[R] mozilla/firefox search engine AMD64 jre1.5 plugin linux
Hi, I have a problem with the help.start() and the search engine on a AMD64 : The search engine use the java plugin but the java plugin is not available for the jre.1.5 ... I have a linux box : fedora 4 on 64bit and R2.1.1 When I start the search engine, I had the message that the java plugin was missing. So I try to install manual the java run time jre-1.5 for the AMD64, but the plugin was missing ( http://forum.java.sun.com/thread.jspa?threadID=568127tstart=75 ) So I instaled the J2RE blackdown 1.4.2 I obtain the plugin for the 64bit and make the link. When I restart R and the search engine, the plugin 1.4.2 correctly reconnize by mozilla ( about:plugins in the URL windows), and I don't have any more the message for the missing plugin, but, then I try a search, mozilla freeze and I have to kill it : help.start() Making links in per-session dir ... If '/usr/bin/firefox' is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... UA: Mozilla/5.0 (X11; U; Linux x86_64; fr; rv:1.7.10) Gecko/20050720 Fedora/1.0.6-1.1.fc4 Firefox/1.0.6:, extra: Firefox/1.0.6 [EMAIL PROTECTED] ~]# ps -eaf | grep mozilla root 13916 13899 0 09:40 pts/1 00:00:00 /bin/sh /usr/lib64/firefox-1.0.6 /run-mozilla.sh /usr/lib64/firefox-1.0.6/firefox-bin -UILocale fr-FR file:///tmp/Rtmpo13829/.R/doc/html/index.html [EMAIL PROTECTED] ~]# kill 13916 [EMAIL PROTECTED] ~]# /usr/lib64/firefox-1.0.6/firefox: line 227: 13916 Complété $dist_bin/run-mozilla.sh $script_args $dist_bin/$MOZILLA_BIN $@ # I am not a system administrator and It's my home computer (so no help ...) So I need your help ;-) - For the AMD64 R users : have you the same problem ? - If yes : How you solve it ? - If it's not possible to solve, is it possible to find an alternative solution (like to acces of the search engine from an other computer (windows, linux 32). I don't care about java plugin on the mozilla 64 bit, I just want the R help !!! Thanks. L. Buffat __ R-help@stat.math.ethz.ch 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] mozilla/firefox search engine AMD64 jre1.5 plugin linux
This is a 64-bit FC* issue. I believe we did a year or so ago run i686 firefox (from mozilla.org) and the Sun Java + plugin on AMD64 FC2. Note that help.search() will do all that the HTML search engine does, and more. On Windows, you would get help for a different version of R, but i686 Linux would be fine. The latter is our solution: we only use AMD64 machines as servers. On Mon, 22 Aug 2005, laurent buffat wrote: Hi, I have a problem with the help.start() and the search engine on a AMD64 : The search engine use the java plugin but the java plugin is not available for the jre.1.5 ... I have a linux box : fedora 4 on 64bit and R2.1.1 When I start the search engine, I had the message that the java plugin was missing. So I try to install manual the java run time jre-1.5 for the AMD64, but the plugin was missing ( http://forum.java.sun.com/thread.jspa?threadID=568127tstart=75 ) So I instaled the J2RE blackdown 1.4.2 I obtain the plugin for the 64bit and make the link. When I restart R and the search engine, the plugin 1.4.2 correctly reconnize by mozilla ( about:plugins in the URL windows), and I don't have any more the message for the missing plugin, but, then I try a search, mozilla freeze and I have to kill it : help.start() Making links in per-session dir ... If '/usr/bin/firefox' is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... UA: Mozilla/5.0 (X11; U; Linux x86_64; fr; rv:1.7.10) Gecko/20050720 Fedora/1.0.6-1.1.fc4 Firefox/1.0.6:, extra: Firefox/1.0.6 [EMAIL PROTECTED] ~]# ps -eaf | grep mozilla root 13916 13899 0 09:40 pts/1 00:00:00 /bin/sh /usr/lib64/firefox-1.0.6 /run-mozilla.sh /usr/lib64/firefox-1.0.6/firefox-bin -UILocale fr-FR file:///tmp/Rtmpo13829/.R/doc/html/index.html [EMAIL PROTECTED] ~]# kill 13916 [EMAIL PROTECTED] ~]# /usr/lib64/firefox-1.0.6/firefox: line 227: 13916 Complété $dist_bin/run-mozilla.sh $script_args $dist_bin/$MOZILLA_BIN $@ # I am not a system administrator and It's my home computer (so no help ...) So I need your help ;-) - For the AMD64 R users : have you the same problem ? - If yes : How you solve it ? - If it's not possible to solve, is it possible to find an alternative solution (like to acces of the search engine from an other computer (windows, linux 32). I don't care about java plugin on the mozilla 64 bit, I just want the R help !!! Thanks. L. Buffat -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch 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] integration
Hello
after reading few nodes from the info docs. I am not
sure if this task can be done using R:
the density function f(x,y) = 12xy(1-y) for
0x1, 0y1
the condition of inequality (x-y) (1/2)
what if the limits of integration are functions of the
variable I am integrating over.
is this somthing which can be done in a simple way,
with R?
examples:
Mathimatic 5.1:
In[2]:=Integrate[12*x*y*(1-y)*Boole[x-y1/2],{y,0,1},{x,0,1}]
Maple:
Doubleint(12*x*y*(1-y)*Heaviside(x-y-1/2),x=0..1,y=0..1);
many thanks
__
R-help@stat.math.ethz.ch 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] integration
Numerical integration: yes.
Symbolic integration: no.
On Mon, 22 Aug 2005, Fred J. wrote:
after reading few nodes from the info docs. I am not
sure if this task can be done using R:
the density function f(x,y) = 12xy(1-y) for
0x1, 0y1
the condition of inequality (x-y) (1/2)
what if the limits of integration are functions of the
variable I am integrating over.
is this somthing which can be done in a simple way,
with R?
examples:
Mathimatic 5.1:
In[2]:=Integrate[12*x*y*(1-y)*Boole[x-y1/2],{y,0,1},{x,0,1}]
Maple:
Doubleint(12*x*y*(1-y)*Heaviside(x-y-1/2),x=0..1,y=0..1);
Symbolic integration: no.
Numerical integration: yes, e.g.
library(adapt)
adapt(2, c(0,0), c(1,1),
functn=function(x) {y=x[2]; x=x[1]; 12*x*y*(1-y)*(x-y1/2)})
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@stat.math.ethz.ch 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] reShape question
Dear R helpers,
The following output, from Hmisc reShape examples, illustrates how to
reshape from a data frame with repeated measures.
I would need to do exactly the opposite ie get sbp1 to 3 and dbp1 to 3
from sbp and and dbp.
Is there a way to do that without subsetting, renaming and binding ?
Many thanks for any help,
Regards, JL
set.seed(33)
n - 4
w - data.frame(age=rnorm(n, 40, 10),
+ sex=sample(c('female','male'), n,TRUE),
+ sbp1=rnorm(n, 120, 15),
+ sbp2=rnorm(n, 120, 15),
+ sbp3=rnorm(n, 120, 15),
+ dbp1=rnorm(n, 80, 15),
+ dbp2=rnorm(n, 80, 15),
+ dbp3=rnorm(n, 80, 15), row.names=letters[1:n])
options(digits=3)
w
agesex sbp1 sbp2 sbp3 dbp1 dbp2 dbp3
a 38.6 female 109 123 131 81.8 90.9 88.9
b 39.6 female 132 120 120 71.1 86.9 110.0
c 50.1 male 131 148 118 73.4 82.8 52.4
d 38.4 female 104 124 125 84.4 83.5 67.1
reShape(w, base=c('sbp','dbp'), reps=3, timevar='week', times=c(0,3,12))
week agesex sbp dbp
a 10 38.6 female 109 81.8
a 23 38.6 female 123 90.9
a 3 12 38.6 female 131 88.9
b 10 39.6 female 132 71.1
b 23 39.6 female 120 86.9
b 3 12 39.6 female 120 110.0
c 10 50.1 male 131 73.4
c 23 50.1 male 148 82.8
c 3 12 50.1 male 118 52.4
d 10 38.4 female 104 84.4
d 23 38.4 female 124 83.5
d 3 12 38.4 female 125 67.1
__
R-help@stat.math.ethz.ch 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] time series plots: labels language tickmarks
On Mon, 22 Aug 2005, javier garcia - CEBAS wrote: My native language is spanish and I would need to do two changes in the default xlabels in timeseries plots: What sort of plots are you talking about here? (Not tsplot or plot.ts, for example.) I think you are perhaps talking about plots of Dates. a) For timeseries that span more than one year, there are just xlabs and tickmarks for the beginning of each year. Could I add extra tick marks for each month easily? See ?axis.Date, if this is about Dates. b) The xlabs appear in my language for months and days (spanish) but I need them in English, how can I change this setting? Use R in an English locale. (If as the posting guide asked you have told us your platform we could have told you how. If you had shown us some reproducible code we would not have had to guess as to what you want to do.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] time series plots: labels language tickmarks
On Mon, 2005-08-22 at 13:04 +0100, Prof Brian Ripley wrote: On Mon, 22 Aug 2005, javier garcia - CEBAS wrote: My native language is spanish and I would need to do two changes in the default xlabels in timeseries plots: What sort of plots are you talking about here? (Not tsplot or plot.ts, for example.) I think you are perhaps talking about plots of Dates. a) For timeseries that span more than one year, there are just xlabs and tickmarks for the beginning of each year. Could I add extra tick marks for each month easily? See ?axis.Date, if this is about Dates. If you want the ticks for months unlabelled, then axis.Date() in R v. 2.1.1 and 2.1.1-patched won't allow this. axis.Date() from R-devel allows you to suppress the labelling of ticks - the change is trivial so you could get the src of axis.Date for R-devel (e.g. it is here in the subversion tree: https://svn.r-project.org/R/trunk/src/library/graphics/R/datetime.R and use that to create a my.axis.Date() and use this function explicitly to add axes to your plot for the monthly ticks - until R 2.2.0 is released anyway - using argument labels = FALSE to suppress the labels for the monthly ticks. HTH G b) The xlabs appear in my language for months and days (spanish) but I need them in English, how can I change this setting? Use R in an English locale. (If as the posting guide asked you have told us your platform we could have told you how. If you had shown us some reproducible code we would not have had to guess as to what you want to do.) -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch 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] vectors of different length in a matrix
HI! I?ve 3 vectors of different length (a,b,c) and want to arrange them in a matrix a,b,c as rows and the figures of these vectors in the columns (with that matrix i want to calculate a distance between thes vectors - vegan - vegdist - horn). Is there a possibilty to create such a matrix and to fill up the missing fields with NA?s automatically Thanx marten winter -- *Marten Winter* ___ UFZ - Umweltforschungszentrum Leipzig-Halle GmbH Sektion Biozoenoseforschung Theodor-Lieser-Straße 4 D-06120 Halle (Saale) Centre for Environmental Research (UFZ) Leipzig-Halle Department of Community Ecology Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany phone: ++49 (0) 345 558-5316 fax:++49 (0) 345 558-5329 E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://www.halle.ufz.de/bzf/ ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] vectors of different length in a matrix
On Mon, 2005-08-22 at 08:56 -0400, Duncan Murdoch wrote: On 8/22/2005 8:45 AM, Marten Winter wrote: HI! I?ve 3 vectors of different length (a,b,c) and want to arrange them in a matrix a,b,c as rows and the figures of these vectors in the columns (with that matrix i want to calculate a distance between thes vectors - vegan - vegdist - horn). Is there a possibilty to create such a matrix and to fill up the missing fields with NA?s automatically Filling with NA's is the hard part; R normally likes to recycle vectors that are too short. Here's one way, probably not the best: x - matrix(NA, 3, max(length(a), length(b), length(c))) x[1,seq(along=a)] - a x[2,seq(along=b)] - b x[3,seq(along=c)] - c Another way to do it would be to extend all the vectors to the same length by appending NAs, then using rbind. Another issue is that this would fail at the next step outlined in the original message (vegan - vegdist - horn), since that step won't accept NAs. So the original schedule was bad. If you fill with zeros, then the 'vegdist' step would work in the sense that it produces numbers. I don't know if these numbers would make any sense if the vectors had nothing to do with each other originally, and columns would be of mixed meaning after stacking into a matrix. If your vector elements had identities (names) originally, then you should stack your data so that entries with the same identity go to the same column. It is difficult to imagine Horn index used in cases where you don't have these identities -- specifically species names. cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ R-help@stat.math.ethz.ch 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] vectors of different length in a matrix
On Mon, 2005-08-22 at 16:13 +0300, Jari Oksanen wrote: On Mon, 2005-08-22 at 08:56 -0400, Duncan Murdoch wrote: On 8/22/2005 8:45 AM, Marten Winter wrote: HI! I?ve 3 vectors of different length (a,b,c) and want to arrange them in a matrix a,b,c as rows and the figures of these vectors in the columns (with that matrix i want to calculate a distance between thes vectors - vegan - vegdist - horn). Is there a possibilty to create such a matrix and to fill up the missing fields with NA?s automatically Filling with NA's is the hard part; R normally likes to recycle vectors that are too short. Here's one way, probably not the best: x - matrix(NA, 3, max(length(a), length(b), length(c))) x[1,seq(along=a)] - a x[2,seq(along=b)] - b x[3,seq(along=c)] - c Another way to do it would be to extend all the vectors to the same length by appending NAs, then using rbind. Another issue is that this would fail at the next step outlined in the original message (vegan - vegdist - horn), since that step won't accept NAs. Uh. It seems that I should read the package documentation (and posting guide which tells me to do so): it seems that vegdist() *can* handle NAs. I do still think that data with NA probably makes no sense with alternative horn. cheers, jari oksanen __ R-help@stat.math.ethz.ch 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 add values on the axes of the 3D bi-variable lrm fit?
Dear r-list, When I try to plot the following 3D lrm fit I obtain only arrows with labels on the three axes of the figure (without values). fit - lrm(y ~ rcs(x1,knots)+rcs(x2,knots), tol=1e-14,X=T,Y=T) dd - datadist(x1,x2);options(datadist='dd'); par(mfrow=c(1,1)) plot(fit,x1=NA, x2=NA, theta=50,phi=25) How can I add values to the axes of this plot? (axes with the range of values of each of the explanatory variables x1x2) Thanks, Jan ___ Ir. Jan Verbesselt Research Associate Group of Geomatics Engineering Department Biosystems ~ M³-BIORES Vital Decosterstraat 102, 3000 Leuven, Belgium Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be/ ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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 add legend of plot.Design function ( method=image)?
Dear Rlist,
How can the Legend of the plot.Design() function can be visualized?
Following the documentation in R, I did the following (see below), only the
'Legend' function doesn't visualize the legend of the
plot (method='image') of the lrmfit. I tried to change par( margin setting)
but this didnt solve it.
How can this be solved?
Thanks a lot,
Jan
library(Design)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate bin
ary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
boundaries - perimeter(age, cholesterol, lowess=TRUE)
plot(age, cholesterol) # show bivariate data density
lines(boundaries)# and perimeter that will be used for 3-D plot
z - plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image')
# draws image() plot
# don't show estimates where data are sparse
# doesn't make sense here since vars don't
interact
if(!.R.)Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability') # gray scale or color legend for prob.
___
Ir. Jan Verbesselt
Research Associate
Group of Geomatics Engineering
Department Biosystems ~ M³-BIORES
Vital Decosterstraat 102, 3000 Leuven, Belgium
Tel: +32-16-329750 Fax: +32-16-329760
http://gloveg.kuleuven.ac.be/
___
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] pdf font embedding --- again
On Mon, 22 Aug 2005 [EMAIL PROTECTED] wrote: dear R wizards--- I would like to do some book-on-demand printing at a popular printer named lulu, but lulu requires inclusion even of the basic postscript fonts. Interestingly, my book itself does not need the 14 base acrobat fonts, only the embedded R figures do. Of course, I really would like to get pdftex to embed the fonts, but how to do this is not obvious either. [This method seems to be what the R help page is indicating... The software including the PostScript plot file should either embed the font outlines (usually from '.pfb' or '.pfa' files) or use DSC comments to instruct the print spooler to do so.) Why not use the fonts your book does use in the figures? (That's how my books are done.) So, I would really, really like to embed the necessary fonts with the R figures. I first reread the discussion in this mailing list about (eps) font embedding earlier this year. This was ultimately not very helpful. First, I do not know how to instruct my embedding program to include the fonts that R figures want. Second, I already start with the pdf device, so distilling eps files is not a good option--and it would seem a bit crazy to first use the wrong output device (postscript), then ship my files over to a windows machine somewhere that has distiller installed, run distiller by hand, then ftp them back to my linux machine---just for getting the fonts embedded. Is it impossible to get R to embed the necessary fonts in its pdf output? Yes, as it has no access to them. They are not Open Source. You may be able to use URW clones, depending on their licensing conditions. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] rgui on windows quiting automatically
Rgui on my computer has started acting funny (though I expect the problem is with my system rather than R, but hopefully someone here can still help). I am working with R version 2.11 on windows 2000. Rgui was working fine, then last week it started acting up. Now when I start Rgui (from shorcuts, or the commandline), the GUI starts up, but before the copyright and version info is printed I get the closing dialog asking me if I want to save the workspace (the same one that I get from q()). If I answer yes or no then R exits nicely, if I click on cancel then I get the windows dialog box saying that the program has performed an illeagle action and will be closed (It says it is creating a log file, but I have yet to find a log file with anything useful in it on why the program was closed). I have tried starting from the command line with the --vanilla switch, but that does not work either. rgui --help and rgui --version do work (but don't run the main program). rgui --verbose causes the error and shutdown without the quit dialog. I tried running the older versions of R that were still installed on my computer, but they behaved the same way (had worked fine before this). I did a complete uninstall of all copies of R on the computer, downloaded a fresh version of R 2.11 and reinstalled that (removing all .Rdata files that it may have accessed) and it is still giving me the same problem. rterm still works, so it is something in the GUI portion. Any help will be appreciated, Greg Snow, Ph.D. Statistical Data Center, LDS Hospital Intermountain Health Care [EMAIL PROTECTED] (801) 408-8111 __ R-help@stat.math.ethz.ch 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] pdf font embedding --- again
dear R wizards--- I would like to do some book-on-demand printing at a popular printer named lulu, but lulu requires inclusion even of the basic postscript fonts. Interestingly, my book itself does not need the 14 base acrobat fonts, only the embedded R figures do. Of course, I really would like to get pdftex to embed the fonts, but how to do this is not obvious either. [This method seems to be what the R help page is indicating... The software including the PostScript plot file should either embed the font outlines (usually from '.pfb' or '.pfa' files) or use DSC comments to instruct the print spooler to do so.) So, I would really, really like to embed the necessary fonts with the R figures. I first reread the discussion in this mailing list about (eps) font embedding earlier this year. This was ultimately not very helpful. First, I do not know how to instruct my embedding program to include the fonts that R figures want. Second, I already start with the pdf device, so distilling eps files is not a good option--and it would seem a bit crazy to first use the wrong output device (postscript), then ship my files over to a windows machine somewhere that has distiller installed, run distiller by hand, then ftp them back to my linux machine---just for getting the fonts embedded. Is it impossible to get R to embed the necessary fonts in its pdf output? help appreciated. regards, /iaw --- ivo welch __ R-help@stat.math.ethz.ch 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 with same axes
I have used the 'par' command to overlay one plot on another. But how do I overlay it with the x-values plotted at the same points on the x-axis? Thank you, Steven __ R-help@stat.math.ethz.ch 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] lm.ridge again
Hello, I have posted this mail a few days ago without any answer: I have the following doubts related with lm.ridge, from MASS package. To show the problem using the Longley example, I have the following doubts: First: I think coefficients from lm(Employed~.,data=longley) should be equal coefficients from lm.ridge(Employed~.,data=longley, lambda=0) why it does not happen? Second: if I have for example Ridge-lm.ridge(Employed~., data=longley, lambda = seq(0,0.1,0.001)), I suppose intercept coefficient is defined implicit, why it does not appear in Ridge$coef? Third: I suppose that if I define 1) y-longley$Employed 2) X-as.matrix(cbind(1,Longley[,1:6]) 3) I as the identity the following should be true: Coef=(X'X+kI)^(-1) X'y and if a take k=Ridge$kHKV, the coefficients should be approx equal to Ridge$Coef[near value of kHKV] and it does not seem to happen, why? Values: Ridge$kHKB [1] 0.004275357 Using the calculation above (third question, third point): Coef= [,1] 1-0.095492310 GNP.deflator -0.052759002 GNP 0.070993540 Unemployed -0.004244391 Armed.Forces -0.005725582 Population -0.413341544 Year 0.048420107 And if I take from Ridgecoef: Ridge$coef[0.004] GNP.deflator -0.03098507 GNP -1.32553151 Unemployed -1.53237769 Armed.Forces -0.63334911 Population -0.88690241 Year 6.82105049 Any help, suggestion or orientation? Thanks in advance Daniel Rozengardt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] read a table ignoring specific rows ?
Dear R users,
First of all sorry for this question, surely quite naive.
(I searched on the R site but was unable to find by myself).
I have a table, called infile :
1 2 3
4 5 6
7 8 9
I would like to read it and ignore the rows with 1st element 3
I do it now with a for loop, and it's ok,
but I was expecting something simpler, like :
intable = read.table(infile);
newtable = intable[isgoodrow(intable)];
where : isgoodrow = function(therow)
{if (therow$V1 3) return(F) else return(T);};
(... but this don't work).
So, could somebody please tell me if there is a way to read
a table ignoring specific rows, without using a for loop ?
... and if yes how ?
Thanks
Vincent
__
R-help@stat.math.ethz.ch 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] plotting with same axes
On Mon, 2005-08-22 at 12:58 -0400, [EMAIL PROTECTED] wrote: I have used the 'par' command to overlay one plot on another. But how do I overlay it with the x-values plotted at the same points on the x-axis? Thank you, Steven The specific answer depends to an extent on the graphics you are plotting and whether there is a need to actually use par(new). In some cases there is an 'add = TRUE' option to plotting functions that allows for this. In others, you can create the initial plot and then use lines(), points() or the like to simply add further plotting components to the existing plot. If all else fails and you need to use par(new), then you will want to explicitly define the x and y axes to the same ranges by using the same 'xlim' and 'ylim' arguments in _both_ plotting functions. A reproducible example of what it is you are doing would enable us to give you more specific guidance, if the above is not helpful. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch 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] read a table ignoring specific rows ?
Can you read in the entire file as a data.frame; and then construct a
new data.frame which excludes some rows?
perhaps something along the lines of...
fred.file - data.frame()
fred.file - edit(fred.file)
fred.file
colA colB colC
1142
2233
3354
4433
552 25
fred.new - fred.file[fred.file$colC = 3,]
fred.new
colA colB colC
1142
2233
4433
s/
On 22/08/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Dear R users,
First of all sorry for this question, surely quite naive.
(I searched on the R site but was unable to find by myself).
I have a table, called infile :
1 2 3
4 5 6
7 8 9
I would like to read it and ignore the rows with 1st element 3
I do it now with a for loop, and it's ok,
but I was expecting something simpler, like :
intable = read.table(infile);
newtable = intable[isgoodrow(intable)];
where : isgoodrow = function(therow)
{if (therow$V1 3) return(F) else return(T);};
(... but this don't work).
So, could somebody please tell me if there is a way to read
a table ignoring specific rows, without using a for loop ?
... and if yes how ?
Thanks
Vincent
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] read a table ignoring specific rows ?
Thank you very much to all of you. Sorry once more for this too simple question. I have to improve my knowledge about the syntax ! Thanks Vincent __ R-help@stat.math.ethz.ch 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] R-help
Diego, Have you checked out the home site for nls2? Specifically the system requirements page? http://www.inra.fr/miaj/public/AB/nls2/available.html That says that nls2 requires a Unix-like operating system. Basically, the script for building the library is for such systems only, it also depends upon a lex (flex) library being available. Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of HM Diego Hernán Sent: 22 August 2005 18:47 To: r-help@stat.math.ethz.ch Subject: [R] R-help Hello I need help with the way to install nls2 library for windows, or the script that can be used for install the nls2 library. Do you know if this library works in windows? Best regards. Diego Rojas Cali-Colombia __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] function for two-part or two-condition models
Hello list, Andrew, and Richard, I wanted to send you a late thanks your for your suggestions and mention that I recently stumbled upon what I was looking for in the VGAM package. If you're interested, see the help file for zapoisson, which is based on both a binomial and a poisson distribution. Richard Quoting Remington, Richard [EMAIL PROTECTED]: Two alternatives to the zero inflated Poisson (ZIP) model are mentioned in Jung, Jhun, and Lee (Biometrics, vol 61, no 2, June 2005, p626): Although the ZIP model is more general than the standard Poisson, count data with many zeros are often more dispersed than the ZIP model. In this case, the use of a zero-inflated negative binomial (ZINB) distribution or a zero-inflated generalized Poisson distribution is a good alternative. best, Richard -- Richard E. Remington Statistician KERN Statistical Services, Inc. PO Box 1046 Boise, ID 83701 Tel: 208.426.0113 KernStat.com Andrew Robinson wrote: Hi Richard, I'm not sure that I can imagine how data can have too many zeros to be fit well with zero-inflated Poisson models. Won't the excess zeros be accommodated by increasing the the inflation? In any case, if you want a model that separates the zeros from the occurrences before fitting a Poisson model to account for variation in abundance then it might be safest to do that split manually. Another angle to try is to treat it as a special case of a finite mixture regression. I think that some of Jim Lindsey's code will fit such models. Google can help you find his wbsite. An MS student of mine explored these models for regeneration modeling. I'd be happy to send you a pdf of his thesis if it would help. Cheers, Andrew On Mon, Jun 27, 2005 at 03:35:30PM -0400, Richard Chandler wrote: Hello, This is an (hopefully) improved question of one I posted several weeks ago. Does anyone know of a function for fitting two-part models? These models are designed to handle count data with so many zeroes that they can't be fit well with zero-inflated Poisson models or other 'typical' GLMs. My understanding is that they work by first fitting a binomial model to separate the zeros from the occurrences (positive integers) before fitting a Poisson model to account for variation in abundance. I have tried help.search(two-part) and many other similar guesses. Thanks, Richard -- Richard Chandler, M.S. Candidate Department of Natural Resources Conservation UMass Amherst (413)545-1237 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Richard Chandler Department of Natural Resources Conservation UMass Amherst (413)545-1237 __ R-help@stat.math.ethz.ch 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] pdf font embedding --- again
Thank you---as always.
still, I remain font-desparate.
I would love to use the fonts from my book, but [a] I cannot figure out
how to do this yet even in the R postscript device; and [b] I am using
the R pdf device, not the postscript device. I guess if I can solve
[a], then I can rewrite all my graphics creations now into the
postscript device, and replace the dev.off() with something that
follows it with ps2pdf. The following attempt, however, does not work:
afmfiles - c(lbr.afm, lbd.afm, lbi.afm, lbdi.afm,
lbms.afm);
Lucida - postscriptFont(Lucida, metrics=afmfiles);
postscript(file=test.ps, family=Lucida);
l- 40:80;
plot(l,l,pch=l);
dev.off();
By the way, if I try postscript(family=afmfiles); then I do not get
an R error, but R 2.1.0 segfaults, which is probably not desirable.
This occurs even if there is no .afm file in the current directory.
Can I make a suggestion to the R team?It would be nice if I could
specify a pdf() device parameter that says choose font settings to
embed all fonts (i.e., do not use fonts that cannot be embedded,
either). Something that guarantees me that I get a figure that I can
give to someone that is fully specified. Right now, accomplishing
this is not easy to figure out, and perhaps not even possible. Yes, in
the list of font families that R recognizes are some fonts that do not
seem among the 13 standard fonts (such as URWbookman). moreover, if I
choose it as my pdf font family, it is smart enough to use a different
symbol file ('StandardSymL'), which I hope is also open and not adobe.
If so, they could be used in principle. How do I get R to embed
URWbookman? ZapfDingbats always seems to be included, so I hope this
is open and embeddable.
more help would be highly appreciated.
Regards,
/iaw
---
ivo welch
-Original Message-
From: Prof Brian Ripley [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Sent: Mon, 22 Aug 2005 17:07:14 +0100 (BST)
Subject: Re: [R] pdf font embedding --- again
On Mon, 22 Aug 2005 [EMAIL PROTECTED] wrote:
dear R wizards--- I would like to do some book-on-demand printing at
a
popular printer named lulu, but lulu requires inclusion even of the
basic postscript fonts. Interestingly, my book itself does not need
the 14 base acrobat fonts, only the embedded R figures do. Of
course,
I really would like to get pdftex to embed the fonts, but how to do
this is not obvious either. [This method seems to be what the R help
page is indicating... The software including the PostScript plot
file
should either embed the font outlines (usually from '.pfb' or '.pfa'
files) or use DSC comments to instruct the print spooler to do so.)
Why not use the fonts your book does use in the figures? (That's how
my books are done.)
So, I would really, really like to embed the necessary fonts with
the R
figures. I first reread the discussion in this mailing list about
(eps) font embedding earlier this year. This was ultimately not very
helpful. First, I do not know how to instruct my embedding program
to
include the fonts that R figures want. Second, I already start with
the pdf device, so distilling eps files is not a good option--and it
would seem a bit crazy to first use the wrong output device
(postscript), then ship my files over to a windows machine somewhere
that has distiller installed, run distiller by hand, then ftp them
back
to my linux machine---just for getting the fonts embedded.
Is it impossible to get R to embed the necessary fonts in its pdf
output?
Yes, as it has no access to them. They are not Open Source. You may be
able to use URW clones, depending on their licensing conditions.
-- Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
__
R-help@stat.math.ethz.ch 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 add legend of plot.Design function (method=image)? (if (!.R.) )
Hi,
When running
z - plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image')
Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability')
And after pointing the cursor to the plot() screen in R, I obtain the
following message:
Using function locator(2) to place opposite corners of image.legend
Error in Legend.plot.Design(z, fun = plogis, at = qlogis(c(0.01, 0.05, :
couldn't find function subplot
*How can I position the legend inside the range? (or solve the following
error message).
Regards,
Jan
-Original Message-
From: Jan Verbesselt [mailto:[EMAIL PROTECTED]
Sent: Monday, August 22, 2005 4:59 PM
To: 'r-help@stat.math.ethz.ch'
Subject: How to add legend of plot.Design function ( method=image)?
Dear Rlist,
How can the Legend of the plot.Design() function can be visualized?
Following the documentation in R, I did the following (see below), only the
'Legend' function doesn't visualize the legend of the
plot (method='image') of the lrmfit. I tried to change par( margin setting)
but this didnt solve it.
How can this be solved?
Thanks a lot,
Jan
library(Design)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate bin
ary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
boundaries - perimeter(age, cholesterol, lowess=TRUE)
plot(age, cholesterol) # show bivariate data density
lines(boundaries)# and perimeter that will be used for 3-D plot
z - plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image')
# draws image() plot
# don't show estimates where data are sparse
# doesn't make sense here since vars don't
interact
if(!.R.)Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability') # gray scale or color legend for prob.
___
Ir. Jan Verbesselt
Research Associate
Group of Geomatics Engineering
Department Biosystems ~ M³-BIORES
Vital Decosterstraat 102, 3000 Leuven, Belgium
Tel: +32-16-329750 Fax: +32-16-329760
http://gloveg.kuleuven.ac.be/
___
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] translating output ( latex()....)
Anne wrote: Dear R-helpers I need to produce statistical output where the annotations are in French (and from time to time in German). I produce plots/tables using extensively the latex() , summary.formula() ...functions of Hmisc which allows me for nice print-out. Up to now I corrected manually my latex code , replacing such headings as missing by valeur manquante etc. Is there a (simple) way of updating the R functions with the translated output? (I would of course gladly make it available to the list) I know my question will sound like an heresy to the vast majority of statisticians and I agree it is a waste of statistician time to do translations, but it is due to work related constraints (and I fear the anti-americanisme primaire encountered in some european countries) Anne, If you were to use a general way to detect the language (using the new facilities that Brian Ripley mentioned) and wanted to use that to enhance print. and latex. methods for the summary.formula family of functions, and know or can learn how to use CVS, we will consider giving you access to the Hmisc CVS repository to make the enhancements you want. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch 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 add legend of plot.Design function (method=image)? (if (!.R.) )
Jan Verbesselt wrote:
Hi,
When running
z - plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image')
Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability')
And after pointing the cursor to the plot() screen in R, I obtain the
following message:
Using function locator(2) to place opposite corners of image.legend
Error in Legend.plot.Design(z, fun = plogis, at = qlogis(c(0.01, 0.05, :
couldn't find function subplot
*How can I position the legend inside the range? (or solve the following
error message).
Regards,
Jan
The if(!.R.) in the example code was for a reason: I couldn't find
subplot in R. If you want to provide code enhancements to do this I
will incorporate your new code. -Frank
-Original Message-
From: Jan Verbesselt [mailto:[EMAIL PROTECTED]
Sent: Monday, August 22, 2005 4:59 PM
To: 'r-help@stat.math.ethz.ch'
Subject: How to add legend of plot.Design function ( method=image)?
Dear Rlist,
How can the Legend of the plot.Design() function can be visualized?
Following the documentation in R, I did the following (see below), only the
'Legend' function doesn't visualize the legend of the
plot (method='image') of the lrmfit. I tried to change par( margin setting)
but this didn’t solve it.
How can this be solved?
Thanks a lot,
Jan
library(Design)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate bin
ary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
boundaries - perimeter(age, cholesterol, lowess=TRUE)
plot(age, cholesterol) # show bivariate data density
lines(boundaries)# and perimeter that will be used for 3-D plot
z - plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image')
# draws image() plot
# don't show estimates where data are sparse
# doesn't make sense here since vars don't
interact
if(!.R.)Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability') # gray scale or color legend for prob.
___
Ir. Jan Verbesselt
Research Associate
Group of Geomatics Engineering
Department Biosystems ~ M³-BIORES
Vital Decosterstraat 102, 3000 Leuven, Belgium
Tel: +32-16-329750 Fax: +32-16-329760
http://gloveg.kuleuven.ac.be/
___
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@stat.math.ethz.ch 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 building dendrograms to use with heatmap()
Hi,
I'm trying to build dendrograms to pass to heatmap().
The dendrograms I build plot properly, but when I pass them to heatmap() I get
the error message row dendrogram ordering gave index of wrong length (see
output log below).
I looked in the code of heatmap() and saw that the error was due to a NULL
return value from order.dendrogram(), which in turn got a NULL return value from
unlist(). But I have no idea why unlist() is returning NULL.
I've included code below which reproduces the problem and below that the output
from a run of that code on my computer.
Any help would be greatly appreciated. Thanks in advance.
-Ben
### begin code ###
version
dendro.leaf - function(label) {
ans - list()
attr(ans, 'members') - 1
attr(ans, 'height') - 0
attr(ans, 'leaf') - T
attr(ans, 'midpoint') - 0
attr(ans, 'label') - label
attr(ans, 'class') - 'dendrogram'
ans
}
dendro.merge - function(d1, d2, height) {
ans - list(d1, d2)
members - attr(d1, 'members') + attr(d2, 'members')
attr(ans, 'members') - members
attr(ans, 'height') - height
attr(ans, 'leaf') - F
attr(ans, 'midpoint') - (members - 1)/2
attr(ans, 'class') - 'dendrogram'
ans
}
lc1 - dendro.leaf('c1')
lc2 - dendro.leaf('c2')
lc3 - dendro.leaf('c3')
nc1 - dendro.merge(lc1, lc2, 0.1)
nc2 - dendro.merge(nc1, lc3, 0.2)
plot(nc2)
lr1 - dendro.leaf('r1')
lr2 - dendro.leaf('r2')
lr3 - dendro.leaf('r3')
nr1 - dendro.merge(lr2, lr3, 0.1)
nr2 - dendro.merge(lr1, nr1, 0.3)
plot(nr2)
x - matrix(seq(-1, 1, length.out=9), nrow=3)
rownames(x) - paste('r', 1:3, sep='')
colnames(x) - paste('c', 1:3, sep='')
heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
order.dendrogram(nr2)
unlist(nr2)
### begin output from run of code above ##
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major2
minor1.1
year 2005
month06
day 20
language R
dendro.leaf - function(label) {
+ ans - list()
+ attr(ans, 'members') - 1
+ attr(ans, 'height') - 0
+ attr(ans, 'leaf') - T
+ attr(ans, 'midpoint') - 0
+ attr(ans, 'label') - label
+ attr(ans, 'class') - 'dendrogram'
+ ans
+ }
dendro.merge - function(d1, d2, height) {
+ ans - list(d1, d2)
+ members - attr(d1, 'members') + attr(d2, 'members')
+ attr(ans, 'members') - members
+ attr(ans, 'height') - height
+ attr(ans, 'leaf') - F
+ attr(ans, 'midpoint') - (members - 1)/2
+ attr(ans, 'class') - 'dendrogram'
+ ans
+ }
lc1 - dendro.leaf('c1')
lc2 - dendro.leaf('c2')
lc3 - dendro.leaf('c3')
nc1 - dendro.merge(lc1, lc2, 0.1)
nc2 - dendro.merge(nc1, lc3, 0.2)
plot(nc2)
lr1 - dendro.leaf('r1')
lr2 - dendro.leaf('r2')
lr3 - dendro.leaf('r3')
nr1 - dendro.merge(lr2, lr3, 0.1)
nr2 - dendro.merge(lr1, nr1, 0.3)
plot(nr2)
x - matrix(seq(-1, 1, length.out=9), nrow=3)
rownames(x) - paste('r', 1:3, sep='')
colnames(x) - paste('c', 1:3, sep='')
heatmap(x, Rowv=nr2, Colv=nc2, scale='none')
Error in heatmap(x, Rowv = nr2, Colv = nc2, scale = none) :
row dendrogram ordering gave index of wrong length
order.dendrogram(nr2)
NULL
unlist(nr2)
NULL
__
R-help@stat.math.ethz.ch 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] cbind and rbind
Hi, I have been trying for a while to use cbind and rbind to add a row and column to the same table but seem to be able only to add one OR the other??? Any help would be most welcome, Tony Evans Australia [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] cbind and rbind
Like this? x - cbind(rnorm(10), rnorm(10)) # add row total x - cbind(x, rowSums(x)) # add col sums x - rbind(x, colSums(x)) The KEY to posting to r-help is writing a small example that helpers can reproduce. When I write one, I often find the answer myself. I often don't and get eviscerated by some R-guru, but that's part of the fun of it all! I hope that helps, Andy -Original Message- From: Tony Evans [mailto:[EMAIL PROTECTED] Sent: Monday, August 22, 2005 8:03 PM To: Andy Bunn Subject: Re: [R] cbind and rbind Sorry, I did read the guide but am very new to this. I have created a table and have made totals of rows and columns using apply() I now want to add these totals to the table. I have been able to add one OR the other using cbind and rbind but have not been able to find a code to add them both. I hope this is better information. Tony Evans Australia - Original Message - From: Andy Bunn [EMAIL PROTECTED] To: Tony Evans [EMAIL PROTECTED] Sent: Tuesday, August 23, 2005 10:02 AM Subject: RE: [R] cbind and rbind Try reading the posting guide and give a small example of what you want to try and do...then we can help better. x - rnorm(10) y - rnorm(10) z - cbind(x,y) w - rbind(z,rnorm(2)) -Andy __ R-help@stat.math.ethz.ch 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 add legend of plot.Design function ( method=image)? (if (!.R.) )
Greg Snow, Ph.D. Statistical Data Center, LDS Hospital Intermountain Health Care [EMAIL PROTECTED] (801) 408-8111 Frank E Harrell Jr [EMAIL PROTECTED] 08/22/05 03:15PM Jan Verbesselt wrote: [snip discussion of subplot not being in R] While R does not have the subplot function there is an alternative. The cnvrt.coords function in the TeachingDemos package has an example (the bottom set) of doing a rough equivalent to subplot. This idea could be used to implement what you want (margins and text sizes may need adjustment). Hope this helps, __ R-help@stat.math.ethz.ch 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 reshape an array avoiding for loops
Have you considered aperm? I found this listed under See Also for ?t. spencer graves Wladimir Eremeev wrote: Dear r-help, I have an array a1 with dimensions [1:660,1:65,1:25] I would like the first dimension to be the last one. That is I want and array [1:65,1:25,1:660] The only way to do this, I know, is tmp.a-array(dim=dim(a1)[c(2,3,1)]) for(i in 1:dim(a1)[1]) tmp.a[,,i]-a1[i,,] a1-tmp.a rm(tmp.a) Is it possible to avoid 'for' loop here? Thank you! --- Best regards, Wladimirmailto:[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch 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] specify seed for Random Number Generator
Have you considered set.seed? This was listed with the first hit for 'RSiteSearch(random number seed)'. spencer graves Dhiren DSouza wrote: I need to generate 100 I.I.D samples from an exponential distribution. I use rexp(100,parameter). Is there anyway to specify a seed to determine the first input for the uniform random number generator used to generate these exponentials? -Dhiren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
