Re: [R] where did the factor name go
Yes, dump() does not dump the attributes of language objects of type LANGSXP. I don't know if that is deliberate or not, but in this case it would not be possible for dump to capture all the information, for note .. ..- attr(*, .Environment)=R_GlobalEnv and hence if you adopt Jim's suggestion, be aware that you will save() the whole of the workspace in order to capture the environment of the formula. On Mon, 28 May 2007, jim holtman wrote: Don't know what it happening, but when I compared the output of 'str(tmp.aov)' before and after the 'source', I saw at least the following differences: before: $ terms:Classes 'terms', 'formula' length 3 y ~ a .. ..- attr(*, variables)= language list(y, a) .. ..- attr(*, factors)= int [1:2, 1] 0 1 .. .. ..- attr(*, dimnames)=List of 2 .. .. .. ..$ : chr [1:2] y a .. .. .. ..$ : chr a .. ..- attr(*, term.labels)= chr a .. ..- attr(*, order)= int 1 .. ..- attr(*, intercept)= int 1 .. ..- attr(*, response)= int 1 .. ..- attr(*, .Environment)=R_GlobalEnv .. ..- attr(*, predvars)= language list(y, a) .. ..- attr(*, dataClasses)= Named chr [1:2] numeric factor .. .. ..- attr(*, names)= chr [1:2] y a after: $ terms: language y ~ a So it would seem some of the attributes are not being saved. You might want to use 'save' instead. Here is the output: tmp - data.frame(y=rnorm(12), a=factor(rep(letters[1:4],3))) tmp y a 1 0.61982575 a 2 -0.05612874 b 3 -0.15579551 c 4 -1.47075238 d 5 -0.47815006 a 6 0.41794156 b 7 1.35867955 c 8 -0.10278773 d 9 0.38767161 a 10 -0.05380504 b 11 -1.37705956 c 12 -0.41499456 d tmp.aov - aov(y ~ a, data=tmp) summary(tmp.aov) Df Sum Sq Mean Sq F value Pr(F) a3 1.3068 0.4356 0.622 0.6204 Residuals8 5.6031 0.7004 save(tmp.aov, file=dumpdata.R) rm(tmp.aov) load(dumpdata.R) ls() summary(tmp.aov) Df Sum Sq Mean Sq F value Pr(F) a3 1.3068 0.4356 0.622 0.6204 Residuals8 5.6031 0.7004 On 5/28/07, Richard M. Heiberger [EMAIL PROTECTED] wrote: tmp - data.frame(y=rnorm(12), a=factor(rep(letters[1:4],3))) tmp y a 1 -0.60866099 a 2 0.55500538 b 3 0.12231693 c 4 -0.24613790 d 5 -0.09253593 a 6 -1.54652581 b 7 0.17204210 c 8 -1.22778942 d 9 1.22151194 a 10 -0.43982577 b 11 -1.25444287 c 12 -0.97251060 d tmp.aov - aov(y ~ a, data=tmp) summary(tmp.aov) Df Sum Sq Mean Sq F value Pr(F) a3 1.5220 0.5073 0.6973 0.5794 Residuals8 5.8209 0.7276 dump(tmp.aov) rm(tmp.aov) source(dumpdata.R) ls() [1] tmp tmp.aov summary(tmp.aov) Df Sum Sq Mean Sq F value Pr(F) NA 3 1.5220 0.5073 0.6973 0.5794 Residuals8 5.8209 0.7276 The factor name in the summary() after dumping and sourcing the aov object is missing. version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.0 year 2007 month 04 day23 svn rev41293 language R version.string R version 2.5.0 (2007-04-23) __ 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 and provide commented, minimal, self-contained, reproducible code. -- 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 and provide commented, minimal, self-contained, reproducible code.
[R] SARIMA in R
Hi, Is R's implementation of Seasonal ARIMA in the arima() function a multiplicative or an additive model? e.g., is an ARIMA(0,1,1)(0,1,1)[12] from arima() the same as Box et al's ARIMA(0,1,1)x(0,1,1)[12] (from Time Series Analysis 1994, p.333). From another post http://tolstoy.newcastle.edu.au/R/help/04/07/0117.html I suspect it's additive but I'm not sure. Thanks, Gad -- Gad Abraham Department of Mathematics and Statistics The University of Melbourne Parkville 3010, Victoria, Australia email: [EMAIL PROTECTED] web: http://www.ms.unimelb.edu.au/~gabraham __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Where to find nprq?
roger koenker wrote: It has been folded into my quantreg package. Thanks a lot - it is working now Rainer url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On May 28, 2007, at 4:32 AM, Rainer M. Krug wrote: Hi I am trying to install the package pheno, but it needs the package nprq by Roger Koenker et al. which I can I find this package? It does not seem to be on CRAN and googling also doesn't give me an URL - is it still somewhere available? Thanks, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell:+27 - (0)83 9479 042 Skype:RMkrug email:[EMAIL PROTECTED] [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 and provide commented, minimal, self-contained, reproducible code. -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-About PLSR
Nitish Kumar Mishra wrote: I have installed PLS package in R and use it for princomp prcomp commands for calculating PCA using its example file(USArrests example). Uhm. These functions and data sets are not in the pls package; they are in the stats and datasets packages that come with R. But How I can use PLS for Partial least square, R square, mvrCv one more think how i can import external file in R. When I use plsr, R2, RMSEP it show error could not find function plsr, RMSEP etc. How I can calculate PLS, R2, RMSEP, PCR, MVR using pls package in R. There is an Rnews article describing the package¹, and a paper in Journal of Statistical Software². ¹Mevik, B.-H. (2006); The pls package; R News 6(3), 12-17. http://cran.r-project.org/doc/Rnews ²Mevik, B.-H., Wehrens, R. (2007); The pls Package: Principal Component and Partial Least Squares Regression in R; Journal of Statistical Software 18(2), 1--24. http://www.jstatsoft.org/v18/i02/v18i02.pdf -- Bjørn-Helge Mevik __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sum per hour
Thank you, I have try your proposition. Seems to be the right way... but I still have an error message. Here is the code I have executing: time-c(2000-10-03 14:00:00,2000-10-03 14:10:00,2000-10-03 14:20:00,2000-10-03 15:30:00,2000-10-03 16:40:00,2000-10-03 16:50:00,2000-10-03 17:00:00,2000-10-03 17:10:00,2000-10-03 17:20:00,2000-10-03 18:30:00,2000-10-04 14:00:00,2000-10-04 14:10:00,2000-10-04 14:20:00,2000-10-04 15:30:00,2000-10-04 16:40:00,2000-10-04 16:50:00,2000-10-04 17:00:00,2000-10-04 17:10:00,2000-10-04 17:20:00,2000-10-04 18:30:00) precipitation-c(0,0.1,0,0,0,0,0.2,0.3,0.5,6,7,8,9,1,0,0,0,0,1,0) library(zoo) z - zoo(precipitation, as.POSIXct(time, tz = GMT)) aggregate(z, function(x) as.POSIXct(trunc(x, hour)), sum(na.rm=TRUE)) Error in FUN(X[[1L]], ...) : argument INDEX is missing, with no default ... I saw you can index a zoo object. I have tried with a vector..but doesn't work. I don't know else what this INDEX argument is... Does anyone have an idea about it ? Thanks in advance, Jessica __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] hierarhical cluster analysis of groups of vectors
I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] hierarhical cluster analysis of groups of vectors
It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- Rafael Duarte Marine Resources Department - DRM IPIMAR - National Research Institute for Agriculture and Fisheries Av. Brasília, 1449-006 Lisbon - Portugal Tel:+351 21 302 7000 Fax:+351 21 301 5948 e-mail: [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 and provide commented, minimal, self-contained, reproducible code.
[R] JGR
Hi, I dont find any site to make suggestions about JGR. It is possible to make a keyboard link do automatic attribution sign - like Emacs use Shift - Thanks Ronaldo -- The most exciting phrase to hear in science, the one that heralds new discoveries, is not Eureka! (I found it!) but That's funny ... -- Isaac Asimov -- Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/Depto. Biologia Geral/Lab. de Ecologia | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8187 | [EMAIL PROTECTED] | [EMAIL PROTECTED] | http://www.ppgcb.unimontes.br/ | ICQ#: 5692561 | LinuxUser#: 205366 __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Function tsmooth
Hi, Assume that we may model the Nottingham temperature data (nottem) or Sunspot data (sunspot) set by a nonparametric autoregressive model of the form Yt = m(Yt-1) + et. Using the kernel estimation method, produce the resulting plots. We may use the fucntion tsmooth(x,y,notmal,bandwidth=0.01). How can i define x and y using data nottem and sunspot? Thanks a lot! Owen __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] pie initial angle
Dear all, I'd like to produce a simple pie chart for a customer (I know it's bad but they insist), and I have some difficulties setting the initial angle. For example: pie(c(60, 40), init.angle=14) and pie(c(80, 20), init.angle=338) both present the slices in the same direction, where: pie(c(60, 40)) pie(c(80, 20)) present the slices in different directions. I read everything I could about init.angle argument, I even played with various formulas to compute it, but I just can't figure it out. How can I preserve the desired *direction* of the slices? Many thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] pie initial angle
Not sure I understand what you want but the clockwise= argument of pie determines whether the slice is drawn clockwise or counter clockwise. On 5/29/07, Adrian Dusa [EMAIL PROTECTED] wrote: Dear all, I'd like to produce a simple pie chart for a customer (I know it's bad but they insist), and I have some difficulties setting the initial angle. For example: pie(c(60, 40), init.angle=14) and pie(c(80, 20), init.angle=338) both present the slices in the same direction, where: pie(c(60, 40)) pie(c(80, 20)) present the slices in different directions. I read everything I could about init.angle argument, I even played with various formulas to compute it, but I just can't figure it out. How can I preserve the desired *direction* of the slices? Many thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Legend outside plotting area
Judith,
Haven't tried it in anger myself, but two things suggest themselves. The first
is to use the lattice package, which seems to draw keys (autokey option)
outside the plot region by default. Look at the last couple of examples in
?xyplot. May save a lot of hassle...
In classical R graphics, have you tried plotting everything explicitly inside a
plot region with margins at zero?
For example:
plot.new()
par(mar=c(0,0,0,0))
plot.window(xlim=c(-2,11), ylim=c(-3,13))
points(1:10,1:10, pch=1)
points(1:10,10:1, pch=19)
par(srt=90)
text(x=-2, y=5, y-axis, pos=1, offset=0.5)
par(srt=0)
text(c(5,5), c(13,-1), labels=c(Title,x-axis), pos=1, offset=0.7,
cex=c(1.5,1))
rect(-0.2,-0.2, 11.2,11.2)
axis(side=1, at=0:10, pos=-0.2)
axis(side=2, at=0:10, pos=-0.2)
legend(x=5, y=-2, xjust=0.5, pch=c(1,19), legend=c(Type 1, Type 19), ncol=2)
All very tedious, but it works. Also, fiddling around with things like pretty()
on the data can automate most of the above positional choices if you're so
inclined. And legend(..., plot=F) returns the legend size and coordinates if
you want to fine-tune the location.
Steve E
[EMAIL PROTECTED] 23/05/2007 13:14:54
Quoting Judith Flores [EMAIL PROTECTED]:
Hi,
I have been trying many of the suggested options
to place a legend outside plotting area, including
something like this:
par(xpd=T,
oma=par()$oma+c(4.5,0,1.5,0),mar=par()$mar+c(1,0,1,0)
But the aspect of the four plots gets compromised
when I change the margin settings. I cannot use mtext
because I need to use colors for the text. I tried
layout, but wouldn't let me include the legend, only
plots.
I would appreciate very much some more help.
Regards,
J
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[R] Odp: pie initial angle
Hi [EMAIL PROTECTED] napsal dne 29.05.2007 12:53:14: Dear all, I'd like to produce a simple pie chart for a customer (I know it's bad but they insist), and I have some difficulties setting the initial angle. For example: pie(c(60, 40), init.angle=14) and pie(c(80, 20), init.angle=338) both present the slices in the same direction, where: I presume you misunderstand init angle. Above statements points an arrow of both slices to the similar direction but slices starts at different initial angles. pie(c(60, 40)) pie(c(80, 20)) present the slices in different directions. The arrow slices point to different direction **but** they both **start** at the same initial angle 0 deg. I read everything I could about init.angle argument, I even played with various formulas to compute it, but I just can't figure it out. How can I preserve the desired *direction* of the slices? You probably need to compute initial angle based on proportions in your pie chart (If you really want each pie chart starting at different position). Regards Petr Many thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] hierarhical cluster analysis of groups of vectors
Thanks. The vectors are produced by PLS-discriminant analysis between groups and the vectors within a group are simply different measurements of the same thing. What I need is a measure of how the different groups cluster. (I assume that I can do some averaging after applying dist, but I can not find the information on how to do it.) Best regards Anders Rafael Duarte wrote: It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- Anders Malmendal, mailto:[EMAIL PROTECTED] Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark. tel: +45 8942 3866 fax: +45 8619 6199 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] hierarhical cluster analysis of groups of vectors
Thanks. The vectors are produced by PLS-discriminant analysis between groups and the vectors within a group are simply different measurements of the same thing. What I need is a measure of how the different groups cluster (relative to each other). (I assume that I can do some averaging after applying dist, but I can not find the information on how to do it.) Best regards Anders Rafael Duarte wrote: It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- Anders Malmendal, mailto:[EMAIL PROTECTED] Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark. tel: +45 8942 3866 fax: +45 8619 6199 __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Odp: pie initial angle
From simple geometry pie(c(x, y), init.angle=(300+y/2*360/100)-360) shall do what you request. Although I am not sure if it is wise. Regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 29.05.2007 13:30:06: Hi [EMAIL PROTECTED] napsal dne 29.05.2007 12:53:14: Dear all, I'd like to produce a simple pie chart for a customer (I know it's bad but they insist), and I have some difficulties setting the initial angle. For example: pie(c(60, 40), init.angle=14) and pie(c(80, 20), init.angle=338) both present the slices in the same direction, where: I presume you misunderstand init angle. Above statements points an arrow of both slices to the similar direction but slices starts at different initial angles. pie(c(60, 40)) pie(c(80, 20)) present the slices in different directions. The arrow slices point to different direction **but** they both **start** at the same initial angle 0 deg. I read everything I could about init.angle argument, I even played with various formulas to compute it, but I just can't figure it out. How can I preserve the desired *direction* of the slices? You probably need to compute initial angle based on proportions in your pie chart (If you really want each pie chart starting at different position). Regards Petr Many thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] hierarhical cluster analysis of groups of vectors
On Tue, 29 May 2007, Anders Malmendal wrote: Thanks. The vectors are produced by PLS-discriminant analysis between groups and the vectors within a group are simply different measurements of the same thing. What I need is a measure of how the different groups cluster (relative to each other). (I assume that I can do some averaging after applying dist, but I can not find the information on how to do it.) I don't think anyone can tell you that: it is a matter of judgement. What you need is a dissimilarity on your groups. Assuming your vectors are numeric (you didn't say) you could use Mahalanobis distance between the centroids, with within-group covariance as the variance matrix. Often that works well, but not always, and you might prefer Euclidean distance between centroids, or minimum Euclidean or Mahalanobis distance Best regards Anders Rafael Duarte wrote: It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- 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 and provide commented, minimal, self-contained, reproducible code.
[R] search path question
Hi R users, Is there a simple function that can add a folder into current R search path? For example, suppose my current work directory is D:\work, but my input files are stored in folder C:\inFiles\, I know I can change work directory or add C:\inFiles\ before files name when I scan them, but I don't want to do that. I want to find a function that can simply add C:\inFiles\ into R's search path, so that we I scan a file R will go to all the search paths to find it. In matlab, path(path,C:\inFiles) will do this job, I'm just wondering if there is a similar function in R can do this job. Thanks, zhiliang [[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 and provide commented, minimal, self-contained, reproducible code.
[R] about the unscaled covariances from a summary.lm object
Hello! I want to clarify something about the unscaled covarinces component of a summary.lm object. So we have the regressor matrix X. If the fitted lm object is lmobj, the inverse of the matrix t(X)%*%X is xx, and the residual variance is sigma^2_e, the variance-covariance matrix of the OLS estimate of the coefficients is given by: xx*sigma^2_e I saw that what the function vcov actually does is simply: vcov=summary(lmobj)$sigma^2 * summary(lmobj)$cov.unscaled So the cov.unscaled component should give the matrix xx. I am right? I tried inverting the matrix t(X)%*%X with solve by issuing: solve(t(X)%*%X), but I get a matrix quite different from the matrix given by cov.unscaled. Is it just computational instability, or I am missing something important? Regards, Martin __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC
I have now read the README file which I should have done before. :-[ Sorry. To summarize: - Install the odbc connector driver (3.51) - Set up the dsn in the file .odbc.ini - It works beautifully and RODBC is super! Prof Brian Ripley wrote: yOn Mon, 28 May 2007, Bill Szkotnicki wrote: Hello, I have installed R2.5.0 from sources ( x86_64 ) and added the package RODBC and now I am trying to connect to a mysql database In windows R after installing the 3.51 driver and creating the dsn by specifying server, user, and password it is easy to connect with channel - odbcConnect(dsn) Does anyone know what needs to be done to make this work from linux? Did you not read the RODBC README file? It is described in some detail with reference to tutorials. -- Bill Szkotnicki Department of Animal and Poultry Science University of Guelph [EMAIL PROTECTED] (519)824-4120 Ext 52253 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] about the unscaled covariances from a summary.lm object
try the following: x1 - rnorm(100) x2 - rep(0:1, each = 50) x3 - runif(100) y - drop(cbind(1, x1, x2, x3) %*% c(1, 2, -1, -3)) + rnorm(100, sd = 2) dat - data.frame(y, x1, x2, x3) ## fit.lm - lm(y ~ x1 + x2 + x3, dat) summ.fit.lm - summary(fit.lm) X - model.matrix(fit.lm) all.equal(solve(crossprod(X)), summ.fit.lm$cov.unscaled) Sigma - summ.fit.lm$sigma^2 * solve(crossprod(X)) all.equal(sqrt(diag(Sigma)), summ.fit.lm$coefficients[, Std. Error]) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Martin Ivanov [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Tuesday, May 29, 2007 3:12 PM Subject: [R] about the unscaled covariances from a summary.lm object Hello! I want to clarify something about the unscaled covarinces component of a summary.lm object. So we have the regressor matrix X. If the fitted lm object is lmobj, the inverse of the matrix t(X)%*%X is xx, and the residual variance is sigma^2_e, the variance-covariance matrix of the OLS estimate of the coefficients is given by: xx*sigma^2_e I saw that what the function vcov actually does is simply: vcov=summary(lmobj)$sigma^2 * summary(lmobj)$cov.unscaled So the cov.unscaled component should give the matrix xx. I am right? I tried inverting the matrix t(X)%*%X with solve by issuing: solve(t(X)%*%X), but I get a matrix quite different from the matrix given by cov.unscaled. Is it just computational instability, or I am missing something important? Regards, Martin __ 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 and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Using ksmooth to produce the resulting plots
Hi, Consider the Nottingham temperature and the Sunspot data: data(nottem) data(sunspot) Assume that we may model each data set by a nonparametic autoregressice model of the form Yt = m(Yt-1) +et, What are the value of x and y for using function ksmooth(x,y,normal,bandwidth=0.01)? Thanks a lot! Owen __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] hierarhical cluster analysis of groups of vectors
Anders;
If you want to _test_ for differences, ANOVA applied to on the (typically)
first principal component scores for each object would give a fairly quick
indication of whether there was a case to answer (though scaling is an issue to
be aware of; a low-variance variable might differ strongly between groups yet
be masked by a larger variance variable wiht no group association unless you
get the scaling right for the circumstances).
If you just want to cluster the 10 groups, I suspect it might be simplest to
average (where average implies some consistent summary statistic for each
variable) your starting vectors, _before_ playing about with your distance
matrix; after all, it is the inter-mean distances you are after, so why not
get the means in the first place?. Of course, scaling is again an issue if
the variables differ in variance...
Steve E
Anders Malmendal [EMAIL PROTECTED] 29/05/2007 10:15:23
I want to do hierarchical cluster analysis to compare 10 groups of
vectors with five vectors in each group (i.e. I want to make a dendogram
showing the clustering of the different groups). I've looked into using
dist and hclust, but cannot see how to compare the different groups
instead of the individual vectors. I am thankful for any help.
Anders
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Re: [R] Odp: Odp: pie initial angle
Thanks Petr and Gabor, On Tuesday 29 May 2007, Petr PIKAL wrote: From simple geometry pie(c(x, y), init.angle=(300+y/2*360/100)-360) shall do what you request. Although I am not sure if it is wise. Yes, this is what I want to do. I agree with all your points re initial angle, I just needed the position of the slices the way they are. My geometry seems to be poor towards innexistent :) All the best, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] ratio distribution - missing attachment
Dear Martin and Vitto,
Please find attached the R function to compute the density of the ratio of 2
dependent normal variates.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Martin Maechler [mailto:[EMAIL PROTECTED]
Sent: Monday, May 28, 2007 5:37 AM
To: Ravi Varadhan
Cc: R-help@stat.math.ethz.ch
Subject: Re: [R] ratio distribution - missing attachment
Thank you, Ravi.
You probably will have noticed, that the attachment didn't make
it to the mailing list.
The reason is that the we let the mailing list software strip
binary attachments which can easily be misused to spread
viruses; see -- http://www.r-project.org/mail.html (search attachment)
or the posting-guide.
OTOH, the software allows attachments with MIME type text/plain.
If you use an e-mail software for sophisticated users, the
software allows you to specify the MIME type of your
attachments;
otherwise (as with most user friendly, modern e-mail
software), attach a *.txt file (Doug Bates uses foo_R.txt)
and it should make it to the lists;
as a third alternative, just cut paste the corresponding
text into your e-mal.
I think your R function should make it to R-help (and its
archives), so I'd be thankful for a repost.
Martin
Ravi == Ravi Varadhan [EMAIL PROTECTED]
on Fri, 25 May 2007 14:24:20 -0400 writes:
Ravi Mike, Attached is an R function to do this, along with
Ravi an example that will reproduce the MathCad plot shown
Ravi in your attached paper. I haven't checked it
Ravi thoroughly, but it seems to reproduce the MathCad
Ravi example well.
Ravi Ravi.
Ravi
Ravi ---
Ravi Ravi Varadhan, Ph.D.
Ravi Assistant Professor, The Center on Aging and Health
Ravi Division of Geriatric Medicine and Gerontology
Ravi Johns Hopkins University
Ravi Ph: (410) 502-2619
Ravi Fax: (410) 614-9625
Ravi Email: [EMAIL PROTECTED]
Ravi Webpage:
Ravi http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
Ravi
Ravi
Ravi -Original Message- From:
Ravi [EMAIL PROTECTED]
Ravi [mailto:[EMAIL PROTECTED] On Behalf Of
Ravi Mike Lawrence Sent: Friday, May 25, 2007 1:55 PM To:
Ravi Lucke, Joseph F Cc: Rhelp Subject: Re: [R] Calculation
Ravi of ratio distribution properties
Ravi According to the paper I cited, there is controversy
Ravi over the sufficiency of Hinkley's solution, hence
Ravi their proposed more complete solution.
Ravi On 25-May-07, at 2:45 PM, Lucke, Joseph F wrote:
The exact ratio is given in
On the Ratio of Two Correlated Normal Random Variables,
D. V. Hinkley, Biometrika, Vol. 56, No. 3. (Dec., 1969),
pp. 635-639.
Ravi -- Mike Lawrence Graduate Student, Department of
Ravi Psychology, Dalhousie University
Ravi Website: http://myweb.dal.ca/mc973993 Public calendar:
Ravi http://icalx.com/public/informavore/Public
Ravi The road to wisdom? Well, it's plain and simple to
Ravi express: Err and err and err again, but less and less
Ravi and less. - Piet Hein
ratio2normals - function(x, mean1,mean2,sd1,sd2,rho){
# A function to compute ratio of 2 normals
# R code written by Ravi Varadhan
# May 25, 2007
# Based on the paper by Pham Gia et al., Comm in Stats (2006)
A - 1 / (2*pi*sd1*sd2*sqrt(1-rho^2))
exponent.num - -sd2^2*mean1^2 - sd1^2*mean2^2 + 2*rho*sd1*sd2*mean1*mean2
exponent.denom - 2*(1-rho^2)*sd1^2*sd2^2
K - A * exp(exponent.num/exponent.denom)
t2x.num - -sd2^2*mean1*x - sd1^2*mean2 + rho*sd1*sd2*(mean2*x + mean1)
t2x.denom - sd1*sd2*sqrt(2*(1-rho^2)*(sd2^2*x^2 - 2*rho*x*sd1*sd2 + sd1^2))
t2x - t2x.num / t2x.denom
erf.term - 2 * pnorm(sqrt(2) * t2x) - 1
Ft2x - sqrt(pi) * t2x * exp(t2x^2) * erf.term + 1
fx - K * Ft2x * 2 * (1 - rho^2) * sd1^2 * sd2^2 / (sd2^2 * x^2 + sd1^2 -
2*x*rho*sd1*sd2)
return(fx)
}
mean1 - 75.25
mean2 - 71.58
sd1 - 6.25
sd2 - 5.45
rho - 0.76
x - seq(0.5,1.5, length=100)
y - ratio2normals(x,mean1,mean2, sd1,sd2,rho)
plot(x,y, type=l)
# compute the mean and variance via quadrature
m1 - function(x, mean1, mean2, sd1, sd2, rho){
x * ratio2normals(x, mean1, mean2, sd1, sd2, rho)
}
m2 - function(x, mean1, mean2, sd1, sd2, rho){
x^2 * ratio2normals(x, mean1, mean2, sd1, sd2, rho)
}
m.1 - integrate(m1, lower=-Inf, upper=Inf, mean1=mean1, mean2=mean2, sd1=sd1,
sd2=sd2, rho=rho,
[R] look for packages
Dear list members, I am analysing some microarray data. I have got the differentially expressed genes and now want to carry out PCA analysis to get the main components that contribute to the variance.I have browsered the CRAN and BioConductor and did not find an appropriate package. Have anybody ever carried out PCA analysis? Is there any package about PCA in R? Thanks for your advice. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Fw: hierarhical cluster analysis of groups of vectors
Hi Rafael, What about multivariate logistic regression? - Forwarded Message From: Rafael Duarte [EMAIL PROTECTED] To: Anders Malmendal [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, May 29, 2007 3:21:11 PM Subject: Re: [R] hierarhical cluster analysis of groups of vectors It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- Rafael Duarte Marine Resources Department - DRM IPIMAR - National Research Institute for Agriculture and Fisheries Av. Brasília, 1449-006 Lisbon - Portugal Tel:+351 21 302 7000 Fax:+351 21 301 5948 e-mail: [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 and provide commented, minimal, self-contained, reproducible code. Send instant messages to your online friends http://uk.messenger.yahoo.com [[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 and provide commented, minimal, self-contained, reproducible code.
[R] exemples, tutorial on lmer
Hi all, I have some difficulties to work with the function lmer from lme4 Does somebody have a tutorial or different examples to use this function? Thanks, Oliver. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] look for packages
Look that: RSiteSearch(PCA Analysis, restrict=functions) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 Ohttp://maps.google.com/maps?f=qhl=enq=Curitiba,+Brazillayer=ie=UTF8z=18ll=-25.448315,-49.276916spn=0.002054,0.005407t=kom=1 On 29/05/07, De-Jian,ZHAO [EMAIL PROTECTED] wrote: Dear list members, I am analysing some microarray data. I have got the differentially expressed genes and now want to carry out PCA analysis to get the main components that contribute to the variance.I have browsered the CRAN and BioConductor and did not find an appropriate package. Have anybody ever carried out PCA analysis? Is there any package about PCA in R? Thanks for your advice. __ 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 and provide commented, minimal, self-contained, reproducible code. [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] normality tests [Broadcast]
False. Box proved ~ca 1952 that standard inferences in the linear regression
model are robust to nonnormality, at least for (nearly) balanced designs.
The **crucial** assumption is independence, which I suspect partially
motivated his time series work on arima modeling. More recently, work on
hierarchical models (e.g. repeated measures/mixed effect models) has also
dealt with lack of independence.
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of wssecn
Sent: Friday, May 25, 2007 2:59 PM
To: r-help
Subject: Re: [R] normality tests [Broadcast]
The normality of the residuals is important in the inference procedures for
the classical linear regression model, and normality is very important in
correlation analysis (second moment)...
Washington S. Silva
Thank you all for your replies they have been more useful... well
in my case I have chosen to do some parametric tests (more precisely
correlation and linear regressions among some variables)... so it
would be nice if I had an extra bit of support on my decisions... If I
understood well from all your replies... I shouldn't pay s much
attntion on the normality tests, so it wouldn't matter which one/ones
I use to report... but rather focus on issues such as the power of the
test...
Thanks again.
On 25/05/07, Lucke, Joseph F [EMAIL PROTECTED] wrote:
Most standard tests, such as t-tests and ANOVA, are fairly resistant to
non-normalilty for significance testing. It's the sample means that have
to be normal, not the data. The CLT kicks in fairly quickly. Testing
for normality prior to choosing a test statistic is generally not a good
idea.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Friday, May 25, 2007 12:04 PM
To: [EMAIL PROTECTED]; Frank E Harrell Jr
Cc: r-help
Subject: Re: [R] normality tests [Broadcast]
From: [EMAIL PROTECTED]
On 25/05/07, Frank E Harrell Jr [EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] wrote:
Hi all,
apologies for seeking advice on a general stats question. I ve run
normality tests using 8 different methods:
- Lilliefors
- Shapiro-Wilk
- Robust Jarque Bera
- Jarque Bera
- Anderson-Darling
- Pearson chi-square
- Cramer-von Mises
- Shapiro-Francia
All show that the null hypothesis that the data come from a normal
distro cannot be rejected. Great. However, I don't think
it looks nice
to report the values of 8 different tests on a report. One note is
that my sample size is really tiny (less than 20
independent cases).
Without wanting to start a flame war, are there any
advices of which
one/ones would be more appropriate and should be reported
(along with
a Q-Q plot). Thank you.
Regards,
Wow - I have so many concerns with that approach that it's
hard to know
where to begin. But first of all, why care about
normality? Why not
use distribution-free methods?
You should examine the power of the tests for n=20. You'll probably
find it's not good enough to reach a reliable conclusion.
And wouldn't it be even worse if I used non-parametric tests?
I believe what Frank meant was that it's probably better to use a
distribution-free procedure to do the real test of interest (if there is
one) instead of testing for normality, and then use a test that assumes
normality.
I guess the question is, what exactly do you want to do with the outcome
of the normality tests? If those are going to be used as basis for
deciding which test(s) to do next, then I concur with Frank's
reservation.
Generally speaking, I do not find goodness-of-fit for distributions very
useful, mostly for the reason that failure to reject the null is no
evidence in favor of the null. It's difficult for me to imagine why
there's insufficient evidence to show that the data did not come from a
normal distribution would be interesting.
Andy
Frank
--
Frank E Harrell Jr Professor and Chair School
of Medicine
Department of Biostatistics
Vanderbilt University
--
yianni
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Re: [R] search path question
Yes, it is.
The original is here
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/92829.html
However, it requires some modifications.
Here they are. Sorry, I can test it only in Windows.
search.source - function(file, path=Sys.getenv(PATH), ...)
{
for(p in strsplit(path,.Platform$path.sep)[[1]]) {
fp - file.path(p, f)
if(file.exists(fp)) return(source(fp, ...))
}
stop(file , sQuote(file), not found)
}
Try also looking here.
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/92821.html
Zhiliang Ma wrote:
Is there a simple function that can add a folder into current R search
path?
For example, suppose my current work directory is D:\work, but my input
files are stored in folder C:\inFiles\, I know I can change work
directory or add C:\inFiles\ before files name when I scan them, but I
don't want to do that. I want to find a function that can simply add
C:\inFiles\ into R's search path, so that we I scan a file R will go to
all the search paths to find it. In matlab, path(path,C:\inFiles) will
do
this job, I'm just wondering if there is a similar function in R can do
this
job.
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View this message in context:
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] exemples, tutorial on lmer
Hi Oliver, You could start with R News 2005, no. 1. Also the PDF associated with lme4, Implementation.pdf. Hnak On May 29, 2007, at 10:35 AM, Olivier MARTIN wrote: Hi all, I have some difficulties to work with the function lmer from lme4 Does somebody have a tutorial or different examples to use this function? Thanks, Oliver. __ 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 and provide commented, minimal, self-contained, reproducible code. Dr. Hank Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: hierarhical cluster analysis of groups of vectors
Yes, of course. But since the initial question referred the use of dist(), (I suppose with Euclidean distances) and hclust on a matrix with a priori known groups, discriminant analysis seemed adequate to me. It was only a suggestion, without having much detail about the problem. Thanks, Rafael Ron Michael wrote: -- Hi Rafael, What about multivariate logistic regression? - Forwarded Message From: Rafael Duarte [EMAIL PROTECTED] To: Anders Malmendal [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, May 29, 2007 3:21:11 PM Subject: Re: [R] hierarhical cluster analysis of groups of vectors It seems that you have already groups defined. Discriminant analysis would probably be more appropriate for what you want. Best regards, Rafael Duarte Anders Malmendal wrote: I want to do hierarchical cluster analysis to compare 10 groups of vectors with five vectors in each group (i.e. I want to make a dendogram showing the clustering of the different groups). I've looked into using dist and hclust, but cannot see how to compare the different groups instead of the individual vectors. I am thankful for any help. Anders __ 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 and provide commented, minimal, self-contained, reproducible code. -- Rafael Duarte Marine Resources Department - DRM IPIMAR - National Research Institute for Agriculture and Fisheries Av. Brasília, 1449-006 Lisbon - Portugal Tel:+351 21 302 7000 Fax:+351 21 301 5948 e-mail: [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 and provide commented, minimal, self-contained, reproducible code. Send instant messages to your online friends http://uk.messenger.yahoo.com -- Rafael Duarte Marine Resources Department - DRM IPIMAR - National Research Institute for Agriculture and Fisheries Av. Brasília, 1449-006 Lisbon - Portugal Tel:+351 21 302 7000 Fax:+351 21 301 5948 e-mail: [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 and provide commented, minimal, self-contained, reproducible code.
[R] AIC for lrm(Hmisc/Design) model.
Dear all, I am adjusting a Logistic Regression Model using lmr() function of Hmisc/Design package. Now I would like to compute AIC for this model. How can I do that? Kind regards, miltinho Brazil __ [[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 and provide commented, minimal, self-contained, reproducible code.
[R] Estimate Fisher Information by Hessian from OPTIM
Dear All, I am trying to find MLE by using OPTIM function. Difficult in differentiating some parameter in my objective function, I would like to use the returned hessian matrix to yield an estimate of Fisher's Information matrix. My question: Since the hessian is calculated by numerical differentiate, is it a reliable estimate? Otherwise I would have to do a lot of work to write a second derivative on my own. Thank you very much in advance [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] AIC for lrm(Hmisc/Design) model.
Milton Cezar Ribeiro wrote: Dear all, I am adjusting a Logistic Regression Model using lmr() function of Hmisc/Design package. Now I would like to compute AIC for this model. How can I do that? Kind regards, miltinho Brazil I like to change AIC to have it on the chi-square scale. For that you can do aic - function(fit) round(unname(fit$stats['Model L.R.'] - 2*fit$stats['d.f.']),2) f - lrm( ) aic(f) If unname doesn't exist in S-Plus as it does in R, you can remove that part. -- 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 and provide commented, minimal, self-contained, reproducible code.
[R] search path question
Hi R users, Is there a simple function that can add a folder into current R search path? For example, suppose my current work directory is D:\work, but my input files are stored in folder C:\inFiles\, I know I can change work directory or add C:\inFiles\ before files name when I scan them, but I don't want to do that. I want to find a function that can simply add C:\inFiles\ into R's search path, so that we I scan a file R will go to all the search paths to find it. In matlab, path(path,C:\inFiles) will do this job, I'm just wondering if there is a similar function in R can do this job. Thanks, zhiliang [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] search path question
Zhiliang Ma wrote:
I want to find a function that can simply add
C:\inFiles\ into R's search path, so that we I scan a file R will go to
all the search paths to find it. In matlab, path(path,C:\inFiles) will do
this job, I'm just wondering if there is a similar function in R can do this
job.
Something like this (not extensively tested):
`sscan` -
function(name, path=options()$scanpath,...){
for(p in path){
file=file.path(p,name)
if(file.exists(file)){
return(scan(file,...))
}
## last resort..
return(scan(name,...))
}
}
Then do:
options(scanpath=/tmp)
and then:
sscan(foo.data)
will look for /tmp/foo.data first, then if that fails it will do the
'last resort' which is to look in the current directory.
My worry is that this will bite you one day - if you have two files
with the same name, it will get the first one in your scanpath - one day
this will not be the one you think it is
Note this only works with 'scan' - you'll have to do the same thing
for read.table, source, etc etc if you want them to behave with a search
path too. Unless there's a lower-level approach. But that really will
bite you!
Barry
Barry
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Re: [R] search path question
On Tue, 29 May 2007, Zhiliang Ma wrote: Hi R users, Is there a simple function that can add a folder into current R search path? This works for adding libraries to your search path, but I don't think it would work for finding data files outside of your getwd() quite as you'd like: .libPaths(c(/home/foo/R/library,.libPaths())) For example, suppose my current work directory is D:\work, but my input files are stored in folder C:\inFiles\, I know I can change work directory or add C:\inFiles\ before files name when I scan them, but I don't want to do that. I want to find a function that can simply add C:\inFiles\ into R's search path, so that we I scan a file R will go to all the search paths to find it. In matlab, path(path,C:\inFiles) will do this job, I'm just wondering if there is a similar function in R can do this job. Thanks, zhiliang [[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 and provide commented, minimal, self-contained, reproducible code. -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] search path question
Thanks, Barry.
In fact, I have a function just like yours, and I'm looking for a simple
alternative function, which is like path in Matlab.
On 5/29/07, Barry Rowlingson [EMAIL PROTECTED] wrote:
Zhiliang Ma wrote:
I want to find a function that can simply add
C:\inFiles\ into R's search path, so that we I scan a file R will go
to
all the search paths to find it. In matlab, path(path,C:\inFiles) will
do
this job, I'm just wondering if there is a similar function in R can do
this
job.
Something like this (not extensively tested):
`sscan` -
function(name, path=options()$scanpath,...){
for(p in path){
file=file.path(p,name)
if(file.exists(file)){
return(scan(file,...))
}
## last resort..
return(scan(name,...))
}
}
Then do:
options(scanpath=/tmp)
and then:
sscan(foo.data)
will look for /tmp/foo.data first, then if that fails it will do the
'last resort' which is to look in the current directory.
My worry is that this will bite you one day - if you have two files
with the same name, it will get the first one in your scanpath - one day
this will not be the one you think it is
Note this only works with 'scan' - you'll have to do the same thing
for read.table, source, etc etc if you want them to behave with a search
path too. Unless there's a lower-level approach. But that really will
bite you!
Barry
Barry
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] parallel processing an lme model
On 5/28/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi All Had anyone of you seen if it is possible to split a large lme() job to be processed by multiple cpus/computers? I am just at the very beginning to understand related things, but does the lme() use solution finding functions like nlm() mle(), and I-dont-know-what-else of the standard R pagage or does lme come with its own? If the former, has onyone seen how to split an mle() function call to be processed by multiple cpus? First, if you want speed and your model can be fit by lmer I would recommend using lmer or lmer2 from the lme4 package. These functions can fit models with crossed or partially crossed random effects which is often the case for models in very large data sets. However, they do not provide the facility for specifying correlation structures or variance functions in addition to those implied by the random effects. Both lme and lmer end up calling nlminb to do the optimization of the log-likelihood or the REML criterion. The lmer2 function does not call nlminb explicitly but does use the underlying code from nlminb. None of these operations are easily parallelizable. The only hope for getting a speed boost from multiple CPU cores or multiple processors is by using a multithreaded accelerated BLAS (Basic linear algebra subroutines) library (see the R Installation and Administration manual for details). However, in some cases we have observed that multithreaded BLAS actually slow down the computation. To check if this is the case for you try the following both with and without multithreaded BLAS. library(lme4) data(star, package = mlmRev) system.time(fm1 - lmer(math ~ sx*eth+ses+gr+cltype +(yrs|id)+(1|tch)+(yrs|sch), star, control = list(grad = 0, nit = 0, msV = 1)) system.time(m1 - lmer2(math ~ sx*eth+ses+gr+cltype +(yrs|id)+(1|tch)+(yrs|sch), star, control = list(msV = 1)) In the case if, I would very much appreicate your hint or point to a source where I can read about. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] rgl.postscript
Hi,
I am having an issue when creating a postscript file from RGL window. It
seems to cut off some of the axis labels. Here is the code I am using.
I created a 3D plot using RGL_0.71 with R 2.5 on Windows XP.
z1-c(5,4,1,4.5,2,3,2,1,1)
z2-c(6,8,7,7.5,5,3.5,4,1,1)
z3-c(3,2,4,7,3,4.5,6,2,3)
x1-seq(1,9)
x2-seq(1,9)
x3-seq(10,18)
y1-seq(8,0)
y2--1*y1
y3-rep(0,9)
m1-cbind(x1,y1,z1)
m2-cbind(x2,y2,z2)
m3-cbind(x3,y3,z3)
m3-rbind(m2[9,],m3)
up1-m1[,-2]
up2-m2[,-2]
lp-m3[,-2]
p1-rbind(up1, lp[-1,])
p2-rbind(up2, lp[-1,])
sp1-spline(p1)
sp2-spline(p2)
sp1m-cbind(sp1$x,sp1$y)
sp2m-cbind(sp2$x,sp2$y)
ge9-(sp1$x=9)
ge9recs-seq(1,length(ge9))[ge9]
b1-sp1m[ge9recs,]
b2-sp2m[ge9recs,]
b1b2-cbind(b1[,2],b2[,2])
bavg-apply(b1b2,1,mean)
blow-cbind(sp1m[ge9recs,1],bavg)
path.one-rbind(sp1m[-ge9recs,],blow)
path.two-rbind(sp2m[-ge9recs,],blow)
uy1-9-path.one[-ge9recs,1]
ly1-rep(0,length(ge9recs))
y1-c(uy1,ly1)
uy2--1*(9-path.two[-ge9recs,1])
ly2-rep(0,length(ge9recs))
y2-c(uy2,ly2)
m1-cbind(path.one,y1)
m2-cbind(path.two,y2)
d.mat-rbind(m1,m2)
open3d()
points3d(x=d.mat[,1],y=d.mat[,3],z=d.mat[,2],size=3)
lines3d(x=m1[,1],y=m1[,3],z=m1[,2],size=3)
lines3d(x=m2[,1],y=m2[,3],z=m2[,2],size=3)
I then added axes using
box3d()
axes3d(c('x--'),tick=TRUE,nticks=5)
axes3d(c('z--'),tick=TRUE,nticks=5)
axes3d(c('z++'),tick=TRUE,nticks=5)
title3d(main = Test 3-D plot, sub = NULL, xlab =Lag, ylab = NULL, zlab =
Dissolved O2, line = NA)
I did some rotation to determine a nicer view of the plot. I now wanted to
create a snapshot of the plot (using rgl.postscript since I will be using in
LATEX). However, it cuts off some of the axis labels. Is there a way to
adjust the area that gets captured to the postscript file? or some other way
to fix this?
Thanks,
Bill
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Re: [R] search path question
Zhiliang Ma wrote: Thanks, Barry. In fact, I have a function just like yours, and I'm looking for a simple alternative function, which is like path in Matlab. Dont think it can be done - if you look at the code for 'scan', it disappears off into internal() calls to do the business of finding and reading a file, so you're going to have trouble changing its behaviour in R. You'd have to patch R's C source to implement a search path. Barry __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] LAPACK and BLAS libraries
Hi, I don't know if I'm sending this to the right place but I've looked throught tens and tens of topics on http://tolstoy.newcastle.edu.au/ and finally found that email address where I can maybe find some help. Well my main goal is to get to use the lapack library within my R package (which can be done using calls from C). But in order to do this I have to create a file src/Makevars with the following line : PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) However when I create this file, my package won't build anymore. Actually the checking results in the following : mingw32\bin\ld.exe: cannot find -lg2c collect2: ld returned 1 exit status make[3]: *** [PACKAGE.dll] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-PACKAGE] Error 2 *** Installation of PACKAGE failed *** I've installed all the following tools : mingw-runtime-3.12.tar.gz w32api-3.9.tar.gz binutils-2.17.50-20060824-1.tar.gz gcc-core-3.4.5-20060117-1.tar.gz gcc-g++-3.4.5-20060117-1.tar.gz gcc-g77-3.4.5-20060117-1.tar.gz So I don't know what to do next for the package to build... Any help would be greatly appreciated. [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] search path question
Actually, it does
if (is.character(file))
if (file == )
file - stdin()
else {
file - file(file, r)
on.exit(close(file))
}
so all the searching is done in the file() connection.
You could do this via a search_file() connection wrapper, but there is a
problem with ensuring connections get closed (which on.exit does here).
On Tue, 29 May 2007, Barry Rowlingson wrote:
Zhiliang Ma wrote:
Thanks, Barry.
In fact, I have a function just like yours, and I'm looking for a simple
alternative function, which is like path in Matlab.
Dont think it can be done - if you look at the code for 'scan', it
disappears off into internal() calls to do the business of finding and
reading a file, so you're going to have trouble changing its behaviour
in R. You'd have to patch R's C source to implement a search path.
Barry
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and provide commented, minimal, self-contained, reproducible code.
--
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] rgl.postscript
On 5/29/2007 1:53 PM, coar wrote:
Hi,
I am having an issue when creating a postscript file from RGL window. It
seems to cut off some of the axis labels. Here is the code I am using.
I created a 3D plot using RGL_0.71 with R 2.5 on Windows XP.
z1-c(5,4,1,4.5,2,3,2,1,1)
z2-c(6,8,7,7.5,5,3.5,4,1,1)
z3-c(3,2,4,7,3,4.5,6,2,3)
x1-seq(1,9)
x2-seq(1,9)
x3-seq(10,18)
y1-seq(8,0)
y2--1*y1
y3-rep(0,9)
m1-cbind(x1,y1,z1)
m2-cbind(x2,y2,z2)
m3-cbind(x3,y3,z3)
m3-rbind(m2[9,],m3)
up1-m1[,-2]
up2-m2[,-2]
lp-m3[,-2]
p1-rbind(up1, lp[-1,])
p2-rbind(up2, lp[-1,])
sp1-spline(p1)
sp2-spline(p2)
sp1m-cbind(sp1$x,sp1$y)
sp2m-cbind(sp2$x,sp2$y)
ge9-(sp1$x=9)
ge9recs-seq(1,length(ge9))[ge9]
b1-sp1m[ge9recs,]
b2-sp2m[ge9recs,]
b1b2-cbind(b1[,2],b2[,2])
bavg-apply(b1b2,1,mean)
blow-cbind(sp1m[ge9recs,1],bavg)
path.one-rbind(sp1m[-ge9recs,],blow)
path.two-rbind(sp2m[-ge9recs,],blow)
uy1-9-path.one[-ge9recs,1]
ly1-rep(0,length(ge9recs))
y1-c(uy1,ly1)
uy2--1*(9-path.two[-ge9recs,1])
ly2-rep(0,length(ge9recs))
y2-c(uy2,ly2)
m1-cbind(path.one,y1)
m2-cbind(path.two,y2)
d.mat-rbind(m1,m2)
open3d()
points3d(x=d.mat[,1],y=d.mat[,3],z=d.mat[,2],size=3)
lines3d(x=m1[,1],y=m1[,3],z=m1[,2],size=3)
lines3d(x=m2[,1],y=m2[,3],z=m2[,2],size=3)
I then added axes using
box3d()
axes3d(c('x--'),tick=TRUE,nticks=5)
axes3d(c('z--'),tick=TRUE,nticks=5)
axes3d(c('z++'),tick=TRUE,nticks=5)
title3d(main = Test 3-D plot, sub = NULL, xlab =Lag, ylab = NULL, zlab =
Dissolved O2, line = NA)
I did some rotation to determine a nicer view of the plot. I now wanted to
create a snapshot of the plot (using rgl.postscript since I will be using in
LATEX). However, it cuts off some of the axis labels. Is there a way to
adjust the area that gets captured to the postscript file? or some other way
to fix this?
You could try resizing, or using Latex to put the labels on the plot,
but there is no parameter to control what gets cut off. You should also
be aware that the Postscript support is somewhat limited, and you might
be better off using a bitmap copy with rgl.snapshot.
Duncan Murdoch
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[R] #include Rmodules/Rlapack.h
Hey Everyone, I'm running R 2.4.0 on Debian etch 4.0, and I'm trying to call some Lapack functions from my C code. Actually, to be honest I'm not really having trouble calling the commands such as La_dgesv from within my C code, but I do get warning when compiling the package saying: GAUSSlkhd.c: In function 'GAUSSlkhd': GAUSSlkhd.c:37: warning: implicit declaration of function 'La_dgesv' GAUSSlkhd.c:37: warning: assignment makes pointer from integer without a cast I tried using: #include Rmodules/Rlapack.h but it won't compile the package at all with that included, complaining that bjl.h:5:30: error: Rmodules/Rlapack.h: No such file or directory Can someone explain to me how I should include the AWESOME wrapper code to the Lapack libraries? Am I not following the proper protocol by using these La_* commands in my package source code? TIA, Brian __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] aggregation of a zoo object
Dear all, I am trying to execute the following example: time-c(2000-10-03 14:00:00,2000-10-03 14:10:00,2000-10-03 14:20:00,2000-10-03 15:30:00,2000-10-03 16:40:00,2000-10-03 16:50:00,2000-10-03 17:00:00,2000-10-03 17:10:00,2000-10-03 17:20:00,2000-10-03 18:30:00,2000-10-04 14:00:00,2000-10-04 14:10:00,2000-10-04 14:20:00,2000-10-04 15:30:00,2000-10-04 16:40:00,2000-10-04 16:50:00,2000-10-04 17:00:00,2000-10-04 18:30:00,2000-10-04 18:30:00,2000-10-04 18:30:00) # remark the last date is occuring 3 times precipitation-c(NA,0.1,0,0,NA,0,0.2,0.3,0.5,6,7,8,9,1,0,0,NA,0,1,0) library(zoo) z - zoo(precipitation, as.POSIXct(time, tz = GMT)) Warning message: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique in: zoo(precipitation, as.POSIXct(time, tz = GMT)) # then I want to do the sum per hour z_sum_per_hour - aggregate(na.omit(z), function(x) as.POSIXct(trunc(x, hour)),sum) Warning message: some methods for “zoo” objects do not work if the index entries in ‘order.by’ are not unique in: zoo(rval[i], x.index[i]) Do anyone has an idea how to avoid that ? Thanks in advance Jessica __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] off-topic: affine transformation matrix
Thanks for the prompt and clear reply! The simplicity of the solution may have been why I initially overlooked this approach... The results look convincing (http://169.237.35.250/~dylan/temp/affine.png), now I just need to verify that the output from coef() is in the format that I need it in. l - lm(cbind(nx,ny) ~ x + y, data=g) coef(l) nx ny (Intercept) 6.87938629 5.515261158 x1.01158806 -0.005449152 y -0.04481893 0.996895878 ## convert to format needed for affine() function in postGIS? t(coef(l)) (Intercept)x y nx6.879386 1.011588063 -0.04481893 ny5.515261 -0.005449152 0.99689588 note that the format that I am looking for looks something like the matrix defined on this page: http://www.geom.uiuc.edu/docs/reference/CRC-formulas/node15.html cheers, dylan On Monday 28 May 2007 15:18, Prof Brian Ripley wrote: Isn't this just a regression (hopefully with a near-zero error). coef(lm(cbind(xnew, ynew) ~ xold + yold)) should do what I think you are asking for. (I am not clear which direction you want the transformation, so choose 'old' and 'new' accordingly.) On Mon, 28 May 2007, Dylan Beaudette wrote: This may sound like a very naive question, but... give two lists of coordinate pairs (x,y - Cartesian space) is there any simple way to compute the affine transformation matrix in R. I have a set of data which is offset from where i know it should be. I have coordinates of the current data, and matching coordinates of where the data should be. I need to compute the composition of the affine transformation matrix, so that I can apply an affine transform the entire dataset. any ideas? thanks in advance! -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] aggregation of a zoo object
On Tue, 29 May 2007 [EMAIL PROTECTED] wrote: # then I want to do the sum per hour z_sum_per_hour - aggregate(na.omit(z), function(x) as.POSIXct(trunc(x, hour)),sum) Warning message: some methods for âzooâ objects do not work if the index entries in âorder.byâ are not unique in: zoo(rval[i], x.index[i]) Do anyone has an idea how to avoid that ? The warning does not come from the aggregate() call, but from the na.omit() call. After omitting the NAs, you have still duplicated time stamps, hence the warning is issued again. After that, aggregating works fine and produces no warnings. Z __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Partially reading a file (particularly)
Hello, I am trying to figure out if there exists some R command that allows one to be particularly selective when reading a file. I'm dealing with large fixed-width data sets that look like 539001.. 639001.. 639001.. ... 539002.. 639002.. ... Presently, I am using read.fwf to read an entire file, but I am interested only in reading those records beginning with 5. I have been unable to find help in any of the suggested resources. I understand this is a SAS example that replicates what I'm looking to do, if it's of any help to anyone. street type nameam traffic pm traffic freeway 408 3684 3459 surface Martin Luther King Jr. Blvd.15901234 freeway 608 4583 3860 freeway 808 2386 2518 surface Lake Shore Dr. 15901234 INPUT type $ @; IF type = 'surface' THEN DELETE; INPUT name $ 9-38 amtraff pmtraff; Any answers, suggestions, or points-in-the-right-direction would be much appreciated. -- Jared Tobin, Student Research Assistant Dept. of Fisheries and Oceans [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 and provide commented, minimal, self-contained, reproducible code.
[R] summing up colum values for unique IDs when multiple ID's exist in data frame
I have data.frame's with IDs and multiple columns. B/c some of IDs showed up
more than once, I need sum up colum values to creat a new dataframe with
unique ids.
I hope there are some cheaper ways of doing it... Because the dataframe is
huge, it takes almost an hour to do the task. Thanks so much in advance!
Young
# - examples are here and sum.dup.r is at the
bottom.
x = data.frame(ID = c('A','B','C','A'), val=c(0.1,0.001,-0.1,0.2))
x
IDval
1 A 0.100
2 B 0.001
3 C -0.100
4 A 0.200
sum.dup(x)
IDval
1 A 0.300
2 B 0.001
3 C -0.100
sum.dup - function( x ){
d.row = which(duplicated(x$ID))
if( length(d.row) 0){
id = x$ID[d.row]
com.val = x[-d.row,]
for(i in 1:length(id)){
s = sum(x$val[ x$ID == id[i] ])
com.val$val[ com.val$ID == id[i] ] = s
}
ix = sort(as.character(com.val[,1]),index.return=T)
return(com.val[ix$ix,])
}else{
ix = sort(as.character(x[,1]),index.return=T)
return(x[ix$ix,])
}
}
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[R] [R-pkgs] Rcmdr 1.3-0 and RcmdrPlugins.TeachingDemos
I'd like to announce a new version, 1.3-0, of the Rcmdr package. The Rcmdr package provides a basic-statistics graphical user interface (GUI) to R. Beyond small changes and additions, this new version of the package makes provision for plug-ins that permit extension of the Rcmdr GUI without altering and rebuilding the Rcmdr source package or modifying the installed package. An R Commander plug-in is an ordinary R package that (1) provides extensions to the R Commander menus is a file named menus.txt located in the package's etc directory; (2) provides call-back functions required by these menus; and (3) in optional Log-Exceptions: and Models: fields in the package's DESCRIPTION file, augments respectively the list of functions for which printed output is suppressed and the list of model objects recognized by the R Commander. The menus provided by a plug-in package are merged with the standard Commander menus. Plug-in packages given in the R Commander plugins option (see ?Commander) are automatically loaded when the Commander starts up. Plug-in packages may also be loaded via the Commander Tools - Load Rcmdr plug-in(s) menu; a restart of the Commander is required to install the new menus. Finally, loading a plug-in package when the Rcmdr is not loaded will load the Rcmdr and activate the plug-in. An illustrative R Commander plug-in package, RcmdrPlugin.TeachingDemos (providing a GUI to some of Greg Snow's TeachingDemos package), is now available on CRAN. (I suggest using this naming convention -- RcmdrPlugin.* -- so that plug-in packages will sort immediately below the Rcmdr package on CRAN. This assumes, of course, that other people will be interested in creating Rcmdr plugins!) Because this is a new feature of the Rcmdr, feedback and suggestions would be appreciated. I'd like to acknowledge Richard Heiberger's suggestions for the design of this plug-in facility. John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] summing up colum values for unique IDs when multiple ID's exist in data frame
Young Cho [EMAIL PROTECTED] writes:
I have data.frame's with IDs and multiple columns. B/c some of IDs
showed up more than once, I need sum up colum values to creat a new
dataframe with unique ids.
I hope there are some cheaper ways of doing it... Because the
dataframe is huge, it takes almost an hour to do the task. Thanks
so much in advance!
Does this do what you want in a faster way?
sum_dup - function(df) {
idIdx - split(1:nrow(df), as.character(df$ID))
whID - match(ID, names(df))
colNms - names(df)[-whID]
ans - lapply(colNms, function(cn) {
unlist(lapply(idIdx,
function(x) sum(df[[cn]][x])),
use.names=FALSE)
})
attributes(ans) - list(names=colNms,
row.names=names(idIdx),
class=data.frame)
ans
}
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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Re: [R] summing up colum values for unique IDs when multiple ID's exist in data frame
On Tue, 29 May 2007, Seth Falcon wrote: Young Cho [EMAIL PROTECTED] writes: I have data.frame's with IDs and multiple columns. B/c some of IDs showed up more than once, I need sum up colum values to creat a new dataframe with unique ids. I hope there are some cheaper ways of doing it... Because the dataframe is huge, it takes almost an hour to do the task. Thanks so much in advance! Does this do what you want in a faster way? rowsum() should probably be faster (but perhaps not much). -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partially reading a file (particularly)
On Tue, 29 May 2007, Tobin, Jared wrote: Hello, I am trying to figure out if there exists some R command that allows one to be particularly selective when reading a file. I'm dealing with large fixed-width data sets that look like 539001.. 639001.. 639001.. ... 539002.. 639002.. ... Presently, I am using read.fwf to read an entire file, but I am interested only in reading those records beginning with 5. I have been unable to find help in any of the suggested resources. Assuming you have 'grep' in your path, res - read.fwf( pipe( grep '^5' my.file ) , other args ) will do it. grep will usually be found on linux/unix systems and Mac OS X. The 'Rtools' toolkit for windows has grep, I believe. I understand this is a SAS example that replicates what I'm looking to do, if it's of any help to anyone. street type nameam traffic pm traffic freeway 408 3684 3459 surface Martin Luther King Jr. Blvd.15901234 freeway 608 4583 3860 freeway 808 2386 2518 surface Lake Shore Dr. 15901234 INPUT type $ @; IF type = 'surface' THEN DELETE; INPUT name $ 9-38 amtraff pmtraff; Any answers, suggestions, or points-in-the-right-direction would be much appreciated. -- Jared Tobin, Student Research Assistant Dept. of Fisheries and Oceans [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 and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] trouble understanding why ...==NaN isn't true
I have the following data: dataset[2,Sample.227] [1]NaN 1558 Levels: -0.000 -0.001 -0.002 -0.003 -0.004 -0.005 -0.006 -0.007 -0.008- 0.009 ... 2.000 However, I'm not sure why this expression is coming back as FALSE: dataset[2,Sample.227]==NaN [1] FALSE Similarly: dataset[2,Sample.227]==NaN [1] NA It seems that since NaN is represented as a character, this expression ==NaN should be TRUE, but it's returning as FALSE. Thanks, Andrew [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble understanding why ...==NaN isn't true
Okay, it turns out that there were leading spaces, so that in the data, it was represented asNaN, hence the expression ==NaN was coming back as false. Is there a way to find out preemptively if there are leading spaces? Thanks, Andrew On 5/29/07, Andrew Yee [EMAIL PROTECTED] wrote: I have the following data: dataset[2,Sample.227] [1]NaN 1558 Levels: -0.000 -0.001 -0.002 -0.003 -0.004 -0.005 -0.006 -0.007 - 0.008 -0.009 ... 2.000 However, I'm not sure why this expression is coming back as FALSE: dataset[2,Sample.227]==NaN [1] FALSE Similarly: dataset[2,Sample.227]==NaN [1] NA It seems that since NaN is represented as a character, this expression ==NaN should be TRUE, but it's returning as FALSE. Thanks, Andrew [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble understanding why ...==NaN isn't true
1. NaN is a character string, **not** NaN; hence is.nan(NaN) yields FALSE. 2. Please read the docs! ?NaN explicitly says: Do not test equality to NaN, or even use identical, since systems typically have many different NaN values. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andrew Yee Sent: Tuesday, May 29, 2007 3:33 PM To: r-help@stat.math.ethz.ch Subject: [R] trouble understanding why ...==NaN isn't true I have the following data: dataset[2,Sample.227] [1]NaN 1558 Levels: -0.000 -0.001 -0.002 -0.003 -0.004 -0.005 -0.006 -0.007 -0.008- 0.009 ... 2.000 However, I'm not sure why this expression is coming back as FALSE: dataset[2,Sample.227]==NaN [1] FALSE Similarly: dataset[2,Sample.227]==NaN [1] NA It seems that since NaN is represented as a character, this expression ==NaN should be TRUE, but it's returning as FALSE. Thanks, Andrew [[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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble understanding why ...==NaN isn't true
Hi, Andrew, Looks like you're reading the data incorrectly. If using ?read.table or the like, try to add a na.strings = c(NA, NaN) argument. Second, Bert's comment: use ?is.nan, rather than ==. --sundar Andrew Yee said the following on 5/29/2007 3:39 PM: Okay, it turns out that there were leading spaces, so that in the data, it was represented asNaN, hence the expression ==NaN was coming back as false. Is there a way to find out preemptively if there are leading spaces? Thanks, Andrew On 5/29/07, Andrew Yee [EMAIL PROTECTED] wrote: I have the following data: dataset[2,Sample.227] [1]NaN 1558 Levels: -0.000 -0.001 -0.002 -0.003 -0.004 -0.005 -0.006 -0.007 - 0.008 -0.009 ... 2.000 However, I'm not sure why this expression is coming back as FALSE: dataset[2,Sample.227]==NaN [1] FALSE Similarly: dataset[2,Sample.227]==NaN [1] NA It seems that since NaN is represented as a character, this expression ==NaN should be TRUE, but it's returning as FALSE. Thanks, Andrew [[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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] summing up colum values for unique IDs when multiple ID's exist in data frame
try this:
x - IDval
+ 1 A 0.100
+ 2 B 0.001
+ 3 C -0.100
+ 4 A 0.200
+
x - read.table(textConnection(x), header=TRUE)
(z - tapply(x$val, x$ID, sum))
A B C
0.300 0.001 -0.100
data.frame(ID=names(z), val=z)
IDval
A A 0.300
B B 0.001
C C -0.100
On 5/29/07, Young Cho [EMAIL PROTECTED] wrote:
I have data.frame's with IDs and multiple columns. B/c some of IDs showed
up
more than once, I need sum up colum values to creat a new dataframe with
unique ids.
I hope there are some cheaper ways of doing it... Because the dataframe
is
huge, it takes almost an hour to do the task. Thanks so much in advance!
Young
# - examples are here and sum.dup.r is at the
bottom.
x = data.frame(ID = c('A','B','C','A'), val=c(0.1,0.001,-0.1,0.2))
x
IDval
1 A 0.100
2 B 0.001
3 C -0.100
4 A 0.200
sum.dup(x)
IDval
1 A 0.300
2 B 0.001
3 C -0.100
sum.dup - function( x ){
d.row = which(duplicated(x$ID))
if( length(d.row) 0){
id = x$ID[d.row]
com.val = x[-d.row,]
for(i in 1:length(id)){
s = sum(x$val[ x$ID == id[i] ])
com.val$val[ com.val$ID == id[i] ] = s
}
ix = sort(as.character(com.val[,1]),index.return=T)
return(com.val[ix$ix,])
}else{
ix = sort(as.character(x[,1]),index.return=T)
return(x[ix$ix,])
}
}
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PLEASE do read the posting guide
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] aggregation of a zoo object
Here is one way of doing it: time-c(2000-10-03 14:00:00,2000-10-03 14:10:00,2000-10-03 14:20:00, + 2000-10-03 15:30:00,2000-10-03 16:40:00,2000-10-03 16:50:00, + 2000-10-03 17:00:00,2000-10-03 17:10:00,2000-10-03 17:20:00, + 2000-10-03 18:30:00,2000-10-04 14:00:00,2000-10-04 14:10:00, + 2000-10-04 14:20:00,2000-10-04 15:30:00,2000-10-04 16:40:00, + 2000-10-04 16:50:00,2000-10-04 17:00:00,2000-10-04 18:30:00, + 2000-10-04 18:30:00,2000-10-04 18:30:00) # remark the last date is occuring 3 times precipitation-c(NA,0.1,0,0,NA,0,0.2,0.3,0.5,6,7,8,9,1,0,0,NA,0,1,0) my.df - data.frame(time=as.POSIXct(time), precip=precipitation) # get only good data my.df - my.df[complete.cases(my.df),] tapply(my.df$precip, as.POSIXct(trunc(my.df$time, 'day')), sum) 2000-10-03 2000-10-04 7.1 26.0 On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear all, I am trying to execute the following example: time-c(2000-10-03 14:00:00,2000-10-03 14:10:00,2000-10-03 14:20:00,2000-10-03 15:30:00,2000-10-03 16:40:00,2000-10-03 16:50:00,2000-10-03 17:00:00,2000-10-03 17:10:00,2000-10-03 17:20:00,2000-10-03 18:30:00,2000-10-04 14:00:00,2000-10-04 14:10:00,2000-10-04 14:20:00,2000-10-04 15:30:00,2000-10-04 16:40:00,2000-10-04 16:50:00,2000-10-04 17:00:00,2000-10-04 18:30:00,2000-10-04 18:30:00,2000-10-04 18:30:00) # remark the last date is occuring 3 times precipitation-c(NA,0.1,0,0,NA,0,0.2,0.3,0.5,6,7,8,9,1,0,0,NA,0,1,0) library(zoo) z - zoo(precipitation, as.POSIXct(time, tz = GMT)) Warning message: some methods for zoo objects do not work if the index entries in 'order.by' are not unique in: zoo(precipitation, as.POSIXct(time, tz = GMT)) # then I want to do the sum per hour z_sum_per_hour - aggregate(na.omit(z), function(x) as.POSIXct(trunc(x, hour)),sum) Warning message: some methods for zoo objects do not work if the index entries in 'order.by' are not unique in: zoo(rval[i], x.index[i]) Do anyone has an idea how to avoid that ? Thanks in advance Jessica __ 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 and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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 and provide commented, minimal, self-contained, reproducible code.
[R] control axis
I have an outlier that I would still like to display, but would prefer to shorten the axis. For example, display 0% - 40%, and 90% - 100%. Is this possible? I am using an xyplot. Thanks Murray -- Murray Pung Statistician, Datapharm Australia Pty Ltd 0404 273 283 [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with optim
Hi,
Unfortunately I don't think it is possible to do exactly what you want, but:
If the numbers reported by 'optim' to the console are enough for you, then
consider using 'capture.output'. Below I used the example from 'optim' help
page, because I could not use yours directly.
hth,
Michal
# -b-e-g-i-n---R---c-o-d-e-
# this is from the 'optim' example
fr - function(x) { ## Rosenbrock Banana function
x1 - x[1]
x2 - x[2]
100 * (x2 - x1 * x1)^2 + (1 - x1)^2
}
# and now optim-ize capturing the output to 'out' and the results to 'o'
out - capture.output(
o - optim( c(-1.2, 1), fr, method=BFGS,
control=c(REPORT=1, trace=1))
)
# 'out' is a character vector storing every line as a separate element
out
# 'o' is returned by optim
o
# to get a grip on the values you could use for example 'strsplit' and then
# extract neccessary info
optimout - function(out)
{
# split by spaces
l - strsplit(out, )
# just return the numbers
rval - sapply(l[-length(l)], function(x) x[length(x)] )
as.numeric(rval)
}
x - optimout(out)
x
plot(x)
# -e-n-d---R---c-o-d-e-
-Wiadomo¶æ oryginalna-
Od: [EMAIL PROTECTED] w imieniu Anup Nandialath
Wys³ano: Wt 2007-05-29 08:33
Do: r-help@stat.math.ethz.ch
Temat: [R] Help with optim
Dear Friends,
I'm using the optim command to maximize a likelihood function. My optim command
is as follows
estim.out - optim(beta, loglike, X=Xmain, Y=Y, hessian=T, method=BFGS,
control=c(fnscale=-1, trace=1, REPORT=1))
Setting the report=1, gives me the likelihood function value (if i'm correct)
at each step. The output from running this is as follows
initial value 3501.558347
iter 2 value 3247.277071
iter 3 value 3180.679307
iter 4 value 3157.201356
iter 5 value 3156.579887
iter 6 value 3017.715292
iter 7 value 2993.349538
iter 8 value 2987.181782
iter 9 value 2986.672719
iter 10 value 2986.658620
iter 11 value 2986.658266
iter 12 value 2986.658219
iter 13 value 2986.658156
iter 13 value 2986.658156
iter 13 value 2986.658135
final value 2986.658135
converged
I just wanted to know if there was any way I could get the value of each
iteration into an object. At present it is dumped on the screen. But is there a
way to get hold of these values through an object??
Thanks in advance
sincerely
Anup
-
The fish are biting.
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Re: [R] control axis
On 5/29/07, Murray Pung [EMAIL PROTECTED] wrote: I have an outlier that I would still like to display, but would prefer to shorten the axis. For example, display 0% - 40%, and 90% - 100%. Is this possible? I am using an xyplot. Could you give an example? If you mean xyplot from the lattice package, using a shingle can be a reasonable approach, perhaps with relation=sliced. -Deepayan __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partially reading a file (particularly)
On 5/29/07, Charles C. Berry [EMAIL PROTECTED] wrote: On Tue, 29 May 2007, Tobin, Jared wrote: Hello, I am trying to figure out if there exists some R command that allows one to be particularly selective when reading a file. I'm dealing with large fixed-width data sets that look like 539001.. 639001.. 639001.. ... 539002.. 639002.. ... Presently, I am using read.fwf to read an entire file, but I am interested only in reading those records beginning with 5. I have been unable to find help in any of the suggested resources. Assuming you have 'grep' in your path, res - read.fwf( pipe( grep '^5' my.file ) , other args ) will do it. grep will usually be found on linux/unix systems and Mac OS X. The 'Rtools' toolkit for windows has grep, I believe. On windows XP we can also use findstr which comes with Windows: res - read.fwf( pipe( findstr /b 5 my.file ) , other args ) __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] http proxies: setting and unsetting
Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] control axis
I have an example below: example - structure(list( patient = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6), group = structure(c(active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active, active,placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo, placebo), .label = c(active, placebo)), visit = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10), var = c(1, 0.8, 0.5, 0.45, 0.3, 0.34, 0.26, 0.25, 0.2, 0.19, 1, 0.6, 0.5, 0.4, 0.35, 0.3, 0.23, 0.2, 0.19, 0.1, 1, 1.2, 0.8, 0.6, 0.56, 0.45, 0.54, 0.34, 0.32, 0.2, 1, 1.2, 1.3, 1.1, 4.2, 1.3, 1.2, 0.9, 0.89, 0.88, 1, 1.3, 1.2, 1.2, 0.9, 0.87, 0.76, 0.8, 0.98, 1.2, 1, 1.2, 1.3, 1.2, 1.15, 1.2, 1.234, 1.4, 1.1, 1)), .Names = c(patient, group, visit, var), class = data.frame, row.names = c(NA, -60)) xyplot(example$var ~ example$visit | example$group, groups = example$patient, col = black, type = b, ylab = Variable, xlab = Visit, bty = n, pch = c(16,16), bty = n, las = 1, #ylim = c(0,5), scales = list( x = list(at = c(1:10), labels = c(Baseline,2,3,4,5,6,7,8,9,End of Study), rot = 40, alternating = 1)) ) On 30/05/07, Anup Nandialath [EMAIL PROTECTED] wrote: did you try the xlim and ylim options on xyplot? you can change the axis using that HTH Anup -- Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panelhttp://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+and lay it on us. -- Murray Pung Statistician, Datapharm Australia Pty Ltd 0404 273 283 [[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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] http proxies: setting and unsetting
Note that Windows XP has 4 types of environment variables and I suspect that the problem stems from not taking that into account: http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_kmmj.mspx?mfr=true On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] http proxies: setting and unsetting
Hi Gabor, Thanks for the reply and link. I took a look at the link -- one thing I don't understand is why if I delete the 'http_proxy' variable via the cmd shell (or equivalent OS dialog box), why I can get R to ignore the proxy, but using Sys.setenv(http_proxy=) won't do that for me (at least for the scope of the session). If there were other variables affecting it, I would think my deleting 'http_proxy' in the OS would also have no effect -- yet it does. Any ideas? Thanks again, Matt -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Tue 5/29/2007 9:49 PM To: Pettis, Matthew (Thomson) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] http proxies: setting and unsetting Note that Windows XP has 4 types of environment variables and I suspect that the problem stems from not taking that into account: http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_kmmj.mspx?mfr=true On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Generating Data using Formulas
Hello,
My name is Christian Falde. I am new to R.
My problem is this. I am attempting to learn R on my own. In so doing I am
using some problems from Davidson and MacKinnon Econometric Theory and Methods
to do so. This is because I can already do the some of the problems in SAS so
I am attempting to rework them using R. Seemed logical to me, now I am stuck
and its really bugging me.
The problem is this
Generate a data set sample size of 25 with the formula y=1+.8*y(t-1)+ u.
Where y is the dependent, y(t-1) is the dependent variable lagged one peroid,
and u is the classical error term. Assume y0=0 and the u is NID(0,1). Use this
sample to compute the OLS estimates B1 (1) and B2(.8). Repeat at least 100
times and find the average of the B's. Use these average to estimate the bias
of the ols estimators.
To start I did the following non lagged program.
final-function(i,j){x-function(i) {10*i}
y-function(i,j) {1+.8*10*i+100*rnorm(j)}
datathreeone- data.frame(replicate(100,coef(lm(y(i,j)~x(i)
rowMeans(datathreeone)}
final(1:25,25)
final(1:50,50)
final(1:100,100)
final(1:200,200)
final(1:1,1)
Now the only thing I need to to is change .8*10*i which is exogenous to
.8* y(t-1) .
There are two reasons why I did it this way. I needed the rnorm(i) to generate
a new set of u's each replication, and I wanted to be able to use the function
as i did to make the results more concise.
For the lag in SAS we used an if then else logic relating to the number of
observation. This in R would have to be linked to the invisable row number. I
think I need an index variable for the row. Perhaps, sorry thinking while
typing.
Another reason why I am stuck, the lag function was seemingly straight forward.
lag (x, k=1)
yet x has to be a matrix so when I tried to do it like above with y as a
function R complained.
I have been working on this for a couple of days now so everything is begining
to not make sense. It just seems to me to get the matrix to work out I would
need to have two matrices.
dependentand explanatory
y1 = sum ( 1 +.8*0 + 100*rnorm(i))
y2 = sum ( 1 +.8* (dependent row 1) + 100*rnorm(i))
etc
I just am not sure how to do that.
Please help and thank you for your time,
christian falde
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Re: [R] http proxies: setting and unsetting
You can have 4 different http_proxy environment variables and if you set one type but try to unset a different type then that will have no effect on the one you originally set. For example, if you originally set it as a system or user environment variable and then try to unset the process environment variable of the same name then that will have no effect on the system or user environment variable. On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi Gabor, Thanks for the reply and link. I took a look at the link -- one thing I don't understand is why if I delete the 'http_proxy' variable via the cmd shell (or equivalent OS dialog box), why I can get R to ignore the proxy, but using Sys.setenv(http_proxy=) won't do that for me (at least for the scope of the session). If there were other variables affecting it, I would think my deleting 'http_proxy' in the OS would also have no effect -- yet it does. Any ideas? Thanks again, Matt -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Tue 5/29/2007 9:49 PM To: Pettis, Matthew (Thomson) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] http proxies: setting and unsetting Note that Windows XP has 4 types of environment variables and I suspect that the problem stems from not taking that into account: http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_kmmj.mspx?mfr=true On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] http proxies: setting and unsetting
OK, I think I get that... do you know which namespace the Sys.setenv() function affects? Do you know if there are functions in R that can alter the user/system/process environment variables? Thanks, Matt -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Tue 5/29/2007 10:20 PM To: Pettis, Matthew (Thomson) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] http proxies: setting and unsetting You can have 4 different http_proxy environment variables and if you set one type but try to unset a different type then that will have no effect on the one you originally set. For example, if you originally set it as a system or user environment variable and then try to unset the process environment variable of the same name then that will have no effect on the system or user environment variable. On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi Gabor, Thanks for the reply and link. I took a look at the link -- one thing I don't understand is why if I delete the 'http_proxy' variable via the cmd shell (or equivalent OS dialog box), why I can get R to ignore the proxy, but using Sys.setenv(http_proxy=) won't do that for me (at least for the scope of the session). If there were other variables affecting it, I would think my deleting 'http_proxy' in the OS would also have no effect -- yet it does. Any ideas? Thanks again, Matt -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Tue 5/29/2007 9:49 PM To: Pettis, Matthew (Thomson) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] http proxies: setting and unsetting Note that Windows XP has 4 types of environment variables and I suspect that the problem stems from not taking that into account: http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_kmmj.mspx?mfr=true On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Antiguo Mueble Con Tocadiscos Y Radio!
MITTWOCH 30. MAI STARTET DIE HAUSSE! Firma: TALKTECH TELEMEDIA (OYQ.F) Kurzel: WKN: 278-104 (OYQ.F) ISIN: US8742781045 Preis: 0.81 (+50% in 1 tag) 3T Prognose: 3 Overall I believe this to be a good work and worth the money if you wish to be introduced to Windows Workflow Foundation. Singer A Pedal - Impecable ! Lote De Dos Frascos Antiguos De Vidrio. This is not your average computer text which gives a chunk of code and then explains what it does. Antiguo Tractor De Chapa . Explain that all of this material will make sense once they start to do the task on the job. Antiguo Autito De Chapa Argo ,usa Juguete, Chapa. However, this enhancement comes with a price, a steep learning curve. Instead, you can spend a few hours each week practicing skills and learning vocabulary. Even if the customer doesn't get all the people required to make the possible profit, the money will be paid out every month. There really is nothing average about this writer and book. Antiguo Juguete Elefante De Goma Piel Roce Ind. And then check out any MLM opportunitiy and see how it looks. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] http proxies: setting and unsetting
That was misleading advice. R is a C program and accesses the environment via the C calls getenv and (on Windows) putenv. This is not Windows scripting (Grothendieck's earlier reference): the C runtime maintains only one environment block. I've re-checked, and suspect the problem is in the following comment in ?download.file These environment variables must be set before the download code is first used: they cannot be altered later by calling 'Sys.setenv'. If I have http_proxy set in the environment, the proxy is not used in any of the following cases: - Calling R from a shortcut with http_proxy= on the target (see the rw-FAQ). - Calling R from a shortcut with no_proxy=* on the target. - Using Sys.unsetenv(http_proxy) right at the start of the R session. - Using Sys.setenv(no_proxy=*) right at the start of the R session. If you set options(internet.info=0) you will see exactly what is tried. Another possibility is that R is being used with --internet2, in which case none of this applies, and the simple answer is not to use --internet2 at home. On Tue, 29 May 2007, Gabor Grothendieck wrote: You can have 4 different http_proxy environment variables and if you set one type but try to unset a different type then that will have no effect on the one you originally set. For example, if you originally set it as a system or user environment variable and then try to unset the process environment variable of the same name then that will have no effect on the system or user environment variable. On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi Gabor, Thanks for the reply and link. I took a look at the link -- one thing I don't understand is why if I delete the 'http_proxy' variable via the cmd shell (or equivalent OS dialog box), why I can get R to ignore the proxy, but using Sys.setenv(http_proxy=) won't do that for me (at least for the scope of the session). If there were other variables affecting it, I would think my deleting 'http_proxy' in the OS would also have no effect -- yet it does. Any ideas? Thanks again, Matt -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Tue 5/29/2007 9:49 PM To: Pettis, Matthew (Thomson) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] http proxies: setting and unsetting Note that Windows XP has 4 types of environment variables and I suspect that the problem stems from not taking that into account: http://www.microsoft.com/technet/scriptcenter/guide/sas_wsh_kmmj.mspx?mfr=true On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am trying to use R at work and at home on the same computer. At work, I have a proxy, and at home, I do not. I have, for work, a User environment variable http_proxy which I set in the OS (Windows XP Pro). When I am at work, and I try to retrieve data from the web with 'read.csv', things work just fine. I assume it knows how to use the proxy. The trouble is when I am at home and have no proxy, R still tries to use my work proxy. I have tried the following: Sys.setenv(http_proxy=) Sys.setenv(no_proxy=TRUE) Sys.setenv(no_proxy=1) none of which seems to work. Whenever I try to use read.csv, it tells me that it cannot find my work proxy, which I am trying to tell R to ignore. I can solve this problem by removing the http_proxy environment variable binding in the OS when at home, but that is a pain, because then I have to reset it when I go back into work. Is there a way to tell R within a session to ignore the proxy? If so, what am I doing wrong? thanks, matt __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code. -- 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] http proxies: setting and unsetting
On 5/29/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: OK, I think I get that... do you know which namespace the Sys.setenv() function affects? Do you know if there are functions in R that can alter the user/system/process environment variables? Use the R Sys.getenv() command to get the process environment variables. To get user and system environment variables, from the Desktop right click on My Computer and choose Properties. Then choose the Advanced tab and click on the Environment Variables button near the bottom of the window that appears. __ 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 and provide commented, minimal, self-contained, reproducible code.
