Reasons not to answer very basic questions in a straightforward way; was: Re: [R] creating a sequence of object names
John wrote:
Thank you, Uwe. I've found a way to do the job by
reading the FAQ 7.21 although it is not giving a
precise explanation to a novice or casual user at
first reading. For example, if you type the first two
But the corresponding help files do so, for sure, and the FAQ 7.21
points you to ?assign and ?get.
lines in the FAQ, you get an error as you do not have
the variable, a, initially.
I am sure that more and more people get interested in
and serious about using R if advanced users are kind
enough to answer simple and silly questions as well
which are already explained in basic documentations.
Or is this community for highly motivated and advanced
R users only?
No, of course it is for novices as well!
BUT we do expect that novices do read basic documentation such as An
Introduction to R and the R FAQ before asking question.
If there are too many silly questions from thousands of R users, nobody
is able to manage the questions any more. And note that those people
answering questions do it on a voluntary basis, and (at least partially)
in their spare time!
Nobody would be subscribed to R-help any more, if there are 1000 mails a
day, 900 of them containing silly questions! It is yet already hard
enough to get through the huge amount of messages in a reasonable amount
of time!
I have answered your question in a way,
1) so that it is up to you to read some documentation. Now you have
seen the FAQs and some help files. And you have learned much more than
you would have learned if I had said Use assign()
2) so that nobody feels too encouraged to ask questions before reading
basic documentation - and my answer still saved you a lot of time!
Uwe Ligges
Regards,
John
--- Uwe Ligges [EMAIL PROTECTED]
wrote:
John wrote:
Hello R-users,
I wanted to generate objects named 'my.ftn1',
'my.ftn2', ... , 'my.ftn10', and tried the
following
code without success. How can I do this?
for ( i in 1:10 ) {
+ sub( , , paste(my.ftn, i)) - NULL
+ }
Error: Target of assignment expands to
non-language
object
Many thanks.
John
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http://www.R-project.org/posting-guide.html
Please do as suggested above, read the posting
guide!
It suggests to read the FAQs. FAQ 7.21 is what you
are looking for: How
can I turn a string into a variable?.
Uwe Ligges
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Re: [R] hist and truehist
Peter thanks for the response. So the results from hist(mydata) and truehist(mydata, h = .5) are the same. OK, but the sum of densities or intensities, for case that I gave, don't sum to 1 but to 2. Look bellow. I have an example where these density values are also up to 4 and sum to 5 (I have attached the PDF of that plot). This is really frustrating for me. What are actually these intensisties and densities, how are they calculated. Why are they the same? mydata - c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,3,4,5) # histogram with frequencies hist(mydata) # histogram with ratios or probabilities hist(mydata, freq = F) # what are that values on vertical axis # lets take a look at values behind x -hist(mydata, freq = F, plot = F); x # Sum values sum(x$intensities) [1] 2.00 R sum(x$density) [1] 2.00 When I think of histogram (the one not with frequencies) I think of gathering records into some classes and then divide the number of records in each class by total number of all records. This is not the case in hist(). Sorry for being pain in the ..., but this is really weird. Above that R-team is really doing a great job. Thanks for such a good tool! -- Lep pozdrav / With regards / Con respeto, Gregor GORJANC --- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si Zootechnical Departmentmail: gregor.gorjanc at bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzalefax: +386 (0)1 72 41 005 Slovenia --- Rplots.pdf Description: Adobe PDF document __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Storing loop output from a function
UweL == Uwe Ligges [EMAIL PROTECTED]
on Sat, 27 Nov 2004 17:09:26 +0100 writes:
UweL Andrew Kniss wrote:
I am attempting to write an R function to aid in time series diagnostics.
The tsdiag() works well, but I would prefer to get a plot with ACF, PACF,
and Ljung-Box p-values of residuals. In my attempt to get to that
point, I
am writing a function to calculate Ljung-Box p-values for residuals at
various lag distances.
ljung - function(fit)
for(i in c(1:24,36,48))
{box-(Box.test(fit$residuals, lag=i, type=Ljung-Box))
print(c(i, box$p.value))}
UweL You need to return() rather than print() the object.
and Andy Liaw correctly remarked that
AndyL Yes, but print() is supposed to return (invisibly) its argument(s)...
Yes.
But I'm pretty sure, Andrew's problem is to get all the p-values back
from his function and not just the last one
Which -- (together with making 'lags' a function argument)
would be something like
ljung - function(fit, lags = c(1:24,36,48))
{
nl - length(lags)
r - numeric(nl)
for(i in 1:nl)
r[i] - Box.test(fit$residuals, lag= lags[i], type=Ljung-Box)
r
}
or, simply, more elegantly and efficiently,
but a bit harder to understand for a beginner,
ljung - function(fit, lags = c(1:24,36,48))
sapply(lags, function(ll)
Box.test(fit$residuals, lag = ll, type=Ljung-Box))
Martin Maechler, ETH Zurich
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Re: [R] hist and truehist
Gregor GORJANC wrote: Peter thanks for the response. So the results from hist(mydata) and truehist(mydata, h = .5) are the same. OK, but the sum of densities or intensities, for case that I gave, don't sum to 1 but to 2. Look bellow. I have an example where these density values are also up to 4 and sum to 5 (I have attached the PDF of that plot). This is really frustrating for me. What are actually these intensisties and densities, how are they calculated. Why are they the same? mydata - c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,3,4,5) # histogram with frequencies hist(mydata) # histogram with ratios or probabilities hist(mydata, freq = F) # what are that values on vertical axis # lets take a look at values behind x -hist(mydata, freq = F, plot = F); x # Sum values sum(x$intensities) [1] 2.00 R sum(x$density) [1] 2.00 Well, look at the breaks! Each has with 0.5 Hence the you have to calculate sum(x$density)*0.5 Uwe Ligges When I think of histogram (the one not with frequencies) I think of gathering records into some classes and then divide the number of records in each class by total number of all records. This is not the case in hist(). Sorry for being pain in the ..., but this is really weird. Above that R-team is really doing a great job. Thanks for such a good tool! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] lm help: using lm when one point is known (not y intercept)
JohnF == John Fox [EMAIL PROTECTED]
on Sat, 27 Nov 2004 23:49:08 -0500 writes:
JohnF Dear Seth,
JohnF You don't say which variable is the explanatory
JohnF variable and which is the response, but assuming that
JohnF prob is to be regressed on effect, you can fit
JohnF lm(prob - 50 ~ I(effect + 37.25) - 1). That is you
JohnF can shift the point through which the regression is
JohnF to go to the origin and then force the regression
JohnF through the origin.
JohnF I hope this helps,
yes, nice!
Even a bit more useful {though slightly uglier} is to use offset():
mfit - lm(prob ~ offset(50+ 0*effect) + I(effect + 37.25) - 1)
such that e.g. predict(mfit, ...) will still predict 'prob'
Note however that for both solutions, the regression abline()
will look wrong {and I hoped it would also be ok when using offset()},
plot(prob ~ effect) ; abline(mfit)
Martin
JohnF John
JohnF
JohnF John Fox
JohnF Department of Sociology
JohnF McMaster University
JohnF Hamilton, Ontario
JohnF Canada L8S 4M4
JohnF 905-525-9140x23604
JohnF http://socserv.mcmaster.ca/jfox
JohnF
-Original Message-
To: [EMAIL PROTECTED]
Subject: [R] lm help: using lm when one point is known (not y intercept)
Hello-
My question is a short one. How can I specify a single point
which through the fitted linear model has to go through? To
illustrate my problem, the fit to following data must go
through the point (-37.25(effect), 50(prob)). Note: you can
ignore the label column.
Effect Prob Label
1 -1143.75 7.142857 L
2 -572.75 21.428571 D
3 -223.75 35.714286GL
4 123.25 50.00DG
5 359.75 64.285714 G
6 374.75 78.571429 DGL
7 821.75 92.857143DL
Thanks in advance!
Seth Imhoff
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RE: [R] Tcl error - brace in argument?
Peter,
Yes c(0,23) works.
Many thanks!
Matthew
-Original Message-
From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Sent: 26 November 2004 16:43
To: Peter Dalgaard
Cc: Matthew Dowle; '[EMAIL PROTECTED]'
Subject: Re: [R] Tcl error - brace in argument?
Peter Dalgaard [EMAIL PROTECTED] writes:
Matthew Dowle [EMAIL PROTECTED] writes:
Hi all,
Does anyone know a solution for this error ?
tkwidget(dlg, iwidgets::spinint, range={0 23})
I suspect you want range=as.tclObj(c(0,23)) or something like that,
i.e. a Tcl list of two numbers, not a five-character string.
On second thoughts: I think range=c(0,23) should do.
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] PlotML
Dear all, Has anybody ever written some plot / hist functions that would return PlotML code? [http://ptolemy.eecs.berkeley.edu/] Regards, Gregoire __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: Reasons not to answer very basic questions in a straightforward way; was: Re: [R] creating a sequence of object names
Dear Uwe,
I must say that I had thanked you for referring me to
the specific and exact FAQ 7.21 and I had solved my
simple problem from it. I alreadly had looked at some
of basic materials like 'An Introduction to R', 'R for
Beginners', 'R Data Import/Export as well as the
FAQ(that is, I know how to use ?assign and ?get). But,
because I am not going to be an expert in R I assume
that I have missed something (even very trivial) in
those documents. Of course, I can read them again and
again until I know everything in them. That is for
more interested enthusiasts, however.
I know very well that it is basic manners to read
those materials before asking questions here, but you
should also understand that people sometimes get stuck
with very simple problems if they are driven by stress
or run down. They can save a lot of time and
concentrate on and develop their primary jobs instead.
And I don't think you should be worried about 900
silly questions out of 1000 messages posted because
they are at least well-educated people who know what
reading basic materials before posting questions
means.
People can learn diverse solutions about their simple
questions, from advanced experienced users, that
sometimes contain much more informations and tips.
It is up to users(not necessarily advanced users)
whether or not they are willing to answer questions
and share their precious (even little) findings in
programming. Volunteers can simply ignore silly
questions if they are not appropriate for answering.
Or I would let them know what to do with their
improper questions in a personal email.
Finally, I do appreciate your answer again and other
people's active replies too. It was really useful to
point me to the specific FAQ rather than to just say
'look at the FAQ'. It simply occurred to my mind that
kindness is the best policy for good education.
I beg your pardon if this message is not relevant to
this help list.
With kind regards,
John
--- Uwe Ligges [EMAIL PROTECTED]
wrote:
John wrote:
Thank you, Uwe. I've found a way to do the job by
reading the FAQ 7.21 although it is not giving a
precise explanation to a novice or casual user at
first reading. For example, if you type the first
two
But the corresponding help files do so, for sure,
and the FAQ 7.21
points you to ?assign and ?get.
lines in the FAQ, you get an error as you do not
have
the variable, a, initially.
I am sure that more and more people get interested
in
and serious about using R if advanced users are
kind
enough to answer simple and silly questions as
well
which are already explained in basic
documentations.
Or is this community for highly motivated and
advanced
R users only?
No, of course it is for novices as well!
BUT we do expect that novices do read basic
documentation such as An
Introduction to R and the R FAQ before asking
question.
If there are too many silly questions from thousands
of R users, nobody
is able to manage the questions any more. And note
that those people
answering questions do it on a voluntary basis, and
(at least partially)
in their spare time!
Nobody would be subscribed to R-help any more, if
there are 1000 mails a
day, 900 of them containing silly questions! It is
yet already hard
enough to get through the huge amount of messages in
a reasonable amount
of time!
I have answered your question in a way,
1) so that it is up to you to read some
documentation. Now you have
seen the FAQs and some help files. And you have
learned much more than
you would have learned if I had said Use assign()
2) so that nobody feels too encouraged to ask
questions before reading
basic documentation - and my answer still saved you
a lot of time!
Uwe Ligges
Regards,
John
--- Uwe Ligges [EMAIL PROTECTED]
wrote:
John wrote:
Hello R-users,
I wanted to generate objects named 'my.ftn1',
'my.ftn2', ... , 'my.ftn10', and tried the
following
code without success. How can I do this?
for ( i in 1:10 ) {
+ sub( , , paste(my.ftn, i)) - NULL
+ }
Error: Target of assignment expands to
non-language
object
Many thanks.
John
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Please do as suggested above, read the posting
guide!
It suggests to read the FAQs. FAQ 7.21 is what you
are looking for: How
can I turn a string into a variable?.
Uwe Ligges
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[R] core dump during make check when building 64-bit R on Solaris 8/9
Hi, I am building a 64-bit R 2.0.1 on Solaris 9. The compiler is Sun Studio 8. Make was successful but I have a core dump during a make check. By the way, this problem also happens on my Solaris 8 machine though I did not get a core dump. I do not have 64-bit versions of the readline, tcl/tk, libncurses, etc libraries so these caused configure not to use them with ELFCLASS32 errors. I use the following flags in config.site: CC=cc -xarch=v9 CFLAGS=-xO5 -xlibmil -dalign F77=f95 -xarch=v9 FFLAGS=-xO5 -xlibmil -dalign CXX=CC -xarch=v9 I pasted the make check error messages below: $ make check collecting examples for package 'base' ... Building/Updating help pages for package 'base' Formats: text html latex example running code in 'base-Ex.R' ...*** Error code 1 make: Fatal error: Command failed for target `base-Ex.Rout' Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples *** Error code 1 make: Fatal error: Command failed for target `test-Examples-Base' Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples *** Error code 1 make: Fatal error: Command failed for target `test-Examples' Current working directory /export/home/cheeseng/R-2.0.1/tests *** Error code 1 make: Fatal error: Command failed for target `test-all-basics' Current working directory /export/home/cheeseng/R-2.0.1/tests *** Error code 1 make: Fatal error: Command failed for target `check' The last few lines in base-Ex.Rout.fail is: ### * kappa flush(stderr()); flush(stdout()) ### Name: kappa ### Title: Estimate the Condition Number ### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri ### Keywords: math ### ** Examples kappa(x1 - cbind(1,1:10))# 15.71 [1] 15.70590 Doing a dbx on the core dump shows that the following: program terminated by signal SEGV (no mapping at the fault address) 0x790fdf54: ___pl_dgesdd_64_+0x1654:std %f4, [%o1] I hope some one have a more successful build and can show how you did it. Thanks, Chee Seng UNIX Administrator Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065 --- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] PlotML
Gregoire Thomas [EMAIL PROTECTED] writes: Dear all, Has anybody ever written some plot / hist functions that would return PlotML code? [http://ptolemy.eecs.berkeley.edu/] Not that I know of, and looking at the design of PlotML, it doesn't look like a nice fit as an R device driver. PlotML works at the level of data sets, bar graphs, axes, etc., not with low-level items like lines, polygons, and text. There are general XML handling tools in the XML package, though. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Call to trellis.focus(); thenpanel.superpose()
The following works fine with the x11 device, though it may well be that an initial plot is overwritten. With a pdf or postscript device, I get two plots, the first of which still has the red border from having the focus, while the second is the plot that I want. library(lattice); library(grid) plt - xyplot(uptake ~ conc, groups=Plant, data=CO2) print(plt) trellis.focus(panel, row=1, column=1) arglist=trellis.panelArgs() arglist$type - l do.call(panel.superpose, args=arglist) trellis.unfocus() Should I be able to use panel.superpose() in this way? The new abilities provided by trellis.focus() etc add greatly to the flexibility of what can be done with lattice plots. The grid-lattice combination is a great piece of software. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Bioinformation Science, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R: nnet questions
hi all i'm new to the area of neural networks. i've been reading some references and seem to understand some of the learning algorithms. i am very familiar with regression and would just like to see how neural nets handle this problem so i've been using the nnet package. i simply want to use a 3 layer neural net, ie 1 input, 1 hidden layer (where the hidden layer is linear, since i want to basically perform regression analysis by means of neural nets) and 1 output layer. the x and y vector was simulated as follows: x-1:100 x [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 [91] 91 92 93 94 95 96 97 98 99 100 y-2+5*x+rnorm(100)*5 y [1] 8.789605 11.151109 14.622276 30.381379 19.328647 29.317038 33.793720 39.557390 51.939294 45.045965 [11] 58.783991 63.191745 72.882202 79.184778 85.034551 94.446000 89.243004 88.223547 106.327683 104.424668 [21] 103.057648 112.855778 111.777823 108.359485 128.956152 127.369102 128.784481 139.760279 151.959887 152.014623 [31] 158.869586 167.030970 166.711160 177.415680 173.542293 182.484224 179.767128 192.284343 196.173830 202.353030 [41] 220.449623 213.410307 216.746041 219.812526 230.440402 230.759429 239.311279 244.151390 248.637023 254.648298 [51] 262.694237 253.619539 276.975714 280.395284 280.173787 286.813617 284.766870 296.705692 295.110064 304.709464 [61] 305.650793 310.128992 314.035624 314.649213 322.958865 333.640203 342.538307 340.546359 342.433629 344.720633 [71] 354.115051 363.631246 371.479886 367.066764 377.184512 386.634677 392.310577 386.151325 400.345393 408.831710 [81] 413.999148 405.009358 418.679828 418.388427 419.282955 432.329471 433.448313 444.166060 447.773185 455.103503 [91] 448.588598 464.410358 465.565875 478.677403 478.306390 479.565728 487.681689 491.422090 502.468491 500.385458 i then went about to use the nnet function: a.net-nnet(y~x,linout=T,size=1) # weights: 4 initial value 8587786.130082 iter 10 value 2086583.979646 final value 2079743.529111 converged NOTE: the function said that four weights were estimated. This is correct as shown below. the model can be represented as: input ---(w1)---hidden ---(w2)--- output x --a1+w1*x -- a2+w2*(a1+w1*x) where: wi are the weights, i=1,2 x is an input pattern further results were: summary(a.net) a 1-1-1 network with 4 weights options were - linear output units b-h1 i1-h1 -276.48 -295.11 b-o h1-o 254.92 764.72 is the following statement correct? (i think that it is!) a1= b-h1 w1= i1-h1 a2= b-o w2= h1-o If the hidden layer and the output layers are both LINEAR then the following should be true: 1. 2= a2+a1*w2 2. 5= w1*w2 THIS IS NOT THE CASE, see the results. The only thing that i can think of thats happening is that the activation function from the hidden layer is not linear. Is this correct since i used the linout=T arguement? are we able to change the activation function from the hidden layer? two other questions: 1. with regard to the size arguement, how does one know how many nodes are in the hidden layer? (this might be a silly question.) e.g we might have 2 hidden layers both with 3 nodes. 2. are we able to plot the drop in the error function as a function of the epochs? hope someone can help thanking you!!!__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RE: Adding a line in the graph of 'plot()'
Yes. See ?abline or ?lines -Original Message- From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Sun 11/28/2004 8:35 PM To: [EMAIL PROTECTED] Cc: Subject: [R]: Adding a line in the graph of 'plot()' Hello. I'm looking for a way to add a line in a plot of a points that should lie along a particular line. Can I add a line to the 'plot()' function, maybe using 'abline()' so that the line is visible in the graph of 'plot()'? How? More generally, can I overlay plots over one another? Thanks. Dean Vrecko Simon Fraser University __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Ts analysis with R: a contribute in Italian language
Dear All, I wish to inform, especially Italian speaking R-users, that on CRAN web site is now available a contribute (in Italian language) about using R in ts analysis. Any comments would be appreciated. Best regards, Vito = Diventare costruttori di soluzioni Became solutions' constructors The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/palese/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] plot problem
Dear all, I am having trouble plotting a PCA result. The plot doesn't appear!!! R goes through without any errors but doesn't make a plot appear!! Could it be wrong window parameters? In this case how do I change them? I am under red hat 9 with the latest version of R! Thanks. Vous manquez despace pour stocker vos mails ? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Building latest version of package
Hi I have a package which was built using R 1.9.1 and everything worked fine. I recently upgraded to R 2.0.1 and tried to re-install my package - and I got: Error in library(mypackage) : 'mypackage' is not a valid package -- installed 2.0.0? So I tried rebuilding it using my new version of R: R CMD BUILD --binary mypackage hhc: not found cp: cannot stat `mypackage.chm': No such file or directory make[1]: *** [chm-mypackage] Error 1 make: *** [pkg-mypackage] Error 2 *** Installation of mypackage failed *** Removing 'f:/tmp/Rbuild.2972/mypackage' ERROR * installation failed I didn't have these problems before. What is hhc and why can't R find it? In general, will I have to re-build my package everytime a new version of R is released? Many thanks Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] plotting data in non-orthogonal coords.
Hi ! I am wondering how to plot data (e.g. f(x,y) ) in a coordinate system spanned by two non-orthogonal basis vectors (e.g. hexagonal symmetry). The data is given on an equally spaced grid in theses coords and i would like to do a contour plot (e.g. with filled.contour). Thanks for your help. Andreas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] non-visible functions in return to methods()
Please point me to the documentation explaining why some of the functions returned by calling methods() are marked as non-visible and whether there is indeed no way of viewing the R code of such functions thanks Steve _ Stay in touch with absent friends - get MSN Messenger http://www.msn.co.uk/messenger __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] non-visible functions in return to methods()
non-visible functions are hidden in a namespace. You can view the code by using getS3method(). -roger steve houghton wrote: Please point me to the documentation explaining why some of the functions returned by calling methods() are marked as non-visible and whether there is indeed no way of viewing the R code of such functions thanks Steve _ Stay in touch with absent friends - get MSN Messenger http://www.msn.co.uk/messenger __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with using transace
I am trying to use the Hmisc function transace to transform predictors test-cbind(flowstress,pressres,alloy) xtrans-transace(x,binary=pressres',monotonic='flowstress', categorical='alloy') and I am getting the following message¨ Error in ace(x[, -i], x[, i], monotone = im, categorical = ic) : unused argument(s) (monotone ...) Any idea? thanks anne thank for your help Anne __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: Reasons not to answer very basic questions in a straightforwa rd way; was: Re: [R] creating a sequence of object names
I'd like to make just a couple of points: R-help is considered by quite a few people to be high-traffic. As such, many have low appetite for very basic questions. (I wouldn't call them silly.) In many cases such questions are answered by pointing to a particular function help page or manual section. In this particular case, it's probably not at the very basic level that would be covered in An Introduction to R. However, it _is_ a bona fide FAQ, thus the entry 7.21 in the R-FAQ. Now, if there's ever one type of questions that many do not like to see in a mailing list, it's one that can be found in the list FAQ, as one of the main reasons for having the FAQ is to prevent such questions from being asked over and over again on the list. Now, if after reading the FAQ entry, you still can't solve the problem, then you should tell us that, as well as how you tried and failed, so people have a much better idea where you went off track, and are more likely to give you more useful help. This is in the Posting Guide, which suggest ways to ask question that maximize the probability of getting useful replies. Reading that is to your own benefit, as well as others on the list. As Duncan Murdoch said in a reply to a poster complaining (essentially about being told to RTFM) on R-devel, we are not asking you to read these things over and over again, nor on a periodic basis, but please do try to at least take a glance before posting. Posts that get less than enthusiastic response are usually ones that showed that posters' unwillingness to do the minimal work to help themselves, not because they are considered `dumb' or `silly'. In such cases people are much less willing to help. Cheers, Andy From: John Dear Uwe, I must say that I had thanked you for referring me to the specific and exact FAQ 7.21 and I had solved my simple problem from it. I alreadly had looked at some of basic materials like 'An Introduction to R', 'R for Beginners', 'R Data Import/Export as well as the FAQ(that is, I know how to use ?assign and ?get). But, because I am not going to be an expert in R I assume that I have missed something (even very trivial) in those documents. Of course, I can read them again and again until I know everything in them. That is for more interested enthusiasts, however. I know very well that it is basic manners to read those materials before asking questions here, but you should also understand that people sometimes get stuck with very simple problems if they are driven by stress or run down. They can save a lot of time and concentrate on and develop their primary jobs instead. And I don't think you should be worried about 900 silly questions out of 1000 messages posted because they are at least well-educated people who know what reading basic materials before posting questions means. People can learn diverse solutions about their simple questions, from advanced experienced users, that sometimes contain much more informations and tips. It is up to users(not necessarily advanced users) whether or not they are willing to answer questions and share their precious (even little) findings in programming. Volunteers can simply ignore silly questions if they are not appropriate for answering. Or I would let them know what to do with their improper questions in a personal email. Finally, I do appreciate your answer again and other people's active replies too. It was really useful to point me to the specific FAQ rather than to just say 'look at the FAQ'. It simply occurred to my mind that kindness is the best policy for good education. I beg your pardon if this message is not relevant to this help list. With kind regards, John --- Uwe Ligges [EMAIL PROTECTED] wrote: John wrote: Thank you, Uwe. I've found a way to do the job by reading the FAQ 7.21 although it is not giving a precise explanation to a novice or casual user at first reading. For example, if you type the first two But the corresponding help files do so, for sure, and the FAQ 7.21 points you to ?assign and ?get. lines in the FAQ, you get an error as you do not have the variable, a, initially. I am sure that more and more people get interested in and serious about using R if advanced users are kind enough to answer simple and silly questions as well which are already explained in basic documentations. Or is this community for highly motivated and advanced R users only? No, of course it is for novices as well! BUT we do expect that novices do read basic documentation such as An Introduction to R and the R FAQ before asking question. If there are too many silly questions from thousands of R users, nobody is able to manage the questions any more. And note that those people answering questions do it on a voluntary basis, and (at least partially) in their spare time! Nobody would be
RE: [R] non-visible functions in return to methods()
You mean something like ?methods, which says: Value: An object of class 'MethodsFunction', a character vector of function names with an 'info' attribute. There is a 'print' method which marks with an asterisk any methods which are not visible: such functions can be examined by 'getS3method' or 'getAnywhere'. ?? Andy From: steve houghton Please point me to the documentation explaining why some of the functions returned by calling methods() are marked as non-visible and whether there is indeed no way of viewing the R code of such functions thanks Steve _ Stay in touch with absent friends - get MSN Messenger http://www.msn.co.uk/messenger __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: Reasons not to answer very basic questions in a straightforwa rd way; was: Re: [R] creating a sequence of object names
lots of good points from Andy and Uwe deleted and perhaps the most important reason for the particular socratic form of teaching on this list are the number of to-be, current, and former faculty members who feel compelled to teach general solutions to the problems (reading the FAQ is a rather general solution, eh?) rather than spoonfeed answers. This is a bit unlike some of the program language mailing lists where the care and feeding of personal egos is also part of the scene. (of course, I'm not referring to the wizards lists...!). best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] non-visible functions in return to methods()
Roger == Roger D Peng [EMAIL PROTECTED]
on Mon, 29 Nov 2004 08:48:04 -0500 writes:
Roger non-visible functions are hidden in a namespace.
yes.
Roger You can view the code by using getS3method().
not always {namely when the hidden function is not an S3 method}
getAnywhere() is more generally useful, but please consider my
post from half a year ago
https://stat.ethz.ch/pipermail/r-help/2004-May/050112.html
which gives more explanations and possibilities.
Roger steve houghton wrote:
Please point me to the documentation explaining why some of the
functions returned
by calling methods() are marked as non-visible and whether there is
indeed no way of
viewing the R code of such functions
thanks
Steve
__
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[R] systemfit - SUR
Hello to everyone, I have 2 problems and would be very pleased if anyone can help me: 1) When I use the package systemfit for SUR regressions, I get two different variance-covariance matrices when I firstly do the SUR regression (The covariance matrix of the residuals used for estimation) and secondly do the OLS regressions. In the manual for systemfit on page 14 I see however, that the variance-covariance matrix for SUR is obtained from OLS. How can this be explained? 2) Is there an easy possibility to test a) the OLS equations, and b) the SUR system for SUR structures? In other words: Is the LM-Test from Breusch and Pagan available in R? Thanks for the attention! Best Regards, Thomas Almer __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] systemfit - SUR
On Monday 29 November 2004 16:42, [EMAIL PROTECTED] wrote: Hello to everyone, I have 2 problems and would be very pleased if anyone can help me: 1) When I use the package systemfit for SUR regressions, I get two different variance-covariance matrices when I firstly do the SUR regression (The covariance matrix of the residuals used for estimation) and secondly do the OLS regressions. In the manual for systemfit on page 14 I see however, that the variance-covariance matrix for SUR is obtained from OLS. How can this be explained? Hi Thomas, I get identical residual covariance matrices: R library(systemfit) R data( kmenta ) R demand - q ~ p + d R supply - q ~ p + f + a R labels - list( demand, supply ) R system - list( demand, supply ) R fitols - systemfit(OLS, system, labels, data=kmenta ) R fitols$rcov [,1] [,2] [1,] 3.725391 4.136963 [2,] 4.136963 5.784441 R fitsur - systemfit(SUR, system, labels, data=kmenta ) R fitsur$rcovest [,1] [,2] [1,] 3.725391 4.136963 [2,] 4.136963 5.784441 Did you do _iterated_ SUR? Best wishes, Arne 2) Is there an easy possibility to test a) the OLS equations, and b) the SUR system for SUR structures? In other words: Is the LM-Test from Breusch and Pagan available in R? Thanks for the attention! Best Regards, Thomas Almer __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Citation
Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratório de Ciências Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] plot problem
Hi William, the 1st example given in ?screeplot works for me (R 2.0.0 on SuSE Linux 9.0): (pc.cr - princomp(USArrests, cor = TRUE)) # inappropriate screeplot(pc.cr) plot appears To help you we need more details. Does normal plotting work? e.g.: plot(rnorm(20),rnorm(20)) Can you plot to a file? (see ?ps, ?pdf or ?png and don't forget dev.off()) Arne On Monday 29 November 2004 13:47, william ritchie wrote: Dear all, I am having trouble plotting a PCA result. The plot doesn't appear!!! R goes through without any errors but doesn't make a plot appear!! Could it be wrong window parameters? In this case how do I change them? I am under red hat 9 with the latest version of R! Thanks. Vous manquez despace pour stocker vos mails ? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Citation
See the function ?citation under 2.0.0 R citation() To cite R in publications use: R Development Core Team (2004). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. HTH, Andy -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Tatiana Fernandes Sent: Monday, November 29, 2004 11:20 AM To: [EMAIL PROTECTED] Subject: [R] Citation Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratório de Ciências Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Citation
Did you see item 2.8 in the R FAQ? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Citing-R Tatiana Fernandes wrote: Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratrio de Cincias Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Citation
Tatiana Fernandes wrote: Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. Please the FAQ more carefully and find how it is cited therein. Or just type citation() at the prompt. Uwe Ligges Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratrio de Cincias Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Citation
citation() Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratrio de Cincias Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Building latest version of package
michael watson (IAH-C) wrote: Hi I have a package which was built using R 1.9.1 and everything worked fine. I recently upgraded to R 2.0.1 and tried to re-install my package - and I got: Error in library(mypackage) : 'mypackage' is not a valid package -- installed 2.0.0? So I tried rebuilding it using my new version of R: R CMD BUILD --binary mypackage hhc: not found cp: cannot stat `mypackage.chm': No such file or directory make[1]: *** [chm-mypackage] Error 1 make: *** [pkg-mypackage] Error 2 *** Installation of mypackage failed *** Removing 'f:/tmp/Rbuild.2972/mypackage' ERROR * installation failed I didn't have these problems before. What is hhc and why can't R find it? hhc is Microsoft's compiled html help compiler. Either edit your MkRules file not to generate chm files, or download and install the required software as mentioned in file readme.packages. In general, will I have to re-build my package everytime a new version of R is released? Well, not always, but yes, if considerable changes have taken place, as it has happend for the change from 1.y.z to 2.0.0. Uwe Ligges Many thanks Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Citation
Tatiana Fernandes [EMAIL PROTECTED] writes: Hello! I would like to know how do I citate R? I have used it during my Master thesis but I dont know how to citate during the text and on the references. Ive looked for it on the web page but only found how to citate the FAQ. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R in publications. ...and if you don't see that when you start R, you need to upgrade! It is in the FAQ too (Q2.8). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Citation
From: Chuck Cleland Did you see item 2.8 in the R FAQ? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Citing-R Or the start-up message, which has, in part: R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Note that last line! Andy Tatiana Fernandes wrote: Hello! I would like to know how do I citate R? I have used it during my Master thesis but I don't know how to citate during the text and on the references. I've looked for it on the web page but only found how to citate the FAQ. Thank you in advance. Tatiana Fernandes Universidade Estadual do Norte Fluminense Laboratório de Ciências Ambientais - CBB Av. Alberto Lamego, 2.000 - Campos dos Goytacazes - RJ 28013-600 - BRASIL Tel: +55 (22) 2726-1469 Fax: +55 (22) 2726-1472 e-mail: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] scan; 1 items
HI the scan function when only one item is read says: scan() 1: 3.3 2: Read 1 items [1] 3.3 I hope my english is not playing a trick on me, but 1 items sounds very strange this makes me feel very anal, and it's really not important and I apologize for it but here it goes anyway __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error using glm with poisson family and identity link
On Thu, 25 Nov 2004, Peter Dalgaard wrote: I haven't got all that much experience with it, but obviously, the various algorithms for constrained optimization (box- or otherwise) at least allow you to find a proper maximum likelihood estimator. It's harder than it looks (well, my experience is with the log-binomial model, but it should be similar). The constraints are not box constraints, but a more general set of linear constraints, and you either have to find the convex hull of the data or use a constraint for every data point. Also, the algorithm in glm.fit, while not perfect, is a little smarter than a simple IRLS. It uses step-halving to back away from the edge, and when the parameter space is convex it has a reasonable chance of creeping along the boundary to the true MLE. I think better glm fitting is worth pursuing: computational difficulties with the log-binomial model have forced many epidemiologists turn to estimators other than the MLE (or contrasts other than the relative risk), which is a pity. -thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] PlotML
Has anybody ever written some plot / hist functions that would return PlotML code? [http://ptolemy.eecs.berkeley.edu/] http://ptolemy.eecs.berkeley.edu/%5D Not that I know of, and looking at the design of PlotML, it doesn't look like a nice fit as an R device driver. PlotML works at the level of data sets, bar graphs, axes, etc., not with low-level items like lines, polygons, and text. There are general XML handling tools in the XML package, though. Thx. I've wrapped up a couple of functions into a package that does what I need. In case somebody is interested I've put it with an example at: http://penyfan.ugent.be/ptplot/ . Note that you might also need to install R2HTML. Regards, Gregoire __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error using glm with poisson family and identity link
Thomas Lumley [EMAIL PROTECTED] writes: Also, the algorithm in glm.fit, while not perfect, is a little smarter than a simple IRLS. It uses step-halving to back away from the edge, and when the parameter space is convex it has a reasonable chance of creeping along the boundary to the true MLE. Hmm. That wasn't my experience. I had a situation where there was like a (virtual) maximum outside the boundary, and the algorithm would basically stay on the path to that peak, banging its little head into the same point of the wall repeatedly, so to speak. (If you make a little drawing of an elliptical contour intersecting a linear boundary, I'm sure you'll see that this process leads to a point-of-no-progress that can be quite far from the maximum along the edge.) I think better glm fitting is worth pursuing: computational difficulties with the log-binomial model have forced many epidemiologists turn to estimators other than the MLE (or contrasts other than the relative risk), which is a pity. Yup... -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Question d'un débutant
On Sun, 28 Nov 2004, HOME - Didier Ledoux wrote: Je suis débutant en R. Je voudrais faire un tableau de statistiques descriptives ou les moyennes seraient calculées en fonction de deux critères: sexe, région Cela donnerait ceci: SEXEREGIONMOYENNE femmeAmoy1 femmeBmoy2 HommeA moy3 HommeB moy4 Comment dois-je faire? Quelles commandes utiliser? ?by -thomas__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] escaping backslash in a string
How can I get a single backslash in a character string? My goal is to escape dots in a string that will be used as a regular expression. I thought I could do it this way: gsub(., \\., x) Unfortunately, \\ does not represent a literal backslash as I expected, but rather a pair of backslashes: \\. [1] \\. \\ [1] \\ Just a backslash and a dot fails too, since that represents an escaped dot: \. [1] . A single backslash works in the middle of strings sometimes,but it depends on what the character following it is (presumably depending on whether the pair of characters represents an escape sequence): a\b [1] a\b x\y [1] xy Is there a way to represent \? This seems like a design problem in the interpreter. R.version _ platform i386-redhat-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.1 year 2004 month11 day 15 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] non-visible functions in return to methods()
On Mon, 29 Nov 2004, steve houghton wrote: Please point me to the documentation explaining why some of the functions returned by calling methods() are marked as non-visible and whether there is indeed no way of viewing the R code of such functions Luke Tierney's article in Volume 3 No 1 of the R Newsletter explains why. How to get the functions is FAQ 7.26. -thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] library(fields) world shift function not working anymore
Hi there. I just upgraded to 2.01 on Mac OS 10.3.6. I used to use the command (on R 1.9.x): world(ylim=c(-30,30), xlim = c(0,360), shift=TRUE, add=TRUE) to draw a world outline over my image plots. My data uses longitude from (0, 360) so I need to use the shift function. After I upgraded, I get the following error: world(ylim=c(-30,30), xlim = c(0,360), shift=TRUE, add=TRUE) Error in world(ylim = c(-30, 30), xlim = c(0, 360), shift = TRUE, add = TRUE) : NAs are not allowed in subscripted assignments Does anyone know a workaround for this? Thank you. Jennifer Fox Graduate Researcher NOAA Aeronomy Laboratory Boulder, CO [EMAIL PROTECTED] [[alternative text/enriched version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] escaping backslash in a string
Dan Lipsitt [EMAIL PROTECTED] writes: How can I get a single backslash in a character string? My goal is to escape dots in a string that will be used as a regular expression. I thought I could do it this way: gsub(., \\., x) Unfortunately, \\ does not represent a literal backslash as I expected, but rather a pair of backslashes: \\. [1] \\. \\ [1] \\ Nononononono If you want to know what is inside a string, use cat() not (implicitly) print() cat( \\.) \. The thing is that print() itself escapes weird characters, including the escape character: x - readLines() # ctr-D terminates (on Linux anyway) \. x [1] \\. Is there a way to represent \? This seems like a design problem in the interpreter. Yes. Not at all. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problem with using transace
[EMAIL PROTECTED] wrote:
I am trying to use the Hmisc function transace to transform predictors
test-cbind(flowstress,pressres,alloy)
xtrans-transace(x,binary=pressres',monotonic='flowstress', categorical='alloy')
and I am getting the following message¨
Error in ace(x[, -i], x[, i], monotone = im, categorical = ic) :
unused argument(s) (monotone ...)
Any idea?
thanks anne
thank for your help
Anne
The corrected version (below) will fix that problem but note that there
is a bug in ace causing it not to allow a monotonicity constraint when a
variable is on the left hand side. This is inconsistent with the ace
documentation. There are other problems in ace in which it checks
column numbers against the number of rows in the x matrix instead of the
number of columns. The internal version of ace defined inside areg.boot
fixes the latter problem. Note that I reported these problems a long
time ago.
Frank
transace - function(x, monotonic=NULL, categorical=NULL, binary=NULL,
pl=TRUE) {
if(.R.) require('acepack') # provides ace, avas
nam - dimnames(x)[[2]]
omit - is.na(x %*% rep(1,ncol(x)))
omitted - (1:nrow(x))[omit]
if(length(omitted)) x - x[!omit,]
p - ncol(x)
xt - x # binary variables retain original coding
if(!length(nam)) stop(x must have column names)
rsq - rep(NA, p)
names(rsq) - nam
for(i in (1:p)[!(nam %in% binary)]) {
lab - nam[-i]
w - 1:(p-1)
im - w[lab %in% monotonic]
ic - w[lab %in% categorical]
if(nam[i] %in% monotonic) im - c(0, im)
if(nam[i] %in% categorical) ic - c(0, ic)
m - 10*(length(im)0)+(length(ic)0)
if(m==11) a - ace(x[,-i], x[,i], mon=im, cat=ic)
else if (m==10) a - ace(x[,-i], x[,i], mon=im)
else if(m==1) a - ace(x[,-i], x[,i], cat=ic)
else a - ace(x[,-i], x[,i])
xt[,i] - a$ty
rsq[i] - a$rsq
if(pl)plot(x[,i], xt[,i], xlab=nam[i], ylab=paste(Transformed,nam[i]))
}
cat(R-squared achieved in predicting each variable:\n\n)
print(rsq)
attr(xt, rsq) - rsq
attr(xt, omitted) - omitted
invisible(xt)
}
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--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] Seeking help with a simple loop construction
Hello, I have a df, pp, with five variables: nobs(pp) q10_1 q10_2 q10_3 q10_4 actcode 16201620162016201620 I want to create a loop to run four xtabs (the first four variables above by the fifth) and then store the results in a matrix. Below I make my intent clear by showing the output of one xtab which is inserted into a matrix. a - xtabs(q10_1 ~ actcode) a actcode 1 2 3 4 5 6 7 8 9 10 7 11 3 60 66 56 21 40 7 8 freq.mat - matrix(0, 4, 10, byrow = TRUE) freq.mat[1,] - a freq.mat [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]7 113 60 66 56 21 407 8 [2,]000000000 0 [3,]000000000 0 [4,]000000000 0 === I have spent a couple of hours searching the web and my texts but continue to strike out in my attempts to construct a correct formulation of this simple loop. Help would be appreciated. Greg Blevins The Market Solutions Group, Inc. Windows XP R 2.0.1 Pentium 4 512 memory __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Log(2) values to log(10) values
Dear group, I am using justRMA in bioconductor to get expression values. Now I computed fold changes. the fold changes i get are log2 values. How can I convert these to log10 values to see them as actual fold change values. thank you. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] escaping backslash in a string
Ah, I see. Thanks. ?print.default and ?cat do not mention this. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Log(2) values to log(10) values
Multiply by log(2)/log(10); e.g., log2(1024) * log(2)/log(10) [1] 3.0103 log(1024, 10) [1] 3.0103 Andy From: Srinivas Iyyer Dear group, I am using justRMA in bioconductor to get expression values. Now I computed fold changes. the fold changes i get are log2 values. How can I convert these to log10 values to see them as actual fold change values. thank you. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Log(2) values to log(10) values
Srinivas Iyyer [EMAIL PROTECTED] writes: Dear group, I am using justRMA in bioconductor to get expression values. Now I computed fold changes. the fold changes i get are log2 values. How can I convert these to log10 values to see them as actual fold change values. Divide by log2(10) or multiply by log10(2). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Seeking help with a simple loop construction
Does this do what you want?
foo.df - data.frame(x = rnorm(12), y = runif(12), z = factor(rep(1:3,4)))
bar.mat - matrix(NA, nrow = ncol(foo.df)-1, ncol = nlevels(foo.df$z))
for(i in 1:(ncol(foo.df)-1))
{
bar.mat[i,] - xtabs(foo.df[,i] ~ foo.df$z)
}
bar.mat
There's probably a slicker way with apply...
HTH, Andy
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Greg Blevins
Sent: Monday, November 29, 2004 1:09 PM
To: [EMAIL PROTECTED]
Subject: [R] Seeking help with a simple loop construction
Hello,
I have a df, pp, with five variables:
nobs(pp)
q10_1 q10_2 q10_3 q10_4 actcode
16201620162016201620
I want to create a loop to run four xtabs (the first four
variables above by the fifth) and then store the results in a
matrix. Below I make my intent clear by showing the output of
one xtab which is inserted into a matrix.
a - xtabs(q10_1 ~ actcode)
a
actcode
1 2 3 4 5 6 7 8 9 10
7 11 3 60 66 56 21 40 7 8
freq.mat - matrix(0, 4, 10, byrow = TRUE)
freq.mat[1,] - a
freq.mat
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]7 113 60 66 56 21 407 8
[2,]000000000 0
[3,]000000000 0
[4,]000000000 0
===
I have spent a couple of hours searching the web and my texts but
continue to strike out in my attempts to construct a correct
formulation of this simple loop. Help would be appreciated.
Greg Blevins
The Market Solutions Group, Inc.
Windows XP
R 2.0.1
Pentium 4
512 memory
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Re: [R] Log(2) values to log(10) values
Srinivas Iyyer wrote: Dear group, I am using justRMA in bioconductor to get expression values. Now I computed fold changes. the fold changes i get are log2 values. How can I convert these to log10 values to see them as actual fold change values. First, a bit of etiquette. It is considered impolite to post the same question to more than one listserv. Second, although this is not a BioC-specific question, that is probably a better place to ask. To answer; log10 values will *not* give you actual fold changes. These will be the same as log2, to a multiplicitive constant. You want to convert back to the natural scale e.g., 2^FC, where FC = your fold changes. Also note that you compute fold change on the log scale by subtraction, not division. HTH, Jim thank you. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Call to trellis.focus(); thenpanel.superpose()
Hi Deepayan Sarkar wrote: On Monday 29 November 2004 04:46, John Maindonald wrote: The following works fine with the x11 device, though it may well be that an initial plot is overwritten. With a pdf or postscript device, I get two plots, the first of which still has the red border from having the focus, while the second is the plot that I want. library(lattice); library(grid) plt - xyplot(uptake ~ conc, groups=Plant, data=CO2) print(plt) trellis.focus(panel, row=1, column=1) arglist=trellis.panelArgs() arglist$type - l do.call(panel.superpose, args=arglist) trellis.unfocus() Should I be able to use panel.superpose() in this way? Yes. The red border should be 'removed', but that's done by grid.remove and maybe it doesn't work on PDF devices. It works, but it works by removing the red rectangle from the list of objects representing the scene and then redrawing the scene, hence a new page. Paul The solution is to use trellis.focus(panel, row=1, column=1, highlight = FALSE) (which happens automatically for non-interactive sessions). The new abilities provided by trellis.focus() etc add greatly to the flexibility of what can be done with lattice plots. The grid-lattice combination is a great piece of software. Yes, it can be especially useful for tasks similar to identify(). Everything else can probably be done by clever enough use of the panel function (though perhaps not as naturally). Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
Hi I am trying to tune an svm by doing the following: tune(svm, similarity ~., data = training, degree = 2^(1:2), gamma = 2^(-1:1), coef0 = 2^(-1:1), cost = 2^(2:4), type = polynomial) but I am getting Error in svm.default(x, y, scale = scale, ...) : wrong type specification! I have to admit I am not sure what I am doing wrong. Could anyone tell me why the parameters I am using are wrong? Plus could anyone tell me how to go about picking the correct ranges for my tuning? Thanks S [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] escaping backslash in a string
I have it working now, I think. Since it's going into a regular expression, I have to escape each of the escape characters, resulting in four backslashes altogether: sub([.], x, a.b) [1] axb sub([.], \., a.b) [1] a.b sub([.], \\., a.b) [1] a.b sub([.], \\\., a.b) [1] a.b sub([.], ., a.b) [1] a\\.b cat(sub([.], ., a.b)) a\.b or cat(sub(\\., ., a.b)) a\.b Dan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: Reasons not to answer very basic questions...
A.J. Rossini wrote: and perhaps the most important reason for the particular socratic form of teaching on this list... Golly, anyone who read Plato's Dialogues would realize that the Socratic method involves patiently leading the questioner stepwise through the solution, not simply writing RTFMeno. Jim __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] library(fields) world shift function not working anymore
I just upgraded to 2.01 on Mac OS 10.3.6. I used to use the command (on R 1.9.x): world(ylim=c(-30,30), xlim = c(0,360), shift=TRUE, add=TRUE) to draw a world outline over my image plots. My data uses longitude from (0, 360) so I need to use the shift function. After I upgraded, I get the following error: world(ylim=c(-30,30), xlim = c(0,360), shift=TRUE, add=TRUE) Error in world(ylim = c(-30, 30), xlim = c(0, 360), shift = TRUE, add = TRUE) : NAs are not allowed in subscripted assignments Does anyone know a workaround for this? Well, a workaround would be: library(maps) map(world2, ylim=c(-30,30), xlim = c(0,360), add = TRUE) (at least until fields is updated). CHANGES IN R VERSION 2.0.0 o Subassignments involving NAs and with a replacement value of length 1 are now disallowed. (They were handled inconsistently in R 2.0.0, see PR#7210.) For data frames they are disallowed altogether, even for logical matrix indices (the only case which used to work). Ray Brownrigg __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] tune()
Hi I am trying to tune an svm by doing the following: tune(svm, similarity ~., data = training, degree = 2^(1:2), gamma = 2^(-1:1), coef0 = 2^(-1:1), cost = 2^(2:4), type = polynomial) but I am getting Error in svm.default(x, y, scale = scale, ...) : wrong type specification! I have to admit I am not sure what I am doing wrong. Could anyone tell me why the parameters I am using are wrong? Plus could anyone tell me how to go about picking the correct ranges for my tuning? Thanks S [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] tune()
Sending a help request once is enough! Even if you don't have an answer after 1 hour. I am trying to tune an svm by doing the following: tune(svm, similarity ~., data = training, degree = 2^(1:2), gamma = 2^(-1:1), coef0 = 2^(-1:1), cost = 2^(2:4), type = polynomial) I think you want to set `kernel' not `type'... but I am getting Error in svm.default(x, y, scale = scale, ...) : wrong type specification! ...checking the argument `type' on ?svm would have told you that. I have to admit I am not sure what I am doing wrong. Could anyone tell me why the parameters I am using are wrong? Plus could anyone tell me how to go about picking the correct ranges for my tuning? Surprisingly, you have to set `ranges' to specify the ranges of the parameters, e.g., obj - tune(svm, Species ~ ., data = iris, ranges = list(degree =2^(1:2), gamma = 2^(-1:1), coef0 = 2^(-1:1), cost = 2^(2:4)), kernel = polynomial) I'm not sure what good ranges are to tune an SVM with a polynomial kernel... hth, Z __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] escaping backslash in a string
Dan Lipsitt danlipsitt at gmail.com writes: : : I have it working now, I think. Since it's going into a regular : expression, I have to escape each of the escape characters, resulting : in four backslashes altogether: : : sub([.], x, a.b) : [1] axb : sub([.], \., a.b) : [1] a.b : sub([.], \\., a.b) : [1] a.b : sub([.], \\\., a.b) : [1] a.b : sub([.], ., a.b) : [1] a\\.b : cat(sub([.], ., a.b)) : a\.b : : or : : cat(sub(\\., ., a.b)) : a\.b : You can use \134 in place of the double backslash if that makes more sense to you. Another possibility is to create a variable backslash - \\ and paste together each string in terms of that variable. Also its sometimes helpful to use nchar(s) on string s just to check how many characters it has. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [BASIC] Solution of creating a sequence of object names
Dear R-users,
I state that this is for beginners, so you may ignore
this in order not to be irritated.
By the way, patience is another important thing,
together with kindness, we should keep in mind when
we teach students and our own children as Jim Lemon
pointed out well in the context of the Socratic
method. You may know that being kind does not mean
giving spoonfed answers to questioners.
-
I was asked for the solution of my problem, and a
couple of answers were given to me in private emails.
I am not sure if it was a mere accident. I post them
now, without their permission, for those who are
interested in learning them. So if you're happy to
know the solution, thanks should go to the person
concerned. I thank all the three people named below.
(1) my solution after reading the R-FAQ 7.21 as Uwe
Ligges pointed out
for ( i in 1:10 ) {
+ assign(paste(my.file., i, sep=), NULL)
+ }
(2) Adai Ramasamy's solution
for(obj in paste(my.ftn, 1:10, sep=))
assign(obj, NULL)
### or
for(i in 1:10) assign(paste(my.ftn, i, sep=),
NULL)
(3) James Holtman's solution
# For example, if you want to generate 10 groups
# of 5 random numbers and store them
# under then names GRPn where n is 1 - 10,
# the following can be used:
#
Result - list() # create the list
for (i in 1:10) Result[[paste(GRP, i, sep='')]] -
runif(5) # store each result
Result# print out the data
$GRP1
[1] 0.2655087 0.3721239 0.5728534 0.9082078 0.2016819
$GRP2
[1] 0.89838968 0.94467527 0.66079779 0.62911404
0.06178627
$GRP3
[1] 0.2059746 0.1765568 0.6870228 0.3841037 0.7698414
$GRP4
[1] 0.4976992 0.7176185 0.9919061 0.3800352 0.7774452
$GRP5
[1] 0.9347052 0.2121425 0.6516738 0.121 0.2672207
$GRP6
[1] 0.38611409 0.01339033 0.38238796 0.86969085
0.34034900
$GRP7
[1] 0.4820801 0.5995658 0.4935413 0.1862176 0.8273733
$GRP8
[1] 0.6684667 0.7942399 0.1079436 0.7237109 0.4112744
$GRP9
[1] 0.8209463 0.6470602 0.7829328 0.5530363 0.5297196
$GRP10
[1] 0.78935623 0.02333120 0.47723007 0.73231374
0.69273156
Regards,
John
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RE: [R] [BASIC] Solution of creating a sequence of object names
You may be missing something. After you create all those objects,
you'll want to use them. Use get():
for (i in 1:10) ... get(paste(object,i,sep=)) ...
It took me about a week to find out how to do this. I waited for a
few days, but before I got to ask this basic/rtfm question, someone
else - fortunately :-) - did.
HTH,
b.
-Original Message-
From: John [mailto:[EMAIL PROTECTED]
Sent: Monday, November 29, 2004 4:03 PM
To: [EMAIL PROTECTED]
Subject: [R] [BASIC] Solution of creating a sequence of object names
Dear R-users,
I state that this is for beginners, so you may ignore
this in order not to be irritated.
By the way, patience is another important thing,
together with kindness, we should keep in mind when
we teach students and our own children as Jim Lemon
pointed out well in the context of the Socratic
method. You may know that being kind does not mean
giving spoonfed answers to questioners.
-
I was asked for the solution of my problem, and a
couple of answers were given to me in private emails.
I am not sure if it was a mere accident. I post them
now, without their permission, for those who are
interested in learning them. So if you're happy to
know the solution, thanks should go to the person
concerned. I thank all the three people named below.
(1) my solution after reading the R-FAQ 7.21 as Uwe
Ligges pointed out
for ( i in 1:10 ) {
+ assign(paste(my.file., i, sep=), NULL)
+ }
(2) Adai Ramasamy's solution
for(obj in paste(my.ftn, 1:10, sep=))
assign(obj, NULL)
### or
for(i in 1:10) assign(paste(my.ftn, i, sep=),
NULL)
(3) James Holtman's solution
# For example, if you want to generate 10 groups
# of 5 random numbers and store them
# under then names GRPn where n is 1 - 10,
# the following can be used:
#
Result - list() # create the list
for (i in 1:10) Result[[paste(GRP, i, sep='')]] -
runif(5) # store each result
Result# print out the data
$GRP1
[1] 0.2655087 0.3721239 0.5728534 0.9082078 0.2016819
$GRP2
[1] 0.89838968 0.94467527 0.66079779 0.62911404
0.06178627
$GRP3
[1] 0.2059746 0.1765568 0.6870228 0.3841037 0.7698414
$GRP4
[1] 0.4976992 0.7176185 0.9919061 0.3800352 0.7774452
$GRP5
[1] 0.9347052 0.2121425 0.6516738 0.121 0.2672207
$GRP6
[1] 0.38611409 0.01339033 0.38238796 0.86969085
0.34034900
$GRP7
[1] 0.4820801 0.5995658 0.4935413 0.1862176 0.8273733
$GRP8
[1] 0.6684667 0.7942399 0.1079436 0.7237109 0.4112744
$GRP9
[1] 0.8209463 0.6470602 0.7829328 0.5530363 0.5297196
$GRP10
[1] 0.78935623 0.02333120 0.47723007 0.73231374
0.69273156
Regards,
John
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[R] Kernel Fisher Discriminant in R?
Dear members, I am wondering if there are any functions to perform the Kernel Fisher Discriminant method, especially for multi-class problems, in R. I would appreciate any kind of information on this. Thanks for your time. Seungho Huh, Ph.D. Research Statistician RTI International North Carolina, USA [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] [BASIC] Solution of creating a sequence of object names
It was enough for me to use the 'assign' function
alone. But I'll remember the 'get' function for future
reference. Thanks a lot for the note.
John
--- bogdan romocea [EMAIL PROTECTED] wrote:
You may be missing something. After you create all
those objects,
you'll want to use them. Use get():
for (i in 1:10) ... get(paste(object,i,sep=))
...
It took me about a week to find out how to do this.
I waited for a
few days, but before I got to ask this basic/rtfm
question, someone
else - fortunately :-) - did.
HTH,
b.
-Original Message-
From: John [mailto:[EMAIL PROTECTED]
Sent: Monday, November 29, 2004 4:03 PM
To: [EMAIL PROTECTED]
Subject: [R] [BASIC] Solution of creating a sequence
of object names
Dear R-users,
I state that this is for beginners, so you may
ignore
this in order not to be irritated.
By the way, patience is another important thing,
together with kindness, we should keep in mind
when
we teach students and our own children as Jim Lemon
pointed out well in the context of the Socratic
method. You may know that being kind does not mean
giving spoonfed answers to questioners.
-
I was asked for the solution of my problem, and a
couple of answers were given to me in private
emails.
I am not sure if it was a mere accident. I post them
now, without their permission, for those who are
interested in learning them. So if you're happy to
know the solution, thanks should go to the person
concerned. I thank all the three people named below.
(1) my solution after reading the R-FAQ 7.21 as Uwe
Ligges pointed out
for ( i in 1:10 ) {
+ assign(paste(my.file., i, sep=), NULL)
+ }
(2) Adai Ramasamy's solution
for(obj in paste(my.ftn, 1:10, sep=))
assign(obj, NULL)
### or
for(i in 1:10) assign(paste(my.ftn, i, sep=),
NULL)
(3) James Holtman's solution
# For example, if you want to generate 10 groups
# of 5 random numbers and store them
# under then names GRPn where n is 1 - 10,
# the following can be used:
#
Result - list() # create the list
for (i in 1:10) Result[[paste(GRP, i, sep='')]]
-
runif(5) # store each result
Result# print out the data
$GRP1
[1] 0.2655087 0.3721239 0.5728534 0.9082078
0.2016819
$GRP2
[1] 0.89838968 0.94467527 0.66079779 0.62911404
0.06178627
$GRP3
[1] 0.2059746 0.1765568 0.6870228 0.3841037
0.7698414
$GRP4
[1] 0.4976992 0.7176185 0.9919061 0.3800352
0.7774452
$GRP5
[1] 0.9347052 0.2121425 0.6516738 0.121
0.2672207
$GRP6
[1] 0.38611409 0.01339033 0.38238796 0.86969085
0.34034900
$GRP7
[1] 0.4820801 0.5995658 0.4935413 0.1862176
0.8273733
$GRP8
[1] 0.6684667 0.7942399 0.1079436 0.7237109
0.4112744
$GRP9
[1] 0.8209463 0.6470602 0.7829328 0.5530363
0.5297196
$GRP10
[1] 0.78935623 0.02333120 0.47723007 0.73231374
0.69273156
Regards,
John
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[R] Labeling charts within a loop
Hi All:
This may turn out to be very simply, but I can't seem to add the name of
the school to a chart. The loop I created is below that subsets a
dataframe and creates a chart for each school based on certain
variables. As it stands now, they title includes the school's ID number.
Instead, I want to replace this with the school's actual name, which is
stored in a variable called schname.
But so far, my attempts have been messy and ugly? Can anyone see a
mistake in my code?
Thanks,
Harold
#This portion of code takes the subset
school.list-as.vector(unique(mansfield.dat$schirn))
for(school.number in school.list){
assign(paste(school, school.number, sep=),
subset(mansfield.dat,mansfield.dat$schirn==school.number))}
for(school.number in school.list){
AV-mean(get(paste(school,school.number,sep=))[[bpra3ccf]])
RP-mean(get(paste(school,school.number,sep=))[[bprr3ccf]])
LT-mean(get(paste(school,school.number,sep=))[[bprl3ccf]])
IT-mean(get(paste(school,school.number,sep=))[[bpri3ccf]])
strengthbar-cbind(AV,RP,LT,IT)
pdf(paste(school,school.number,rel, .pdf,sep=))
barplot(strengthbar,names=c(AV, RP, LT,
IT),width=c(.5,.5,.5,.5),ylim = c(0, 4),col=(salmon))
legend(1.0,3.8,legend=c(1=Relative Weakness, 2=Similar to District,
3=Relative Strength))
title(main=(paste(Grade 3 Relative Strengths and Weaknesses, \n,
School , school.number,sep=)))
dev.off()
}
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Re: [R] Labeling charts within a loop
Doran, Harold [EMAIL PROTECTED] writes:
Hi All:
This may turn out to be very simply, but I can't seem to add the name of
the school to a chart. The loop I created is below that subsets a
dataframe and creates a chart for each school based on certain
variables. As it stands now, they title includes the school's ID number.
Instead, I want to replace this with the school's actual name, which is
stored in a variable called schname.
But so far, my attempts have been messy and ugly? Can anyone see a
mistake in my code?
No overt mistakes, but multiple infelicities. Don't listen to guys who
want to create sequences of variable names, it is (almost) invariably
the wrong idea.
#This portion of code takes the subset
school.list-as.vector(unique(mansfield.dat$schirn))
for(school.number in school.list){
assign(paste(school, school.number, sep=),
subset(mansfield.dat,mansfield.dat$schirn==school.number))}
Lessee, that was basically
byschool - split(mansfield.dat, mansfield.dat$schirn)
below, you use only 4 variables from the data frame and under
different names, so maybe first extract and rename them and have
#--
# code should be executable from here on
vars - c(bpra3ccf, bprr3ccf, bprl3ccf, bpri3ccf)
d2 - mansfield.dat[vars]
names(d2) - c(AV, RP, LT, IT)
byschool - split(d2, mansfield.dat$schirn)
# now to get the averages, you can do
mnList - lapply(byschool, colMeans)
# now, let's do a little function to do one of your plots. It will have
# three arguments, the mean vector, the number of the school, and the
# name of the school
doPlot - function(mn, no, name)
{
# (I won't argue with your filename scheme)
pdf(file=paste(school, no, rel.pdf, sep=)
# The barplot should get the names right automagically now:
barplot(mn, width=c(.5,.5,.5,.5), ylim = c(0, 4), col=(salmon))
legend(1.0,3.8,legend=c(1=Relative Weakness,
2=Similar to District, 3=Relative Strength))
title(main=(paste(Grade 3 Relative Strengths and Weaknesses, \n,
School:, name, sep=)))
dev.off()
}
# All set, now
num - names(mnList)
mapply(doPlot, mnList, num, schname[num])
# done! End executable code
#--
Obviously, not having your data, all the above is untested, and most
likely not entirely bugfree.
for(school.number in school.list){
AV-mean(get(paste(school,school.number,sep=))[[bpra3ccf]])
RP-mean(get(paste(school,school.number,sep=))[[bprr3ccf]])
LT-mean(get(paste(school,school.number,sep=))[[bprl3ccf]])
IT-mean(get(paste(school,school.number,sep=))[[bpri3ccf]])
strengthbar-cbind(AV,RP,LT,IT)
pdf(paste(school,school.number,rel, .pdf,sep=))
barplot(strengthbar,names=c(AV, RP, LT,
IT),width=c(.5,.5,.5,.5),ylim = c(0, 4),col=(salmon))
legend(1.0,3.8,legend=c(1=Relative Weakness, 2=Similar to District,
3=Relative Strength))
title(main=(paste(Grade 3 Relative Strengths and Weaknesses, \n,
School , school.number,sep=)))
dev.off()
}
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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RE: Reasons not to answer very basic questions in a straightforward way; was: Re: [R] creating a sequence of object names
Your statement seems innocent enough on the face of it, but there are two facets that I think are worthy of note. The first is that of time, and more specifically who's time. As a user of other lists I can say that this is the best list in terms of getting the answer to my problem, albeit sometime's obliquely. I intermittently respond to questions generally of the type you refer to. I say intermittently because I don't have the time to do more than that. Why do I respond to these questions? Well I made some of the same basic errors. As a much more knowledgeable user, I think twice (well more like six times) before I post because I understand the amount of time it takes to create a response that is worthwhile. I'll get to the reason for not creating simple answers in the next point. If I had to pay for the quality of support that I get on this list, there is no way that I could afford it. I take what I get and I am grateful for the time given by so many. To assume that my time is more important than those who will give me the answer is disrespectful. Secondly is a process referred to as crowding out. With reference to the list there is a danger that it would cease to be a source of wisdom and start being a repetitive FAQ. As the list stands now I learn much more from other people's questions than I do from my own. I read about different ways of approaching various tasks and while I barely comprehend some of the more difficult questions they provoke my curiosity. I can read an FAQ anytime, I can read all of the manuals, they won't go away. At the moment the list is full of variation with the odd thread like this, which sparks more of a philosophical content. If 90% of the list was full of questions that are tiresome because of dullness or more succinctly tedious, why would I continue to either ask questions of it or respond to them. In essence what I find useful on the list would be crowded out by repetitive questions. Experience has shown me that where you have a demand for quick solutions from people busy getting on with their lives, it can overwhelm your own life. One such experience happened the last time I was in London, I happened to be standing next to one of those little currency exchange booths waiting for a friend. I heard some people having trouble working out where the British Museum was. I gave them some help. It was only after a while that I thought to start counting how many requests I received (well I was on Tottenham Court Rd) but eventually I counted 35. One can maintain that sort of help for a while, but I couldn't stand there all day. I was abused by a couple for eventually leaving and not answering their question. I know there are users of R who will not use the mailing list because they are intimidated by the manner of the list, but the users I have talked to acknowledge that they are looking for an easy solution and are not interested in contributing to the list. Th! ey have also pointed out that they can see why the list does what it does. I get the feeling that a lot of subscribers to this list would understand where you are coming from, even though they may not look at the list the same way that you do. The bottom line is that I have had a reply to every question that I have put on the list and those replies have always helped me to solve my problem. Show that you've put some effort in and people will match that effort and more*. Your note had effort and consequently was treated as meritorious, although the answers may not have been what you wished. Tom Mulholland * K9, Dr Who, BBC Television -Original Message- ... I know very well that it is basic manners to read those materials before asking questions here, but you should also understand that people sometimes get stuck with very simple problems if they are driven by stress or run down. They can save a lot of time and concentrate on and develop their primary jobs instead. And I don't think you should be worried about 900 silly questions out of 1000 messages posted because they are at least well-educated people who know what reading basic materials before posting questions means. ... I beg your pardon if this message is not relevant to this help list. With kind regards, John --- Uwe Ligges [EMAIL PROTECTED] wrote: John wrote: Thank you, Uwe. I've found a way to do the job by reading the FAQ 7.21 although it is not giving a precise explanation to a novice or casual user at first reading. For example, if you type the first two But the corresponding help files do so, for sure, and the FAQ 7.21 points you to ?assign and ?get. lines in the FAQ, you get an error as you do not have the variable, a, initially. I am sure that more and more people get interested in and serious about using R if advanced users are kind enough to answer simple and silly questions as well which are already explained in basic documentations. Or is this
RE: [R] Tetrachoric and polychoric ceofficients (for sem) - any tips?
Dear Michael,
I had some time this evening, so I programmed the two-step procedure
described in the article that I mentioned. This isn't the ML estimate of the
correlation, but apparently it performs reasonably well and it is quite
fast. I checked the function on some examples and it appears to work
correctly. I'd be curious to see how the this function compares with the one
that you received.
A more complete solution would take a data frame and, as appropriate,
calculate polychoric, polyserial, and product-moment correlations among its
columns. I don't think that writing a polyserial-correlation function would
be any more difficult. Perhaps I'll add this to the sem package; I hesitate
to do so because the resulting standard errors and likelihoods from sem()
won't be right.
I'm taking the liberty of copying this reply to the r-help list, since the
question was originally raised there. I hope that's OK.
Regards,
John
-- snip
polychor - function (x, y){
# x: a contingency table of counts or an ordered categorical variable
# y: if x is a variable, a second ordered categorical variable
# returns the polychoric correlation for the table
# or between x and y, using the two-step approximation
# to the ML estimate described in F. Drasgow, Polychoric and
# polyserial correlations, in S. Kotz and N. Johnson, eds.
# The Encyclopedia of Statistics, Volume 7, New York: Wiley,
# 1986.
f - function(rho) {
P - matrix(0, r, c)
R - matrix(c(1, rho, rho, 1), 2, 2)
for (i in 1:r){
for (j in 1:c){
P[i,j] - pmvnorm(lower=c(row.cuts[i], col.cuts[j]),
upper=c(row.cuts[i+1], col.cuts[j+1]),
corr=R)
}
}
- sum(tab * log(P))
}
tab - if (missing(y)) x else table(x, y)
r - nrow(tab)
c - ncol(tab)
n - sum(tab)
row.cuts - c(-Inf, qnorm(cumsum(rowSums(tab))/n))
col.cuts - c(-Inf, qnorm(cumsum(colSums(tab))/n))
optimise(f, interval=c(0, 1))$minimum
}
-Original Message-
From: Michael Dewey [mailto:[EMAIL PROTECTED]
Sent: Monday, November 29, 2004 1:38 PM
To: John Fox
Subject: RE: [R] Tetrachoric and polychoric ceofficients (for
sem) - any tips?
At 18:07 28/11/04, you wrote:
Dear Michael,
I'm not aware of pre-existing R code for tetrachoric or polychoric
correlations. I may at some point incorporate such functions
into the
sem package but I don't have concrete plans for doing so. On
the other
hand, I don't think that it would be very hard to do so. (A
discussion,
references, and an example are in Kotz and Johnson, eds.,
Encyclopedia
of Statistics, Vol 7.)
Someone has kindly emailed me some code for the polychoric
case (which he says is quite slow) I will try it out, it may
be better to treat the 2 by 2 case separately. If it is OK I
plan to write an equivalent to cor for matrices of
tetrachoric/polychoric. It will not happen any time soon now,
but if I do manage t would you be interested in it for sem?
As you say there remains the problem that they are estimates
and introduce further uncertainties.
Tetrachoric and polychoric correlations are estimates, and in
subsequently estimating a SEM from these, one should take
that into account.
Michael Dewey
[EMAIL PROTECTED]
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Re: [R] Error using glm with poisson family and identity link
On 29 Nov 2004 18:07:40 +0100, Peter Dalgaard [EMAIL PROTECTED] wrote: I had a situation where there was like a (virtual) maximum outside the boundary, and the algorithm would basically stay on the path to that peak, banging its little head into the same point of the wall repeatedly, so to speak. I love that image: the little optimizer that couldn't. I hope the fortunes maintainer is listening... Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to plot a 3D picture
Hi, Suppose I have a 4 by 4 matrix as following: 10 6 3 1 8 4 3 2 6 2 4 3 9 3 4 2 The x axis is the column index of the matrix, the y axis is the row index of the matrix and the z axis is the value in the corresponding position of the matrix. I tried to use contour and image. They are not the ones I want. You help is greatly appreciated. Peter [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to plot a 3D picture
On Monday 29 November 2004 21:07, Peter Yang wrote: Hi, Suppose I have a 4 by 4 matrix as following: 10 6 3 1 8 4 3 2 6 2 4 3 9 3 4 2 The x axis is the column index of the matrix, the y axis is the row index of the matrix and the z axis is the value in the corresponding position of the matrix. I tried to use contour and image. They are not the ones I want. You are probably looking for ?persp. Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] New trellis settings
I've just upgraded to 2.0.1 and was taken by surprise by the changes
in graphical parameter handling for lattice plots. I'd previously
been using 1.9.1. The old settings seem to have been replaced by a
daunting number of new options. I've poked around a bit and have not
seen any discussion of the changes in the newsletter or on r-help but
maybe I'm overlooking something?
Specifically, I have some code that in the past changed the relative
proportions of text versus the plot area using:
trellis.par.set('fontsize', list(text=8))
which caused all text to get smaller, and the plot area to grow to
fill the larger available space. Now, the plot area does not grow on
its own. I've tried fiddling with layout.heights, layout.widths, and
axis.components but there are dozens of settings available. For many
of these settings, I have no idea what quantity I'm actually changing,
other than by trial and error. Is there an easier way?
-- Dave
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Re: [R] New trellis settings
Hi, Dear all R users: Does someone know whether R can calculate the Receiver Operating Characteristic (ROC) Curves? I didn't find it from the packages. Thanks a lot. --- Xin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] New trellis settings
On Monday 29 November 2004 22:39, [EMAIL PROTECTED] wrote:
I've just upgraded to 2.0.1 and was taken by surprise by the changes
in graphical parameter handling for lattice plots. I'd previously
been using 1.9.1. The old settings seem to have been replaced by a
daunting number of new options.
Not really. The old settings are essentially what they were, the new
'options' are for things that used to be hard-coded in previous
versions.
I've poked around a bit and have not
seen any discussion of the changes in the newsletter or on r-help but
maybe I'm overlooking something?
Specifically, I have some code that in the past changed the relative
proportions of text versus the plot area using:
trellis.par.set('fontsize', list(text=8))
which caused all text to get smaller, and the plot area to grow to
fill the larger available space. Now, the plot area does not grow on
its own.
That does seem to have been a side-effect in 1.9.1, but it was never
intended. I would consider that behaviour a bug, not a feature.
I've tried fiddling with layout.heights, layout.widths, and
axis.components but there are dozens of settings available. For many
of these settings, I have no idea what quantity I'm actually
changing, other than by trial and error. Is there an easier way?
Not really. The recommended thing to change is the settings (not the
options) which all default to 1:
str(trellis.par.get()$layout.heights)
List of 18
$ top.padding : num 1
$ main : num 1
$ main.key.padding : num 1
$ key.top : num 1
$ key.axis.padding : num 1
...
I was hoping that the names would be enough of a hint. Anything with
'padding' in the name is space, and probably the ones you want to
change.
Deepayan
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Re: [R] About ROC curves
package ROC from bioconductor, eg: http://www.bioconductor.org/repository/release1.5/package/Win32/ Cheers! Christoph Xin Qi wrote: Hi, Dear all R users: Does someone know whether R can calculate the Receiver Operating Characteristic (ROC) Curves? I didn't find it from the packages. Thanks a lot. --- Xin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] About ROC curves
There is a package, Lexis, not officil though, which contains a function ROC (and some other stuff for epidemiology). You can find it in: http://biostat.ku.dk/~bxc/SPE/library/ Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc -- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Xin Qi Sent: Tuesday, November 30, 2004 5:49 AM To: [EMAIL PROTECTED] Subject: [R] About ROC curves Hi, Dear all R users: Does someone know whether R can calculate the Receiver Operating Characteristic (ROC) Curves? I didn't find it from the packages. Thanks a lot. --- Xin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
