[R] proportional curves
hie I know this might not be the right forum but can anyone tell me what parameters i can possibly use to generate proportional survival curves using rweibull(n,shape,scale). if I plot the curves and they do not cross does it neccesarily mean that they are proprotional. thanks __ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R segmented package
Dear Maura, For package-specific questions, it is probably advisable to contact privately the author.. BTW: However I cannot understand if a break-point per independent variable (regressor) is handled when there are many independent variables in the model, or if segmented can handle many breakpoints for the same independent variable (time in my case) ... ? Yes, both the statements are true. Virtually segmented is able to handle GLMs with any number of (linear) exaplanatory variables + any number of `segmented' variables, and multiple breakpoints are allowed for *each* `segmented' variable. See the relevant help files. All the best, vito PS: I am sending you some further documentation via off-list best, vito Maura E Monville ha scritto: Most of the data sets I'm dealing with exhibit a time trend. We would like to get rid of the time trend. The plot shows in some cases a monotonic increase of the dependent variable with time. This is the easiest case. In some other cases the plot shows a time trend where the dependent variable changes slope 4-5 times along the observations measurement period. I've attempted a segmented regression and estimated the break-point empirically. This is a tedious error-prone process. I just found out that R includes a package, called segmented, which can estimate the break-point discriminating between two regression models. I have browsed through the on-line documentation. It is stated multiple break-points are supported by segmented. However I cannot understand if a break-point per independent variable (regressor) is handled when there are many independent variables in the model, or if segmented can handle many breakpoints for the same independent variable (time in my case) ... ? I would greatly appreciate some explanations and suggestions on the use of segmented. Thank you very much in advance. Regards, -- Vito M.R. Muggeo Dip.to Sc Statist e Matem `Vianelli' Università di Palermo viale delle Scienze, edificio 13 90128 Palermo - ITALY tel: 091 6626240 fax: 091 485726/485612 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] miscalculate AUC
Dear R-helper,
I have subject 1, 2, 3 and formulation S, MF, MM. I
have a problem in calculating AUC. The AUC (0~t) in
formulation MF and MM were miscalculated, but I don’t
know where my problem is. Here is my code and output.
test-function( InVVTestindex,
separateWindows=TRUE)
{
for( i in 1:length(unique
(InVVTestindex$subject))){
x-InVVTestindex$time[InVVTestindex$subject==i]
y-InVVTestindex$concentration[InVVTestindex$subject==i]
v-InVVTestindex$formulation[InVVTestindex$subject==i]
w-InVVTestindex$pH[InVVTestindex$subject==i]
#calculate AUC
add-function(time,concentration){
auc-0
for(i in 2:length(time)) {
auc[i]-1/2*(time[i]-time[i-1])*(concentration[i]+concentration[i-1])
auc[i]-auc[i]+auc[i-1]
}
return(list(auc=auc))
}
add-add(x,y)
AUC-add$auc
#Output
cat( Output \n)
output-data.frame(w,i,v,x,y,AUC)
colnames(output)-list(pH,subject,formulation,time,concentration,AUC(0~t))
show(output)
cat(\n\n)
}
}
Output
pH subject formulation time concentration
AUC(0~t)
1 6.8 1 S 0.0 0.00
0.
2 6.8 1 S 0.5110.26
27.5650
3 6.8 1 S 1.0116.17
84.1725
4 6.8 1 S 1.5130.20
145.7650
5 6.8 1 S 2.0145.77
214.7575
6 6.8 1 S 3.0123.75
349.5175
7 6.8 1 S 4.0123.05
472.9175
8 6.8 1 S 5.0 82.35
575.6175
9 6.8 1 S 6.0 48.62
641.1025
10 6.8 1 S 8.0 26.51
716.2325
11 6.8 1 S 10.0 3.04
745.7825
12 6.8 1 S 12.0 2.87
751.6925
13 6.8 1 S 24.0 2.74
785.3525
14 6.8 1 MF 0.0 0.00 752.4725
15 6.8 1 MF 0.5 91.67
775.3900
16 6.8 1 MF 1.0216.78
852.5025
17 6.8 1 MF 1.5179.91
951.6750
18 6.8 1 MF 2.0187.02
1043.4075
19 6.8 1 MF 3.0176.15
1224.9925
20 6.8 1 MF 4.0171.24
1398.6875
21 6.8 1 MF 5.0157.83
1563.2225
22 6.8 1 MF 6.0149.15
1716.7125
23 6.8 1 MF 8.0142.18
2008.0425
24 6.8 1 MF 10.0107.56
2257.7825
25 6.8 1 MF 12.0 86.37
2451.7125
26 6.8 1 MF 24.0 9.30
3025.7325
27 6.8 1 MM 0.0 0.00
2914.1325
28 6.8 1 MM 0.5114.18
2942.6775
29 6.8 1 MM 1.0160.72
3011.4025
30 6.8 1 MM 1.5152.28
3089.6525
31 6.8 1 MM 2.0125.05
3158.9850
32 6.8 1 MM 3.0118.97
3280.9950
33 6.8 1 MM 4.0123.26
3402.1100
34 6.8 1 MM 5.0143.46
3535.4700
35 6.8 1 MM 6.0137.00
3675.7000
36 6.8 1 MM 8.0 91.48
3904.1800
37 6.8 1 MM 10.0 52.46
4048.1200
38 6.8 1 MM 12.0 15.39
4115.9700
39 6.8 1 MM 24.0 8.00
4256.3100
Best regards,
Hsin-Ya Lee
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Re: [R] postscript(), used from a pre R-2.6.0 workspace
I find that if start R-2.6.0 in a workspace with no .RData file, load one of my workspaces from R-2.5.1 or earlier into R-2.6.0, and then before doing anything else type postscript(file=z.ps), I get:: ls() character(0) load(url(http://www.maths.anu.edu.au/~johnm/r/test5.RData;)) postscript(file=z.ps) Error in postscript(file = z.ps) : Invalid font type In addition: Warning messages: 1: closing unused connection 3 (gzcon(http://www.maths.anu.edu.au/~johnm/r/test5.RData) ) 2: In postscript(file = z.ps) : font family not found in PostScript font database 3: In postscript(file = z.ps) : font family not found in PostScript font database Or R may be started in a workspace with such a .RData file, or with a .RData file from R-2.5.1 or earlier. This behavior persists even if I take such an image file, load it, clear the workspace, and save it. An instance of such a .RData file has the url: http://www.maths.anu.edu.au/~johnm//r/test5.RData It makes no difference whether I load the file into R-2.6.0 on a MacOS X or Windows system, or whether I use the current R-patched (2007-10-27 r43288). I do not know whether the source of the original .RData file matters, or how it may depend on what I have done in that earlier workspace. For moving my .RData files across without messing up use of postscript() [or pdf()], a workaround is to dump the contents of the earlier workspace, then start R in a working directory whose .RData file, if any, has the proper R-2.6.0 pedigree, and source the dumped file. I do not want to have to directly run the function that creates the database each time I start a session. Has anyone else hit this? John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting question: how to plot SNP location data?
Hello,
I would like to plot specific SNPs with their exact locations on a
chromosome. Based on my genotyping results I would like to separate
these SNPs in three different categories: 1, 2 and 3 and use different
colours to represent these categories. The script below generates the
sample data. I can plot these with the image function using the
following:
val - 1:3
samp - sample(val, 100, replace=TRUE)
z - matrix(samp, nrow=20, ncol=4, byrow=TRUE)
SNP - 1:20
siblings - 1:4
opar - par(cex=0.7)
image(SNP, siblings, z, col=c(blue, red, black), axes=FALSE,
ann=FALSE)
axis(1, at=1:20, labels=paste(rep(SNP, 20), 1:20), las=2)
axis(2, at=1:4)
mtext(sibling, 2, line=3)
title(main=Specific SNPs in Chr 1)
par(opar)
In addition to having the data for the above colour matrix, I also have
data including the exact locations of the SNPs on a chromosome (snploc).
I would like to plot the SPNs using the colour codes from above (z) and
include the exact locations of each SNP. Is it possible to do that using
the image-function? Below I have tried to solve the problem using the
basic plot function but I cannot include the colors to that plot. How
would that be possible?
colnames(z) - c(sib1,sib2,sib3,sib4)
rownames(z) - paste(rep(SNP, 20), 1:20)
z.t - t(z)
#snploc$location represents the location of the SNP in the chromosome
snploc - data.frame(SNP=paste(rep(SNP, 20), 1:20),
location=c(4.2,5.8,6.9,3,8,7,5,4,3.6,4.3,4.6,6.6,5.2,6,9,9.4,12,16,14,12
.3))
snploc$SNP - factor(snploc$SNP, levels=unique(snploc$SNP))
temp - as.data.frame(sapply(levels(snploc$SNP), function(x){ z.t[,x]
- snploc$location[snploc$SNP == x];
z.t[,x]
}))
temp1 - as.list(temp)
#Plot the location of the SNP
x11()
for (i in names(temp1)) {
opar - par(new=TRUE)
plot(temp1[[i]], 1:4, pch=|, ann=FALSE, col=blue,
xlim=c(0, 20), ylim=c(1,4), yaxp=c(1,4,3))
par(opar)
}
mtext(SNP location, 1, line=3)
mtext(sibling, 2, line=3)
opar - par(cex=0.7)
axis(3, at=snploc$location, labels=snploc$SNP, las=3)
par(opar)
Originally my z.t data.frame has dimensios 33*4000 so looping through
this data.frame is tedious.
Thanks,
Lauri
***
Lauri Nikkinen
Finnish Red Cross Blood Service
www.bloodservice.fi
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Re: [R] postscript(), used from a pre R-2.6.0 workspace
John Maindonald wrote: I find that if start R-2.6.0 in a workspace with no .RData file, load one of my workspaces from R-2.5.1 or earlier into R-2.6.0, and then before doing anything else type postscript(file=z.ps), I get:: ls() character(0) load(url(http://www.maths.anu.edu.au/~johnm/r/test5.RData;)) postscript(file=z.ps) Error in postscript(file = z.ps) : Invalid font type In addition: Warning messages: 1: closing unused connection 3 (gzcon(http://www.maths.anu.edu.au/~johnm/r/test5.RData) ) 2: In postscript(file = z.ps) : font family not found in PostScript font database 3: In postscript(file = z.ps) : font family not found in PostScript font database Or R may be started in a workspace with such a .RData file, or with a .RData file from R-2.5.1 or earlier. This behavior persists even if I take such an image file, load it, clear the workspace, and save it. An instance of such a .RData file has the url: http://www.maths.anu.edu.au/~johnm//r/test5.RData It makes no difference whether I load the file into R-2.6.0 on a MacOS X or Windows system, or whether I use the current R-patched (2007-10-27 r43288). I do not know whether the source of the original .RData file matters, or how it may depend on what I have done in that earlier workspace. For moving my .RData files across without messing up use of postscript() [or pdf()], a workaround is to dump the contents of the earlier workspace, then start R in a working directory whose .RData file, if any, has the proper R-2.6.0 pedigree, and source the dumped file. I do not want to have to directly run the function that creates the database each time I start a session. Has anyone else hit this? I get a slightly different scenario: R R version 2.6.0 (2007-10-03) load(url(http://www.maths.anu.edu.au/~johnm/r/test5.RData;)) postscript(file=z.ps) Error in postscript(file = z.ps) : failed to load encoding In addition: Warning message: In postscript(file = z.ps) : failed to load encoding file 'macRoman' ls(all=T) [1] .Last.projection.Last.value .PostScript.Options [4] .Provided .Random.seed.Traceback [7] .call .ess.lvsave .formula [10] .map.range .rdired.objects .required [13] .rpart.parms.2 .rpart.parms.3 .rpart.parms.4 [16] .rpart.parms.5 rm(.PostScript.Options) postscript(file=z.ps) You might try and do likewise -p -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Query installing R on Mac OS X Leopard (new release)...
MacOS X users, please note: - https://stat.ethz.ch/mailman/listinfo/r-sig-mac R Special Interest Group on Development for Mac OS X. This list might be used also for bug reports or feature requests on the R application for OS X. - which contains threads on this issue. It's the best place for help on MacOS-specific problems (although I understand many MacOS users will have no idea what other OSes do, surely the installer and GUI console are clearly MacOS-specific). On Tue, 30 Oct 2007, Rob Hodgkinson wrote: Thanks to Mark, Moshe and David for helpful responses to my query on Regression. I am now trying to install R-2.6.0.dmg on my Macbook Pro running OS X 10.5 (ie Leopard) since last weeken, so far without issue. At the prompt ³Installation Type² (after destination drive is selected) the 4 parts to be checked are all grayed out and so also is the (Install) button. I can¹t seem to continue nor work around this ? I am wondering whether this is related to Leopard (documentation says OK for Mac OS X 10.4.4 or higher). Has anyone observed/worked around this problem please, or might suggest a solution ? Sorry again if the wrong forum, I saw no R/Install query group. Thanks.../Rob [[alternative HTML version deleted]] -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] axis title on two lines
Hello,I am searching for the possibility to make a two lines axis title. This
suggestion:ylab=expression(paste(log rate\n[ fluor.,inc. %.% cell^{-1} %.%
sec^{-1}, ]))results in two lines left not centered and with a large gap.any
suggestions.ThanksMarcel
__
Marcel Sandow
Leibniz Institute of Marine Sciences - IFM-Geomar
Experimental Ecology: Foodwebs
Düsternbrooker Weg 20
24105 Kiel
Germany
Fon: +49-431-600-4404
Fax: +49-431-600-1515
Homepage: http://www.ifm-geomar.de
E-mail: [EMAIL PROTECTED]
[[alternative HTML version deleted]]
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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] postscript(), used from a pre R-2.6.0 workspace
postscript() is supposed to read and write .PostScript.Options from a private environment, so one question is how .PostScript.Options got to be in the workspace: I suspect a much older version of R put it there, not least because it would seem to be using an encoding (and case) relevant to Classic MacOS. There are a couple of 'inherits=FALSE' missing in postscript.R: one of them is stopping font initialization if .PostScript.Options exists on the search path. On Tue, 30 Oct 2007, Peter Dalgaard wrote: John Maindonald wrote: I find that if start R-2.6.0 in a workspace with no .RData file, load one of my workspaces from R-2.5.1 or earlier into R-2.6.0, and then before doing anything else type postscript(file=z.ps), I get:: ls() character(0) load(url(http://www.maths.anu.edu.au/~johnm/r/test5.RData;)) postscript(file=z.ps) Error in postscript(file = z.ps) : Invalid font type In addition: Warning messages: 1: closing unused connection 3 (gzcon(http://www.maths.anu.edu.au/~johnm/r/test5.RData) ) 2: In postscript(file = z.ps) : font family not found in PostScript font database 3: In postscript(file = z.ps) : font family not found in PostScript font database Or R may be started in a workspace with such a .RData file, or with a .RData file from R-2.5.1 or earlier. This behavior persists even if I take such an image file, load it, clear the workspace, and save it. An instance of such a .RData file has the url: http://www.maths.anu.edu.au/~johnm//r/test5.RData It makes no difference whether I load the file into R-2.6.0 on a MacOS X or Windows system, or whether I use the current R-patched (2007-10-27 r43288). I do not know whether the source of the original .RData file matters, or how it may depend on what I have done in that earlier workspace. For moving my .RData files across without messing up use of postscript() [or pdf()], a workaround is to dump the contents of the earlier workspace, then start R in a working directory whose .RData file, if any, has the proper R-2.6.0 pedigree, and source the dumped file. I do not want to have to directly run the function that creates the database each time I start a session. Has anyone else hit this? I get a slightly different scenario: R R version 2.6.0 (2007-10-03) load(url(http://www.maths.anu.edu.au/~johnm/r/test5.RData;)) postscript(file=z.ps) Error in postscript(file = z.ps) : failed to load encoding In addition: Warning message: In postscript(file = z.ps) : failed to load encoding file 'macRoman' ls(all=T) [1] .Last.projection.Last.value .PostScript.Options [4] .Provided .Random.seed.Traceback [7] .call .ess.lvsave .formula [10] .map.range .rdired.objects .required [13] .rpart.parms.2 .rpart.parms.3 .rpart.parms.4 [16] .rpart.parms.5 rm(.PostScript.Options) postscript(file=z.ps) You might try and do likewise -p -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave line length
Hello, I am trying to add R code to my dissertation and the length of a line of text that Sweave generates is longer than the right margin in my dissertation. I have found no way to tell Sweave how to set the line length. I am using an iMac with tiger ver. 10.4.10, and R: ver. 2.5.1. Here is the R code that is longer than my right margin: input to Sweave: legend(topleft,c(obs, theo,hi,lo),lty = c(1,2,3,4),col=c(1,2,6,4,0), cex=1.5,pt.cex=c(3,6), bty='o',inset=.05) output from Sweave: legend(topleft, c(obs, theo, hi, lo), lty = c(1, 2, 3, 4), col = c(1, + 2, 6, 4, 0), cex = 1.5, pt.cex = c(3, 6), bty = o, inset = 0.05) The line is about eleven (11) characters too long. Thanks, Keith Jones __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave line length
Keith Jones wrote: Hello, I am trying to add R code to my dissertation and the length of a line of text that Sweave generates is longer than the right margin in my dissertation. I have found no way to tell Sweave how to set the line length. I am using an iMac with tiger ver. 10.4.10, and R: ver. 2.5.1. Here is the R code that is longer than my right margin: input to Sweave: legend(topleft,c(obs, theo,hi,lo),lty = c(1,2,3,4),col=c(1,2,6,4,0), cex=1.5,pt.cex=c(3,6), bty='o',inset=.05) output from Sweave: legend(topleft, c(obs, theo, hi, lo), lty = c(1, 2, 3, 4), col = c(1, + 2, 6, 4, 0), cex = 1.5, pt.cex = c(3, 6), bty = o, inset = 0.05) The line is about eleven (11) characters too long. Thanks, Keith Jones I'm not sure if it affects the echoed commands too, but inserting a code chunk like options(width=60) @ (replace 60 with the width you need) controls the width of the R output. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to test combined effects?
Gang Chen gangchen at mail.nih.gov writes: Suppose I have a mixed-effects model where yij is the jth sample for the ith subject: yij= beta0 + beta1(age) + beta2(age^2) + beta3(age^3) + beta4(IQ) + beta5(IQ^2) + beta6(age*IQ) + beta7(age^2*IQ) + beta8(age^3 *IQ) +random intercepti + eij In R how can I get an F test against the null hypothesis of beta6=beta7=beta8=0? In SAS I can run something like contrast age*IQ 1, age^2*IQ 1, age^3 *IQ 1, but is there anything similar in R? Check packages multcomp and gmodels for contrast tests that work with lme. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave line length
On 10/30/2007 8:55 AM, Kevin E. Thorpe wrote: Keith Jones wrote: Hello, I am trying to add R code to my dissertation and the length of a line of text that Sweave generates is longer than the right margin in my dissertation. I have found no way to tell Sweave how to set the line length. I am using an iMac with tiger ver. 10.4.10, and R: ver. 2.5.1. Here is the R code that is longer than my right margin: input to Sweave: legend(topleft,c(obs, theo,hi,lo),lty = c(1,2,3,4),col=c(1,2,6,4,0), cex=1.5,pt.cex=c(3,6), bty='o',inset=.05) output from Sweave: legend(topleft, c(obs, theo, hi, lo), lty = c(1, 2, 3, 4), col = c(1, + 2, 6, 4, 0), cex = 1.5, pt.cex = c(3, 6), bty = o, inset = 0.05) The line is about eleven (11) characters too long. Thanks, Keith Jones I'm not sure if it affects the echoed commands too, but inserting a code chunk like options(width=60) @ (replace 60 with the width you need) controls the width of the R output. You can also set keep.source=TRUE as an Sweave option, in which case the formatting of R code will match what you have in your source file. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Some matrix and sandwich questions
Dear R-help, I have a four-part question about regression, matrices, and sandwich package. 1) In the sandwich package, I would like to better understand the meat() function. From the bread() documentation, for a simple OLS regression, bread() returns (1/n * X'X)^(-1) That is, for a simple regression (per the documentation on bread()): MyLM - lm(y ~ x) bread(MyLM) solve(crossprod(cbind(1, x))) * length(y) (The last two terms above produce the same output, the matrix described above.) In terms of the basic data matrix and coefficients, what does meat() return for a simple OLS regression? (I don't know the term empirical estimating functions from the documentation of meat(). Is this the score vector set equal to zero?) 2) Is there an easy way to convert the right-hand side of a formula into a matrix, lm( y ~ x + factor(i) ) Is there an easy way to get a matrix like this: X = cbind(vector of 1's, x, matrix of 1's and 0's for the dummy variables based on i) Obviously one could construct this by hand, but it seems as if the X used for the last regression would be useful. 3) Is there an easy way, e.g., based on crossprod(), to compute a weighted cross-product of a matrix with itself or of two matrices: X'WX X'WY where W is a diagonal weighting matrix? (This would be similar to the matrix accum commands in Stata if that gives any useful guidance regarding the desired product.) 4) Is there a straightforward way to implement the computation of the variance covariance matrix for two-step estimation per Murphy and Topel (1985)? That aim is the underlying reason for questions (1)-(3). Thank you very much for your consideration. Best, Michael -- Michael Ash, Associate Professor of Economics and Public Policy Department of Economics and CPPA University of Massachusetts Amherst, MA 01003 Tel +1-413-545-6329 Fax +1-413-545-2921 Email [EMAIL PROTECTED] http://people.umass.edu/maash __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Some matrix and sandwich questions
Dear R-help, I have a four-part question about regression, matrices, and sandwich package. 1) In the sandwich package, I would like to better understand the meat() function. From the bread() documentation, for a simple OLS regression, bread() returns (1/n * X'X)^(-1) That is, for a simple regression (per the documentation on bread()): MyLM - lm(y ~ x) bread(MyLM) solve(crossprod(cbind(1, x))) * length(y) (The last two terms above produce the same output, the matrix described above.) In terms of the basic data matrix and coefficients, what does meat() return for a simple OLS regression? (I don't know the term empirical estimating functions from the documentation of meat(). Is this the score vector set equal to zero?) 2) Is there an easy way to convert the right-hand side of a formula into the X matrix used for the regresssion: lm( y ~ x + factor(i) ) Is there an easy way to get a matrix like this: X = cbind(vector of 1's, x, matrix of 1's and 0's for the dummy variables based on i) Obviously one could construct this by hand, but it seems as if the X used for the regression would be useful. 3) Is there an easy way, e.g., based on crossprod(), to compute a weighted cross-product of a matrix with itself or of two matrices: X'WX X'WY where W is a diagonal weighting matrix? (This would be similar to the matrix accum commands in Stata if that gives any useful guidance regarding the desired entity.) 4) Is there a straightforward way to implement the computation of the variance covariance matrix for two-step estimation per Murphy and Topel (1985)? That aim is the underlying reason for questions (1)-(3). Thank you very much for your consideration. Best, Michael -- Michael Ash, Associate Professor of Economics and Public Policy Department of Economics and CPPA University of Massachusetts Amherst, MA 01003 Tel +1-413-545-6329 Fax +1-413-545-2921 Email [EMAIL PROTECTED] http://people.umass.edu/maash __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave line length
Kevin, Your suggestion got me on the right track. The R command: option(width=50), sets the text width for R to 50 columns per line. When Sweave is run it breaks lines into 50 columns per line. The only exception to this is when there is a command like setwd(/Users/keithjones/Documents/DataFiles/TexasTechhd/Dissertation II/MathematicaFiles/PointPatternAnalysis/) it keeps the line in one piece. It will not break a line in between the quotes in a line. I will have to do that myself. 95% of the lines coded is a lot better then none. Thanks, Keith Jones Keith Jones wrote: Hello, I am trying to add R code to my dissertation and the length of a line of text that Sweave generates is longer than the right margin in my dissertation. I have found no way to tell Sweave how to set the line length. I am using an iMac with tiger ver. 10.4.10, and R: ver. 2.5.1. Here is the R code that is longer than my right margin: input to Sweave: legend(topleft,c(obs, theo,hi,lo),lty = c(1,2,3,4),col=c(1,2,6,4,0), cex=1.5,pt.cex=c(3,6), bty='o',inset=.05) output from Sweave: legend(topleft, c(obs, theo, hi, lo), lty = c(1, 2, 3, 4), col = c(1, + 2, 6, 4, 0), cex = 1.5, pt.cex = c(3, 6), bty = o, inset = 0.05) The line is about eleven (11) characters too long. Thanks, Keith Jones I'm not sure if it affects the echoed commands too, but inserting a code chunk like options(width=60) @ (replace 60 with the width you need) controls the width of the R output. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] axis title on two lines
You might want to replace the xlab with mtext?
aa - 1:10
plot(aa, xlab='')
mtext(label one \n label number two , side=1,
line=3)
--- Marcel Sandow [EMAIL PROTECTED] wrote:
Hello,I am searching for the possibility to make a
two lines axis title. This
suggestion:ylab=expression(paste(log rate\n[
fluor.,inc. %.% cell^{-1} %.% sec^{-1},
]))results in two lines left not centered and with
a large gap.any suggestions.ThanksMarcel
__
Marcel Sandow
Leibniz Institute of Marine Sciences - IFM-Geomar
Experimental Ecology: Foodwebs
Düsternbrooker Weg 20
24105 Kiel
Germany
Fon: +49-431-600-4404
Fax: +49-431-600-1515
Homepage: http://www.ifm-geomar.de
E-mail: [EMAIL PROTECTED]
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Re: [R] axis title on two lines
Thanksmtext is exactly what I am looking for. Using \n inside gave the same
results as before. But using two independent mtext code lines with defferent
line settings worked perfectly.- Ursprüngliche Nachricht -Von: John
Kane Datum: Dienstag, Oktober 30, 2007 2:56 pmBetreff: Re: [R] axis title on
two linesAn: Marcel Sandow , [EMAIL PROTECTED] You might want to replace the
xlab with mtext? aa - 1:10 plot(aa, xlab='') mtext(label one \n label
number two , side=1, line=3) --- Marcel Sandow wrote: Hello,I am
searching for the possibility to make a two lines axis title. This
suggestion:ylab=expression(paste(log rate\n[ fluor.,inc. %.% cell^{-1} %.%
sec^{-1}, ]))results in two lines left not centered and with a large
gap.any suggestions.ThanksMarcel
__
Marcel SandowLeibniz Institute of Marine Sciences - IFM-Geomar
Experimental Ecology: Foodwebs Düsternbrooker Weg 20 24105 Kiel
GermanyFon: +49-431-600-4404 Fax: +49-431-600-1515Homepage:
http://www.ifm-geomar.de E-mail: [EMAIL PROTECTED]
[[alternative HTML version deleted]]
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__
Marcel Sandow
Leibniz Institute of Marine Sciences - IFM-Geomar
Experimental Ecology: Foodwebs
Düsternbrooker Weg 20
24105 Kiel
Germany
Fon: +49-431-600-4404
Fax: +49-431-600-1515
Homepage: http://www.ifm-geomar.de
E-mail: [EMAIL PROTECTED]
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[R] How to switch off accepting the shortcut of column names
Dear R-users, currently I am working with the R version 2.4.1. I realized it has a feature, which might be wonderful (as so many things in R), but in this case might be a bit dangerous as well. It seems that columns of a data frame can be called just by indicating the first letter of the name of the column. For example: first_item - seq(1,10) second_item - seq(11,20) dat - data.frame(first_item, second_item) names(dat) # [1] first_item second_item dat$f # [1] 1 2 3 4 5 6 7 8 9 10 dat$s # [1] 11 12 13 14 15 16 17 18 19 20 The good thing is, that if there is more than one column starting with the same letter(s), more than one letter has to be given to call the column. However, I would appreciate if I could choose an option in my workspace, whether this type of shortcut is allowed or not. Is there such an option? Thanks for any potential hints. Best wishes, P. Olsson [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting a string
Thanks a lot for all who've provided help!
Yes the accusation of obfuscation is well-justified. Sorry I was not
specific enough in the original post. But I'm lost at this point.
What I want to do is this:
contrast(ModelFit, list(Trust=T, Sex=levels(Model$Sex),
Freq=levels(Model$Freq)), list(Trust=U, Sex=levels(Model$Sex),
Freq=levels(Model$Freq)), type=average)
However the 2nd and 3rd arguments (the two list's) are pre-defined as
one string of characters contr
contr
[1] list(Trust=\T\,Sex=levels(Model$Sex),Freq=levels(Model
$Freq)),list(Trust=\U\,Sex=levels(Model$Sex),Freq=levels(Model$Freq))
If I define
args - strsplit(contr, 'list')
args
[[1]]
[1]
[2] (Trust=\T\,Sex=levels(Model$Sex),Freq=levels(Model$Freq)),
[3] (Trust=\U\,Sex=levels(Model$Sex),Freq=levels(Model$Freq))
The following still doesn't work as Bert Gunter has pointed out:
contrast(fit.lme, eval(parse(text=args[[1]][2])), eval(parse
(text=args[[1]][3])), type=average)
Error in parse(text = args[[1]][2]) : unexpected ',' in (Trust=T,
I also tried to use parse and eval for one inner layer further, but
it didn't work either. So any better approach to dealing with the pre-
defined string? Or giving up pre-defining the string?
Thanks,
Gang
On Oct 29, 2007, at 6:31 PM, Bert Gunter wrote:
...
Of course if arg1 and arg2 are expressions (as characters strings)
that
themselves contain commas, then this won't work. So the poster
does, indeed,
seem to have achieved near obfuscation optimality.
Of course this is yet another case where Lumley's principle (at
least I
think it's his) holds: if you have to use eval(parse(...)) rethink --
there's a better way.
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On
Behalf Of Tim Calkins
Sent: Monday, October 29, 2007 3:16 PM
To: Gang Chen
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Converting a string
Hi -
you can split the string using strsplit().
if your function uses Argument1 as a string, then you're all set. If
that's not the case then you can get() the object.
myfunc - function(arg1, arg2) {
+ arg1 - get(arg1)
+ arg2 - get(arg2)
...
}
args - argument1,argument2 # easier with no after the ,
myfunc(strsplit(args)[[1]][1],strsplit(args)[[1]][2])
This seems needlessly complicated: if obfuscation is your goal, you're
well on your way to success. Of course, that may be a feature of my
solution -- obfuscation is often MY goal.
HTH.
tim
On 10/30/07, Gang Chen [EMAIL PROTECTED] wrote:
Thanks for the help.
One case is like this: With function MyFunc(Argument1,
Argument2, ...) I have the first two arguments defined as one
variable tempstr, a string of characters, like
tempstr - Argument1, Argument2
The question is how I can feed tempstr into MyFunc to make it
executable?
Gang
On Oct 29, 2007, at 5:42 PM, jim holtman wrote:
Can you provide an example of your input and what you expect the
output to be. You can always use 'as.numeric'.
On 10/29/07, Gang Chen [EMAIL PROTECTED] wrote:
This must be very simple, but I'm stuck. I have a command line in R
defined as a variable of a string of characters. How can I convert
the variable so that I can execute it in R?
Really appreciate any help,
Gang
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--
Tim Calkins
0406 753 997
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[R] data format
Hi, How can I analyze the data collected in database formatting (with labels) rather than splitted by individual columns (almost in excel)? For example (comma separated data); Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 etc... ks.test or chisq.test can be done. Splitting the data into new columns is not applicable cos' I'll use R-integration in another software. Thanks for your concern Emre -- --- Emre ÜNAL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bitmap patterns in R fill
Is there a way in R to specify a bitmap pattern and have it fill a region or polygon? This feature is available in many MAC programs and Adobe illustrator, and I know how to do this programming in postscript, But I can't find anything in the documentation relating how to do this in R. Thanks, Jonathan Lees __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] proportional curves
On Tue, 30 Oct 2007, raymond chiruka wrote: hie I know this might not be the right forum but can anyone tell me what parameters i can possibly use to generate proportional survival curves using rweibull(n,shape,scale). For the Weibull family, curves with different scale and the same shape have proportional hazards if I plot the curves and they do not cross does it neccesarily mean that they are proprotional. No. -thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] flexible processing
Hello, unfortunately, I don't know a better subject. I would like to be very flexible in how to process my data. Assume the following dataset: par1 - seq(0,1,length.out = 100) par2 - seq(1,100) fac1 - factor(rep(c(group1, group2), each = 50)) fac2 - factor(rep(c(group3, group4, group5, group6), each = 25)) df - data.frame(par1, par2, fac1, fac2) Now, I would like to calculate e.g. the sum for par1 grouping by fac1 and the mean and sd for par2 grouping by fac1. I would like to determine this method as a string. In the end, I would like to have something like this: fac1.analysis: par1.sumpar2.mean par2.sd group1xxx xxx xxx group2xxx xxx xxx fac2.analysis: ... Does anybody have any idea how to realize it? Antje __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Polygon shading line colors
Hi there, I'm having trouble working out how to change the colors of polygon shading lines. If I plot a polygon with polygon(poly,density=30,borders=gray(0.5)) I get gray borders but black shading lines; I have tried adding col=gray(0.5), bg=gray(0.5) and fg=gray(0.5), but no luck. How can I change the colors of the shading? The help file doesn't seem to detail this, so any suggestions would be greatly appreciated. Many thanks Luke Spadavecchia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Polygon shading line colors
On Tue, 30 Oct 2007, Luke Spadavecchia wrote: Hi there, I'm having trouble working out how to change the colors of polygon shading lines. If I plot a polygon with polygon(poly,density=30,borders=gray(0.5)) I get gray borders but black shading lines; I have tried adding col=gray(0.5), bg=gray(0.5) and fg=gray(0.5), but no luck. Really? col should work, and does for me. What will not work is 'borders' : it is 'border'. A working example based on the help page is plot(c(1,9), 1:2, type=n) polygon(1:9, c(2,1,2,1,NA,2,1,2,1), density=5, col=blue, border=gray(0.5)) How can I change the colors of the shading? The help file doesn't seem to detail this, so any suggestions would be greatly appreciated. Many thanks Luke Spadavecchia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. As it says, working code is expected. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Where can I find package segmented ?
I tried to install segmented from three different repositories but I keep getting the following message on R window: ... Please, advice where to find this package. Thank you in advance. Maura utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: package 'segmented' is in use and will not be installed utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed setRepositories() utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type = type) : no packages were specified chooseCRANmirror() utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Some matrix and sandwich questions
Dear Michael, as to questions 1) and 2): The following article by A. Zeileis provides more details on the package 'sandwich': http://www.jstatsoft.org/v16/i09/ (see also the references). Use 'model.matrix' to construct a design matrix: x - runif(10,0,10) model.matrix(~x) Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to switch off accepting the shortcut of column names
If you had updated your R before posting (as the posting guide suggested) you would have found such an option under ?options. It was new in R 2.6.0. On Tue, 30 Oct 2007, P. Olsson wrote: Dear R-users, currently I am working with the R version 2.4.1. I realized it has a feature, which might be wonderful (as so many things in R), but in this case might be a bit dangerous as well. It seems that columns of a data frame can be called just by indicating the first letter of the name of the column. Well, this applies to lists not just data frame, and to partial matching not just the first letter. If you want only exact matches I suggest you use other operators, e.g. dat[[f]] will warn in 2.6.x and fail in R-devel. For example: first_item - seq(1,10) second_item - seq(11,20) dat - data.frame(first_item, second_item) names(dat) # [1] first_item second_item dat$f # [1] 1 2 3 4 5 6 7 8 9 10 dat$s # [1] 11 12 13 14 15 16 17 18 19 20 The good thing is, that if there is more than one column starting with the same letter(s), more than one letter has to be given to call the column. However, I would appreciate if I could choose an option in my workspace, whether this type of shortcut is allowed or not. Is there such an option? Thanks for any potential hints. Best wishes, P. Olsson [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Please do. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Where can I find package segmented ?
This is an FAQ: rw-FAQ 4.8. On Tue, 30 Oct 2007, Maura E Monville wrote: I tried to install segmented from three different repositories but I keep getting the following message on R window: ... Please, advice where to find this package. Thank you in advance. Maura utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: package 'segmented' is in use and will not be installed utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed setRepositories() utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type = type) : no packages were specified chooseCRANmirror() utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] flexible processing
Hi,
No is the more elegant way
analysis -
lapply(c(fac1, fac2), function(x){
cbind.data.frame(par1.sum= do.call(rbind,lapply(lapply(split(df,
eval(parse(text=x))), [[, 1), sum)),
par2.mean=do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))),
[[, 2), mean)),
par2.sd= do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))), [[,
2), mean)))
})
On 30/10/2007, Antje [EMAIL PROTECTED] wrote:
Hello,
unfortunately, I don't know a better subject. I would like to be very
flexible
in how to process my data.
Assume the following dataset:
par1 - seq(0,1,length.out = 100)
par2 - seq(1,100)
fac1 - factor(rep(c(group1, group2), each = 50))
fac2 - factor(rep(c(group3, group4, group5, group6), each = 25))
df - data.frame(par1, par2, fac1, fac2)
Now, I would like to calculate e.g. the sum for par1 grouping by fac1
and
the mean and sd for par2 grouping by fac1.
I would like to determine this method as a string.
In the end, I would like to have something like this:
fac1.analysis:
par1.sumpar2.mean par2.sd
group1xxx xxx xxx
group2xxx xxx xxx
fac2.analysis:
...
Does anybody have any idea how to realize it?
Antje
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--
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Re: [R] flexible processing
analysis -
lapply(c(fac1, fac2), function(x){
cbind.data.frame(par1.sum= do.call(rbind,lapply(lapply(split(df,
eval(parse(text=x))), [[, 1), sum)),
par2.mean=do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))),
[[, 2), mean)),
par2.sd= do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))), [[,
2), sd)))
})
On 30/10/2007, Henrique Dallazuanna [EMAIL PROTECTED] wrote:
Hi,
No is the more elegant way
analysis -
lapply(c(fac1, fac2), function(x){
cbind.data.frame(par1.sum= do.call(rbind,lapply(lapply(split(df,
eval(parse(text=x))), [[, 1), sum)),
par2.mean=do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))),
[[, 2), mean)),
par2.sd= do.call(rbind,lapply(lapply(split(df, eval(parse(text=x))),
[[, 2), mean)))
})
On 30/10/2007, Antje [EMAIL PROTECTED] wrote:
Hello,
unfortunately, I don't know a better subject. I would like to be very
flexible
in how to process my data.
Assume the following dataset:
par1 - seq(0,1,length.out = 100)
par2 - seq(1,100)
fac1 - factor(rep(c(group1, group2), each = 50))
fac2 - factor(rep(c(group3, group4, group5, group6), each =
25))
df - data.frame(par1, par2, fac1, fac2)
Now, I would like to calculate e.g. the sum for par1 grouping by
fac1 and
the mean and sd for par2 grouping by fac1.
I would like to determine this method as a string.
In the end, I would like to have something like this:
fac1.analysis:
par1.sumpar2.mean par2.sd
group1xxx xxx xxx
group2xxx xxx xxx
fac2.analysis:
...
Does anybody have any idea how to realize it?
Antje
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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[R] calculate spatial distance
Hi, I have a set of locations defined by longitude and latitude (in degrees), and want to calculate the spatial (or geographic) distance among all locations. I did not find such a function in the spatial-related packages. (I *cannot* use 'dist', as I have geographic, not cartesian coordinates). thanks! Robert Robert Ptacnik Norwegian Institute for Water Research (NIVA) Gaustadalléen 21 NO-0349 Oslo mobile +47 982 277 81 FON NIVA +47 22 18 51 00 FAX +47 22 18 52 00 -- NIVAs hovedkontor har flyttet til nye lokaler i CIENS - Forskningssenter for miljø og samfunn; Gaustadalléen 21, 0349 Oslo. Meld deg på vårt nyhetsbrev på www.niva.no __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] time difference error
Hello! I posted this question earlier but it seems that something went wrong, so I post it again. I have a problem making a new variabel in a dataframe that consists of a time difference. It seems that the new variable gets into the dataframe but I cant look at it anymoore. Here is what happens. tdiff- difftime(Kontrolltid, Starttid, units=auto) tdiff Time differences in mins [1] 168 NA NA 165 175 140 191 195 130 160 135 165 330 178 141 NA 119 90 70 [20] 99 115 70 65 90 90 65 90 75 85 93 52 75 60 90 105 70 65 60 [39] 85 110 65 60 98 62 71 61 41 80 67 83 72 73 attr(,tzone)[1] givnona- data.frame(givnona, tdiff) names(givnona) [1] Vanna Datum StarttidKontrolltid Zo.Höger [6] Zo.Vänster Mm.HögerMm.Vänster tot.zo tot.mm [11] tdiff fix(givnona) Error in edit.data.frame(get(subx, envir = parent), title = subx, ...) : can only handle vector and factor elements tdiff -structure(c(168, NA, NA, 165, 175, 140, 191, 195, 130, 160, 135, 165, 330, 178, 141, NA, 119, 90, 70, 99, 115, 70, 65, 90, 90, 65, 90, 75, 85, 93, 52, 75, 60, 90, 105, 70, 65, 60, 85, 110, 65, 60, 98, 62, 71, 61, 41, 80, 67, 83, 72, 73), tzone = , units = mins, class = difftime) Any solution?cheers/Jojje _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] flexible processing
Check out summaryBy in the doBy package: library(doBy) summaryBy(. ~ fac1, data = df, FUN = c(sum, mean, sd))[c(1,2,5,7)] fac1 par1.sum par2.mean par2.sd 1 group1 12.37374 25.5 14.57738 2 group2 37.62626 75.5 14.57738 summaryBy(. ~ fac2, data = df, FUN = c(sum, mean, sd))[c(1,2,5,7)] fac2 par1.sum par2.mean par2.sd 1 group3 3.03030313 7.3598 2 group4 9.34343438 7.3598 3 group5 15.65656663 7.3598 4 group6 21.96969788 7.3598 If you don't mind a few extra columns you can omit the [c(...)] part. On Oct 30, 2007 10:18 AM, Antje [EMAIL PROTECTED] wrote: Hello, unfortunately, I don't know a better subject. I would like to be very flexible in how to process my data. Assume the following dataset: par1 - seq(0,1,length.out = 100) par2 - seq(1,100) fac1 - factor(rep(c(group1, group2), each = 50)) fac2 - factor(rep(c(group3, group4, group5, group6), each = 25)) df - data.frame(par1, par2, fac1, fac2) Now, I would like to calculate e.g. the sum for par1 grouping by fac1 and the mean and sd for par2 grouping by fac1. I would like to determine this method as a string. In the end, I would like to have something like this: fac1.analysis: par1.sumpar2.mean par2.sd group1xxx xxx xxx group2xxx xxx xxx fac2.analysis: ... Does anybody have any idea how to realize it? Antje __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] kernlab/ ksvm: class.weights prob.model in binary classification
Hello list, I am faced with a two-class classification problem with highly asymetric class sizes (class one: 99%, class two: 1%). I'd like to obtain a class probability model, also introducing available information on the class prior. Calling kernlab/ksvm with the line ksvm_model1-ksvm(as.matrix(slides), as.factor(Class), class.weights= c(0 =99, 1 =1), prob.model=T) or ksvm_model1-ksvm(as.matrix(slides), as.factor(Class), class.weights=wts, prob.model=T) with the named vector wts 0 1 99 1 I get the following output: Using automatic sigma estimation (sigest) for RBF or laplace kernel Error in inherits(x, factor) : only 0's may be mixed with negative subscripts In addition: Warning message: Variable(s) `' constant. Cannot scale data. in: .local(x, ...) My data is a balanced set of 2500 examples, most of the 65 features are binary with some real numbers in between. I am using kernlab in version 0.9-5. Best regards, Dominik Gallus -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Some matrix and sandwich questions
On 10/30/07, Christian Ritz [EMAIL PROTECTED] wrote: Use 'model.matrix' to construct a design matrix: x - runif(10,0,10) model.matrix(~x) Thanks! That's super helpful. The following article by A. Zeileis provides more details on the package 'sandwich': http://www.jstatsoft.org/v16/i09/ (see also the references). This is also very helpful, although I still have questions about terminology (because I am unfamiliar with the phrase empirical estimating function). Is the term empirical estimating function equivalent to the expectation of the score set equal to zero where score is the vector of first derivatives of the (log) likelihood function? I think that the paper is written at a higher level of abstraction about estimators than I am used to. I'd be grateful if someone could briefly help me understand the Zeileis paper using either MLE, or even OLS, *examples*. Thanks very much. Best, Michael -- Michael Ash, Associate Professor of Economics and Public Policy Department of Economics and CPPA University of Massachusetts Amherst, MA 01003 Tel +1-413-545-6329 Fax +1-413-545-2921 Email [EMAIL PROTECTED] http://people.umass.edu/maash __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Splitting up the micEcon package?
Dear R Users: The functions of our micEcon package [1,2] can be subdivided into three categories: - microeconomic demand and firm models - sample selection models (mainly selection()) - routines for (likelihood) maximisation (e.g. maxLik(), maxNR(), maxBHHH()) (mainly used for ML estimation of sample selection models) Although sample selection models are often used in microeconomic analyses, they are also used in several other disciplines. Therefore, we are unsure whether it is better to keep these different functionalities in the micEcon package or to move the sample selection models and the routines for (likelihood) maximisation into one or two new package(s) (increasing the long list of R packages even further). What is the recommendation of the R community? Thank you, Ott Arne Note: We have asked this question already on R-devel five days ago [3], but we did not receive an answer yet. References: [1] http://cran.r-project.org/src/contrib/Descriptions/micEcon.html [2] http://www.micecon.org/ [3] http://tolstoy.newcastle.edu.au/R/e3/devel/07/10/0222.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ pgpzNvMq9FrkT.pgp Description: PGP signature __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to switch off accepting the shortcut of column names
You cannot call a column on a dataframe using the first letter (or first few letters) if the letters match more than one name. Extraction methods for data frames allow partially matching row names, but if the result is undefined you get NULL in return. Try this. first_item - seq(1,10) second_item - seq(11,20) dat - data.frame(first_item, second_item) dat$s [1] 11 12 13 14 15 16 17 18 19 20 #Now add an extra column with matching name ssecond_item - seq(21,30) dat - data.frame(dat,ssecond_item) dat$s NULL Julian P. Olsson wrote: Dear R-users, currently I am working with the R version 2.4.1. I realized it has a feature, which might be wonderful (as so many things in R), but in this case might be a bit dangerous as well. It seems that columns of a data frame can be called just by indicating the first letter of the name of the column. For example: first_item - seq(1,10) second_item - seq(11,20) dat - data.frame(first_item, second_item) names(dat) # [1] first_item second_item dat$f # [1] 1 2 3 4 5 6 7 8 9 10 dat$s # [1] 11 12 13 14 15 16 17 18 19 20 The good thing is, that if there is more than one column starting with the same letter(s), more than one letter has to be given to call the column. However, I would appreciate if I could choose an option in my workspace, whether this type of shortcut is allowed or not. Is there such an option? Thanks for any potential hints. Best wishes, P. Olsson [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data format
Here is how to read it in. Then you can run your analysis: x - read.csv(textConnection(Label,Value + Good,10 + Bad,12 + Good,15 + Good,18 + Good,12 + Bad,15 + Bad,10)) x Label Value 1 Good10 2 Bad12 3 Good15 4 Good18 5 Good12 6 Bad15 7 Bad10 On 10/30/07, Emre Unal [EMAIL PROTECTED] wrote: Hi, How can I analyze the data collected in database formatting (with labels) rather than splitted by individual columns (almost in excel)? For example (comma separated data); Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 etc... ks.test or chisq.test can be done. Splitting the data into new columns is not applicable cos' I'll use R-integration in another software. Thanks for your concern Emre -- --- Emre ÜNAL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Where can I find package segmented ?
I think you already have it installed and loaded. Try search() and see if it appears. --- Maura E Monville [EMAIL PROTECTED] wrote: I tried to install segmented from three different repositories but I keep getting the following message on R window: ... Please, advice where to find this package. Thank you in advance. Maura utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: package 'segmented' is in use and will not be installed utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed setRepositories() utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type = type) : no packages were specified chooseCRANmirror() utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] force interactive
I'd like to invoke R using a fifo for input. The following unix commands gets me almost completely there: mkfifo R.fifo R --no-save R.fifo R.out in a separate window, I would enter the command eg printf capabilities() R.fifo the expected output goes into R.out; but the process stops. How to I make R persist so I can send multiple commands to the fifo? Also, would this be possible in windows? // George -- George Georgalis, information system scientist IXOYE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Some matrix and sandwich questions
Hi again, in the MLE setting the score function (no expectation taken) is the estimating function. So for the OLS situation the basic estimating function is: (in the terminology of Zeileis' paper) psi(x,y,beta) = (y - x^t beta) x^t Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Some matrix and sandwich questions
On Tue, 30 Oct 2007, Michael Ash wrote: On 10/30/07, Christian Ritz [EMAIL PROTECTED] wrote: in the MLE setting the score function (no expectation taken) is the estimating function. So for the OLS situation the basic estimating function is: (in the terminology of Zeileis' paper) psi(x,y,beta) = (y - x^t beta) x^t Thanks! That was extremely helpful---maybe it could even be added to the documentation of estfun() and meat() Sorry for coming so late to the thread (and thanks to Christian for pointing out how sandwich works :-)). The estimating function is the derivative of the objective function wrt to the parameter vector. The empirical estimating function is the estimating function evaluated at the observed data and the estimated parameters. This is explained in Section 4.2 of the JSS 16(9) paper which is contained in the package as vignette(sandwich-OOP, package = sandwich) But I'll follow your suggestion and add a bit more detail to the man page as well. (Having the OLS example in the bread() documentation made it much easier for me to understand the broader concept.) There is the analogous example in the examples section of the estfun() documentation. If you want to see more details about the OLS case, have a look at http://www.jstatsoft.org/v11/i10/ which is also contained in the package as vignette(sandwich, package = sandwich) Best, Z __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strwidth of bold font
Perhaps: strwidth(expression(bold(text))) On 30/10/2007, Roland Kaiser [EMAIL PROTECTED] wrote: Hi! Is there a way to get the string width of the bold typefaces? like: strwidth(text, family = serif, font = 2). Thanks Roland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting up the micEcon package?
Dear Arne and Ott-Simm It always seemed weird to me mixing demand and firm models with SSel. models on a single package. Separating them would seem the logical thing to do. On the other hand, one more R package :/ , I´m not too big of a fan of increasing this list ad infinitum. My take on this is that it would be worth it to split it if you think you´ll keep expanding the SSel. models under the new package. Otherwise keep it the way it is. I still dream of contributing a package that offers a group of SSel. models under a wide variety of settings, but still haven´t found the time to do so, nor it seems i´ll have it in the near future. On the other hand, judging by the low number of replies it seems to me that the audiece for SSel. in R is still quite limited. My two cents, greetings robert On 10/30/07, Arne Henningsen [EMAIL PROTECTED] wrote: Dear R Users: The functions of our micEcon package [1,2] can be subdivided into three categories: - microeconomic demand and firm models - sample selection models (mainly selection()) - routines for (likelihood) maximisation (e.g. maxLik(), maxNR(), maxBHHH()) (mainly used for ML estimation of sample selection models) Although sample selection models are often used in microeconomic analyses, they are also used in several other disciplines. Therefore, we are unsure whether it is better to keep these different functionalities in the micEcon package or to move the sample selection models and the routines for (likelihood) maximisation into one or two new package(s) (increasing the long list of R packages even further). What is the recommendation of the R community? Thank you, Ott Arne Note: We have asked this question already on R-devel five days ago [3], but we did not receive an answer yet. References: [1] http://cran.r-project.org/src/contrib/Descriptions/micEcon.html [2] http://www.micecon.org/ [3] http://tolstoy.newcastle.edu.au/R/e3/devel/07/10/0222.html -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data format
There are many ways. A simple one is to use split() to divide your
'Value' column using your 'Label' column as index. For example,
# Create dataset
mydata=data.frame(Label=c('Good','Bad','Good','Good','Good','Bad','Bad'),
Value=c(10,12,15,18,12,15,10))
# Split the data
mydata=split(mydata$Value,mydata$Label)
# Do a ks test
ks.test(mydata[[1]],mydata[[2]])
Julian
Emre Unal wrote:
Hi,
How can I analyze the data collected in database formatting (with labels)
rather than splitted by individual columns (almost in excel)?
For example (comma separated data);
Label,Value
Good,10
Bad,12
Good,15
Good,18
Good,12
Bad,15
Bad,10
etc...
ks.test or chisq.test can be done.
Splitting the data into new columns is not applicable cos' I'll use
R-integration in another software.
Thanks for your concern
Emre
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Re: [R] strwidth of bold font
Thanks it does the trick! Perhaps: strwidth(expression(bold(text))) On 30/10/2007, Roland Kaiser [EMAIL PROTECTED] wrote: Hi! Is there a way to get the string width of the bold typefaces? like: strwidth(text, family = serif, font = 2). Thanks Roland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Place a string into the header/footer of a pdf file generated during a plot session
Dear useRs, Do you know, by any chance, if it is possible to write a string in the header/footer of a pdf file created during a plot session? To make sure that I know what R script generated a certain chart, I would like to add the path to the working directory into the header/footer of the corresponding pdf file. Thank you. Tudor -- Tudor Dan Bodea Georgia Institute of Technology School of Civil and Environmental Engineering Web: http://www.prism.gatech.edu/~gtg757i __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Place a string into the header/footer of a pdf file generated during a plot session
Perhaps you can use mtext: plot(rnorm(100), col=red, pch=16) mtext(getwd(), side=1, line=3, outer=F, adj=0, cex=0.7) -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 30/10/2007, Tudor Bodea [EMAIL PROTECTED] wrote: Dear useRs, Do you know, by any chance, if it is possible to write a string in the header/footer of a pdf file created during a plot session? To make sure that I know what R script generated a certain chart, I would like to add the path to the working directory into the header/footer of the corresponding pdf file. Thank you. Tudor -- Tudor Dan Bodea Georgia Institute of Technology School of Civil and Environmental Engineering Web: http://www.prism.gatech.edu/~gtg757i __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Implementing R through Oracle
I have been looking for a statistical package that I can implement in our application and I came across R. We run an n-Tier environment with an Oracle 10g backend. Our design is to keep all business logic in the backend. What I would like to do is call R from pl/sql. I noticed that ROracle is designed to connect with and process from a client perspective. I actually would be running in the database preparing the data and then apply the statistics to the result set for additional information. Then I would take the results from R and apply additional processing. Has anyone done this? Thanks. -- View this message in context: http://www.nabble.com/Implementing-R-through-Oracle-tf4719929.html#a13493204 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] timezone conversion difficulties with the new US daylight saving time switch over
I'm having difficulties with daylight saving times in US time zones. (Apologies for the long post, but the problem seems subtle and complex, unless I'm doing something completely wrong, in which case it should be evident from the first 10 lines below.) This is what I see, using a (slightly modified) example from ?as.POSIXlt : as.POSIXlt((d - Sys.time()), EST5EDT) # the current time in New York [1] 2007-10-30 12:38:47 EST d [1] 2007-10-30 11:38:47 Mountain Daylight Time The problem is that Mountain Time is 2 hours behind Eastern Time and the US is still on Daylight Saving Time - the current time in New York should be reported as 13:38:47 EDT, not 12:38:47 EST. This is running on Windows XP 64 bit (SP2), and I see the same behavior on Windows XP 32 bit and on Windows 2000 Server (SP4). AFAICS, this problem only occurs this week, and this week is unusual in that it is the first year that Daylight Saving Time in the US ends on the first Sunday in November rather than the last Sunday in October (I don't know whether this is the cause of the problem, but it seems likely). I see the same problem around the same week last year, but before and after this week in both years, the conversions are fine: # *** problem in 2007 as.POSIXlt(as.POSIXct(2007-10-30 11:38:47), EST5EDT) [1] 2007-10-30 12:38:47 EST # before the problem week 2007 as.POSIXlt(as.POSIXct(2007-10-20 11:38:47), EST5EDT) [1] 2007-10-20 13:38:47 EDT # after the problem week 2007 as.POSIXlt(as.POSIXct(2007-11-05 11:38:47), EST5EDT) [1] 2007-11-05 13:38:47 EST # *** problem in 2006 as.POSIXlt(as.POSIXct(2006-10-30 11:38:47), EST5EDT) [1] 2006-10-30 12:38:47 EST # before the problem week 2006 as.POSIXlt(as.POSIXct(2006-10-27 11:38:47), EST5EDT) [1] 2006-10-27 13:38:47 EDT # after the problem week 2006 as.POSIXlt(as.POSIXct(2006-11-07 11:38:47), EST5EDT) [1] 2006-11-07 13:38:47 EST My computer is set to the Mountain Daylight timezone, and is set to automatically adjust for Daylight Saving Time changes. sessionInfo() R version 2.6.0 Patched (2007-10-11 r43143) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Sys.timezone() [1] Mountain Daylight Time If I explicitly set env var TZ, the conversion problems go away, but the time reported by Sys.time() is inappropriately not in daylight saving time: Sys.time() [1] 2007-10-30 13:14:38 Mountain Daylight Time Sys.setenv(TZ=MST7MDT) Sys.time() [1] 2007-10-30 12:14:51 MST If I set my system timezone to Eastern Daylight Time, and restart R, I also get problematic behavior (as.POSIXlt inappropriately adjusting a time by an hour on the day after Daylight saving time ends): Sys.timezone() [1] Eastern Daylight Time as.POSIXlt((d - Sys.time()), EST5EDT) [1] 2007-10-30 12:57:40 EST d [1] 2007-10-30 13:57:40 Eastern Daylight Time # *** problem week 2007 as.POSIXlt(as.POSIXct(2007-10-30 11:38:47), EST5EDT) [1] 2007-10-30 10:38:47 EST # before the problem week 2007 as.POSIXlt(as.POSIXct(2007-10-20 11:38:47), EST5EDT) [1] 2007-10-20 11:38:47 EDT # after the problem week 2007 as.POSIXlt(as.POSIXct(2007-11-05 11:38:47), EST5EDT) [1] 2007-11-05 11:38:47 EST # *** problem week 2006 - the day is after the switch, but # the time gets adjusted by one hour as.POSIXlt(as.POSIXct(2006-10-30 11:38:47), EST5EDT) [1] 2006-10-30 10:38:47 EST # before the problem week 2006 as.POSIXlt(as.POSIXct(2006-10-27 11:38:47), EST5EDT) [1] 2006-10-27 11:38:47 EDT # after the problem week 2006 as.POSIXlt(as.POSIXct(2006-11-10 11:38:47), EST5EDT) [1] 2006-11-10 11:38:47 EST The problem in 2006 goes away if I set TZ=EST5EDT: Sys.setenv(TZ = EST5EDT) Sys.timezone() [1] EST as.POSIXlt(as.POSIXct(2006-10-30 11:38:47), EST5EDT) [1] 2006-10-30 11:38:47 EST Questions: (1) should I be using a different way to convert times between time zones? (2) is there a problem in how R is interacting with the system time conversion facilities? (3) if the answer to (2) is yes, does anyone have any good hints for where to start looking for a solution? It looks to me like unclass(as.POSIXlt(as.POSIXct(2007-10-30 11:38:47), EST5EDT))$isdst is inappropriately zero. I tried following the code in src/main/datetime.c:do_asPOSIXlt, and it looks like this isdst value comes from a call to localtime() from localtime0() ... thanks in advance for any help, Tony Plate PS. I do not see the same problem in an old version of R (2.2.1) running under Ubuntu Linux: Sys.timezone() [1] as.POSIXlt((d - Sys.time()), EST5EDT) [1] 2007-10-29 14:56:49 EDT d [1] 2007-10-29 12:56:49 MDT # ok in 2007 as.POSIXlt(as.POSIXct(2007-10-30 11:38:47), EST5EDT) [1] 2007-10-30 13:38:47 EDT # before the problem week 2007
Re: [R] calculate spatial distance
I don't know of such a function, but you have several options:
1. Assume that Euclidean distance is good enough - probably
reasonable over a limited geographic region (and commonly done).
2. Use your GIS software to do the calculations since it already
understands projections and distances on a sphere.
3. Write a function to do this yourself and make it available to
other researchers who need this capability. Assuming that
great circle distances on a perfect sphere are good enough, it
isn't that hard to do.
Eh, I talked myself into it (runs, but otherwise untested):
geogdist - function(lat1, lon1, lat2, lon2)
{
# takes latitude and longitue for points 1 and 2
# returns great circle distances in km
# south and west are negative
rad - function(x) { (x/360) * 2 * pi }
deg - function(x) { (x/(2 * pi)) * 360 }
gd - (sin(rad(lat1)) * sin(rad(lat2))) + (cos(rad(lat1)) *
cos(rad(lat2)) * cos(rad(abs(lon2-lon1
gd - deg(acos(gd))
111.23 * gd
}
On Oct 30, 2007 11:49 AM, [EMAIL PROTECTED] wrote:
Hi,
I have a set of locations defined by longitude and latitude (in degrees),
and want to calculate the spatial (or geographic) distance among all
locations.
I did not find such a function in the spatial-related packages. (I *cannot*
use 'dist', as I have geographic, not cartesian coordinates).
thanks!
Robert
--
Sarah Goslee
http://www.functionaldiversity.org
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculate spatial distance
RSiteSearch(longitude distance)
pops up a bunch of results that seem pertinent. e.g.
R: Distance Between Geographic Coordinates (score: 4)
R: Distance Along Great Circle Arc (score: 2)
??
On Tue, 30 Oct 2007, Sarah Goslee wrote:
I don't know of such a function, but you have several options:
1. Assume that Euclidean distance is good enough - probably
reasonable over a limited geographic region (and commonly done).
2. Use your GIS software to do the calculations since it already
understands projections and distances on a sphere.
3. Write a function to do this yourself and make it available to
other researchers who need this capability. Assuming that
great circle distances on a perfect sphere are good enough, it
isn't that hard to do.
Eh, I talked myself into it (runs, but otherwise untested):
geogdist - function(lat1, lon1, lat2, lon2)
{
# takes latitude and longitue for points 1 and 2
# returns great circle distances in km
# south and west are negative
rad - function(x) { (x/360) * 2 * pi }
deg - function(x) { (x/(2 * pi)) * 360 }
gd - (sin(rad(lat1)) * sin(rad(lat2))) + (cos(rad(lat1)) *
cos(rad(lat2)) * cos(rad(abs(lon2-lon1
gd - deg(acos(gd))
111.23 * gd
}
On Oct 30, 2007 11:49 AM, [EMAIL PROTECTED] wrote:
Hi,
I have a set of locations defined by longitude and latitude (in degrees),
and want to calculate the spatial (or geographic) distance among all
locations.
I did not find such a function in the spatial-related packages. (I *cannot*
use 'dist', as I have geographic, not cartesian coordinates).
thanks!
Robert
--
Sarah Goslee
http://www.functionaldiversity.org
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Reading a file with read.csv: two character rows not interpreted as I hope
Hi Folks... been playing with this for a while, with no luck, so I¹m hoping someone knows it off the top of their head... Difficult to find this nuance in the archives, as so many msgs deal with read.csv! I¹m trying to read a data file with the following structure (a little piece of the actual data, they are actually csv just didn¹t paste with the commas): wavelength SampleA SampleB SampleC SampleD color green black black green class Class 1 Class 2 Class 2 Class 1 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01 432 1.42E-01 1.50E-01 1.62E-01 1.48E-01 Columns after the first one are sample names. 2nd row is the list of colors to use in later plotting. 3rd row is the class for later manova. The rest of it is x data in the first column with y1, y2...following for plotting. I can read the file w/o the color or class rows with read.csv just fine, makes a nice data frame with proper data types. The problem comes when parsing the 2nd and 3rd rows. Here¹s the code: data = read.csv(filename, header=TRUE) # read in data color = data[1,]; color = data[-1] # capture color info throw out 1st value class = data[2,]; class = class[-1] # capture category info throw out 1st value cleaned.data = data[-1,] # remove color category info for matrix operations cleaned.data = data[-1,] freq = data[,1] # capture frequency info What happens is that freq is parsed as factors, and the color and class are parsed as a data frames of factors. I need color and class to be characters which I can pass to functions in the typical way one uses colors and levels. I need the freq the cleaned.data info as numeric for plotting. I don¹t feel I¹m far off from things working, but that¹s where you all come in! Seems like an argument of as.something is needed, but the ones I¹ve tried don¹t work. Would it help to put color and class above the x,y data in the file, then clean it off? Btw, I¹m on a Mac using R 2.6.0. Thanks in advance, Bryan * Bryan Hanson Professor of Chemistry Biochemistry [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R installation on SuSE 10.3
I have downloaded the source code for Linux. the ./configure procedure can find gcc but cannot find f77 or f2c I have looked for the above compiler with Test and installed all what pertains to Fortran. Still not even the man pages for f77 anf fc2 work . Where is f77 and f2c with linux 10.3 ?? Thank you do much -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculate spatial distance
Check out rdist.earth in the fields package. On Oct 30, 2007 11:49 AM, [EMAIL PROTECTED] wrote: Hi, I have a set of locations defined by longitude and latitude (in degrees), and want to calculate the spatial (or geographic) distance among all locations. I did not find such a function in the spatial-related packages. (I *cannot* use 'dist', as I have geographic, not cartesian coordinates). thanks! Robert Robert Ptacnik Norwegian Institute for Water Research (NIVA) Gaustadalléen 21 NO-0349 Oslo mobile +47 982 277 81 FON NIVA +47 22 18 51 00 FAX +47 22 18 52 00 -- NIVAs hovedkontor har flyttet til nye lokaler i CIENS - Forskningssenter for miljø og samfunn; Gaustadalléen 21, 0349 Oslo. Meld deg på vårt nyhetsbrev på www.niva.no __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] data.frame, ggplot vs matplot
Hello, I've been trying to use ggplot, but I cannot seem to get my data in the correct form. I usually have a vector x, and a matrix y and I would usually use matplot(x,y) to plot the columns of y against x. Now, if i understand correctly, I should cast x and y into a data.frame and do something like ggplot(x,y,data=data). I think I'm missing something here: do I really need to reshape y into a single vector, replicate x accordingly, and put both vectors in a data frame? I've tried it, but the reshape function is still very obscure to me. Any help appreciated! Small example: x-seq(from=1,by=1,length=10) y-sin(x)%*%t(x) columns-c(1:10) matplot(x,y) legend(topleft, (x,y), columns) # the version below is not working require(ggplot2) data.frame(cbind(x,y))-dataS wide - reshape(dataS, direction=wide,timevar=c(1:length(columns))) dataL-reshape(wide,direction=long) # this clearly doesn't work as I would have thought qplot(x, y, data = dataL) Best regards, baptiste __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] high RAM on Linux or Solaris platform
On Tue, 30 Oct 2007, David Bickel wrote: To help me make choices regarding a platform for running high-memory R processes in parallel, I would appreciate any responses to these questions: 1. Does the amount of RAM available to an R session depend on the processor (Intel vs. Sun) or on the OS (various Linux distributions vs. Solaris)? Yes. It depends on whether R uses 64-bit or 32-bit pointers. For 64-bit R you need a 64-bit processor, an operating system that will run 64-bit programs, and a compiler that will produce them. I'm not sure what the current Intel offerings are, but you can compile and run 64-bit on AMD Opteron (Linux) and Sun (Solaris) systems. 2. Does R have any built-in limitations of RAM available to a session? For example, could it make use of 16 GB in one session given the right processor/OS platform? R does have built-in limitations even in a 64-bit system, but they are large. It is certainly possible to use more than 16Gb of memory. The main limit is that the length of a vector is stored in a C int, and so is no more than 2^31-1, or about two billion. A numeric vector of that length would take up 16Gb on its own. 3. Is there anything else I should consider before choosing a processor and OS? I don't think there is anything else R-specific. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R installation on SuSE 10.3
Maura E Monville wrote: I have downloaded the source code for Linux. the ./configure procedure can find gcc but cannot find f77 or f2c I have looked for the above compiler with Test and installed all what pertains to Fortran. Still not even the man pages for f77 anf fc2 work . Where is f77 and f2c with linux 10.3 ?? Thank you do much In SuSE 10.2 I found it in the gcc-fortran package. I don't recall if it is required, but there is also a gcc41-fortran. It may well be the same in SuSE 10.3. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Homework help: Is this how CI using t dist are constructed?
I'm trying to replicate some of the examples from my textbook in R (my text uses Minitab). In this problem, I'm trying to construct a 95% confidence interval for these distance measurements [1]: # Case Study 7.4.1, p. 483 x - scan() 1: 62 52 68 23 34 45 27 42 83 56 40 12: Read 11 items alpha-.95 mean(x) + qt(c((1-alpha)/2, 1-((1-alpha)/2)), df=length(x)-1) * sd(x) / sqrt(length(x)) [1] 36.21420 60.51307 Are confidence intervals with the t distribution constructed using this type of equation, or am I overlooking a more concise, 'canned' approach that's already been programmed? Any suggestions on simplifying this? Thanks for all your advice and help. -Kevin [1] An Introduction to Mathematical Statistics and its Applications, fourth ed., Larsen and Marx. Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R installation on SuSE 10.3
Hi, On Tue, 30 Oct 2007 14:44:17 -0500 Maura E Monville [EMAIL PROTECTED] wrote: I have downloaded the source code for Linux. the ./configure procedure can find gcc but cannot find f77 or f2c I have looked for the above compiler with Test and installed all what pertains to Fortran. Still not even the man pages for f77 anf fc2 work . Where is f77 and f2c with linux 10.3 ?? In 10.3 they provide gcc-fortran (or f77). Just search for fortran in yast2. If you want to use a precompiled binary you can find one there: http://download.opensuse.org/repositories/home:dsteuer/openSUSE_10.3 or just type r-base in the search box on http://software.opensuse.org/search Hope that helps Detlef Thank you do much -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Keinen Gedanken zweimal denken, außer er ist schön. Unbekannte Quelle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] markov regime switching models
Hi, I am looking for a package to estimate regime switching models (states following a markov chain). I found packages for Hidden Markov Models but I am looking for something a little different: In the HMM the conditional distribution of the observations (give the state) is a known distribution (normal or others), while the package I need should allow to set a conditional distribution (given the state) which can be still modelled (for example with mean-reversion or jump diffusion...). I think the theory under this estimation technique is in James D. Hamilton, A New Approach to the Economic Analysis of Nonstationary Time Series and the Business Cycle (1989) Thanks very much for any help! Valentina Bonetti Master student at Bocconi University, Milan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: data format
Excuse me for less detailed e-mail I've sent before, I guess there's a misunderstanding here. My problem is to use the data in the order I've typed below without splitting it. Is it possible? I really don't know. Some statistics packages do it. Original Data is; Good,Bad 10,12 15,15 18,10 12 But I have the data in the following form, Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 And I want to analyze the data without splitting it. I guessed whether there's a quick/simple solution to my problem. Array functions do solve this problem in general. Now I'm reading the help files about How to deal with arrays in R environment?. Thx a lot for your concern Emre -- Forwarded message -- From: Emre Unal [EMAIL PROTECTED] Date: Oct 30, 2007 4:39 PM Subject: data format To: r-help@r-project.org Hi, How can I analyze the data collected in database formatting (with labels) rather than splitted by individual columns (almost in excel)? For example (comma separated data); Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 etc... ks.test or chisq.test can be done. Splitting the data into new columns is not applicable cos' I'll use R-integration in another software. Thanks for your concern Emre -- --- Emre ÜNAL -- --- Emre ÜNAL http://www.geocities.com/dusemre http://dusemre.blogspot.com ICQ: 5712269 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] NAIVE BAYES with 10-fold cross validation
hi there!! i am trying to implement the code of the e1071 package for naive bayes, but it doens't really work, any ideas?? i am very glad about any help!! i need a naive bayes with 10-fold cross validation: code: library(e1071) model - naiveBayes(code ~ ., mydata) tune.control - tune.control(random = FALSE, nrepeat = 1, repeat.aggregate = min, sampling = c(cross), sampling.aggregate = mean, cross = 10, best.model = TRUE, performances = TRUE) pred - predict(model, mydata[,-12], type=class) tune(naiveBayes, code~., mydata, predict.fun=pred, tune.control) thx for your help! cheers, julia -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Homework help: Is this how CI using t dist are constructed?
On Tue, 30 Oct 2007, Zembower, Kevin wrote: I'm trying to replicate some of the examples from my textbook in R (my text uses Minitab). In this problem, I'm trying to construct a 95% confidence interval for these distance measurements [1]: # Case Study 7.4.1, p. 483 x - scan() 1: 62 52 68 23 34 45 27 42 83 56 40 12: Read 11 items alpha-.95 mean(x) + qt(c((1-alpha)/2, 1-((1-alpha)/2)), df=length(x)-1) * sd(x) / sqrt(length(x)) [1] 36.21420 60.51307 Are confidence intervals with the t distribution constructed using this type of equation, or am I overlooking a more concise, 'canned' approach that's already been programmed? Any suggestions on simplifying this? R offers a confint() generic with methods for various types of models. If you consider estimation of the mean as a simple linear model (with only an intercept) you can do fm - lm(x ~ 1) fm to estimate the mean and then confint(fm) to get the confidence interval (by default at 0.95 level). hth, Z Thanks for all your advice and help. -Kevin [1] An Introduction to Mathematical Statistics and its Applications, fourth ed., Larsen and Marx. Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Homework help: Is this how CI using t dist are constructed?
Zembower, Kevin wrote: I'm trying to replicate some of the examples from my textbook in R (my text uses Minitab). In this problem, I'm trying to construct a 95% confidence interval for these distance measurements [1]: # Case Study 7.4.1, p. 483 x - scan() 1: 62 52 68 23 34 45 27 42 83 56 40 12: Read 11 items alpha-.95 mean(x) + qt(c((1-alpha)/2, 1-((1-alpha)/2)), df=length(x)-1) * sd(x) / sqrt(length(x)) [1] 36.21420 60.51307 Are confidence intervals with the t distribution constructed using this type of equation, or am I overlooking a more concise, 'canned' approach that's already been programmed? Any suggestions on simplifying this? Thanks for all your advice and help. You mean like t.test(x)? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] high RAM on Linux or Solaris platform
On Tue, 30 Oct 2007, Thomas Lumley wrote: On Tue, 30 Oct 2007, David Bickel wrote: To help me make choices regarding a platform for running high-memory R processes in parallel, I would appreciate any responses to these questions: 1. Does the amount of RAM available to an R session depend on the processor (Intel vs. Sun) or on the OS (various Linux distributions vs. Solaris)? Yes. It depends on whether R uses 64-bit or 32-bit pointers. For 64-bit R you need a 64-bit processor, an operating system that will run 64-bit programs, and a compiler that will produce them. I'm not sure what the current Intel offerings are, but you can compile and run 64-bit on AMD Opteron (Linux) and Sun (Solaris) systems. That is both Sparc Solaris and x86_64 Solaris (although for the latter you seem to need to use the SunStudio compilers). As far as I know all current desktop Intel processors run x86_64, and Xeons seem to have a price-performance edge at the moment. We have several boxes with dual quad-core Xeons and lots of RAM. (Not all for use with R, some Linux, some Windows.) Core 2 Duos do, and are commonplace in quite low-end systems. 2. Does R have any built-in limitations of RAM available to a session? For example, could it make use of 16 GB in one session given the right processor/OS platform? R does have built-in limitations even in a 64-bit system, but they are large. It is certainly possible to use more than 16Gb of memory. The main limit is that the length of a vector is stored in a C int, and so is no more than 2^31-1, or about two billion. A numeric vector of that length would take up 16Gb on its own. ?Memory-limits documents them. 3. Is there anything else I should consider before choosing a processor and OS? I don't think there is anything else R-specific. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] NAIVE BAYES with 10-fold cross validation
am trying to implement the code of the e1071 package for naive bayes, but it doens't really work, any ideas?? am very glad about any help!! need a naive bayes with 10-fold cross validation: The caret package will do this. Use fit - train( x, y, method = nb, trControl = trainControl(method = cv, number = 10)) (there is no formula interface yet). It will use the naïve Bayes implementation in klaR. Unless you specify otherwise, it will train naïve Bayes models with and without using kernel density estimation (but you can change that). The object fit$finalModel will contain the model fit that is cv optimal. For example: fit - train( +iris[,-5], iris$Species, nb, +trControl = trainControl(method = cv, number = 10)) Iter 1 Values: TRUE Loading required package: MASS Loading required package: class Iter 2 Values: FALSE fit Call: train.default(x = iris[, -5], y = iris$Species, method = nb, trControl = trainControl(method = cv, number = 10)) 150 samples 4 predictors summary of cross-validation (10 fold) sample sizes: 135, 135, 135, 135, 135, 135, ... cv resampled training results across tuning parameters: usekernel Accuracy Kappa Accuracy SD Kappa SD Optimal FALSE 0.953 0.93 0.0706 0.106 TRUE 0.96 0.94 0.0562 0.0843* Accuracy was used to select the optimal model Max -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Julia Kröpfl Sent: Tuesday, October 30, 2007 4:46 PM To: r-help@r-project.org Subject: [R] NAIVE BAYES with 10-fold cross validation hi there!! i am trying to implement the code of the e1071 package for naive bayes, but it doens't really work, any ideas?? i am very glad about any help!! i need a naive bayes with 10-fold cross validation: code: library(e1071) model - naiveBayes(code ~ ., mydata) tune.control - tune.control(random = FALSE, nrepeat = 1, repeat.aggregate = min, sampling = c(cross), sampling.aggregate = mean, cross = 10, best.model = TRUE, performances = TRUE) pred - predict(model, mydata[,-12], type=class) tune(naiveBayes, code~., mydata, predict.fun=pred, tune.control) thx for your help! cheers, julia -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Homework help: Is this how CI using t dist are constructed?
Yes, exactly. In fact, I had already discovered this, too. I don't know why I didn't think of it before asking this question. Thanks for your patience with me. -Kevin -Original Message- From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: Tuesday, October 30, 2007 4:54 PM To: Zembower, Kevin Cc: r-help@r-project.org Subject: Re: [R] Homework help: Is this how CI using t dist are constructed? Zembower, Kevin wrote: I'm trying to replicate some of the examples from my textbook in R (my text uses Minitab). In this problem, I'm trying to construct a 95% confidence interval for these distance measurements [1]: snip You mean like t.test(x)? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Homework help: Is this how CI using t dist are constructed?
On 31/10/2007, at 9:52 AM, Achim Zeileis wrote:
On Tue, 30 Oct 2007, Zembower, Kevin wrote:
I'm trying to replicate some of the examples from my textbook in R
(my
text uses Minitab). In this problem, I'm trying to construct a 95%
confidence interval for these distance measurements [1]:
# Case Study 7.4.1, p. 483
x - scan()
1: 62 52 68 23 34 45 27 42 83 56 40
12:
Read 11 items
alpha-.95
mean(x) + qt(c((1-alpha)/2, 1-((1-alpha)/2)), df=length(x)-1) * sd
(x)
/ sqrt(length(x))
[1] 36.21420 60.51307
Are confidence intervals with the t distribution constructed using
this
type of equation, or am I overlooking a more concise, 'canned'
approach
that's already been programmed? Any suggestions on simplifying this?
R offers a confint() generic with methods for various types of models.
If you consider estimation of the mean as a simple linear model
(with only
an intercept) you can do
fm - lm(x ~ 1)
fm
to estimate the mean and then
confint(fm)
to get the confidence interval (by default at 0.95 level).
This is using a sledgehammer to crack a peanut.
The use of t.test() as suggested by Peter Dalgaard is much more
appropriate.
cheers,
Rolf Turner
##
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Re: [R] How to test combined effects?
Dieter,
Thank you very much for the help!
I tried both glht() in multcomp and estimable() in gmodels, but
couldn't get them work as shown below. Basically I have trouble
specifying those continuous variables. Any suggestions?
Also it seems both glht() and estimable() would give multiple t
tests. Is there a way to obtain sort of partial F test?
ModelFit-lme(mct~ IQ*age+IQ*I(age^2)+IQ*I(age^3), MyData,
random=~1|ID)
anova(ModelFit)
mDF denDF F-value p-value
(Intercept) 1 257 54393.04 .0001
IQ 1 215 3.02 0.0839
age 1 25746.06 .0001
I(age^2)1 257 8.80 0.0033
I(age^3)1 25721.30 .0001
IQ:age 1 257 1.18 0.2776
IQ:I(age^2) 1 257 0.50 0.4798
IQ:I(age^3) 1 257 0.23 0.6284
library(multcomp)
glht(ModelFit, linfct = c(IQ:age = 0, IQ:I(age^2) = 0, IQ:I
(age^3) = 0))
Error in coefs(ex[[3]]) :
cannot interpret expression 'I''age^2' as linear function
library(gmodels)
estimable(ModelFit, rbind('IQ:age'=0, 'IQ:I(age^2) = 0', 'IQ:I
(age^3) = 0'))
Error in FUN(newX[, i], ...) :
`param' has no names and does not match number of coefficients of
model. Unable to construct coefficient vector
Thanks,
Gang
On Oct 30, 2007, at 9:08 AM, Dieter Menne wrote:
Gang Chen gangchen at mail.nih.gov writes:
Suppose I have a mixed-effects model where yij is the jth sample for
the ith subject:
yij= beta0 + beta1(age) + beta2(age^2) + beta3(age^3) + beta4(IQ) +
beta5(IQ^2) + beta6(age*IQ) + beta7(age^2*IQ) + beta8(age^3 *IQ)
+random intercepti + eij
In R how can I get an F test against the null hypothesis of
beta6=beta7=beta8=0? In SAS I can run something like contrast age*IQ
1, age^2*IQ 1, age^3 *IQ 1, but is there anything similar in R?
Check packages multcomp and gmodels for contrast tests that work
with lme.
Dieter
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[R] R 2.6.0 crashes when opening some .R files
Why would R 2.6.0 crash when opening .R files created with an older version of R, but apparently not when opening .R files created with the current version? Even cutting and pasting text from older .R files does not prevent this from happening. Richard Anderson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data.frame, ggplot vs matplot
baptiste Auguié-2 wrote: Hello, I've been trying to use ggplot, but I cannot seem to get my data in the correct form. I usually have a vector x, and a matrix y and I would usually use matplot(x,y) to plot the columns of y against x. Now, if i understand correctly, I should cast x and y into a data.frame and do something like ggplot(x,y,data=data). I think I'm missing something here: do I really need to reshape y into a single vector, replicate x accordingly, and put both vectors in a data frame? I've tried it, but the reshape function is still very obscure to me. Any help appreciated! Small example: x-seq(from=1,by=1,length=10) y-sin(x)%*%t(x) columns-c(1:10) matplot(x,y) legend(topleft, (x,y), columns) dataL = melt(dataS,id=x) qplot(x,value,data=dataL) qplot(x,value,data=dataL,colour=variable) cheers Ben Bolker -- View this message in context: http://www.nabble.com/data.frame%2C-ggplot-vs-matplot-tf4721042.html#a13498585 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] data types changing
List,
I am attempting to take a row of data from one matrix to another if it
satisfies a certain condition. When R puts the data in the new matrix it is
changing the characters to integers and giving them values which aren't very
helpful to my analysis. I would use as.character, but I need to keep the
double values as is. Is there a way to copy the entry exactly as is to the new
matrix, without having to use a separate statement for each entry. I've
included some code below. In my example all but row 5 are factors and should
be kept as characters, and column 7 has 2 levels, 1 or 2. Column 5, the
response is a double. Thanks for the help.
l = nrow(data)
n = 1
k = 1
data1trip = as.data.frame(rbind(1:7))
data2trip = as.data.frame(rbind(1:7))
colnames(data1trip) =...#my column names for data1trip
colnames(data2trip) =...#data2trip
for(i in 1:l){
if (data[i,7]==1){
data1trip[k,] = data[i,]; k=k+1 }
else {
data2trip[n,] = data[i,]; n = n+1}
}
is the only other way to do what i want
for(i in 1:l){
if (data[i,7]==1){
data1trip[k,1] = as.char(data[i,1]
data1trip[k,2] = as.char(data[i,2]
data1trip[k,3] = data[i,]
...
else {
and the same for those which have a 2 value in data[i,7]?
}
This second way seems a bit sloppy and i wanted to check if there existed a
more professional way to do it.
Thanks again,
Dave Mitchell
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[R] Difficulty Compiling RSQLite on Solaris x86 Using Studio 12 Compilers
Apologies if this is not the best list on which to ask for help. I have
compiled R 2.6.0 using Sun Studio 12 compilers. I can install most CRAN
and bioconductor packages that I need, with the exception of RSQLite.
Unfortunately this is critical for other packages that I need. I have
tried to compile it using R CMD INSTALL to generate a config.log file.
I don't know how to fix the reported error. I have tried commenting
out most of the test language in the configure file, but then there are
other complaints.
I used Studio 12 to build 2.5.1 and it worked perfectly. The only issue
with the 2.6.0 build is that 'make test' fails and this did not happen
with 2.5.1. However, it appears to run fine.
Any ideas of how I can get RSQLite to compile? Or is there another list
to which I should address my question.
thanks,
aric
Here is an except from the config.log:
/usr/bin/uname -p = i386
/bin/uname -X = System = SunOS
Node = solenv
Release = 5.11
KernelID = snv_69
Machine = i86pc
## --- ##
## Core tests. ##
## --- ##
configure:1313: checking for gcc
configure:1339: result: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64
configure:1583: checking for C compiler version
configure:1586: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 --version /dev/null 5
./configure: line 1587: dmake:: command not found
configure:1589: $? = 127
configure:1591: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 -v /dev/null 5
./configure: line 1592: dmake:: command not found
configure:1594: $? = 127
configure:1596: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 -V /dev/null 5
./configure: line 1597: dmake:: command not found
configure:1599: $? = 127
configure:1622: checking for C compiler default output file name
configure:1625: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
-xO5 -xc99 -xlibmieee -xlibmil -nofstore conftest.c 5
./configure: line 1626: dmake:: command not found
configure:1628: $? = 127
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME
| #define PACKAGE_TARNAME
| #define PACKAGE_VERSION
| #define PACKAGE_STRING
| #define PACKAGE_BUGREPORT
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:1667: error: C compiler cannot create executables
See `config.log' for more details.
## - ##
## Output variables. ##
## - ##
-xO5 -xc99 -xlibmieee -xlibmil -nofstore'
/opt/studio12/SUNWspro/bin/cc -m64'
/opt/studio12/SUNWspro/bin/cc -m64'
CC='dmake: defaulting to parallel mode.
CFLAGS='dmake: defaulting to parallel mode.
CPP=''
CPPFLAGS=''
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EXEEXT=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
PKG_CPPFLAGS=''
PKG_LIBS=''
SHELL='/bin/bash'
See the man page dmake(1) for more information on setting up
the .dmakerc file.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
ac_ct_CC='dmake: defaulting to parallel mode.
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## --- ##
## confdefs.h. ##
## --- ##
#define PACKAGE_BUGREPORT
#define PACKAGE_NAME
#define PACKAGE_STRING
#define PACKAGE_TARNAME
#define PACKAGE_VERSION
configure: exit 77
--
IMPORTANT WARNING: This email (and any attachments) is ...{{dropped:8}}
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Re: [R] Reading a file with read.csv: two character rows not interpreted as I hope
Here is one way. You will probably use 'file' instead of textConnection
x.in - textConnection('wavelength SampleA SampleB SampleC SampleD
+ color green black black green
+ class Class 1 Class 2 Class 2 Class 1
+ 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
+ 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+ 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
+ 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+ 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+ 432 1.42E-01 1.50E-01 1.62E-01 1.48E-01')
c.names - scan(x.in, what='', nlines=1) # read column names
Read 5 items
c.options - read.table(x.in, as.is=TRUE, nrows=2) # get lines 2-3
c.data - read.table(x.in) # rest of the data
colnames(c.data) - c.names
close(x.in)
c.options # here are lines 2-3
V1 V2 V3 V4 V5
1 color green black black green
2 class Class 1 Class 2 Class 2 Class 1
c.data # your data
wavelength SampleA SampleB SampleC SampleD
1403 0.194 0.214 0.211 0.183
2409 0.192 0.189 0.200 0.182
3415 0.170 0.199 0.194 0.186
4420 0.159 0.191 0.216 0.174
5426 0.150 0.166 0.172 0.158
6432 0.142 0.150 0.162 0.148
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Hi Folks... Œbeen playing with this for a while, with no luck, so I¹m hoping
someone knows it off the top of their head... Difficult to find this nuance
in the archives, as so many msgs deal with read.csv!
I¹m trying to read a data file with the following structure (a little piece
of the actual data, they are actually csv just didn¹t paste with the
commas):
wavelength SampleA SampleB SampleC SampleD
color green black black green
class Class 1 Class 2 Class 2 Class 1
403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
432 1.42E-01 1.50E-01 1.62E-01 1.48E-01
Columns after the first one are sample names. 2nd row is the list of colors
to use in later plotting. 3rd row is the class for later manova. The rest
of it is x data in the first column with y1, y2...following for plotting.
I can read the file w/o the color or class rows with read.csv just fine,
makes a nice data frame with proper data types. The problem comes when
parsing the 2nd and 3rd rows. Here¹s the code:
data = read.csv(filename, header=TRUE) # read in data
color = data[1,]; color = data[-1] # capture color info throw out 1st
value
class = data[2,]; class = class[-1] # capture category info throw out 1st
value
cleaned.data = data[-1,] # remove color category info for matrix
operations
cleaned.data = data[-1,]
freq = data[,1] # capture frequency info
What happens is that freq is parsed as factors, and the color and class are
parsed as a data frames of factors.
I need color and class to be characters which I can pass to functions in the
typical way one uses colors and levels.
I need the freq the cleaned.data info as numeric for plotting.
I don¹t feel I¹m far off from things working, but that¹s where you all come
in! Seems like an argument of as.something is needed, but the ones I¹ve
tried don¹t work. Would it help to put color and class above the x,y data
in the file, then clean it off?
Btw, I¹m on a Mac using R 2.6.0.
Thanks in advance, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
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--
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+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] R installation on Linux/SuSE10.3
I am installing in /usr/local/bin where I have to be root even if I changed the access right to some sub directories by chmod. The installation completed fine (all stages: /config, make, make install). But no icon was created on my desktop. It works just typing in on the command line. It has no GUI. How come ? The README file does not even touch such problem. In spite of hating Windows I have to confess that R is much more friendly on Windows. Is there any way to make R run more smoothly on Linux/SuSE as well ?? Thank you in advance. Regards, Maura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reversing perspective plot axis
Hi, I am trying to create a perspective plot with Time on the x-axis, Underlying Price on the y-axis, and Option Price on the z-axis. But I don't like the way my x-axis is setup. Right now, Time is this sequence. Time = seq(from = 1/52, to = 1, by=1/52) That results in the x-axis going from 0 at the back, to 1 near the foreground corner.(If that makes any sense) I want to do the exact opposite. When I try this sequence: Time = seq(from = 1, to = 1/52, by=-1/52) I get this error message: Error in persp.default(x = Time, y = S, z = Price, xlab = Time, ylab = S, : increasing 'x' and 'y' values expected So it seems that I can't use a descending sequence for my perspective plot. Is that true? Is there a way to work around this? persp(x=Time, y=S, z=Price, xlab=Time, ylab=S, zlab=TypeFlag, ...) Essentially, what I'm trying to create is something that looks like this. http://www.insightful.com/products/finmetrics/opSensitivity1_lg.gif You can see how Time on the x-axis diminishes as it moves to the foreground corner. Thanks in advance. James __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reversing perspective plot axis
On 30 October 2007 at 20:17, James wrote: | I am trying to create a perspective plot with Time on the x-axis, | Underlying Price on the y-axis, and Option Price on the z-axis. But Can't help with persp, but see http://dirk.eddelbuettel.com/code/rquantlib-rgl.html for some animated gifs using Rgl and the RQuantLib pricers. Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading a file with read.csv: two character rows not interpreted as I hope
Jim, thanks for the suggestion. There is still something subtle
non-intuitive going on here. I adapted your code with minor changes as
follows (I had to add the sep argument) but get different behavior:
c.names - scan(file.csv, what='', nlines=1, sep=,) # read column names
c.options - read.table(file.csv, as.is=TRUE, nrows=2, sep=,) # get
lines 2-3
c.data - read.table(file.csv, sep=,) # rest of the data
colnames(file.csv) - c.names
Your code works perfectly (you knew that!). My adaptation runs, but
c.options contains the first two lines, not lines 2 3, and c.data contains
the contents of the entire file as *factors* (data type of c.names
c.options is correct - character). How strange!
Also, and this is an observation rather than a question: in your code, you
call scan and get the first line as characters, then you do read.table which
gets lines 2 3 presumably because the first line, from read.table's
perspective is a hidden label (?), then the second time you use read.table
the hidden first line is ignored, as are the two lines with character data.
I really don't understand these behaviors, which is probably why I'm having
trouble parsing the file!
Thanks, Bryan
On 10/30/07 8:40 PM, jim holtman [EMAIL PROTECTED] wrote:
Here is one way. You will probably use 'file' instead of textConnection
x.in - textConnection('wavelength SampleA SampleB SampleC SampleD
+ color green black black green
+ class Class 1 Class 2 Class 2 Class 1
+ 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
+ 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+ 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
+ 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+ 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+ 432 1.42E-01 1.50E-01 1.62E-01 1.48E-01')
c.names - scan(x.in, what='', nlines=1) # read column names
Read 5 items
c.options - read.table(x.in, as.is=TRUE, nrows=2) # get lines 2-3
c.data - read.table(x.in) # rest of the data
colnames(c.data) - c.names
close(x.in)
c.options # here are lines 2-3
V1 V2 V3 V4 V5
1 color green black black green
2 class Class 1 Class 2 Class 2 Class 1
c.data # your data
wavelength SampleA SampleB SampleC SampleD
1403 0.194 0.214 0.211 0.183
2409 0.192 0.189 0.200 0.182
3415 0.170 0.199 0.194 0.186
4420 0.159 0.191 0.216 0.174
5426 0.150 0.166 0.172 0.158
6432 0.142 0.150 0.162 0.148
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Hi Folks... Œbeen playing with this for a while, with no luck, so I¹m hoping
someone knows it off the top of their head... Difficult to find this nuance
in the archives, as so many msgs deal with read.csv!
I¹m trying to read a data file with the following structure (a little piece
of the actual data, they are actually csv just didn¹t paste with the
commas):
wavelength SampleA SampleB SampleC SampleD
color green black black green
class Class 1 Class 2 Class 2 Class 1
403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
432 1.42E-01 1.50E-01 1.62E-01 1.48E-01
Columns after the first one are sample names. 2nd row is the list of colors
to use in later plotting. 3rd row is the class for later manova. The rest
of it is x data in the first column with y1, y2...following for plotting.
I can read the file w/o the color or class rows with read.csv just fine,
makes a nice data frame with proper data types. The problem comes when
parsing the 2nd and 3rd rows. Here¹s the code:
data = read.csv(filename, header=TRUE) # read in data
color = data[1,]; color = data[-1] # capture color info throw out 1st
value
class = data[2,]; class = class[-1] # capture category info throw out 1st
value
cleaned.data = data[-1,] # remove color category info for matrix
operations
cleaned.data = data[-1,]
freq = data[,1] # capture frequency info
What happens is that freq is parsed as factors, and the color and class are
parsed as a data frames of factors.
I need color and class to be characters which I can pass to functions in the
typical way one uses colors and levels.
I need the freq the cleaned.data info as numeric for plotting.
I don¹t feel I¹m far off from things working, but that¹s where you all come
in! Seems like an argument of as.something is needed, but the ones I¹ve
tried don¹t work. Would it help to put color and class above the x,y data
in the file, then clean it off?
Btw, I¹m on a Mac using R 2.6.0.
Thanks in advance, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
[R] survey weights in sample with replacement
Hi, I am trying to draw a random sample from an household survey with sample weight. Is there any function in R or Splus which allows this. Regards, *** Mehtabul Azam Department of Economics Southern Methodist University Dallas TX 75275-0496 Tel: (214) 214 938 3906 Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: http://people.smu.edu/mazam __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] survey weights in sample with replacement
On 31/10/07 4:03 PM, Azam, Mehtabul wrote: I am trying to draw a random sample from an household survey with sample weight. Is there any function in R or Splus which allows this. I'm not sure if this what you're after, but R's pps package lets you sample with probability proportional to size. Hope this helps, James -- James Reilly Department of Statistics, University of Auckland Private Bag 92019, Auckland, New Zealand __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reversing perspective plot axis
On 30/10/2007 10:42 PM, Dirk Eddelbuettel wrote: On 30 October 2007 at 20:17, James wrote: | I am trying to create a perspective plot with Time on the x-axis, | Underlying Price on the y-axis, and Option Price on the z-axis. But Can't help with persp, but see http://dirk.eddelbuettel.com/code/rquantlib-rgl.html for some animated gifs using Rgl and the RQuantLib pricers. Animations are easier in the latest release: see spin3d to set a spin rate, par3dinterp to interpolate between views, movie3d to take regular snapshots, or play3d to just play them. Duncan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading a file with read.csv: two character rows not interpreted as I hope
Try:
inFile - file(file.csv, r)
Then use inFile where you have file.csv. You are reopening the file
on each call; this keeps the file open.
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Jim, thanks for the suggestion. There is still something subtle
non-intuitive going on here. I adapted your code with minor changes as
follows (I had to add the sep argument) but get different behavior:
c.names - scan(file.csv, what='', nlines=1, sep=,) # read column names
c.options - read.table(file.csv, as.is=TRUE, nrows=2, sep=,) # get
lines 2-3
c.data - read.table(file.csv, sep=,) # rest of the data
colnames(file.csv) - c.names
Your code works perfectly (you knew that!). My adaptation runs, but
c.options contains the first two lines, not lines 2 3, and c.data contains
the contents of the entire file as *factors* (data type of c.names
c.options is correct - character). How strange!
Also, and this is an observation rather than a question: in your code, you
call scan and get the first line as characters, then you do read.table which
gets lines 2 3 presumably because the first line, from read.table's
perspective is a hidden label (?), then the second time you use read.table
the hidden first line is ignored, as are the two lines with character data.
I really don't understand these behaviors, which is probably why I'm having
trouble parsing the file!
Thanks, Bryan
On 10/30/07 8:40 PM, jim holtman [EMAIL PROTECTED] wrote:
Here is one way. You will probably use 'file' instead of textConnection
x.in - textConnection('wavelength SampleA SampleB SampleC SampleD
+ color green black black green
+ class Class 1 Class 2 Class 2 Class 1
+ 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
+ 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+ 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
+ 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+ 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+ 432 1.42E-01 1.50E-01 1.62E-01 1.48E-01')
c.names - scan(x.in, what='', nlines=1) # read column names
Read 5 items
c.options - read.table(x.in, as.is=TRUE, nrows=2) # get lines 2-3
c.data - read.table(x.in) # rest of the data
colnames(c.data) - c.names
close(x.in)
c.options # here are lines 2-3
V1 V2 V3 V4 V5
1 color green black black green
2 class Class 1 Class 2 Class 2 Class 1
c.data # your data
wavelength SampleA SampleB SampleC SampleD
1403 0.194 0.214 0.211 0.183
2409 0.192 0.189 0.200 0.182
3415 0.170 0.199 0.194 0.186
4420 0.159 0.191 0.216 0.174
5426 0.150 0.166 0.172 0.158
6432 0.142 0.150 0.162 0.148
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Hi Folks... Œbeen playing with this for a while, with no luck, so I¹m
hoping
someone knows it off the top of their head... Difficult to find this
nuance
in the archives, as so many msgs deal with read.csv!
I¹m trying to read a data file with the following structure (a little piece
of the actual data, they are actually csv just didn¹t paste with the
commas):
wavelength SampleA SampleB SampleC SampleD
color green black black green
class Class 1 Class 2 Class 2 Class 1
403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
432 1.42E-01 1.50E-01 1.62E-01 1.48E-01
Columns after the first one are sample names. 2nd row is the list of
colors
to use in later plotting. 3rd row is the class for later manova. The rest
of it is x data in the first column with y1, y2...following for plotting.
I can read the file w/o the color or class rows with read.csv just fine,
makes a nice data frame with proper data types. The problem comes when
parsing the 2nd and 3rd rows. Here¹s the code:
data = read.csv(filename, header=TRUE) # read in data
color = data[1,]; color = data[-1] # capture color info throw out 1st
value
class = data[2,]; class = class[-1] # capture category info throw out 1st
value
cleaned.data = data[-1,] # remove color category info for matrix
operations
cleaned.data = data[-1,]
freq = data[,1] # capture frequency info
What happens is that freq is parsed as factors, and the color and class are
parsed as a data frames of factors.
I need color and class to be characters which I can pass to functions in
the
typical way one uses colors and levels.
I need the freq the cleaned.data info as numeric for plotting.
I don¹t feel I¹m far off from things working, but that¹s where you all come
in! Seems like an argument of as.something is needed, but the ones I¹ve
tried don¹t work. Would it help to put color and class above the x,y data
in the file, then clean it off?
Btw, I¹m on a Mac using R 2.6.0.
Thanks in advance, Bryan
Re: [R] Reading a file with read.csv: two character rows not interpreted as I hope
Also, your statement should be:
colnames(c.data) - c.names
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Jim, thanks for the suggestion. There is still something subtle
non-intuitive going on here. I adapted your code with minor changes as
follows (I had to add the sep argument) but get different behavior:
c.names - scan(file.csv, what='', nlines=1, sep=,) # read column names
c.options - read.table(file.csv, as.is=TRUE, nrows=2, sep=,) # get
lines 2-3
c.data - read.table(file.csv, sep=,) # rest of the data
colnames(file.csv) - c.names
Your code works perfectly (you knew that!). My adaptation runs, but
c.options contains the first two lines, not lines 2 3, and c.data contains
the contents of the entire file as *factors* (data type of c.names
c.options is correct - character). How strange!
Also, and this is an observation rather than a question: in your code, you
call scan and get the first line as characters, then you do read.table which
gets lines 2 3 presumably because the first line, from read.table's
perspective is a hidden label (?), then the second time you use read.table
the hidden first line is ignored, as are the two lines with character data.
I really don't understand these behaviors, which is probably why I'm having
trouble parsing the file!
Thanks, Bryan
On 10/30/07 8:40 PM, jim holtman [EMAIL PROTECTED] wrote:
Here is one way. You will probably use 'file' instead of textConnection
x.in - textConnection('wavelength SampleA SampleB SampleC SampleD
+ color green black black green
+ class Class 1 Class 2 Class 2 Class 1
+ 403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
+ 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+ 415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
+ 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+ 426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+ 432 1.42E-01 1.50E-01 1.62E-01 1.48E-01')
c.names - scan(x.in, what='', nlines=1) # read column names
Read 5 items
c.options - read.table(x.in, as.is=TRUE, nrows=2) # get lines 2-3
c.data - read.table(x.in) # rest of the data
colnames(c.data) - c.names
close(x.in)
c.options # here are lines 2-3
V1 V2 V3 V4 V5
1 color green black black green
2 class Class 1 Class 2 Class 2 Class 1
c.data # your data
wavelength SampleA SampleB SampleC SampleD
1403 0.194 0.214 0.211 0.183
2409 0.192 0.189 0.200 0.182
3415 0.170 0.199 0.194 0.186
4420 0.159 0.191 0.216 0.174
5426 0.150 0.166 0.172 0.158
6432 0.142 0.150 0.162 0.148
On 10/30/07, Bryan Hanson [EMAIL PROTECTED] wrote:
Hi Folks... Œbeen playing with this for a while, with no luck, so I¹m
hoping
someone knows it off the top of their head... Difficult to find this
nuance
in the archives, as so many msgs deal with read.csv!
I¹m trying to read a data file with the following structure (a little piece
of the actual data, they are actually csv just didn¹t paste with the
commas):
wavelength SampleA SampleB SampleC SampleD
color green black black green
class Class 1 Class 2 Class 2 Class 1
403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
432 1.42E-01 1.50E-01 1.62E-01 1.48E-01
Columns after the first one are sample names. 2nd row is the list of
colors
to use in later plotting. 3rd row is the class for later manova. The rest
of it is x data in the first column with y1, y2...following for plotting.
I can read the file w/o the color or class rows with read.csv just fine,
makes a nice data frame with proper data types. The problem comes when
parsing the 2nd and 3rd rows. Here¹s the code:
data = read.csv(filename, header=TRUE) # read in data
color = data[1,]; color = data[-1] # capture color info throw out 1st
value
class = data[2,]; class = class[-1] # capture category info throw out 1st
value
cleaned.data = data[-1,] # remove color category info for matrix
operations
cleaned.data = data[-1,]
freq = data[,1] # capture frequency info
What happens is that freq is parsed as factors, and the color and class are
parsed as a data frames of factors.
I need color and class to be characters which I can pass to functions in
the
typical way one uses colors and levels.
I need the freq the cleaned.data info as numeric for plotting.
I don¹t feel I¹m far off from things working, but that¹s where you all come
in! Seems like an argument of as.something is needed, but the ones I¹ve
tried don¹t work. Would it help to put color and class above the x,y data
in the file, then clean it off?
Btw, I¹m on a Mac using R 2.6.0.
Thanks in advance, Bryan
*
Bryan Hanson
Professor of Chemistry Biochemistry
[R] DBI Package
Hello everyone! Congratulations by this gorgeous software. My name is Germán Carrillo, I'm writting from Colombia. I don't have much experience with R, reason why I use the R-GUI (version 2.5.1) on Windows. I have some problems with DBI package, I want to connect to PostgreSQL database but I don't know the way to do it. I was reading the DBI manual and I tried write in my R Console the next command: pg - dbDriver(PostgreSQL) But R says: Error en do.call(as.character(drvName), list(...)) : no se pudo encontrar la función PostgreSQL I don't know what's happen, I would like to receive some help about this topic, I was looking for in the internet but there's few documentation about this package. Thanks in advance. Best regards. Pdt: Sorry by my english, I'm learning... :) -- --- |\__ (:__)( |/ Soluciones Geoinformáticas Libres http://geotux.tuxfamily.org/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
