, func = func,
...
)
}
,
doc = tokens, stop = stopwords, func = my.func
)
cat(Terminating at , date(), .\n, sep = )
This script reaches the same point in approx. 1:09 hours, a little under 70
minutes!
What I am noticing now is a severe lack of real memory. Activity Monitor
shows about 20MB of real memory free. R, running in 64-bit mode, is using
6.75GB of real and 10GB of virtual memory. I see lots of disk activity. This
is undoubtedly the swapping between real and virtual memory. CPU activity is
very low. I suppose I could run the script twice, each time on half the
tokens. That would give me two lists, which I would have to combine into a
single one.
Regards,
Richard
On Thu, 12 Nov 2009 18:53:34 -0500, jim holtman wrote
Run the script on a small subset of the data and use Rprof to profile
the code. This will give you an idea of where time is being spent
and where to focus for improvement. I would suggest that you do not
convert the output of the 'table(t)' do a dataframe. You can just
extract the 'names' to get the words. You might be spending some of
the time in the accessing the information in the dataframe, which is
really not necessary for your code.
On Thu, Nov 12, 2009 at 2:12 AM, Richard R. Liu richard@pueo-
owl.ch wrote:
I am running the following code on a MacBook Pro 17 Unibody early 2009 with
8GB RAM, OS X 10.5.8, R 2.10.0 Patch from Nov. 2, 2009, in 64-bit mode.
freq.stopwords - numeric(0)
freq.nonstopwords - numeric(0)
token.tables - list(0)
i.ss - c(0)
cat(Beginning at , date(), .\n)
for (i.d in 1:length(tokens)) {
tt - list(0)
for (i.s in 1:length(tokens[[i.d]])) {
t - tolower(tokens[[i.d]][[i.s]])
t - sub(^[[:punct:]]*, , t)
t - sub([[:punct:]]*$, , t)
t - as.data.frame(table(t))
i.m - match(t$t, stopwords)
i.m.is.na - is.na(i.m)
i.ss - i.ss + 1
freq.stopwords[i.ss] - sum(t$Freq * !i.m.is.na)
freq.nonstopwords[i.ss] - sum(t$Freq * i.m.is.na)
tt[[i.s]] - data.frame(token = t$t, freq = t$Freq,
matches.stopword = i.m)
}
token.tables[[i.d]] - tt
if (i.d %% 5 == 0) cat(i.d, reports completed at , date(), .\n)
}
cat(Terminating at , date(), .\n)
The object in the innermost loop are:
* tokens: a list of lists. In the expression tokens[[i.d]][[i.s]], the
first index runs over 1697 reports, the second over the sentences in the
report, each of which consists of a vector of tokens, i.e., the character
strings between the white spaces in the sentence. One of the largest
reports takes up 58MB on the harddisk. Thus, the number of sentences can be
quite large, and some of the sentences are quite long (measure in tokens as
well as in characters).
* stopwords: is a vector of 571 words that occur very often in written
English.
The code operates on sentences, converting each token in the sentence to
lowercase, removing punctuation at the beginning and end of the token,
tabulating the frequency of the unique
Re: [R] replace a whole word with sub()
Do you want to replace the whole word or the whole string? If the latter, use sub(^Ig.*, 0, x) (Matching is greedy, so .* matches are many characters as possible, here the rest of the string.) If 'whole word', we need a precise definition of word, but sub(^Ig\\w*, 0, x) is one conventional one (a word is alphanumeric: but you might not allow numbers). On Fri, 13 Nov 2009, Giulio Di Giovanni wrote: Dear all, I cannot figure out how to solve a small problem (well, not for me), surely somebody can help me in few seconds. I have a series of strings in a vector X of the type xxx, yyy, zzz, IgA, IgG, kkk, IgM, aaa. I want to substitute every ENTIRE string beginning with Ig with 0. So, I'd like to have xxx, yyy, zzz, 0, 0, kkk, 0, aaa. I can easily identify these strings with grep(^Ig, X), but if I use this criterion in the sub() function (sub(^Ig, 0, X) I obviously get 0A, 0G etc. I didn't expect to do it in this way and I tried with metacharacters and regexps in order to grep and substitute the whole word (\b \, $). I don't post here my tryings, because they were obviously wrong. Please can you help me? Giulio _ Carica e scarica in un clic. Fino a 25 GB su SkyDrive [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] NetCDF output in R
Dear Users,
I have corrected the errors. Many thanks.
For this error,
[1] put.var.ncdf: warning: you asked to write 1440 values, but the passed
data array has 37440 entries!
I added start= c(1,1,1), count=c(length(lons),length(lats),length(nt)) in the
put.var.ncdf function.
so put.var.ncdf(ncid, var, data)
became put.var.ncdf(ncid, var, data, start= c(1,1,1),
count=c(length(lons),length(lats),length(nt)))
For this,
Warning message:
In 1:nt : numerical expression has 26 elements: only the first used
I replaced times with nt in the tdim in the dim.def.ncdf function.
so
tdim - dim.def.ncdf('time','days since 1980-01-01', times, unlim=TRUE)
became
tdim - dim.def.ncdf('time','days since 1980-01-01', nt, unlim=TRUE)
Thanks all.
Nana Browne
There is no key to happiness. The door is always open.
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[R] How to show all the functions and classes that are defined in a library?
library(some_library_name) Suppose I load a library. I'm wondering what command I should use to list all the functions, classes and variables defined in the library. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] vignettes: .png graphics or pre-compiled .pdf
In a package I'm working on there is a vignette with a number of graphs
that result in huge .pdf files, so
the .pdf for the vignette is around 17 Mb. If these graphs are
converted to .png, and the .tex file
is compiled with pdflatex, the resulting .pdf is ~1 Mb.
I'm reluctant to put the .Rnw file into the package as is, generating
the huge .pdf for the vignette.
I first tried installing the smaller .pdf file in the package by itself
(no .Rnw)
together with a file inst/doc/index.html as recommended
in 'Writing R Extensions.' However, when the package is installed,
vignette() can't find it
vignette(package=Guerry)
no vignettes found
vignette(MultiSpat)
Warning message:
vignette 'MultiSpat' *not* found
Alternatively, is there a way to generate .png graphs from the .Rnw file
so that those are used in building
the .pdf for the package? AFAICS, \SweaveOpts{} offers only the choices
of eps/pdf = {TRUE/FALSE}.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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[R] Craddock-Flood Test in R?
Hello The Craddock-Flood Test is recommended for large tables with small degrees of freedom and low-frequency cells. Is there an R procedure and/or package which does the test? Thank you for your help! Sören Vogel -- Sören Vogel, Dipl.-Psych. (Univ.), PhD-Student, Eawag, Dept. SIAM http://www.eawag.ch, http://sozmod.eawag.ch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to show all the functions and classes that are defined in a library?
On 11/13/2009 04:53 PM, Peng Yu wrote: library(some_library_name) Suppose I load a library. You mean package right ? A library is a set of packages I'm wondering what command I should use to list all the functions, classes and variables defined in the library. Check ?ls : ls( package:some_package_name ) ls( package:some_package_name, all = TRUE ) Sometimes you want to see even those that are not exported from the namespace: ls( asNamespace( some_package_name ) ) ls( asNamespace( some_package_name ), all = TRUE ) Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/EAD5 : LondonR slides |- http://tr.im/BcPw : celebrating R commit #5 `- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] vignettes: .png graphics or pre-compiled .pdf
On Fri, 13 Nov 2009, Michael Friendly wrote:
In a package I'm working on there is a vignette with a number of graphs that
result in huge .pdf files, so
the .pdf for the vignette is around 17 Mb. If these graphs are converted to
.png, and the .tex file
is compiled with pdflatex, the resulting .pdf is ~1 Mb.
I'm reluctant to put the .Rnw file into the package as is, generating the
huge .pdf for the vignette.
I first tried installing the smaller .pdf file in the package by itself (no
.Rnw)
together with a file inst/doc/index.html as recommended
in 'Writing R Extensions.' However, when the package is installed,
vignette() can't find it
vignette(package=Guerry)
no vignettes found
vignette(MultiSpat)
Warning message:
vignette 'MultiSpat' *not* found
Alternatively, is there a way to generate .png graphs from the .Rnw file so
that those are used in building
the .pdf for the package? AFAICS, \SweaveOpts{} offers only the choices of
eps/pdf = {TRUE/FALSE}.
Yes, but you can call the png() device yourself within the code chunk
=
png(file = fig1.png, ...)
...
dev.off()
@
and then put
\includegraphics{fig1}
manually into the LaTeX. It's certainly not as nice as Sweave's automatic
handling of figures but will work and still keep the file self-contained.
Z
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology
Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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[R] shrink list by mathed entries
Hello
a - c(Mama, Papa, Papa; Mama, , Sammy; Mama; Papa)
a - strsplit(a, ; )
mama - rep(F, length(a))
mama[sapply(a, function(x) { sum(x==Mama) }, simplify=T) 0] - T
papa - rep(F, length(a))
papa[sapply(a, function(x) { sum(x==Papa) }, simplify=T) 0] - T
# ... more variables
... produces the variables mama and papa correctly. But how do I
remove all Mama list entries in a in the same run, that is, shrink
the list by what was already matched?
Thank you for your help!
Sören Vogel
--
Sören Vogel, Dipl.-Psych. (Univ.), PhD-Student, Eawag, Dept. SIAM
http://www.eawag.ch, http://sozmod.eawag.ch
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Re: [R] p-value 1
Thank you for your reply. The only contact address of the maintainer is http://www-stat.stanford.edu/~tibs/SAM However, one find no contact when one visit this page. I am not a mathematician, therefore, it is strange for me to get probability bigger that 1, if it is like that should I trust the p-value of 0.004332? Sorry for these questions. Best wishes, Amor --- Peter Dalgaard p.dalga...@biostat.ku.dk schrieb am Fr, 13.11.2009: Von: Peter Dalgaard p.dalga...@biostat.ku.dk Betreff: Re: [R] p-value 1 An: amor Gandhi amorigan...@yahoo.de CC: r-h...@stat.math.ethz.ch Datum: Freitag, 13. November 2009, 15:24 amor Gandhi wrote: Dear all, I am trying to use SAMr-library(samr), it gives me p-value = 1.001, any idea why? Well, the package maintainer might be a better place to ask. (Bring an example if you do.) However, as a generic matter, the result is obviously nonsensical, and could be due to a sloppy approximation of a distribution function, or maybe it is a (say) Bonferroni-adjusted p-value which is really an upper bound for the correct p-value. Notice, though, that you should only very rarely care about the exact p-value. As soon as it is above 0.1, the message is just that you have not proven that there is an effect. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ z gegen Massenmails. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] p-value 1
The maintainer's email address is listed in the package documentation... as I think is the case with all CRAN packages. -Ista On Fri, Nov 13, 2009 at 11:20 AM, amor Gandhi amorigan...@yahoo.de wrote: Thank you for your reply. The only contact address of the maintainer is http://www-stat.stanford.edu/~tibs/SAM However, one find no contact when one visit this page. I am not a mathematician, therefore, it is strange for me to get probability bigger that 1, if it is like that should I trust the p-value of 0.004332? Sorry for these questions. Best wishes, Amor --- Peter Dalgaard p.dalga...@biostat.ku.dk schrieb am Fr, 13.11.2009: Von: Peter Dalgaard p.dalga...@biostat.ku.dk Betreff: Re: [R] p-value 1 An: amor Gandhi amorigan...@yahoo.de CC: r-h...@stat.math.ethz.ch Datum: Freitag, 13. November 2009, 15:24 amor Gandhi wrote: Dear all, I am trying to use SAMr-library(samr), it gives me p-value = 1.001, any idea why? Well, the package maintainer might be a better place to ask. (Bring an example if you do.) However, as a generic matter, the result is obviously nonsensical, and could be due to a sloppy approximation of a distribution function, or maybe it is a (say) Bonferroni-adjusted p-value which is really an upper bound for the correct p-value. Notice, though, that you should only very rarely care about the exact p-value. As soon as it is above 0.1, the message is just that you have not proven that there is an effect. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ z gegen Massenmails. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to show all the functions and classes that are defined in a library?
On Fri, Nov 13, 2009 at 9:53 AM, Peng Yu pengyu...@gmail.com wrote: library(some_library_name) Try help(package = some_library_name) Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] random numbers in C
I need some random numbers in my C program. Here a small example:
#include R.h
void rand (int* n)
{
int len = *n;
for (int i = 0; i len; i++)
Rprintf(%1.5f , unif_rand());
}
dyn.load(rand.dll)
.C(rand, as.integer(10))
dyn.unload(rand.dll)
But this gives me 10 times the number 0.0 (I need 10 numbers between 0
and 1). Can somebody give me a hint what I'm doing wrong (or misunderstand).
Thanks in advance
Thomas
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[R] Problems by saving Rprofile.site under vista
Hello, I am trying to save some changes I have done on the Rprofile.site under vista and it doesn´t let me save the file saying that it can´t create the following file (Rprofile.site) and that I should check the pathfile or the file name. -- View this message in context: http://old.nabble.com/Problems-by-saving-Rprofile.site-under-vista-tp26339605p26339605.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package tm fails to remove the with remove stopwords
Sam, Thanks for the example. Removing stop words after the DocumentTermMatrix has been created works fine if one is working with single words, but what if one is creating a dtm of possible combinations of words? Wouldn't one want to remove them from the corpus? Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 399-1219 Skype No Voicemail please On Thu, Nov 12, 2009 at 12:04 PM, Sam Thomas sam.tho...@revelanttech.comwrote: I'm not sure what's wrong with your approach, but this seems to strip the require(tm) params - list(minDocFreq = 1, removeNumbers = TRUE, stemming = TRUE, stopwords = TRUE, weighting = weightTf) myDocument - c(the rain in Spain, falls mainly on the plain, jack and jill ran up the hill, to fetch a pail of water) text.corp - Corpus(VectorSource(myDocument)) dtm - DocumentTermMatrix(text.corp, control = params) dtm dtm.mat - as.matrix(dtm) dtm.mat *From:* Mark Kimpel [mailto:mwkim...@gmail.com] *Sent:* Thursday, November 12, 2009 11:30 AM *To:* r-help@r-project.org; feine...@logic.at; Sam Thomas *Subject:* package tm fails to remove the with remove stopwords I am using code that previously worked to remove stopwords using package tm. Even manually adding the to the list does not work to remove the. This package has undergone extensive redevelopment with changes to the function syntax, so perhaps I am just missing something. Please see my simple example, output, and sessionInfo() below. Thanks! Mark require(tm) myDocument - c(the rain in Spain, falls mainly on the plain, jack and jill ran up the hill, to fetch a pail of water) text.corp - Corpus(VectorSource(myDocument)) # text.corp - tm_map(text.corp, stripWhitespace) text.corp - tm_map(text.corp, removeNumbers) text.corp - tm_map(text.corp, removePunctuation) ## text.corp - tm_map(text.corp, stemDocument) text.corp - tm_map(text.corp, removeWords, c(the, stopwords(english))) dtm - DocumentTermMatrix(text.corp) dtm dtm.mat - as.matrix(dtm) dtm.mat dtm.mat Terms Docs falls fetch hill jack jill mainly pail plain rain ran spain the water 1 0 0000 00 01 0 1 1 0 2 1 0000 10 10 0 0 0 0 3 0 0111 00 00 1 0 0 0 4 0 1000 01 00 0 0 0 1 R version 2.10.0 Patched (2009-10-27 r50222) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] chron_2.3-33 RWeka_0.3-23 tm_0.5-1 loaded via a namespace (and not attached): [1] grid_2.10.0 rJava_0.8-1 slam_0.1-6 tools_2.10.0 Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 399-1219 Skype No Voicemail please [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] linear model and by()
Hello R list, This is a question for anyone who has used the by() command. I would like to perform a regression on a data frame by several factors. Using by() I think that I have able to perform this using the following: lm.r - by(master, list(Sectionf=Sectionf, startd=startd), function(x) lm (tot.c ~ starttime, data = x)) So that is, I would like to perform separate regressions for each level of Sectionf for each level of startd. Now I can get the coefficients and intercepts from all the fitted models. However, I am now unsure how to glean more information from the regressions. If I follow up with this command I get this: summary(lm.r) 9-09-04.Length 9-09-04.Class 9-09-04.Mode 12lmlist 12lmlist 12lmlist 9-09-11.Length 9-09-11.Class 9-09-11.Mode 12lmlist 12lmlist 12lmlist Under normal circumstances, this usually ends up giving me more info about the fitted model, but some reason when using the by() command it doesn't. Beacuase the results are a layer deeper than summary is describing; Try: lapply(lm.r, summary) Nice. Thanks I get it now. (this theory tested with one of the standard datasets, Indometh: library(utils) data(Indometh) reglist - by(Indometh, Indometh$Subject, function(x) lm(conc~time, data=x) ) summary(reglist) Length Class Mode 1 12 lmlist 4 12 lmlist 2 12 lmlist 5 12 lmlist 6 12 lmlist 3 12 lmlist Whereas, without the assignment to reglist I got a series of expected lm output, so by works. Similarly, although I wasn't hopeful that this would work, when I tried to examine the residuals, I get these warning messages: similarly: lapply(lm.r, plot) This definitely worked quite well. Any thoughts on how to get titles from the list to appear on the diagnostic plots? plot(lm.r$fit,lm.r$res,xlab=Fitted,ylab=Residuals) Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf So my question might be answered by someone saying that this isn't a good way to do this. Still, can anyone suggest some strategies that might help me out here? Specifically, how might I be able work with these regressions once I have fitted all the models. Obviously I need to examine the residuals, look at the model fit, etc. Any suggestions on what I might be doing wrong would be much appreciated. I am also including a subset of the data and the commands I used in case that is helpful. I am using Ubuntu 9.04 and R 2.8.1 Thanks in advance! Sam Sorry to not use your data but it's not in a form that lends itself very well to quick testing. If you had included the input commands I might have tried it. No problem not use my data. For future reference, would it have been easier to attach a .csv file and then include the appropriate read.csv command? I realized that the easier one makes it to help, the easier it is to get a response. Thanks a lot for your help! Ista- To be fair, I did include Sectionf - factor(Section) below. ;) attach(master) Sectionf - factor(Section) startd=as.Date(startdate, format=%d/%m/%Y) lm.r - by(master, list(Sectionf=Sectionf, startd=startd), function(x) lm (tot.c ~ starttime, data = x)) Data: Section,starttime,startdate,tot.c Upstream,0,04/09/09,0.17 Upstream,0,04/09/09,0.19 Upstream,0,04/09/09,0.14 Middle,0,04/09/09,0.2 Middle,0,04/09/09,0.13 Middle,0,04/09/09,0.11 Downstream,0,04/09/09,0.16 Downstream,0,04/09/09,0.17 Downstream,0,04/09/09,0.17 Upstream,25,04/09/09,0.17 Upstream,25,04/09/09,0.19 Upstream,25,04/09/09,0.14 Middle,25,04/09/09,0.2 Middle,25,04/09/09,0.13 Middle,25,04/09/09,0.11 Downstream,25,04/09/09,0.16 Downstream,25,04/09/09,0.17 Downstream,25,04/09/09,0.17 Upstream,50.06,04/09/09,0.17 Upstream,50.06,04/09/09,0.19 Upstream,50.06,04/09/09,0.14 Middle,50.06,04/09/09,0.2 Middle,50.06,04/09/09,0.13 Middle,50.06,04/09/09,0.11 Downstream,50.06,04/09/09,0.16 Downstream,50.06,04/09/09,0.17 Downstream,50.06,04/09/09,0.17 Upstream,75.42,04/09/09,0.17 Upstream,75.42,04/09/09,0.19 Upstream,75.42,04/09/09,0.14 Middle,75.42,04/09/09,0.2 Middle,75.42,04/09/09,0.13 Middle,75.42,04/09/09,0.11 Downstream,75.42,04/09/09,0.16 Downstream,75.42,04/09/09,0.17 Downstream,75.42,04/09/09,0.17 Upstream,100.14,04/09/09,0.17 Upstream,100.14,04/09/09,0.19 Upstream,100.14,04/09/09,0.14 Middle,100.14,04/09/09,0.2 Middle,100.14,04/09/09,0.13 Middle,100.14,04/09/09,0.11 Downstream,100.14,04/09/09,0.16 Downstream,100.14,04/09/09,0.17 Downstream,100.14,04/09/09,0.17 Upstream,125.31,04/09/09,0.17 Upstream,125.31,04/09/09,0.19 Upstream,125.31,04/09/09,0.14
[R] R and HDF5 Question
Hello All,
I just signed up to this list, so I apologize if this question has been
asked before.
I am trying to load an hdf5 file into R and running into some problems. Here
are the steps I took to configure my environment:
* R 2.10.0 (x64) on Mac OS X 10.6
* hdf5 1.8.3 installed via macports
* hdf5_1.6.9.tar.gz from CRAN
I suspect the problem I am having relates to incompatibilities in my version
of HDF5 and the one the R module expects. For completeness here is how I
installed the R module:
R CMD INSTALL --configure-vars='CPPFLAGS=-I/opt/local/include'
--configure-args='--with-hdf5=/opt/local' hdf5_1.6.9.tar.gz
This builds fine. The library seems to load without issue, but no data is
returned when I try to load a file:
library(hdf5)
hdf5load(test.h5)
NULL
Yet,
osx:data scott$ h5dump test.h5 HDF5 test.h5 { GROUP / { DATASET
dset { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 31 ) / ( 31 ) } DATA {
(0): 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, (14):
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, (22):
4194304, 8388608, 16777216, 33554432, 67108864, 134217728, (28): 268435456,
536870912, 1073741824 } } } }
Any thoughts?
Thanks in advance.
Scott
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Re: [R] processing log file
Thanks, that's helpful because I can see the individuals and how many times
they accessed:
The 'plyr' solution of Karl Ove Hufthammer gives me the exact summary
statistics that I'm looking for.
Jab
--- On Fri, 13/11/09, markle...@verizon.net markle...@verizon.net wrote:
From: markle...@verizon.net markle...@verizon.net
Subject: Re: Re: [R] processing log file
To: jabez...@yahoo.co.uk
Date: Friday, 13 November, 2009, 16:36
Hi: I think below does what you want but it doesn't come out formatted very
nicely. Maybe someone can show you
the formatting ? Good luck.
table.users - read.table(textConnection(Date UserName Machine
2008-11-25 John 641
2008-11-25 Clive 611
2008-11-25 Jeremy 641
2008-11-25 Walt 722
2008-11-25 Tony 645
2008-11-26 Tony 645
2008-11-26 Tony 641
2008-11-26 Tony 641
2008-11-26 Walt 641
2008-11-26 Walt 645
2008-11-30 John 641
2008-11-30 Clive 611
2008-11-30 Tony 641
2008-11-30 John 641
2008-11-30 John 641),header=TRUE,as.is=TRUE)
print(table.users)
print(str(table.users))
lapply(split(table.users,table.users$Date),function(.df) {
table(.df$Machine)
})
lapply(split(table.users,table.users$Date),function(.df) {
table(.df$UserName)
})
On Nov 13, 2009, Karl Ove Hufthammer k...@huftis.org wrote:
On Fri, 13 Nov 2009 11:03:31 + (GMT) Jabez Wilson
jabez...@yahoo.co.uk wrote:
What I want to do is to find out how many unique users logged
on each day, and how many individual machines where accessed per day.
Use the 'plyr' package:
library(plyr)
ddply(table.users, .(Date), summarise,
users=length(unique(Username)),
machines=length(unique(Machine)))
--
Karl Ove Hufthammer
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Re: [R] Step Function Freezing R
I can't fully answer all these questions, but I'll do my best - There have not been any updates of Windows, and I did not update R during the period, although I did reinstall it after the problem started. There have been no changes to Norton or any other software that uses system resources in that way. The one thing I can think of is that I installed a program called Digitizer (creates data tables/ csds from visually analyzing line charts) around the same time it started freezing. I have completely uninstalled it and deleted all related files. The problem should not be with the data, which is fine. I am running Windows XP Professional and Excel 2007. I have allowed the process to run overnight on two separate occasions. The first time it was completely frozen and there was no progress. Last night it actually made progress, but the fact remains that a process that used to take an hour at the most still has not even halfway completed after over 8 hours. I even installed extra RAM on the system so that there is more than when the process used to work. I agree that it is probably a change in software, but I can't figure out what has changed or what I can do about it. Thanks for your help, JGS On Nov 12, 7:05 pm, J Dougherty j...@surewest.net wrote: There are some points of information you should include. One, have there been recent updates of Windows that may have altered system behaviour? Two, have you updated R during the same period? Three, have you installed software that uses system resources that were available to R before - e.g. has Norton or whatever you use to guard your system upgraded? Four, what versions of Windows and Excel are you running? Five, have you inspected your data for corruption? Six, what changes (data entry, editing, recoding, etc.) have you done that might coincide with the changed behaviour? Seven, have you allowed the process to simply run - say overnight? Nine, how big is you database? In essence, your problem sounds like system problem. The most likely cause is a change in software, but without some really clear information on changes on your system that could potentially have caused this, you are unlikely to find it easily. One possibility is that a change in software has resulted in smaller available resource space. JWDougherty On Thursday 12 November 2009 09:05:34 am Jgabriel wrote: I have a question that might not be kosher here, but I'm running out of options and need some help. Basically using the function step is freezingR. I am running a model that includes a number of interactions on a large data set with a number of dummy variables representing whether an event occurred or not. Here's a simplified example - fit = lm(a~b*(c+d+e)*(f+g+h)*(i+j+k)) regs = step(fit) at this point R freezes and alternates between Not Responding and Running in Windows task manager. It wasn't always this way. I was able to run the same model on the same dataset a couple weeks ago and while it took the step function 20-30 minutes to compute the best AIC and didn't exclude all the insignificant variables/interactions, it served its purpose. Even after uninstalling and reinstalling R and RExcel (which I used to load the data set), the problem persists. I tried it on a smaller data set and still no luck. This is more of a computing issue, so if anyone can point me to a forum better equipped to help me out, I will owe you my eternal gratitude. I hate to fill up space with such an uninspired question, but like I said I'm running out of options. Thanks, JGS __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R installation on UNIX machine
Hello All, I have downloaded and untarred R 2.10.0 onto my SUN UNIX machine. When I run ./configure, it runs through a series of questions and stops at this (and I get this when I try the make command): checking for iconv.h... yes checking for iconv... in libiconv checking whether iconv accepts UTF-8, latin1 and UCS-*... no configure: error: a suitable iconv is essential # make make: not found Could someone decipher this and tell me how I would get a suitable iconv? And is that indeed what it causing make to not be found? I did find this info below in the admin manual appendix. However, when I click on the link and run the suggested install, I get the same results. A suitably comprehensive iconv function is essential. The R usage requires iconv to be able to translate between latin1 and UTF-8, to recognize as the current encoding and to translate to and from the Unicode wide-character formats UCS-[24][BL]E - this is true for glibc but not of most commercial Unixes. However, you can make use of GNU libiconv (possibly as a plug-in replacement: see http://www.gnu.org/software/libiconv/. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simple if else statement problem
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else statements
with the same syntax working. Thanks in advance
--
View this message in context:
http://old.nabble.com/Simple-if-else-statement-problem-tp26340336p26340336.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Trellis settings get lost when printing to pdf
Hi all, I've got some problems when changing the trellis settings for the lattice plots. The plots look exactly as I want them to when calling show.settings() as well as when plotting them in the graphical window. But when printing to a pdf file, none of the settings are used!? Does anyone know what might have happened? Because the when changing the trellis settings, these should remain in the new state until you close R right..? # Change settings for the boxplot appearance new.dot=trellis.par.get(box.dot) new.rectangle=trellis.par.get(box.rectangle) new.umbrella=trellis.par.get(box.umbrella) new.symbol=trellis.par.get(plot.symbol) new.strip.background=trellis.par.get(strip.background) new.strip.shingle=trellis.par.get(strip.shingle) new.dot$pch=| new.dot$col=black new.rectangle$col=black new.rectangle$fill=grey65 new.umbrella$col=black new.umbrella$lty=1 # Continous line, not dotted new.symbol$col=black new.strip.background$col=grey87 # Background colour in the upper label new.strip.shingle$col=black # Border colour around the upper label trellis.par.set(box.dot=new.dot, box.rectangle=new.rectangle, box.umbrella=new.umbrella, plot.symbol=new.symbol, strip.background=new.strip.background, strip.shingle=new.strip.shingle) Best regards, Joel _ Nya Windows 7 - Hitta en dator som passar dig! Mer information. http://windows.microsoft.com/shop [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple if else statement problem
align the else with the curly brackets
if (yes){
be happy
}else{
complain
}
b
On Nov 13, 2009, at 3:33 PM, anna_l wrote:
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else
statements
with the same syntax working. Thanks in advance
--
View this message in context:
http://old.nabble.com/Simple-if-else-statement-problem-tp26340336p26340336.html
Sent from the R help mailing list archive at Nabble.com.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple if else statement problem
Anna,
I think the else needs to be on the same line
as the curly bracket like this } else.
P1 - 1
P2 - 2
if( P2 P1)
{
P-P2
} else
{
P-P1
}
Good luck,
Jim
anna_l wrote:
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else statements
with the same syntax working. Thanks in advance
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Trellis settings get lost when printing to pdf
Did you make the changes before or after starting the device: library(lattice) ## before doesn't change the settings on the device: trellis.par.set(plot.symbol = list(col = red)) trellis.device(pdf, file = tmp.pdf) xyplot(1 ~ 1) dev.off() ## after does trellis.device(pdf, file = tmp.pdf) trellis.par.set(plot.symbol = list(col = red)) xyplot(1 ~ 1) dev.off() I never do things like this, though. I would suggest creating a theme instead and supplying it to xyplot (or whatever plot you're using) using par.settings: my.theme - list(plot.symbol = list(col = red)) trellis.device(pdf, file = tmp.pdf) xyplot(1 ~ 1, par.settings = my.theme) dev.off() HTH, --sundar 2009/11/13 Joel Fürstenberg-Hägg joel_furstenberg_h...@hotmail.com: Hi all, I've got some problems when changing the trellis settings for the lattice plots. The plots look exactly as I want them to when calling show.settings() as well as when plotting them in the graphical window. But when printing to a pdf file, none of the settings are used!? Does anyone know what might have happened? Because the when changing the trellis settings, these should remain in the new state until you close R right..? # Change settings for the boxplot appearance new.dot=trellis.par.get(box.dot) new.rectangle=trellis.par.get(box.rectangle) new.umbrella=trellis.par.get(box.umbrella) new.symbol=trellis.par.get(plot.symbol) new.strip.background=trellis.par.get(strip.background) new.strip.shingle=trellis.par.get(strip.shingle) new.dot$pch=| new.dot$col=black new.rectangle$col=black new.rectangle$fill=grey65 new.umbrella$col=black new.umbrella$lty=1 # Continous line, not dotted new.symbol$col=black new.strip.background$col=grey87 # Background colour in the upper label new.strip.shingle$col=black # Border colour around the upper label trellis.par.set(box.dot=new.dot, box.rectangle=new.rectangle, box.umbrella=new.umbrella, plot.symbol=new.symbol, strip.background=new.strip.background, strip.shingle=new.strip.shingle) Best regards, Joel _ Nya Windows 7 - Hitta en dator som passar dig! Mer information. http://windows.microsoft.com/shop [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple if else statement problem
Ok Jim it worked, thank you! it´s funny because it worked with the first
syntax in some cases...
anna_l wrote:
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else
statements with the same syntax working. Thanks in advance
--
View this message in context:
http://old.nabble.com/Simple-if-else-statement-problem-tp26340336p26340642.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] processing log file
You can use aggregate to get this too:
aggregate(table.users[,c('UserName', 'Machine')], table.users['Date'],
function(x)length(unique(x)))
On Fri, Nov 13, 2009 at 3:01 PM, Jabez Wilson jabez...@yahoo.co.uk wrote:
Thanks, that's helpful because I can see the individuals and how many times
they accessed:
The 'plyr' solution of Karl Ove Hufthammer gives me the exact summary
statistics that I'm looking for.
Jab
--- On Fri, 13/11/09, markle...@verizon.net markle...@verizon.net wrote:
From: markle...@verizon.net markle...@verizon.net
Subject: Re: Re: [R] processing log file
To: jabez...@yahoo.co.uk
Date: Friday, 13 November, 2009, 16:36
Hi: I think below does what you want but it doesn't come out formatted very
nicely. Maybe someone can show you
the formatting ? Good luck.
table.users - read.table(textConnection(Date UserName Machine
2008-11-25 John 641
2008-11-25 Clive 611
2008-11-25 Jeremy 641
2008-11-25 Walt 722
2008-11-25 Tony 645
2008-11-26 Tony 645
2008-11-26 Tony 641
2008-11-26 Tony 641
2008-11-26 Walt 641
2008-11-26 Walt 645
2008-11-30 John 641
2008-11-30 Clive 611
2008-11-30 Tony 641
2008-11-30 John 641
2008-11-30 John 641),header=TRUE,as.is=TRUE)
print(table.users)
print(str(table.users))
lapply(split(table.users,table.users$Date),function(.df) {
table(.df$Machine)
})
lapply(split(table.users,table.users$Date),function(.df) {
table(.df$UserName)
})
On Nov 13, 2009, Karl Ove Hufthammer k...@huftis.org wrote:
On Fri, 13 Nov 2009 11:03:31 + (GMT) Jabez Wilson
jabez...@yahoo.co.uk wrote:
What I want to do is to find out how many unique users logged
on each day, and how many individual machines where accessed per day.
Use the 'plyr' package:
library(plyr)
ddply(table.users, .(Date), summarise,
users=length(unique(Username)),
machines=length(unique(Machine)))
--
Karl Ove Hufthammer
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25° 25' 40 S 49° 16' 22 O
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Re: [R] Step Function Freezing R
Jgabriel wrote: I can't fully answer all these questions, but I'll do my best - There have not been any updates of Windows, and I did not update R during the period, although I did reinstall it after the problem started. There have been no changes to Norton or any other software that uses system resources in that way. The one thing I can think of is that I installed a program called Digitizer (creates data tables/ csds from visually analyzing line charts) around the same time it started freezing. I have completely uninstalled it and deleted all related files. The problem should not be with the data, which is fine. I am running Windows XP Professional and Excel 2007. I have allowed the process to run overnight on two separate occasions. The first time it was completely frozen and there was no progress. Last night it actually made progress, but the fact remains that a process that used to take an hour at the most still has not even halfway completed after over 8 hours. I even installed extra RAM on the system Aha! Please ask your local IT experts to check the RAM and if that is fine ask them to proceed. I have already seen too many machines with RAM problems during the last years. It is hardly an R problem. Uwe Ligges so that there is more than when the process used to work. I agree that it is probably a change in software, but I can't figure out what has changed or what I can do about it. Thanks for your help, JGS On Nov 12, 7:05 pm, J Dougherty j...@surewest.net wrote: There are some points of information you should include. One, have there been recent updates of Windows that may have altered system behaviour? Two, have you updated R during the same period? Three, have you installed software that uses system resources that were available to R before - e.g. has Norton or whatever you use to guard your system upgraded? Four, what versions of Windows and Excel are you running? Five, have you inspected your data for corruption? Six, what changes (data entry, editing, recoding, etc.) have you done that might coincide with the changed behaviour? Seven, have you allowed the process to simply run - say overnight? Nine, how big is you database? In essence, your problem sounds like system problem. The most likely cause is a change in software, but without some really clear information on changes on your system that could potentially have caused this, you are unlikely to find it easily. One possibility is that a change in software has resulted in smaller available resource space. JWDougherty On Thursday 12 November 2009 09:05:34 am Jgabriel wrote: I have a question that might not be kosher here, but I'm running out of options and need some help. Basically using the function step is freezingR. I am running a model that includes a number of interactions on a large data set with a number of dummy variables representing whether an event occurred or not. Here's a simplified example - fit = lm(a~b*(c+d+e)*(f+g+h)*(i+j+k)) regs = step(fit) at this point R freezes and alternates between Not Responding and Running in Windows task manager. It wasn't always this way. I was able to run the same model on the same dataset a couple weeks ago and while it took the step function 20-30 minutes to compute the best AIC and didn't exclude all the insignificant variables/interactions, it served its purpose. Even after uninstalling and reinstalling R and RExcel (which I used to load the data set), the problem persists. I tried it on a smaller data set and still no luck. This is more of a computing issue, so if anyone can point me to a forum better equipped to help me out, I will owe you my eternal gratitude. I hate to fill up space with such an uninspired question, but like I said I'm running out of options. Thanks, JGS __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package tm fails to remove the with remove stopwords
Mark, It looks like removeWords removed the in all instances except when the was the first word in your text. Maybe there is a parameter that needs to be set? I couldn't find anything on the help page. Here's an example of what I am seeing using the crude dataset #function removeWords does not appear to remove the first word require(tm) data(crude) crude[[1]] removeWords(crude[[1]], Shamrock) #Second word removed removeWords(crude[[1]], Diamond) #First word not removed Sam Thomas From: Mark Kimpel [mailto:mwkim...@gmail.com] Sent: Friday, November 13, 2009 11:47 AM To: Sam Thomas Cc: r-help@r-project.org; feine...@logic.at Subject: Re: package tm fails to remove the with remove stopwords Sam, Thanks for the example. Removing stop words after the DocumentTermMatrix has been created works fine if one is working with single words, but what if one is creating a dtm of possible combinations of words? Wouldn't one want to remove them from the corpus? Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 399-1219 Skype No Voicemail please On Thu, Nov 12, 2009 at 12:04 PM, Sam Thomas sam.tho...@revelanttech.com wrote: I'm not sure what's wrong with your approach, but this seems to strip the require(tm) params - list(minDocFreq = 1, removeNumbers = TRUE, stemming = TRUE, stopwords = TRUE, weighting = weightTf) myDocument - c(the rain in Spain, falls mainly on the plain, jack and jill ran up the hill, to fetch a pail of water) text.corp - Corpus(VectorSource(myDocument)) dtm - DocumentTermMatrix(text.corp, control = params) dtm dtm.mat - as.matrix(dtm) dtm.mat From: Mark Kimpel [mailto:mwkim...@gmail.com] Sent: Thursday, November 12, 2009 11:30 AM To: r-help@r-project.org; feine...@logic.at; Sam Thomas Subject: package tm fails to remove the with remove stopwords I am using code that previously worked to remove stopwords using package tm. Even manually adding the to the list does not work to remove the. This package has undergone extensive redevelopment with changes to the function syntax, so perhaps I am just missing something. Please see my simple example, output, and sessionInfo() below. Thanks! Mark require(tm) myDocument - c(the rain in Spain, falls mainly on the plain, jack and jill ran up the hill, to fetch a pail of water) text.corp - Corpus(VectorSource(myDocument)) # text.corp - tm_map(text.corp, stripWhitespace) text.corp - tm_map(text.corp, removeNumbers) text.corp - tm_map(text.corp, removePunctuation) ## text.corp - tm_map(text.corp, stemDocument) text.corp - tm_map(text.corp, removeWords, c(the, stopwords(english))) dtm - DocumentTermMatrix(text.corp) dtm dtm.mat - as.matrix(dtm) dtm.mat dtm.mat Terms Docs falls fetch hill jack jill mainly pail plain rain ran spain the water 1 0 0000 00 01 0 1 1 0 2 1 0000 10 10 0 0 0 0 3 0 0111 00 00 1 0 0 0 4 0 1000 01 00 0 0 0 1 R version 2.10.0 Patched (2009-10-27 r50222) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] chron_2.3-33 RWeka_0.3-23 tm_0.5-1 loaded via a namespace (and not attached): [1] grid_2.10.0 rJava_0.8-1 slam_0.1-6 tools_2.10.0 Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 399-1219 Skype No Voicemail please [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why the same values cannot be judged to be the same in R
Thanks all. %in% is what i need. 2009/11/13 jim holtman jholt...@gmail.com I think you want to use '%in%' instead of '=='. Try debugging (or understanding) what is happening by evaluating the subexpressions of the compares you have in your original posting. Also take a look at the 'recycling' of arguments and then you may understand what is happening: data2[(data2$x1 %in% data_1$x1) (data2$y1 %in% data_1$y1) (data2$tag == 0),] areaid x1 y1 tag 2 1 1.53 2.34 0 4 1 1.52 2.35 0 On Thu, Nov 12, 2009 at 10:04 PM, rusers.sh rusers...@gmail.com wrote: Hi Rusers, I found sometimes that the same values cannot be judged to be the same in R. Anybody knows the probelm? I think i ignored some minor detail. Thanks. Here is the example. data1-matrix(data=c(1,1.2,1.3,3/23/2004,1,1.5,2.3,3/22/2004,2,0.2,3.3,4/23/2004,3,1.5,1.3,5/22/2004),nrow=4,ncol=4,byrow=TRUE) data1-data.frame(data1);names(data1)-c(areaid,x,y,date) data2-matrix(data=c(1,1.22,1.32,1, 1.53, 2.34,1, 1.21, 1.37,1, 1.52, 2.35,2, 0.21, 3.33,2, 0.23, 3.35,3, 1.57, 1.31,3, 1.59, 1.33),nrow=8,ncol=3,byrow=TRUE) data2-data.frame(data2);names(data2)-c(areaid,x1,y1) data2$tag-0 data1_1-data1[1,] data2_1-data2[data2$areaid==data1_1$areaid data2$tag==0,] ran_1-sample(c(1:length(data2_1)),2, replace = FALSE) data2_1-data2_1[ran_1,] data_1-merge(data1_1,data2_1) #data_1 # areaid x y date x1 y1 tag #1 1 1.2 1.3 3/23/2004 1.52 2.35 0 #2 1 1.2 1.3 3/23/2004 1.53 2.34 0 data2[data_1$x1==data2$x1 data_1$y1==data2$y1 data2$tag==0,] #data2[c(data_1$x1==data2$x1 data_1$y1==data2$y1 data2$tag==0),] #areaid x1y1 tag #2 11.53 2.34 0 There should be two same observations between data_1 and data2, but here only one was identified. Thanks a lot. -- - Jane Chang Queen's [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- - Jane Chang Queen's [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers in C
Ups... I've overlooked that part. Thanks a lot for the fast response!
On Fri, Nov 13, 2009 at 6:05 PM, Duncan Murdoch murd...@stats.uwo.cawrote:
On 11/13/2009 11:41 AM, Thomas Unternaehrer wrote:
I need some random numbers in my C program. Here a small example:
#include R.h
void rand (int* n)
{
int len = *n;
for (int i = 0; i len; i++)
Rprintf(%1.5f , unif_rand());
}
dyn.load(rand.dll)
.C(rand, as.integer(10))
dyn.unload(rand.dll)
But this gives me 10 times the number 0.0 (I need 10 numbers between 0
and 1). Can somebody give me a hint what I'm doing wrong (or
misunderstand).
At a minimum, you forgot to call GetRNGState and PutRNGState. See Writing
R Extensions for details. But if you are running this from outside of R,
you'll also need to read about building a standalone Mathlib.
Duncan Murdoch
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Re: [R] linear model and by()
On Fri, Nov 13, 2009 at 11:49 AM, Sam Albers tonightstheni...@gmail.com wrote: snip No problem not use my data. For future reference, would it have been easier to attach a .csv file and then include the appropriate read.csv command? I realized that the easier one makes it to help, the easier it is to get a response. Thanks a lot for your help! Ista- To be fair, I did include Sectionf - factor(Section) below. ;) True enough, sorry I missed it! snip __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple if else statement problem
On 11/13/2009 12:54 PM, anna_l wrote:
Ok Jim it worked, thank you! it´s funny because it worked with the first
syntax in some cases...
If R knows the whole thing is incomplete, it will accept an else on its
own line. If the first 4 lines make a complete statement, R will
evaluate it, and not accept the following else.
So putting braces around the whole thing is another workaround, but
putting the else on the same line as the first closing brace is probably
better.
Duncan Murdoch
anna_l wrote:
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else
statements with the same syntax working. Thanks in advance
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Re: [R] Unsuccessful in reproducing README file in package build .zip and R library installed package folder
[Going through some old and from what I see unanswered messages See Writing R Extensions: The contents of subdirectory ./inst will be copied to top level during package installation (i.e. also for making binary packages). Best wishes, Uwe Ligges morp...@comcast.net wrote: My OS is Windows XP. Writing R Extensions, Section 1.1 states ‘README’ or ‘ChangeLog’ will be ignored by R, but may be useful to end-users. I see examples of README files in packages grDevices folder afm and nlme folder mlbook. The README file was placed at the top level of the package source folder, after the DESCRIPTION file. After running R CMD check, build, and INSTALL --build, the README file was found in the tar.gz file. However, it was not found in the zip file, the package Rcheck folder, and the R library package folder. How is the README put into build such that it is reproduced in the R library installed package folder? Bill Morphet, Ph.D. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers in C
On 11/13/2009 11:41 AM, Thomas Unternaehrer wrote:
I need some random numbers in my C program. Here a small example:
#include R.h
void rand (int* n)
{
int len = *n;
for (int i = 0; i len; i++)
Rprintf(%1.5f , unif_rand());
}
dyn.load(rand.dll)
.C(rand, as.integer(10))
dyn.unload(rand.dll)
But this gives me 10 times the number 0.0 (I need 10 numbers between 0
and 1). Can somebody give me a hint what I'm doing wrong (or misunderstand).
At a minimum, you forgot to call GetRNGState and PutRNGState. See
Writing R Extensions for details. But if you are running this from
outside of R, you'll also need to read about building a standalone Mathlib.
Duncan Murdoch
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[R] multivariate meta-analysis with the metafor package
Dear Wolfgang Viechtbauer and R users, I have few questions regarding the development of the package 'metafor. As you suggested , I post to the R-help mailing list. I read you're planning an extension of this method to the multivariate case. I think it would be a useful tool. I'm currently performing some analyses with R on multiple outcomes, using the Stata command mvmeta to get meta-analytic multivariate estimates, then coming back to R to use these results. Obviously, it's irritating to switch software every time. Briefly: - Are you still planning this extension? And in this case, do you have a planned date? - What are likely to be the advantages and limitations of a potential 'rma.multi' if compared to Stata's 'mvmeta'? Thank you for your time Regards, Antonio Gasparrini Public and Environmental Health Research Unit (PEHRU) London School of Hygiene Tropical Medicine Keppel Street, London WC1E 7HT, UK Office: 0044 (0)20 79272406 - Mobile: 0044 (0)79 64925523 Skype contact: a.gasparrini http://www.lshtm.ac.uk/people/gasparrini.antonio ( http://www.lshtm.ac.uk/pehru/ ) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] roc plot with zero length labels error
[Going through some old and from what I see unanswered messages
Hard to tell what is going on without telling us the data. Works with
the examples, so may be related to one of the objects scicomp5.model1,
pred, T, or auc.
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Best wishes,
Uwe Ligges
Chris Anderson wrote:
I am trying to create the roc plot bootstrap method from library(verification), and when I set the plot =both or emp then I get the following error. The roc.plot works fine when the plot is set to binorm. This is my first time using this function in R and am not sure what this error means or how to resolve the issue. It seems to work ok with the example dataset. Is there an option or data formatting I need to due to resolve this error?
roc.plot((scicomp5.model1[164]==High Price), pred, CI = T, n.boot = 100, plot = 'both',binormal = TRUE,
+ main = paste('AREA UNDER CURVE (AUC) =', round(auc$A, 2)))
Error in text.default(DAT[id, 3, i], DAT[id, 2, i], plot.thres[id2], pos = 4, :
zero length 'labels'
Chris Anderson
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[R] sum(row1==y) if row2=x
Hi to all is there any construct to sum data=data.frame(row1=c(1,1,3,1,2,3,2,2,1,3,4,5,2,3,2,1) , row2=c(2,2,1,1,1,2,1,2,1,1,1,1,2,2,2,1) ) Means I would like to get all y of row1 if in row2 of the data.frame is an x f.e row1=3 and row2=2 so I would like to get 6 And is there another construct to get the count of pairs where row1=3 and row2=2 means the result should be 2 I could do this with loop but I am wondering whether there is any better way. Regards Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 'R CMD check' fails with evaluation nested too deeply: infinite recursion
[Going through some old and from what I see unanswered messages No, you cannot have a cycle in Imports / Depends / LinkingTo otherwise you will run into an the chicken or the egg problem: That declaration means that the other packages must be loadable on installation, for example. You can try to declare Depends in one and to use Suggests in the one with less strong dependencies. If the dependency is too strong: Why not merge these essential parts of the functionality that depend on each other into one package? Best wishes, Uwe Ligges Joerg van den Hoff wrote: I get the error Error : evaluation nested too deeply: infinite recursion / options(expressions=)? during a 'R CMD check ...' on one of my packages. The reason seems to be that this package is mutually dependent on another one (i.e. the DESCRIPTION files of package A lists package B under Depends and vice versa). this might be bad design (having bits in both packages needed by the other), but I believe prior to R 2.9. this did not cause trouble. now the log file of the 'check' is something like Installing *source* package 'roiutils' ... ** R ** exec ** preparing package for lazy loading Loading required package: roiutils Loading required package: fzrutils ===CUT (many more of the same) Loading required package: roiutils Loading required package: fzrutils Loading required package: roiutils Error : evaluation nested too deeply: infinite recursion / options(expressions=)? i.e. it seems that R loads both packages again and again. what am I missing/doing wrong? thanks in advance joerg PS: platform powerpc-apple-darwin8.11.1 arch powerpc os darwin8.11.1 system powerpc, darwin8.11.1 status major 2 minor 9.2 year 2009 month 08 day24 svn rev49384 language R version.string R version 2.9.2 (2009-08-24) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Escaping regular expressions
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Hadley Wickham
Sent: Friday, November 13, 2009 5:34 AM
To: r-help
Subject: [R] Escaping regular expressions
Hi all,
Is there a method for escaping strings to be used regular expressions?
i.e. if I have a user supplied string that I'd like to use as a fixed
component is there a method that will turn (e.g.) .$^ into
\\.\\$\\^ ?
I've used the following:
asFixedRegex - function(pattern) {
gsub(([][^${}().?*+\\]), \\1, pattern)
}
E.g.,
asFixedRegex(.$^)
[1] \\.\\$\\^
or
x - c(C:\\Program Files\\word, P[[:alnum:]]{2,3},
(x+y)[1*3])
regexpr(paste(collapse=|, asFixedRegex(x)), x)
[1] 1 1 1
attr(,match.length)
[1] 21 17 10
nchar(x) # expect same as match.length
[1] 21 17 10
Is there a standard function to do this? If so, I'd
like to know its name.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Thanks,
Hadley
--
http://had.co.nz/
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] sum(row1==y) if row2=x
Hi Knut, Try sum(subset(df, row1 == 3 row2 == 2)[,1]) and nrow(subset( df, row1 == 3 row2 == 2) ) HTH, Jorge On Fri, Nov 13, 2009 at 1:59 PM, Knut Krueger wrote: Hi to all is there any construct to sum data=data.frame(row1=c(1,1,3,1,2,3,2,2,1,3,4,5,2,3,2,1) , row2=c(2,2,1,1,1,2,1,2,1,1,1,1,2,2,2,1) ) Means I would like to get all y of row1 if in row2 of the data.frame is an x f.e row1=3 and row2=2 so I would like to get 6 And is there another construct to get the count of pairs where row1=3 and row2=2 means the result should be 2 I could do this with loop but I am wondering whether there is any better way. Regards Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sum(row1==y) if row2=x
Try this: sum(data[with(data, row1 == 3 row2 == 2),1]) and sum(with(data, row1 == 3 row2 == 2)) On Fri, Nov 13, 2009 at 4:59 PM, Knut Krueger r...@krueger-family.de wrote: Hi to all is there any construct to sum data=data.frame(row1=c(1,1,3,1,2,3,2,2,1,3,4,5,2,3,2,1) , row2=c(2,2,1,1,1,2,1,2,1,1,1,1,2,2,2,1) ) Means I would like to get all y of row1 if in row2 of the data.frame is an x f.e row1=3 and row2=2 so I would like to get 6 And is there another construct to get the count of pairs where row1=3 and row2=2 means the result should be 2 I could do this with loop but I am wondering whether there is any better way. Regards Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to quit unwanted execution immediately?
[Going through some old and from what I see unanswered messages] R can or cannot response immediately depending on the underlying C sources. If the underlying source code is written carefully enough, there are more or less regular checks for events such as this one. If you are using some contributed package, it may be an issue in this package's source code. Best wishes, Uwe Ligges Peng Yu wrote: Occasionally, I start a command (taking long time to finish) that I did not really want to start. I type 'ctrl+C' to try to quit the execution. However, R does not quit the execution of the command immediately. I'm wondering if R could response to ctrl+C immediately. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Utility function to rotate log files?
I am wondering if there is a CRAN package that includes a utility function that will rotate file names, in the same sense that operating systems sometimes rotate log files. Or maybe there's something in base R. That is, we have a set of file names, say file1, file2, file3, and when the function is called, file3 is deleted, file2 is renamed file3, file1 is renamed file2, and the name of file1 is returned to the user's script, which then writes to file1. I've done some searching (RSiteSearch) but haven't found anything. Thanks -Don -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Utility function to rotate log files?
You can try something about like this:
foo - function() {
unlink(file3.txt)
file.rename(file2.txt, file3.txt)
file.rename(file1.txt, file2.txt)
sink(file1.txt)
cat(test file1)
sink()
}
On Fri, Nov 13, 2009 at 5:20 PM, Don MacQueen m...@llnl.gov wrote:
I am wondering if there is a CRAN package that includes a utility function
that will rotate file names, in the same sense that operating systems
sometimes rotate log files. Or maybe there's something in base R.
That is, we have a set of file names, say file1, file2, file3, and when the
function is called, file3 is deleted, file2 is renamed file3, file1 is
renamed file2, and the name of file1 is returned to the user's script, which
then writes to file1.
I've done some searching (RSiteSearch) but haven't found anything.
Thanks
-Don
--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple if else statement problem
anna_l wrote:
Ok Jim it worked, thank you! it´s funny because it worked with the first
syntax in some cases...
No, it did not. R doesn't randomly work in different
ways on different days.
-Peter Ehlers
anna_l wrote:
Hello, I am getting an error with the following code:
if( P2 P1)
+ {
+ P-P2
+ }
else
Erro: unexpected 'else' in else
{
+ P-P1
+ }
I checked the syntax so I don´t understand, I have other if else
statements with the same syntax working. Thanks in advance
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Re: [R] LINEAR MIXED EFFECT
Hi Ana, you did again :-) require(fortunes) fortune(dog) Firstly, don't call your matrix 'matrix'. Would you call your dog 'dog'? Anyway, it might clash with the function 'matrix'. -- Barry Rowlingson R-help (October 2004) if you call your data data you will crach data() function. cheers milton On Fri, Nov 13, 2009 at 8:30 AM, ANARPCG a.gouvei...@imperial.ac.uk wrote: Douglas Bates-2 wrote: On Thu, Nov 12, 2009 at 10:14 AM, milton ruser milton.ru...@gmail.com wrote: Hi Ana, I am not quite sure if it is the problem, but if you call your data.frame as exp, you will crash exp() function... try use another name for your data.frame. By the way, I suggest you not use attach(). Try something like model-lme(weight~date*diet, data=yourdataframe) good luck and include the random specification in the call to lme, not as a separate assignment. milton On Thu, Nov 12, 2009 at 5:43 AM, ANARPCG a.gouvei...@imperial.ac.uk wrote: Milton's point is dead-on, and I would highly encourage you to give the posting guide a look. That said... you might try na.action = na.omit in your call to... actually, we don't know what function you are using (see first point). Regardless, sounds like you have missing data and na.action is set to na.fail (ie, fail if any missing data). cheers, Dave milton ruser wrote: Dear Ana Golveia, It is completelly impossible someone realise what kind or help you need or what is happening. I suggest you give a look on the posting guide, mainly that part about a minimum reproducible code with self explaining information, etc. Cheers milton On Wed, Nov 11, 2009 at 7:22 AM, ANARPCG a.gouvei...@imperial.ac.uk wrote: CAN ANYONE PLEASE HELP ME WITH THIS i HAVE TO DO A MIXED EFFECT LINEAR MODEL WITH MY DATA DUE TO THE FACT THAT I have pseudoreplication! Although after reading and trying it for several times can get around due to Error in na.fail.default(list(date = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, : missing values in object I uploaded my data file Thank you so much Kind regards AG http://old.nabble.com/file/p26300394/rawoctobercalciumexperiment2.txt rawoctobercalciumexperiment2.txt -- View this message in context: http://old.nabble.com/LINEAR-MIXED-EFFECT-tp26300394p26300394.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. sorry I am new on this things the point is after trying to run the model all that happens is: exp-read.table(file=file.choose(),header=T) attach(exp) names(exp) [1] group date diet weightthickness length [7] width liplength lipwidth exp$diet=factor(exp$diet,levels=c(zeropercent,tenpercent,twentypercent,thirtypercent,fortypercent,cuttleprecent)) exp=na.omit(exp) library(nlme) random=~date model-lme(weight~date*diet) Error in na.fail.default(list(date = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, : missing values in object I have pseudoreplications due to the fact that the measurements of the replicates have different starting points so I was advised to do lme. I never used it before and I cant get arround with it! the help I wanted from you is to help me to understand how to do a runable model! http://old.nabble.com/file/p26315302/rawoctobercalciumexperiment2.txt rawoctobercalciumexperiment2.txt -- View this message in context: http://old.nabble.com/LINEAR-MIXED-EFFECT-tp26300394p26315302.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]]
Re: [R] LINEAR MIXED EFFECT
On Fri, 13 Nov 2009, milton ruser wrote: Hi Ana, you did again :-) require(fortunes) fortune(dog) Firstly, don't call your matrix 'matrix'. Would you call your dog 'dog'? Anyway, it might clash with the function 'matrix'. -- Barry Rowlingson R-help (October 2004) if you call your data data you will crach data() function. No. It won't. Except in some fairly unusual circumstances, R can distinguish functions from other objects and find the one it needs. The point is that code will usually be easier to read if you have different names for different things. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] when use which()
Hello: # some code to assign with and without which q - 1:20; q[c(9, 12, 14)] - NA r - 1:20; r[c(8:9, 12:15)] - NA s - 1:20; s[c(8:9, 12:15)] - NA r[q 16] - 0 s[which(q 16)] - 0 r;s # both: 0 0 0 0 0 0 0 0 NA 0 0 NA 0 NA 0 16 17 18 19 20 r - 1:20; r[c(8:9, 12:15)] - NA s - 1:20; s[c(8:9, 12:15)] - NA r[is.na(q)] - 30 s[which(is.na(q))] - 30 r;s # both: 1 2 3 4 5 6 7 NA 30 10 11 30 NA 30 NA 16 17 18 19 20 So it appears to me that a[b] - c delivers the same results as a[which(b)] - c. Is there any situation where the assignment with/ out which indeed makes a difference? Thanks for help Regards Sören __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] naive collinear weighted linear regression
On Wed, 11 Nov 2009, David Winsemius wrote: On Nov 11, 2009, at 7:45 PM, Mauricio Calvao wrote: When I try: fit_mod - lm(y~x,weights=1/error^2) I get Warning message: In lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : extra arguments weigths are just disregarded. (Actually the weights are for adjusting for sampling, and I do not see any sampling in your design.) No, the weights are not for adjusting for sampling. You will get the wrong standard errors if you put sampling weights into the `weights` argument. The warning is saying that he had misspelt 'weights' as 'weigths' (and so the code he posted wasn' t the same as the code he ran). -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] when use which()
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of soeren.vo...@eawag.ch Sent: Friday, November 13, 2009 12:24 PM To: r-help@r-project.org Subject: [R] when use which() Hello: # some code to assign with and without which q - 1:20; q[c(9, 12, 14)] - NA r - 1:20; r[c(8:9, 12:15)] - NA s - 1:20; s[c(8:9, 12:15)] - NA r[q 16] - 0 s[which(q 16)] - 0 r;s # both: 0 0 0 0 0 0 0 0 NA 0 0 NA 0 NA 0 16 17 18 19 20 r - 1:20; r[c(8:9, 12:15)] - NA s - 1:20; s[c(8:9, 12:15)] - NA r[is.na(q)] - 30 s[which(is.na(q))] - 30 r;s # both: 1 2 3 4 5 6 7 NA 30 10 11 30 NA 30 NA 16 17 18 19 20 So it appears to me that a[b] - c delivers the same results as a[which(b)] - c. Is there any situation where the assignment with/ out which indeed makes a difference? When using [ there should be no difference between using x[condition] and x[which(condition)]. which() is just a waste of typing, cpu time, and memory there. If you want all x that don't satisfy the condition x[!condition] works but x[-which(condition)] silently gives the wrong answer when all(condition==FALSE). There is one weird case, in [[, not [, where there is a difference, and this might be considered a bug: list(a=10,b=20,c=30)[[c(FALSE,TRUE,FALSE)]] Error in list(a = 10, b = 20, c = 30)[[c(FALSE, TRUE, FALSE)]] : attempt to select less than one element list(a=10,b=20,c=30)[[which(c(FALSE,TRUE,FALSE))]] [1] 20 [[ is treating the vector of logicals as a vector of integers and it can only work if all of them are TRUE and the list has at least 3 levels of recursion list(list(list(10,20),list(30,40)))[[c(TRUE,TRUE,TRUE)]] [1] 10 Of course, someone can write a package that defines a method for [ that doesn't work this way, but that would be unfriendly. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com Thanks for help Regards Sören __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
