Re: [R] Cannot save histogram picture when run from script
Ng Stanley stanleyngkl at gmail.com writes: I am faced with a strange problem. My picture file is empty when the following statements were run from R script. But the picture file shows up correctly, when the commands are individually run from Rgui. png(file=histogram_correlation.png, bg = white) require(stats) histogram( ~ height | voice.part, data = singer, nint = 17, endpoints = c(59.5, 76.5), layout = c(2,4), aspect = 1, xlab = Height (inches)) dev.off() The FAQ of FAQs, but admittely confusing (I remember Douglas Bates calling Deepayan in the middle of the night in India): lattice graphics must be printed in this context. I usually do it in two steps: p = histogram(...) print(p,(add layout if required here)) 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.
[R] Reformatting data into data frame and plotting it in ggplot2
Hello, I am sure this must have been asked before, but my nabble search did not turn anything useful. Just pointer where to look will also be nice. So, I have the following data: x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) These represent time series or frequency spectra, possibly sampled with different sampling frequencies, but obviously having different lengths. The physical meaning of X and Y is the same for the three series above - as I said, time or frequency in my case. Now I want to plot them on the same graph with the legend test1, test2 and test3. ggplot PDF manual says that the data frame is the preferable format for the data to plot. I guess that turning the above data into a data frame would be useful in many other situations as well. So how can I do that? __ 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] Reformatting data into data frame and plotting it in ggplot2
Tribo, Use data.frame() and rbind() to combine the vectors. x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) dataset - rbind(data.frame(Test = Test 1, x = x_test1, y = y_test1), data.frame(Test = Test 2, x = x_test2, y = y_test2), data.frame(Test = Test 3, x = x_test3, y = y_test3)) dataset$Test - factor(dataset$Test) library(ggplot2) ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Tribo Laboy Verzonden: vrijdag 1 februari 2008 9:59 Aan: r-help@r-project.org Onderwerp: [R] Reformatting data into data frame and plotting it in ggplot2 Hello, I am sure this must have been asked before, but my nabble search did not turn anything useful. Just pointer where to look will also be nice. So, I have the following data: x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) These represent time series or frequency spectra, possibly sampled with different sampling frequencies, but obviously having different lengths. The physical meaning of X and Y is the same for the three series above - as I said, time or frequency in my case. Now I want to plot them on the same graph with the legend test1, test2 and test3. ggplot PDF manual says that the data frame is the preferable format for the data to plot. I guess that turning the above data into a data frame would be useful in many other situations as well. So how can I do that? __ 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] Accessing the elements of a list
Hi R,
I wanted to know how do we access the elements of a list. In particular,
v=list(c(1,2,3,4,5),c(1,2,33,4,5),c(1,2,333,4,5),c(1,2,,4,5))
I want to access all the thirds items of the elements of the list. i.e.,
I want to access the elements, 3,33,333,. This can be done through
sapply as:
sapply(v,function(x) x[3])
But I need to access this without using 'sapply'. Like in a data frame,
we do df[2,3] etc Any ideas?
BR, Shubha
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
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and provide commented, minimal, self-contained, reproducible code.
[R] Building a formula using paste
Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? Regards John Seers sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] pixmap_0.4-7 gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 rcom_1.5-2.2 [6] nnet_7.2-38 e1071_1.5-17 class_7.2-38 tree_1.0-26 mgcv_1.3-29 [11] MASS_7.2-38 car_1.2-7 RODBC_1.2-2 RWinEdt_1.7-9 --- __ 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] Building a formula using paste
use as.formula() rather than just formula(). Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of john seers (IFR) Sent: Friday, 1 February 2008 7:31 PM To: [EMAIL PROTECTED] Subject: [R] Building a formula using paste Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? Regards John Seers sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] pixmap_0.4-7 gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 rcom_1.5-2.2 [6] nnet_7.2-38 e1071_1.5-17 class_7.2-38 tree_1.0-26 mgcv_1.3-29 [11] MASS_7.2-38 car_1.2-7 RODBC_1.2-2 RWinEdt_1.7-9 --- __ 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] R2WinBUGS is broken
Dear John,
this is a new bug caused by a side effect from a new bugs.log function
by Jouni Kerman that improves many other things. I have fixed it in the
master sources on sourceforge right now and a bugfix release will appear
on CRAN within a couple of days.
Best,
Uwe Ligges
John Smith wrote:
Dear R-users,
I am trying to use the following code to reproduce results from Prof.
Gelman's book, but have the listed error for R2WinBUGS version (the openbugs
version is good). I am using R-2.6.1 on windows XP, and all the R packages
are most current ones. schools.bug can be found at
http://www.stat.columbia.edu/~gelman/bugsR/runningbugs.html . Can anyone
help me to figure out what's going wrong?
rm(list=ls())
library(R2WinBUGS)
library ('BRugs')
setwd('C:/bayesian/bda/codes/example_5_5')
data(schools)
J - nrow(schools)
y - schools$estimate
sigma.y - schools$sd
data - list(J=J, y=y, sigma.y=sigma.y)
inits - function()
list(theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
sigma.theta=runif(1,0,100))
parameters - c('theta', 'mu.theta', 'sigma.theta')
schools.sim - bugs(data, inits, parameters, model.file='schools.bug',
n.chains=3, n.iter=1000, clearWD=TRUE)
## schools.sim - bugs(data, inits, parameters, model.file='schools.bug',
## n.chains=3, n.iter=1000, clearWD=TRUE,
## program = 'openbugs')
print(schools.sim)
plot(schools.sim)
Error in matrix(unlist(mx), ncol = n.cols, byrow = TRUE) :
invalid 'nrow' value (too large or NA)
Thanks
[[alternative HTML version deleted]]
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Re: [R] Accessing the elements of a list
I find it hard to imagine you need to do it without using sapply. If
you get over your phobia, you might like to try
sapply(v, [, 3)
If the elements of the list are all the same length, as in your example,
you could do
data.frame(v)[3, ]
I think we need to know more about why you think you can't use sapply
before we can really help you, though.
Bill Venables.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Shubha Vishwanath Karanth
Sent: Friday, 1 February 2008 7:05 PM
To: [EMAIL PROTECTED]
Subject: [R] Accessing the elements of a list
Hi R,
I wanted to know how do we access the elements of a list. In particular,
v=list(c(1,2,3,4,5),c(1,2,33,4,5),c(1,2,333,4,5),c(1,2,,4,5))
I want to access all the thirds items of the elements of the list. i.e.,
I want to access the elements, 3,33,333,. This can be done through
sapply as:
sapply(v,function(x) x[3])
But I need to access this without using 'sapply'. Like in a data frame,
we do df[2,3] etc Any ideas?
BR, Shubha
This e-mail may contain confidential and/or privileged
i...{{dropped:13}}
__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Building a formula using paste
Please disregard my previous reply. Now that I have read your question, all becomes clear. To do what you want to do is a bit tricky. Here is one way f1 - as.name(F1) fm - eval(bquote(aov(.(f1) ~ sensoryTerm, data = vdata))) Them fm is the fitted model object, suitably formed. EOE, of course! Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Venables, Bill (CMIS, Cleveland) Sent: Friday, 1 February 2008 7:45 PM To: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [R] Building a formula using paste use as.formula() rather than just formula(). Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of john seers (IFR) Sent: Friday, 1 February 2008 7:31 PM To: [EMAIL PROTECTED] Subject: [R] Building a formula using paste Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? Regards John Seers sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] pixmap_0.4-7 gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 rcom_1.5-2.2 [6] nnet_7.2-38 e1071_1.5-17 class_7.2-38 tree_1.0-26 mgcv_1.3-29 [11] MASS_7.2-38 car_1.2-7 RODBC_1.2-2 RWinEdt_1.7-9 --- __ 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-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] Building a formula using paste
[EMAIL PROTECTED] wrote: use as.formula() rather than just formula(). Hm? That doesn't seem to cut it for me: f - as.formula(y~x) lm(f) Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 summary(lm(f)) Call: lm(formula = f) Residuals: Min 1Q Median 3Q Max -1.2780 -0.4229 -0.3208 0.7534 1.3073 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0.064370.61961 0.1040.920 x -0.097140.09986 -0.9730.359 Residual standard error: 0.907 on 8 degrees of freedom Multiple R-Squared: 0.1058, Adjusted R-squared: -0.005995 F-statistic: 0.9464 on 1 and 8 DF, p-value: 0.3591 etc. The problem is that we get the call and not the formula, and this appears to be the case whether you use formula or as.formula. Also identical(as.formula(y~x), formula(y~x)) [1] TRUE I see two workarounds: (a) Extract the formula explicitly and print it along with the output formula(m) y ~ x m Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 (b) substitution tricks, e.g. eval(bquote(lm(.(f Call: lm(formula = y ~ x) Coefficients: (Intercept)x 0.06437 -0.09714 Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? -- 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] Accessing the elements of a list
Shubha Vishwanath Karanth wrote: Hi R, I wanted to know how do we access the elements of a list. In particular, v=list(c(1,2,3,4,5),c(1,2,33,4,5),c(1,2,333,4,5),c(1,2,,4,5)) I want to access all the thirds items of the elements of the list. i.e., I want to access the elements, 3,33,333,. This can be done through sapply as: sapply(v,function(x) x[3]) But I need to access this without using 'sapply'. Like in a data frame, we do df[2,3] etc Any ideas? Hi, not the most elegant, but this works: cmd unlist(as.data.frame(v)[3,]) c.1..2..3..4..5. c.1..2..33..4..5. c.1..2..333..4..5. c.1..2....4..5. 3 33 333 Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Manipulating the ... args.
Hi,
foo-x(...)
{ # Need to remove bad characters from string arguments ...
# here.
# Pass on the modified string arguments.
bar(...)
}
I need to modify string arguments passed in to function foo
as ... and then pass the modified arguments on to function
bar. Is there a way to access the contents of ... for
in-place modification?
I know I can use args - list(...), but presumably that
takes a copy. Unless there is a way to pass the list
as ... in the call to bar?
Regards,
David.
--
[David Keegan [EMAIL PROTECTED] 353 1 2710818]
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Re: [R] Manipulating the ... args.
I'm no guru, but can you not use do.call here?
i.e. does
foo-function(...) #Not x(...)
{
arglist-list(...)
#remove bad characters from arglist here.
# then
do.call(bar,arglist)
}
do what you want?
David Keegan [EMAIL PROTECTED] 01/02/2008 11:00:15
Hi,
foo-x(...)
{ # Need to remove bad characters from string arguments ...
# here.
# Pass on the modified string arguments.
bar(...)
}
I need to modify string arguments passed in to function foo
as ... and then pass the modified arguments on to function
bar. Is there a way to access the contents of ... for
in-place modification?
I know I can use args - list(...), but presumably that
takes a copy. Unless there is a way to pass the list
as ... in the call to bar?
Regards,
David.
--
[David Keegan [EMAIL PROTECTED] 353 1 2710818]
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[R] Reformatting data into data frame and plotting it in ggplot2
Hello, I am sure this must have been asked before, but my nabble search did not turn anything useful. Just pointer where to look will also be nice. So, I have the following data: x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) These represent time series or frequency spectra, possibly sampled with different sampling frequencies, but obviously having different lengths. The physical meaning of X and Y is the same for the three series above - as I said, time or frequency in my case. Now I want to plot them on the same graph with the legend test1, test2 and test3. ggplot PDF manual says that the data frame is the preferable format for the data to plot. I guess that turning the above data into a data frame would be useful in many other situations as well. So how can I do that? __ 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] Saving a big table or matrix
?save ?load Gabor ps. although i'm not sure what an Rdata-project means, so maybe you need something else On Fri, Feb 01, 2008 at 08:24:32AM +0200, Atte Tenkanen wrote: Dear R-users, How do you save a big table or matrix as an independent object and attach it to your Rdata-project when needed? Atte Tenkanen University of Turku, Finland Department of Musicology +023335278 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] re placing values in a matrix
Actually, you don't need apply. If there are no NA's then it is very easy: m[] - y[ col(m) ] If you want to keep the NA's then it is a bit more tricky: m[] - 0*m + y[ col(m) ] G. On Thu, Jan 31, 2008 at 07:03:51PM -0800, dxc13 wrote: useR's, Consider: y - c(20, 25, 30) m - matrix(c(0.0,1,NA,0.5,1.25,0.75, 0.5, NA, NA),byrow=TRUE,nrow=3,ncol=3) m [,1] [,2] [,3] [1,] 0.0 1.00 NA [2,] 0.5 1.25 0.75 [3,] 0.5 NA NA For each numeric value, I want to replace them with their corresponding y-value. The result should look like (here, each row represents a variable rather than the columns): [,1] [,2] [,3] [1,] 20 25 NA [2,] 20 25 30 [3,] 20 NA NA Does anyone know how I can do this using apply()? Or is there an easier way? Thanks in advance. Derek -- View this message in context: http://www.nabble.com/replacing-values-in-a-matrix-tp15219764p15219764.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] problem getting multiple densityplots on one page
Hi,
I used the following statements to generate unsuccessfully a 5 by 5 multiple
densityplots on a single page. If I use plot, the whole thing works.
data - matrix(rnorm(25), 5, 5)
op - par(mfrow = c(5, 5))
for (x in 1:5) {densityplot(data[,x])}
par(op)
Thanks
Stanley
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[R] random forest and vegetation data
Hi there, I am an environmental studies masters student trying to get my thesis out the door. I am also newbie at trees in general, but I like what I see in the literature about the random forest algorithm. I think I get the general gist of things, but even after reading stuff I’m unclear about how I could be getting the results I’m seeing. I obviously am missing something about how the split points in the final tree are decided. I’ve been using random forests in image classification by entering split values into decision tree classifiers, and that has seemed work very well. The map output appears legitimate and withheld data gives confusion matrices similar to the predictive errors from the random forest. This leads me to assume that the split points are effective. However now that I’ve turned to the ecological portion of my analysis, with a data set that contains few variable levels and lots of zeros, suddenly the splitting node information is not making sense. Here is my situation. I have a matrix of study plots that each belong to one of three elevation classes and which each have percent cover class data for 15 plant species associated with them. plotelevsp1 sp2 sp3… sp15 1 3 0 2 6… 5 2 0 0 0 1… 0 etc. The species data are ordered factors from 0-9. When I run the algorithm using species cover values to predict elevation class, two species alone come up as the best predictors. That makes ecological sense in this setting, given the species ranges in question. Here’s my difficulty though. The split point values can’t be interpreted, as far as I can tell. I’m getting split points of, say, 1.5 and 2.5 for a species who’s cover is either 0 (absent) or 4 and above. So obviously the split points in the final tree are being generated in some way I don’t understand. Averaged? I’ve tried running the tree using the data as factors, using the data as ordered factors, and using the data as numerical variables, just to see if I could gain insight into what’s going on, but I’m coming up clueless. My literature hunt reveals repeated instances of folks saying that the final tree can’t be interpreted the way other trees are, but I’m not getting a lot on just why that might be. Some folks talk about the final tree being “averaged,” others say that “mode,” is employed (which doesn’t make sense to me if I’m getting 1.5 and 2.5 split values). If the trees are only good as black box predictors (which is of course a very useful thing in itself), should I even be using the node information in my image classifications? As you see, I’m missing some rather important point or other here. Can you enlighten? Thanks, A __ 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] Saving a big table or matrix
Dear R-users, How do you save a big table or matrix as an independent object and attach it to your Rdata-project when needed? Atte Tenkanen University of Turku, Finland Department of Musicology +023335278 __ 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] Reformatting data into data frame and plotting it in ggplot2
Hi, Thierry, That was exactly what I was looking for. Thanks. Now I have a data frame with the series data in my workspace, and a plot on the graphics device with color lines and respective color patches on the legend. My next question is about ggplot. Is it possible to make the legend show not only the aesthetics (color in this case), but also the geometry (lines). It would look much better if it showed colored lines or colored dots (if it were) instead of just the patch. But again the ggplot manual didn't have an example for that. Also, what if I wanted to plot with lines+symbol, do I have to use multiple layers? Is it (easily) achievable? Too many questions... I guess it shows I am quite new to R, but I hope to pick it up quickly with some help and shift all my plotting from Matlab to R. On Fri, Feb 1, 2008 at 6:09 PM, ONKELINX, Thierry [EMAIL PROTECTED] wrote: Tribo, Use data.frame() and rbind() to combine the vectors. x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) dataset - rbind(data.frame(Test = Test 1, x = x_test1, y = y_test1), data.frame(Test = Test 2, x = x_test2, y = y_test2), data.frame(Test = Test 3, x = x_test3, y = y_test3)) dataset$Test - factor(dataset$Test) library(ggplot2) ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Tribo Laboy Verzonden: vrijdag 1 februari 2008 9:59 Aan: r-help@r-project.org Onderwerp: [R] Reformatting data into data frame and plotting it in ggplot2 Hello, I am sure this must have been asked before, but my nabble search did not turn anything useful. Just pointer where to look will also be nice. So, I have the following data: x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) These represent time series or frequency spectra, possibly sampled with different sampling frequencies, but obviously having different lengths. The physical meaning of X and Y is the same for the three series above - as I said, time or frequency in my case. Now I want to plot them on the same graph with the legend test1, test2 and test3. ggplot PDF manual says that the data frame is the preferable format for the data to plot. I guess that turning the above data into a data frame would be useful in many other situations as well. So how can I do that? __ 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] problem getting multiple densityplots on one page
On 01/02/2008, Ng Stanley [EMAIL PROTECTED] wrote:
Hi,
I used the following statements to generate unsuccessfully a 5 by 5
multiple
densityplots on a single page. If I use plot, the whole thing works.
data - matrix(rnorm(25), 5, 5)
op - par(mfrow = c(5, 5))
for (x in 1:5) {par(new=TRUE);densityplot(data[,x], xlim=c(...))}
See changes in line above. par(new=TRUE) to overplot and xlim() to have
same x limits. The y-limits can be set the same way if necessary.
untested!
Rainer
par(op)
Thanks
Stanley
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Plant Conservation Unit Department of Botany
University of Cape Town
Rondebosch 7701
South Africa
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building a formula using paste
Thank you very much. That problem has been niggling me for some time. I slotted in your code and it worked. I just need to spend a bit of time understanding it ... Thanks again. John Seers --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: 01 February 2008 09:57 To: [EMAIL PROTECTED]; john seers (IFR); [EMAIL PROTECTED] Subject: RE: [R] Building a formula using paste Please disregard my previous reply. Now that I have read your question, all becomes clear. To do what you want to do is a bit tricky. Here is one way f1 - as.name(F1) fm - eval(bquote(aov(.(f1) ~ sensoryTerm, data = vdata))) Them fm is the fitted model object, suitably formed. EOE, of course! Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Venables, Bill (CMIS, Cleveland) Sent: Friday, 1 February 2008 7:45 PM To: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [R] Building a formula using paste use as.formula() rather than just formula(). Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of john seers (IFR) Sent: Friday, 1 February 2008 7:31 PM To: [EMAIL PROTECTED] Subject: [R] Building a formula using paste Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? Regards John Seers sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] pixmap_0.4-7 gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 rcom_1.5-2.2 [6] nnet_7.2-38 e1071_1.5-17 class_7.2-38 tree_1.0-26 mgcv_1.3-29 [11] MASS_7.2-38 car_1.2-7 RODBC_1.2-2 RWinEdt_1.7-9 --- __ 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-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] Building a formula using paste
Thanks for the help. Regards John Seers --- -Original Message- From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: 01 February 2008 10:04 To: [EMAIL PROTECTED] Cc: john seers (IFR); [EMAIL PROTECTED] Subject: Re: [R] Building a formula using paste [EMAIL PROTECTED] wrote: use as.formula() rather than just formula(). Hm? That doesn't seem to cut it for me: f - as.formula(y~x) lm(f) Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 summary(lm(f)) Call: lm(formula = f) Residuals: Min 1Q Median 3Q Max -1.2780 -0.4229 -0.3208 0.7534 1.3073 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0.064370.61961 0.1040.920 x -0.097140.09986 -0.9730.359 Residual standard error: 0.907 on 8 degrees of freedom Multiple R-Squared: 0.1058, Adjusted R-squared: -0.005995 F-statistic: 0.9464 on 1 and 8 DF, p-value: 0.3591 etc. The problem is that we get the call and not the formula, and this appears to be the case whether you use formula or as.formula. Also identical(as.formula(y~x), formula(y~x)) [1] TRUE I see two workarounds: (a) Extract the formula explicitly and print it along with the output formula(m) y ~ x m Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 (b) substitution tricks, e.g. eval(bquote(lm(.(f Call: lm(formula = y ~ x) Coefficients: (Intercept)x 0.06437 -0.09714 Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? -- 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.
[R] Mixed models
Hello Folks, I'm after some help regarding mixed models. Basically I have sampled a number of different animals at 10 independent sites and am trying to create a mixed model to account for the variation between sites my current model looks like this: mm-glmm.admb(Hep~Sex+Mass, random=~Mouse, group=Location, data=alan, family=binomial, link=logit) I numbered each animal within each site 1-n to create the Mouse variable, then grouped this by Location, it is the variance component of the site that I am interested in so when I get my output with the SD for Mouse is that what I want or have I structured the model incorrectly?? Any help much appreciated, Thanks Alan. Alan Harrison Quercus Queen's University Belfast MBC, 97 Lisburn Road Belfast BT9 7BL T: 02890 972219 M: 07798615682 [[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] Reformatting data into data frame and plotting it in ggplot2
just the patch. But again the ggplot manual didn't have an example for that. Also, what if I wanted to plot with lines+symbol, do I have to use multiple layers? Is it (easily) achievable? Not yet, but I hope to have that working (automatically) in the next version. I'm working on the legend code at the moment, so we'll see how it goes. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem getting multiple densityplots on one page
Sorry - I thought about plot(density())
should read more carefull...
On 01/02/2008, Gavin Simpson [EMAIL PROTECTED] wrote:
On Fri, 2008-02-01 at 14:00 +0200, Rainer M Krug wrote:
On 01/02/2008, Ng Stanley [EMAIL PROTECTED] wrote:
Hi,
I used the following statements to generate unsuccessfully a 5 by 5
multiple
densityplots on a single page. If I use plot, the whole thing works.
data - matrix(rnorm(25), 5, 5)
op - par(mfrow = c(5, 5))
for (x in 1:5) {par(new=TRUE);densityplot(data[,x],
xlim=c(...))}
See changes in line above. par(new=TRUE) to overplot and xlim() to have
same x limits. The y-limits can be set the same way if necessary.
untested!
Rainer
That can't work as densityplot() is a lattice function and thus i) needs
to be wrapped in print( densityplot() ) when in a for loop or similar,
and ii) you can't mix base graphics layout with lattice.
One way to do this is to stack the data one on another and add an ID
variable. stack() does this for you, but there are others or you can
cook it yourself.
dat - data.frame(matrix(rnorm(25), 5, 5))
dat
sdat - stack(dat) ## generates variables 'values' and 'ind'
densityplot(~ values | ind, data = sdat)
HTH
G
par(op)
Thanks
Stanley
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--
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
--
--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT)
Plant Conservation Unit Department of Botany
University of Cape Town
Rondebosch 7701
South Africa
[[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] Reformatting data into data frame and plotting it in ggplot2
Have a look at scale_manual on http://had.co.nz/ggplot2/ This code will give you a key with lines instead of tiles. ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() + scale_colour_manual(values = c(red, blue, green), guide = line) If you want both lines and dots. ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() + geom_point() ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() + geom_point() + scale_colour_manual(values = c(red, blue, green), guide = line) I haven't found a way to get both the lines and the points in the key. But on the other hand do you realy need to have lines in the key? Suppose you want to combine to datasets in one graph: eg. points representing the raw data, dotted lines representing a smoother on the raw data and a continuous lines representing a model based on the raw data. Then the colours would group the points, smoother and model for each level. So what you you put in the key. Points? Dotted lines? Lines? Or all possible combinations of colour (level) and symbol? In such cases I prefer a key with the different colours for each level and a tile is fine for that. The difference between point, dotted line and line can go to the caption of the graph. HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: Tribo Laboy [mailto:[EMAIL PROTECTED] Verzonden: vrijdag 1 februari 2008 12:27 Aan: ONKELINX, Thierry CC: r-help@r-project.org Onderwerp: Re: [R] Reformatting data into data frame and plotting it in ggplot2 Hi, Thierry, That was exactly what I was looking for. Thanks. Now I have a data frame with the series data in my workspace, and a plot on the graphics device with color lines and respective color patches on the legend. My next question is about ggplot. Is it possible to make the legend show not only the aesthetics (color in this case), but also the geometry (lines). It would look much better if it showed colored lines or colored dots (if it were) instead of just the patch. But again the ggplot manual didn't have an example for that. Also, what if I wanted to plot with lines+symbol, do I have to use multiple layers? Is it (easily) achievable? Too many questions... I guess it shows I am quite new to R, but I hope to pick it up quickly with some help and shift all my plotting from Matlab to R. On Fri, Feb 1, 2008 at 6:09 PM, ONKELINX, Thierry [EMAIL PROTECTED] wrote: Tribo, Use data.frame() and rbind() to combine the vectors. x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) dataset - rbind(data.frame(Test = Test 1, x = x_test1, y = y_test1), data.frame(Test = Test 2, x = x_test2, y = y_test2), data.frame(Test = Test 3, x = x_test3, y = y_test3)) dataset$Test - factor(dataset$Test) library(ggplot2) ggplot(data = dataset, aes(x = x, y = y, colour = Test)) + geom_line() HTH, Thierry -- -- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Tribo Laboy Verzonden: vrijdag 1 februari 2008 9:59 Aan: r-help@r-project.org Onderwerp: [R] Reformatting data into data frame and plotting it in ggplot2 Hello, I am sure this must have been asked before, but my nabble search did not turn anything useful. Just pointer where to look will also be nice. So, I have the following data: x_test1 - c(1:10) y_test1-rnorm(10) x_test2 - c(1:15) y_test2-rnorm(15) x_test3 - c(1:20) y_test3-rnorm(20) These represent time series or frequency spectra, possibly sampled with different sampling frequencies, but obviously having different lengths. The physical meaning of X and Y is
Re: [R] x11() and Xinerama settings
On Friday 07 December 2007, Thomas Zumbrunn wrote: Since I changed my X11 settings to a Xinerama setup, calls to x11() result in windows with a width half the size of the one specified by the corresponding parameter. Furthermore, x axis labels are overlapping. Other devices (e.g. pdf()), are not affected by these distortions. Did anybody have the same problem, and if so, how did you solve it? ( I'm using openSUSE 10.3 on a x86 architecture.) I reply to my own question in order to provide a short summary of what I found out since it might be helpful for some GNU/Linux users of R. Because I got no answer on the this list, I - which was wrong - filed a bug against R. Prof. Ripley pointed out that my X11 settings must be wrong and that most probably the DisplaySize setting in xorg.conf is wrong. This was actually the case. In my Xinerama setup, the DisplaySize width value was the sum of both devices. The xorg.conf was generated by the openSUSE tool SaX2, and I therefore filed a bug against it: https://bugzilla.novell.com/show_bug.cgi?id=357597 The bug is now fixed, and the DisplaySize width value is now only representing the widht of the corresponding device. For those who are also affected by this problem: To fix distorted R x11() windows, simply fix the DisplaySize values in your xorg.conf file and restart your X server. Thanks go to Prof. Ripley for pointing me in the right direction and also to Marc Schwartz and Hin-Tak Leung for further useful advice. __ 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] re placing values in a matrix
Derek, the 0*m part zeros out everything in the matrix, expect for the NA's, 0*NA=NA by definition. If we add this to the y[ col(m) ] matrix, then NA+anything=NA, but 0+anything=anything. G. ps. please answer to the list (as well) On Fri, Feb 01, 2008 at 08:52:50AM -0500, Derek Cyr wrote: Thank you, that works very nicely. I am a little curious as to why you need to do 0*m and add that to y[col(m)] in the second expression. It works perfectly, but I am just not sure how, lol. Thanks D [...] Actually, you don't need apply. If there are no NA's then it is very easy: m[] - y[ col(m) ] If you want to keep the NA's then it is a bit more tricky: m[] - 0*m + y[ col(m) ] G. On Thu, Jan 31, 2008 at 07:03:51PM -0800, dxc13 wrote: useR's, Consider: y - c(20, 25, 30) m - matrix(c(0.0,1,NA,0.5,1.25,0.75, 0.5, NA, NA),byrow=TRUE,nrow=3,ncol=3) m [,1] [,2] [,3] [1,] 0.0 1.00 NA [2,] 0.5 1.25 0.75 [3,] 0.5 NA NA For each numeric value, I want to replace them with their corresponding y-value. The result should look like (here, each row represents a variable rather than the columns): [,1] [,2] [,3] [1,] 20 25 NA [2,] 20 25 30 [3,] 20 NA NA Does anyone know how I can do this using apply()? Or is there an easier way? Thanks in advance. Derek -- View this message in context: http://www.nabble.com/replacing-values-in-a-matrix-tp15219764p15219764.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] fastest way to compute the squared Euclidean distance between two vectors in R
Jason Liao [EMAIL PROTECTED] writes:
I have a program which needs to compute squared Euclidean distance
between two vectors million of times, which the Rprof shows is the
bottleneck. I wondered if there is any faster way than my own simple
function
distance2 = function(x1, x2)
{
temp = x1-x2
sum(temp*temp)
}
You might try:
distance2 - function(x1, x2) crossprod(x1-x2)
And if you do not have to pass the distance2 function itself to some
other function, you might also spare the indirection trhough the
distance2 function and call crossprod directly (replacing the comma by
a minus sign :-).
--
François Pinard http://pinard.progiciels-bpi.ca
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[R] using VSS
hi, i start working with PCA method i found VSS package it is very helpfull it show me residual matrix with the number of components to extract now i want to verify the normality of residual matrix and than to simulate can every one help me please . THANK YOU and excuse me for my bad english. - [[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] Reformatting data into data frame and plotting it in ggplot2
Tribo That function was added during the latest update. So you should update to this version (0.5.7). You can update packages with update.packages() Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: Tribo Laboy [mailto:[EMAIL PROTECTED] Verzonden: vrijdag 1 februari 2008 15:18 Aan: ONKELINX, Thierry CC: r-help@r-project.org Onderwerp: Re: [R] Reformatting data into data frame and plotting it in ggplot2 For some reason I get the following error: Error: could not find function scale_colour_manual so I couldn't make the plots. Otherwise I completely agree that color is good way to summarize in the key several different models and operations performed on the same data (it is always a trick to find colors that print clearly in black and white). But in my case I just want to plot the raw data and to distinguish it in the key. Regards. __ 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] Concatenate a Variable
Hi Carla, Try paste(VAR: ,a,sep=) Jorge On 2/1/08, Carla Rebelo [EMAIL PROTECTED] wrote: Good morning! I do not speak English very well and so I will try to explain the best I can. I have this: tabela[,1] [1] a a b b a c b a c c c c c Levels: a b c unique(tabela[,1]) [1] a b c Levels: a b c var-unique(tabela[,1])[1] var [1] a Levels: a b c But if I concatenate like this cat(VAR: , var, \n) I obtain VAR: 1 and I want to obtain VAR: a How can I do this? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reformatting data into data frame and plotting it in ggplot2
Hi Hadley, Thanks for ggplot. Great piece of work. Very intuitive. The legend always seems to be the most difficult part to implement in any plotting package. gnuplot and RLplot come to mind. Good luck! On Fri, Feb 1, 2008 at 10:17 PM, hadley wickham [EMAIL PROTECTED] wrote: just the patch. But again the ggplot manual didn't have an example for that. Also, what if I wanted to plot with lines+symbol, do I have to use multiple layers? Is it (easily) achievable? Not yet, but I hope to have that working (automatically) in the next version. I'm working on the legend code at the moment, so we'll see how it goes. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Concatenate a Variable
Good morning! I do not speak English very well and so I will try to explain the best I can. I have this: tabela[,1] [1] a a b b a c b a c c c c c Levels: a b c unique(tabela[,1]) [1] a b c Levels: a b c var-unique(tabela[,1])[1] var [1] a Levels: a b c But if I concatenate like this cat(VAR: , var, \n) I obtain VAR: 1 and I want to obtain VAR: a How can I do this? Thanks! __ 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] Bug with curve?
Dear All, Take this code: f - function(x) exp(-x)*x-0.05 g - function(x) 0 curve(f,0,5) curve(g,add=T) Error in xy.coords(x, y) : 'x' and 'y' lengths differ However, with g - function(x) x-x no error is generated. Is this a bug? I am using version _ platform i386-redhat-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major 2 minor 6.1 year 2007 month 11 day26 svn rev43537 language R version.string R version 2.6.1 (2007-11-26) Thanks in advance, Paul __ 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] Is it possible with two random effects in lme()?
Dear all, Is it possible with two random effects in lme()? lmefit1- lme(Handling ~ Mass + factor(Prey)+ Mass*factor(Prey), random = ~ 1 |Place+Age) Here I use Place as random effect, but I also want to add Age as a random effect. Since there could be an effect of Age (continous variable), but I like to control for it rather than locking at the effect of Age on handling time, since Mass and Prey type are of main interest. Regards Kes, [[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] problem getting multiple densityplots on one page
hits=-2.6 tests=BAYES_00
X-USF-Spam-Flag: NO
On Fri, 2008-02-01 at 14:00 +0200, Rainer M Krug wrote:
On 01/02/2008, Ng Stanley [EMAIL PROTECTED] wrote:
Hi,
I used the following statements to generate unsuccessfully a 5 by 5
multiple
densityplots on a single page. If I use plot, the whole thing works.
data - matrix(rnorm(25), 5, 5)
op - par(mfrow = c(5, 5))
for (x in 1:5) {par(new=TRUE);densityplot(data[,x], xlim=c(...))}
See changes in line above. par(new=TRUE) to overplot and xlim() to have
same x limits. The y-limits can be set the same way if necessary.
untested!
Rainer
That can't work as densityplot() is a lattice function and thus i) needs
to be wrapped in print( densityplot() ) when in a for loop or similar,
and ii) you can't mix base graphics layout with lattice.
One way to do this is to stack the data one on another and add an ID
variable. stack() does this for you, but there are others or you can
cook it yourself.
dat - data.frame(matrix(rnorm(25), 5, 5))
dat
sdat - stack(dat) ## generates variables 'values' and 'ind'
densityplot(~ values | ind, data = sdat)
HTH
G
par(op)
Thanks
Stanley
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Re: [R] Concatenate a Variable
Carla Rebelo wrote: Good morning! I do not speak English very well and so I will try to explain the best I can. I have this: tabela[,1] [1] a a b b a c b a c c c c c Levels: a b c unique(tabela[,1]) [1] a b c Levels: a b c var-unique(tabela[,1])[1] var [1] a Levels: a b c But if I concatenate like this cat(VAR: , var, \n) I obtain VAR: 1 and I want to obtain VAR: a How can I do this? Thanks! The devil is in the Details -section of help(cat): Other types of R object should be converted (e.g. by 'as.character' or 'format') before being passed to 'cat'. cat(VAR: , factor(a), \n) VAR: 1 cat(VAR: , format(factor(a)), \n) VAR: a cat(VAR: , as.character(factor(a)), \n) VAR: a __ 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. -- 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.
[R] Off-topic - FORM/SORM
Greetings: FORM/SORM (First/Second Order Reliability Methods) are very popular among some structural engineers but almost never discussed among statisticians. I am quite predudiced as to the reasons for this, but would enquire among the world's statistical thinkers for their perspectives on these methods. Any comments, pro or con, would be greatly appreciated. Since this is off-topic, you may wish to reply directly to me and I will summarize the comments to the group. Thank you. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com [[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] Concatenate a Variable
Carla Rebelo wrote: Good morning! I do not speak English very well and so I will try to explain the best I can. I have this: tabela[,1] [1] a a b b a c b a c c c c c Levels: a b c unique(tabela[,1]) [1] a b c Levels: a b c var-unique(tabela[,1])[1] var [1] a Levels: a b c But if I concatenate like this cat(VAR: , var, \n) I obtain VAR: 1 and I want to obtain VAR: a How can I do this? Thanks! 'a' is a factor, thus you are getting the underlying numeric code as the output. Note from ?cat: Currently only atomic vectors (and so not lists) and names are handled. Character strings are output ‘as is’ (unlike print.default which escapes non-printable characters and backslash — use encodeString if you want to output encoded strings using cat). Other types of R object should be converted (e.g. by as.character or format) before being passed to cat. Thus: var - factor(a, levels = c(a, b, c)) var [1] a Levels: a b c is.vector(var) [1] FALSE So 'var' is not an atomic vector and you must therefore coerce it to a character vector using as.character() before passing it to cat(): cat(VAR: , as.character(var), \n) VAR: a HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bug with curve?
Paul Smith wrote: f - function(x) exp(-x)*x-0.05 g - function(x) 0 curve(f,0,5) curve(g,add=T) Error in xy.coords(x, y) : 'x' and 'y' lengths differ However, with g - function(x) x-x no error is generated. Is this a bug? No; simplify it: g1 - function(x) 0 g2 - function(x) x - x g1(anything) will return (scalar) 0 g2(scalar) will return (scalar) 0, g2(vector) will return (vector) 0, g2(matrix) will return (matrix) 0. So, in your original problem, f and (first) g have different behaviours. Alberto Monteiro __ 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] Reformatting data into data frame and plotting it in ggplot2
For some reason I get the following error: Error: could not find function scale_colour_manual so I couldn't make the plots. Otherwise I completely agree that color is good way to summarize in the key several different models and operations performed on the same data (it is always a trick to find colors that print clearly in black and white). But in my case I just want to plot the raw data and to distinguish it in the key. Regards. __ 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] Bug with curve?
Paul Smith phhs80 at gmail.com writes: Dear All, Take this code: f - function(x) exp(-x)*x-0.05 g - function(x) 0 curve(f,0,5) curve(g,add=T) Error in xy.coords(x, y) : 'x' and 'y' lengths differ However, with g - function(x) x-x no error is generated. The first paragraph of details in the help page says: . 'x(t)' or 'expr' (with 'x' inside) must return a numeric of the same length as the argument 't' or 'x'. So no, technically this is not a bug. The R idiom for adding a horizontal line to the plot is abline(h=...) cheers Ben Bolker __ 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] Building a formula using paste
This is discussed in this thread: http://tolstoy.newcastle.edu.au/R/e2/help/07/01/9353.html This mostly goes over the ground discussed here plus there is a do.call based solution there too. On Feb 1, 2008 7:10 AM, john seers (IFR) [EMAIL PROTECTED] wrote: Thanks for the help. Regards John Seers --- -Original Message- From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: 01 February 2008 10:04 To: [EMAIL PROTECTED] Cc: john seers (IFR); [EMAIL PROTECTED] Subject: Re: [R] Building a formula using paste [EMAIL PROTECTED] wrote: use as.formula() rather than just formula(). Hm? That doesn't seem to cut it for me: f - as.formula(y~x) lm(f) Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 summary(lm(f)) Call: lm(formula = f) Residuals: Min 1Q Median 3Q Max -1.2780 -0.4229 -0.3208 0.7534 1.3073 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0.064370.61961 0.1040.920 x -0.097140.09986 -0.9730.359 Residual standard error: 0.907 on 8 degrees of freedom Multiple R-Squared: 0.1058, Adjusted R-squared: -0.005995 F-statistic: 0.9464 on 1 and 8 DF, p-value: 0.3591 etc. The problem is that we get the call and not the formula, and this appears to be the case whether you use formula or as.formula. Also identical(as.formula(y~x), formula(y~x)) [1] TRUE I see two workarounds: (a) Extract the formula explicitly and print it along with the output formula(m) y ~ x m Call: lm(formula = f) Coefficients: (Intercept)x 0.06437 -0.09714 (b) substitution tricks, e.g. eval(bquote(lm(.(f Call: lm(formula = y ~ x) Coefficients: (Intercept)x 0.06437 -0.09714 Hi All I have looked but cannot find an answer to this. I want to build a formula dynamically (in a function), using for example paste, and using it in a model: fr-F1 f1-formula(paste(fr, ~ SensoryTerm)) m1-aov(f1, data=vdata) So this is the equivalent of m1-aov(F1 ~ SensoryTerm, data=vdata) This works fine but the problem is the formula appears as f1 in the summary(m1) of the model and not F1 ~ SensoryTerm. With many models this can be a bit confusing Is there a way to code this so the formula appears in the model summary? -- 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. __ 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] Log rank test power
Does anyone have any ideas how I could do a power calculation for a log rank test. I would like to know what the suggested sample sizes would be to pick a difference when the control to active are in a ratio of 80% to 20%. Power for a log-rank test is the same as power for a Cox model. For a 2-arm study d = (qnorm(.975) + qnorm(.85))^2 / (.2 *.8 * coef^2) d = # deaths required .975 = two sided alpha=.05 .85 = power of .85 .2, .8 = proportion in each group coef = Cox model coef you want power against. So for a 50% difference in hazard rates (or median survival times) coef = log(1.5). For a 50% change I get d=341. Now for the hard part of sample size in a survival study: how many people to you need to enroll and how long will you need to follow them, to observe 341 total deaths? This second step is usually a mix of prior knowlege, enrollment expectations, and wild speculation. In the words of a prior director of research at U of Rochester: At the commencement of a study the incidence of the disease in question will drop by one half, and will not return to its former levels until the study ends or the principle investigator retires, whichever comes first. L.L. Terry Therneau __ 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] Bug with curve?
On Feb 1, 2008 2:46 PM, Martin Maechler [EMAIL PROTECTED] wrote: Take this code: f - function(x) exp(-x)*x-0.05 g - function(x) 0 curve(f,0,5) curve(g,add=T) Error in xy.coords(x, y) : 'x' and 'y' lengths differ However, with g - function(x) x-x no error is generated. BB The first paragraph of details in the help page BB says: BB . 'x(t)' or 'expr' (with 'x' inside) must return a numeric of the same BB length as the argument 't' or 'x'. yes, thanks Ben. BB So no, technically this is not a bug. why only technically? Paul wouldn't also be able to integrate(g, .), just the error message would be slightly more helpful : Error in integrate(g, 0, 1) : evaluation of function gave a result of wrong length BB The R idiom for adding a horizontal line to the plot is BB abline(h=...) BB cheers BB Ben Bolker Thanks to all for the clarification. Paul __ 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] multiple functions with three dots
Dear all,
I am creating functions with the three dot strategy. I wold like to have
suggestion when writing multiple functions that calls multiple functions
with
I will give you a couple of example:
a=1:5
b=6:10
d=3:7
example=function(x,y, z, ...){
plot(x,y, ...)
points(x,z, ...)
}
example(a,b,d)
how can I set different parameters for points and plot functions? for
example in plot I want to have bigger dots (lwd=3), while in the points I
want to have green dots.
any suggestion?
thank you.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving a big table or matrix
I had a problem: I saved a matrix: save(Tondistmatrix1, file=/Users/atte/Skriptit/Tondistmatrix1) then I tried to open it with R: Tondistmatrix1=load(/Users/atte/Skriptit/Tondistmatrix1) Tondistmatrix1[1:10,] Error in Tondistmatrix1[1:10, ] : incorrect number of dimensions dim(Tondistmatrix1) NULL So, this didn't work but then I noticed that this is enough load(/Users/atte/Skriptit/Tondistmatrix1) dim(Tondistmatrix1) [1] 3938 3938 No problems any more... Atte Tenkanen University of Turku, Finland Department of Musicology +023335278 - Original Message - From: Gabor Csardi [EMAIL PROTECTED] Date: Friday, February 1, 2008 1:43 pm Subject: Re: [R] Saving a big table or matrix ?save ?load Gabor ps. although i'm not sure what an Rdata-project means, so maybe you need something else On Fri, Feb 01, 2008 at 08:24:32AM +0200, Atte Tenkanen wrote: Dear R-users, How do you save a big table or matrix as an independent object and attach it to your Rdata-project when needed? Atte Tenkanen University of Turku, Finland Department of Musicology +023335278 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] dynamic SQL query in RMySQL
Is there a way to perform a dynamic SQL query in R, using RMySQL? Thanks My D. Coyne [[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] Concatenate a Variable
R is treating tablea[,1] as a factor. Try converting it to character. --- Carla Rebelo [EMAIL PROTECTED] wrote: Good morning! I do not speak English very well and so I will try to explain the best I can. I have this: tabela[,1] [1] a a b b a c b a c c c c c Levels: a b c unique(tabela[,1]) [1] a b c Levels: a b c var-unique(tabela[,1])[1] var [1] a Levels: a b c But if I concatenate like this cat(VAR: , var, \n) I obtain VAR: 1 and I want to obtain VAR: a How can I do this? Thanks! __ 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. Looking for the perfect gift? Give the gift of Flickr! __ 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] Bug with curve?
BB == Ben Bolker [EMAIL PROTECTED] on Fri, 1 Feb 2008 14:03:15 + (UTC) writes: BB Paul Smith phhs80 at gmail.com writes: Dear All, Take this code: f - function(x) exp(-x)*x-0.05 g - function(x) 0 curve(f,0,5) curve(g,add=T) Error in xy.coords(x, y) : 'x' and 'y' lengths differ However, with g - function(x) x-x no error is generated. BB The first paragraph of details in the help page BB says: BB . 'x(t)' or 'expr' (with 'x' inside) must return a numeric of the same BB length as the argument 't' or 'x'. yes, thanks Ben. BB So no, technically this is not a bug. why only technically? Paul wouldn't also be able to integrate(g, .), just the error message would be slightly more helpful : Error in integrate(g, 0, 1) : evaluation of function gave a result of wrong length BB The R idiom for adding a horizontal line to the plot is BB abline(h=...) BB cheers BB Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replace Null with NA
Try this: x[x==] - NA On 01/02/2008, My Coyne [EMAIL PROTECTED] wrote: I would like to replace all null () in a column of a matrix to NA, how would I do that without a do loop? Thanks --mc [[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. -- 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] replace Null with NA
I would like to replace all null () in a column of a matrix to NA, how would I do that without a do loop? Thanks --mc [[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] as.numeric rounds up
Hi list, It seems that as.numeric is rounding up my numbers that are in a character format. Example: a [1] 776554.45 776985.31 776076.03 776092.01 776151.42 776276.97 b - as.numeric(a) b [1] 776554.4 776985.3 776076.0 776092.0 776151.4 776277.0 I've tried as.numeric(a,2) and as.numeric(a, digits = 2) but it didn't work, nor ? as.numeric gave me any clues. How can i transform my character numbers in numeric without loosing the decimal digits? Thanks, Monica _ [[elided Hotmail spam]] __ 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] multiple functions with three dots
You can try something like:
a - 1:5
b - 6:10
d - 3:7
example - function(x,y, z, ..., plot.dots, points.dots){
plot.list - list(x=x,y=y)
plot.list - c(plot.list,list(...), as.list(plot.dots))
do.call(plot, plot.list)
points.list - list(x=x,y=z)
points.list - c(points.list, list(...), as.list(points.dots) )
do.call(points, points.list)
}
example(a,b,d, pch=0, plot.dots=list(cex=2),
points.dots=list(col='green'))
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of John Lande
Sent: Friday, February 01, 2008 7:34 AM
To: r-help@r-project.org
Subject: [R] multiple functions with three dots
Dear all,
I am creating functions with the three dot strategy. I wold
like to have suggestion when writing multiple functions that
calls multiple functions with
I will give you a couple of example:
a=1:5
b=6:10
d=3:7
example=function(x,y, z, ...){
plot(x,y, ...)
points(x,z, ...)
}
example(a,b,d)
how can I set different parameters for points and plot
functions? for example in plot I want to have bigger dots
(lwd=3), while in the points I want to have green dots.
any suggestion?
thank you.
[[alternative HTML version deleted]]
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Re: [R] as.numeric rounds up
options(digits=10) b or just print(b, 10) On 01/02/2008, Monica Pisica [EMAIL PROTECTED] wrote: Hi list, It seems that as.numeric is rounding up my numbers that are in a character format. Example: a [1] 776554.45 776985.31 776076.03 776092.01 776151.42 776276.97 b - as.numeric(a) b [1] 776554.4 776985.3 776076.0 776092.0 776151.4 776277.0 I've tried as.numeric(a,2) and as.numeric(a, digits = 2) but it didn't work, nor ? as.numeric gave me any clues. How can i transform my character numbers in numeric without loosing the decimal digits? Thanks, Monica _ [[elided Hotmail spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] as.numeric rounds up - Thanks!
So this is only a cosmetic printing and actually my numbers do have 2 decimal numbers . Thanks, Monica Date: Fri, 1 Feb 2008 16:27:00 -0200 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: Re: [R] as.numeric rounds up CC: r-help@r-project.org options(digits=10) b or just print(b, 10) On 01/02/2008, Monica Pisica [EMAIL PROTECTED] wrote:Hi list, It seems that as.numeric is rounding up my numbers that are in a character format. Example: a [1] 776554.45 776985.31 776076.03 776092.01 776151.42 776276.97b - as.numeric(a) b [1] 776554.4 776985.3 776076.0 776092.0 776151.4 776277.0 I've tried as.numeric(a,2) and as.numeric(a, digits = 2) but it didn't work, nor ? as.numeric gave me any clues. How can i transform my character numbers in numeric without loosing the decimal digits? Thanks, Monica _ [[elided Hotmail spam]] __ 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 _ Helping your favorite cause is as easy as instant messaging. You IM, we give. [[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] the union of several data frame rows
It's ugly, but you could use something like sum(tmp[i,] == A) 0 on each column. pax, Scott On Fri, Feb 1, 2008 at 1:58 PM, Scot W. McNary [EMAIL PROTECTED] wrote: Hi, I have a question about how to obtain the union of several data frame rows. I'm trying to create a common key for several tests composed of different items. Here is a small scale version of the problem. These are keys for 4 different tests, not all mutually exclusive: id q1 q2 q3 q4 q5 q6 1 A C 2 B D 3 A D B 4 C D B D I would like to create a single key all test versions, the union of the above: id q1 q2 q3 q4 q5 q6 key A C D B B D Here is what I have (unsuccessfully) tried so far: key - + matrix(c(1, A, C, , , , , + 2, , , , , B, D, + 3, A, , D, B, , , + 4, , C, D, , B, D), +byrow=TRUE, ncol = 7) k1 - key[1, 2:7] k2 - key[2, 2:7] k3 - key[3, 2:7] k4 - key[4, 2:7] itemid - c(q1, q2, q3, q4, q5, q6) k1 - cbind(itemid, k1) k2 - cbind(itemid, k2) k3 - cbind(itemid, k3) k4 - cbind(itemid, k4) tmp - merge(k1, k2, by = itemid) tmp - merge(tmp, k3, by = itemid) tmp - merge(tmp, k4, by = itemid) t(tmp) [,1] [,2] [,3] [,4] [,5] [,6] itemid q1 q2 q3 q4 q5 q6 k1 A C k2 B D k3 A D B k4C D B D The actual problem involves 300 or so items instead of 6 and 10 different keys instead of four. Any suggestions welcome. Thanks in advance, Scot McNary version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 6.1 year 2007 month 11 day26 svn rev43537 language R version.string R version 2.6.1 (2007-11-26) -- Scot McNary smcnary at charm dot net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the union of several data frame rows
Perhaps: data - data.frame(key, row.names=1) names(data) - paste(q, 1:6, sep=) apply(data, 2, function(x)unique(x)[unique(x) != ]) On 01/02/2008, Scot W. McNary [EMAIL PROTECTED] wrote: Hi, I have a question about how to obtain the union of several data frame rows. I'm trying to create a common key for several tests composed of different items. Here is a small scale version of the problem. These are keys for 4 different tests, not all mutually exclusive: id q1 q2 q3 q4 q5 q6 1 A C 2 B D 3 A D B 4 C D B D I would like to create a single key all test versions, the union of the above: id q1 q2 q3 q4 q5 q6 key A C D B B D Here is what I have (unsuccessfully) tried so far: key - + matrix(c(1, A, C, , , , , + 2, , , , , B, D, + 3, A, , D, B, , , + 4, , C, D, , B, D), +byrow=TRUE, ncol = 7) k1 - key[1, 2:7] k2 - key[2, 2:7] k3 - key[3, 2:7] k4 - key[4, 2:7] itemid - c(q1, q2, q3, q4, q5, q6) k1 - cbind(itemid, k1) k2 - cbind(itemid, k2) k3 - cbind(itemid, k3) k4 - cbind(itemid, k4) tmp - merge(k1, k2, by = itemid) tmp - merge(tmp, k3, by = itemid) tmp - merge(tmp, k4, by = itemid) t(tmp) [,1] [,2] [,3] [,4] [,5] [,6] itemid q1 q2 q3 q4 q5 q6 k1 A C k2 B D k3 A D B k4C D B D The actual problem involves 300 or so items instead of 6 and 10 different keys instead of four. Any suggestions welcome. Thanks in advance, Scot McNary version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 6.1 year 2007 month 11 day26 svn rev43537 language R version.string R version 2.6.1 (2007-11-26) -- Scot McNary smcnary at charm dot net __ 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] the union of several data frame rows
Hi, I have a question about how to obtain the union of several data frame rows. I'm trying to create a common key for several tests composed of different items. Here is a small scale version of the problem. These are keys for 4 different tests, not all mutually exclusive: id q1 q2 q3 q4 q5 q6 1 A C 2 B D 3 A D B 4 C D B D I would like to create a single key all test versions, the union of the above: id q1 q2 q3 q4 q5 q6 key A C D B B D Here is what I have (unsuccessfully) tried so far: key - + matrix(c(1, A, C, , , , , + 2, , , , , B, D, + 3, A, , D, B, , , + 4, , C, D, , B, D), +byrow=TRUE, ncol = 7) k1 - key[1, 2:7] k2 - key[2, 2:7] k3 - key[3, 2:7] k4 - key[4, 2:7] itemid - c(q1, q2, q3, q4, q5, q6) k1 - cbind(itemid, k1) k2 - cbind(itemid, k2) k3 - cbind(itemid, k3) k4 - cbind(itemid, k4) tmp - merge(k1, k2, by = itemid) tmp - merge(tmp, k3, by = itemid) tmp - merge(tmp, k4, by = itemid) t(tmp) [,1] [,2] [,3] [,4] [,5] [,6] itemid q1 q2 q3 q4 q5 q6 k1 A C k2 B D k3 A D B k4C D B D The actual problem involves 300 or so items instead of 6 and 10 different keys instead of four. Any suggestions welcome. Thanks in advance, Scot McNary version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 6.1 year 2007 month 11 day26 svn rev43537 language R version.string R version 2.6.1 (2007-11-26) -- Scot McNary smcnary at charm dot net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random forest and vegetation data
First things first: There's no final tree in random forests. You get
a set of trees (i.e., a forest). Secondly, a forest cannot be
interpreted because of the complexity, not because the splits can't
possibly make sense. You can try to interpret the trees, as long as you
understand the potential pitfalls of doing that.
Here's how ordered factors are handled in randomForest. Since the tree
algorithm only make use of the ranks, there's basically no difference
between numerical and ordinal variables. Thus ordered factors are
simply treated as integers 1 through K where K is the number or levels,
and the underlying algorithm is told that this is just a numeric
variable. This is how a split point of something like 3.5 appears.
Hope that make some sense.
Best,
Andy
From: [EMAIL PROTECTED]
Hi there,
I am an environmental studies masters student trying to get
my thesis out the door. I am also newbie at trees in
general, but I like what I see in the literature about the
random forest algorithm. I think I get the general gist of
things, but even after reading stuff I'm unclear about how I
could be getting the results I'm seeing. I obviously am
missing something about how the split points in the final
tree are decided.
I've been using random forests in image classification by
entering split values into decision tree classifiers, and
that has seemed work very well. The map output appears
legitimate and withheld data gives confusion matrices similar
to the predictive errors from the random forest. This leads
me to assume that the split points are effective.
However now that I've turned to the ecological portion of my
analysis, with a data set that contains few variable levels
and lots of zeros, suddenly the splitting node information is
not making sense.
Here is my situation. I have a matrix of study plots that
each belong to one of three elevation classes and which each
have percent cover class data for 15 plant species associated
with them.
plot elevsp1 sp2 sp3... sp15
1 3 0 2 6... 5
2 0 0 0 1... 0
etc.
The species data are ordered factors from 0-9. When I run
the algorithm using species cover values to predict elevation
class, two species alone come up as the best predictors.
That makes ecological sense in this setting, given the
species ranges in question.
Here's my difficulty though. The split point values can't be
interpreted, as far as I can tell. I'm getting split points
of, say, 1.5 and 2.5 for a species who's cover is either 0
(absent) or 4 and above. So obviously the split points in
the final tree are being generated in some way I don't
understand. Averaged?
I've tried running the tree using the data as factors, using
the data as ordered factors, and using the data as numerical
variables, just to see if I could gain insight into what's
going on, but I'm coming up clueless. My literature hunt
reveals repeated instances of folks saying that the final
tree can't be interpreted the way other trees are, but I'm
not getting a lot on just why that might be.
Some folks talk about the final tree being averaged, others
say that mode, is employed (which doesn't make sense to me
if I'm getting 1.5 and 2.5 split values). If the trees are
only good as black box predictors (which is of course a very
useful thing in itself), should I even be using the node
information in my image classifications?
As you see, I'm missing some rather important point or other
here. Can you enlighten?
Thanks,
A
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[R] latent class analysis
Hi, does some one know how to run the latent class analysis in R? like which package and command I should use? thanks a lot, Suyan Tian __ 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] overlapping intervals
hi!! Below I have 4 columns vector of c and d which are unequal in length.These c and d have 2 columns each where these 2 columns represent an interval values. How am I going to get an overlapping over these interval values?? Please help me sort this problem!! Thanks in advance.. c d 17130612 17587118 17712302 18100404 17712302 18221688 21203780 21387314 21225764 21387314 25012714 30748348 25012714 30748348 33852816 34384588 33852816 34480192 34794536 35996440 36012944 36209144 36252300 36280276 36737468 36971144 43693832 43878548 - [[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] Phase Shift
On Fri, 1 Feb 2008, stephen sefick wrote: Is there any implementation in R for finding the phase shift between two continuous signals. I would like to find the average phase shift for tow signals over two years. Following the _posting guide_, we have: RSiteSearch(phase shift) Also, you might look at ?acf example( acf ) HTH, Chuck thanks Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. 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.
Re: [R] overlapping intervals
On Fri, 1 Feb 2008, mohamed nur anisah wrote: hi!! Below I have 4 columns vector of c and d which are unequal in length.These c and d have 2 columns each where these 2 columns represent an interval values. How am I going to get an overlapping over these interval values?? Please help me sort this problem!! Thanks in advance.. Perhaps this is what you need: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/60815.html If not, you should repost showing what you think the answer should be for your problem below. HTH, Chuck c d 17130612 17587118 17712302 18100404 17712302 18221688 21203780 21387314 21225764 21387314 25012714 30748348 25012714 30748348 33852816 34384588 33852816 34480192 34794536 35996440 36012944 36209144 36252300 36280276 36737468 36971144 43693832 43878548 - [[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. 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.
Re: [R] latent class analysis
try flexmix. On Feb 1, 2008 3:23 PM, Suyan Tian [EMAIL PROTECTED] wrote: Hi, does some one know how to run the latent class analysis in R? like which package and command I should use? thanks a lot, Suyan Tian __ 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. -- === WenSui Liu ChoicePoint Precision Marketing Phone: 678-893-9457 Email : [EMAIL PROTECTED] Blog : statcompute.spaces.live.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Confidence intervals for PCA scores/eigenvalues
On Fri, 1 Feb 2008, Markus Loecher wrote:
Very sorry about my incomplete email from 2 days ago, here is the full
version.
---
Dear all,
I have read various descriptions of employing resampling techniques, such as
the bootstrap, to estimate the uncertainties of the eigenvalues/vectors
computed by PCA.
Let's say I define my test statistic T to be the percent of variance
captured by the first 2 principal components.
I am struggling with a conceptual issue here. Since PCA maximizes the
variance concentration, wouldn't the bootstrapped distribution of T be
biased upward due to the effectively reduced sample size ?
If that is true, how could one obtain an unbiased confidence interval for T
?
Any insight would be helpful !
See
@article{beran1985bta,
title={{Bootstrap Tests and Confidence Regions for Functions of a
Covariance Matrix}},
author={Beran, R. and Srivastava, M.S.},
journal={The Annals of Statistics},
volume={13},
number={1},
pages={95--115},
year={1985},
publisher={JSTOR}
}
@article{beran1987cbt,
title={{Correction: Bootstrap Tests and Confidence Regions for Functions
of a Covariance Matrix}},
author={Beran, R. and Srivastava, M.S.},
journal={The Annals of Statistics},
volume={15},
number={1},
pages={470--471},
year={1987},
publisher={Institute of Mathematical Statistics}
}
and browse thru these perhaps:
http://scholar.google.com/scholar?hl=enlr=cites=1040478970084047991
HTH,
Chuck
Thanks,
Markus
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Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
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Re: [R] overlapping intervals
Here is one way of doing it:
c.i - read.table(textConnection( 17130612 17587118
+ 17712302 18221688
+ 21225764 21387314
+ 25012714 30748348
+ 33852816 34480192
+ 36012944 36209144
+ 36252300 36280276
+ 36737468 36971144
+ 43693832 43878548))
d.i - read.table(textConnection( 17712302 18100404
+ 21203780 21387314
+ 25012714 30748348
+ 33852816 34384588
+ 34794536 35996440))
closeAllConnections()
# setup data.frame for comparing
x - rbind(data.frame(t=c.i$V1, oper=1, type='c'),
+ data.frame(t=c.i$V2, oper=-1, type='c'),
+ data.frame(t=d.i$V1,oper=1, type='d'),
+ data.frame(t=d.i$V2, oper=-1, type='d'))
# put in time order
x - x[order(x$t),]
# determine overlaps
x$over - cumsum(x$oper)
x
t oper type over
1 171306121c1
10 17587118 -1c0
2 177123021c1
19 177123021d2
24 18100404 -1d1
11 18221688 -1c0
20 212037801d1
3 212257641c2
12 21387314 -1c1
25 21387314 -1d0
4 250127141c1
21 250127141d2
13 30748348 -1c1
26 30748348 -1d0
5 338528161c1
22 338528161d2
27 34384588 -1d1
14 34480192 -1c0
23 347945361d1
28 35996440 -1d0
6 360129441c1
15 36209144 -1c0
7 362523001c1
16 36280276 -1c0
8 367374681c1
17 36971144 -1c0
9 436938321c1
18 43878548 -1c0
# assuming that c d don't overlap themselves, oper=2 indicate an overlap
overlap - which(x$over == 2)
# print overlaps
for (i in overlap){
+ print(x[i + c(-1,0,1,2),])
+ }
t oper type over
2 177123021c1
19 177123021d2
24 18100404 -1d1
11 18221688 -1c0
t oper type over
20 212037801d1
3 212257641c2
12 21387314 -1c1
25 21387314 -1d0
t oper type over
4 250127141c1
21 250127141d2
13 30748348 -1c1
26 30748348 -1d0
t oper type over
5 338528161c1
22 338528161d2
27 34384588 -1d1
14 34480192 -1c0
On Feb 1, 2008 4:03 PM, mohamed nur anisah [EMAIL PROTECTED] wrote:
hi!!
Below I have 4 columns vector of c and d which are unequal in length.These c
and d have 2 columns each where these 2 columns represent an interval values.
How am I going to get an overlapping over these interval values?? Please help
me sort this problem!! Thanks in advance..
c d
17130612 17587118 17712302 18100404
17712302 18221688 21203780 21387314
21225764 21387314 25012714 30748348
25012714 30748348 33852816 34384588
33852816 34480192 34794536 35996440
36012944 36209144
36252300 36280276
36737468 36971144
43693832 43878548
-
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What is the problem you are trying to solve?
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[R] best text editor for Linux?
Hi all, I know this question has been asked in the past, but I am wondering if anyone running R on Linux has any guidance as to a text editor that works well with R. At the present time I am running R on Windows and using TINN-R. For a number of reasons I want to switch to Linux, but can't find much in the way of a text editor in sync with R. Any experiences, recommendations would be appreciated. Wade Wall [[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] ARCH LM test for univariant time series
Hi, Does anyone know if R has a Lagrange multiplier (LM) test for ARCH effects for univariant time series? Thanks! -- Tom [[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] best text editor for Linux?
Wade, I switched from R-Windows to R-Linux about 9 months ago and have had great success with GNU-Emacs with the ESS add-on. Your distro should have Emacs available for install, if it does not you can get the source at: http://ftp.gnu.org/pub/gnu/emacs/ ESS can be found at: http://ess.r-project.org/ There is a special help-list for ESS at: [EMAIL PROTECTED] Good Luck, Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpelatgmaildotcom ** Wade Wall wrote: Hi all, I know this question has been asked in the past, but I am wondering if anyone running R on Linux has any guidance as to a text editor that works well with R. At the present time I am running R on Windows and using TINN-R. For a number of reasons I want to switch to Linux, but can't find much in the way of a text editor in sync with R. Any experiences, recommendations would be appreciated. Wade Wall [[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.
[R] (no subject)
r-help c(2.43, 3.22, 6.9, 3.03, 5.36, 6.9, 2.29, 6.13, 6.11, 4.25, 3.85, 5.09, 7.44, 2.86, 2.82, 3.64, 3.22, 7, 2.65, 4.5, 3.73, 5.09, 5.8, 7.87, 2.87, 2.9, 6.63, 6.8, 2.45, 7.68, 2.56, 2.54, 7.35, 4.61, 2.58, 3.27, 5.8, 3.13, 3.29, 2.56, 5.79, 2.67, 7.55, 7.13, 8.4, 6.16, 3.34, 6.49, 1.85, 7.4, 7.89, 3.3, 6.28, 6.52, 6.07, 4.26, 4.4, 3.1, 5.97, 6.69, 3.69, 4.62, 5.79, 2.54, 8.91, 3.48, 2.35, 7.28, 6.75, 6.97, 7.29, 2.28, 3.36, 4.79, 2.41, 7.93, 6.17, 2.19, 4.27, 7.17, 2.12, 3.05, 4.4, 5.35, 2.96, 3.54, 3.31, 7.28, 2.47, 2.27, 7.43, 3.69, 3.32, 2.61, 2.19, 5.67, 5.03, 7.58, 5.27, 2.25, 2.59, 4.16, 1.71, 3.64, 2.93, 7.2, 5.99, 7.68, 4.14, 5.83, 3.87, 7.29, 5.95, 3.4, 2.45, 2.85, 6.77, 3.58, 4.31, 5.83, 6.19, 2.56, 6.69, 7.2, 5.04, 4.34, 2.66, 7.68, 6.8, 2.5, 1.95, 7.12, 3.02, 2.58, 3.39, 3.78, 3.53, 4.42, 6.64, 2.19, 4.79, 5.75, 5.55, 5.57, 3.94, 7.27, 3.39, 6.64, 6.13, 4.55, 6.75, 3.79, 1.82, 5.95, 5.88, 2.64, 5.43, 7.9, 3.14, 5.38, 7.97, 5.83, 3.18, 2.47, 3.33, 6.98, 6.35, 6.1, 7.11, 7.34, 5.08, 2, 3.13, 2.96, 2.43, 2.12, 3.24, 3.13, 2.6, 5.15, 3.34, 7.07, 5.42, 3.1, 2.66, 2.42, 7.3, 3.28, 4.68, 5.9, 6.64, 4.79, 1.84, 6.78, 6.1, 3.29, 2.35, 2.16, 6.36, 6.41, 5.39, 2.48, 7.35, 5.87, 6.77, 5.66, 2.81, 5.27, 2.95, 7.01, 2.55, 3.4, 2.84, 2.35, 6.36, 4.31, 7.44, 3.35, 6.42, 5.86, 3.14, 6.95, 5.27, 2.05, 4.85, 3.37, 2.28, 7.59, 6.99, 5.68, 4.5, 2.81, 6.07, 5.27, 6.32, 5.25, 3.69, 3.89, 3.23, 3.5, 6.2, 6.78, 2.51, 5.87, 7, 6.99, 7.27, 7.62, 6.87, 2.38, 6.78, 3.11, 4.28, 7.57, 5.65, 3.32, 2.53, 3.09, 4.99, 2.19, 6.37, 2.68, 7.22, 2.47, 3.05, 4.92, 2.82, 7.72, 3.67, 6.76, 6.38, 3.18, 3.02, 6.2, 3.47, 3.02, 7.22, 2.21, 7.33, 7.58, 6.58, 2.98, 6.7, 2.64, 6, 2.72, 2, 6.35, 5.36, 6.74, 5.29, 6.22, 3.14, 7.15, 4.45, 2.34, 2.63, 4.62, 7.51, 7.4, 3.16, 5.99, 7.07, 4.85, 3.11, 4.6, 6.55, 2.63, 3.15, 5.16, 5.81, 3.99, 6.12, 4.08, 3.69, 3.32, 3.13, 2.41, 2.95, 2.88, 5.79, 5.83, 2.49, 3.8, 4.62, 3.71, 3.18, 7.41, 7.3, 6.51, 2.27, 7.15, 6.04, 8.11, 7.74, 7.09, 7.21, 2.54, 6.74, 3.48, 7.8, 6.41, 5.64, 5.11, 4.91, 2.25, 3.31, 3.95, 6.58, 5.38, 5.45, 3.46, 2.4, 5.79, 3.34, 3.32, 1.97, 2.49, 3.29, 5.69, 1.75, 4.57, 7.04, 5.29, 7.79, 7.84, 3.02, 4.36, 6.87, 2.14, 5.43, 4.11, 7.51, 2.13, 5.33, 2.91, 2.87, 5.95, 2.29, 2.08, 7.78, 3.96, 4.55, 2.82, 2.63, 3.13, 3.43, 5.96, 2.39, 4.98, 3.51, 6.26, 4.03, 2.41, 6.8, 7.64, 3.3, 2.66, 6.51, 3.33, 5.64, 2.5, 6.09, 2.63, 2.55, 2.52, 4.15, 5.3, 6.11, 5.13, 3.42, 7.42, 1.87, 6.64, 4.63, 3.25, 1.97, 5.44, 7.96, 6.67, 7.14, 5.12, 5.27, 7.48, 7.25, 2.51, 4.5, 2.87, 6.7, 2.09, 6.85, 2.16, 6.37, 3.01, 3.55, 4.5, 2.69, 3.52, 5.7, 3.02, 5.94, 7.38, 6.45, 5.33, 2.8, 4.83, 3.01, 6.34, 2.99, 1.98, 3.02, 3.11, 8.65, 6.38, 7.08, 7.74, 6.19, 7.97, 2.7, 5.05, 6.61, 3.75, 5.24, 6.59, 5.91, 2.02, 6.95, 3.05, 2.89, 5.09, 4.9, 6.78, 5.79, 5.42, 3.13, 3.97, 2.24, 5.91, 6.28, 3.44, 6.14, 2.41, 8.03, 3.39, 3.33, 3.21, 2.04, 4.49, 4.94, 3, 7.59, 6.84, 2.11, 6.36, 2.63, 2.01, 2.73, 4.94, 2.7, 2.65) bgchen [EMAIL PROTECTED] 2007-10-19 __ 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] ARCH LM test for univariant time series
Hi, Tom: The 'arch' function in the 'vars' package is supposed to be able to do that. Unfortunately, I was unable to make it work for a univariate series. Bernhard Pfaff, the author of 'vars', said that if I read the code for 'arch', I could easily retrieve the necessary lines and put them in my own function; I have not so far found the time to try that. If you do, or if you get a better answer than this, would you please let me know? I would like to have this capability for the 'FinTS' package, and I would happily write a help page if someone would contribute the function -- or use a function in another package. Tsay (2005) Analysis of Financial Time Series, 2nd ed. (Wiley) includes an example on p. 103 that could be used for a reference. Hope this helps. Spencer Graves tom soyer wrote: Hi, Does anyone know if R has a Lagrange multiplier (LM) test for ARCH effects for univariant time series? Thanks! __ 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] best text editor for Linux?
On Linux platform, nothing beats Emacs + ESS. Shige On Feb 2, 2008 11:06 AM, Wade Wall [EMAIL PROTECTED] wrote: Hi all, I know this question has been asked in the past, but I am wondering if anyone running R on Linux has any guidance as to a text editor that works well with R. At the present time I am running R on Windows and using TINN-R. For a number of reasons I want to switch to Linux, but can't find much in the way of a text editor in sync with R. Any experiences, recommendations would be appreciated. Wade Wall [[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. [[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] ARCH LM test for univariant time series
Spencer, how about something like this:
archTest=function (x, lags= 16){
#x is a vector
require(vars)
s=embed(x,lags)
y=VAR(s,p=1,type=const)
result=arch(y,multi=F)$arch.uni[[1]]
return(result)
}
can you, or maybe Bernhard, check and see whether this function gives the
correct result?
thanks,
On 2/1/08, Spencer Graves [EMAIL PROTECTED] wrote:
Hi, Tom:
The 'arch' function in the 'vars' package is supposed to be able
to do that. Unfortunately, I was unable to make it work for a
univariate series. Bernhard Pfaff, the author of 'vars', said that if I
read the code for 'arch', I could easily retrieve the necessary lines
and put them in my own function; I have not so far found the time to
try that. If you do, or if you get a better answer than this, would you
please let me know? I would like to have this capability for the
'FinTS' package, and I would happily write a help page if someone would
contribute the function -- or use a function in another package. Tsay
(2005) Analysis of Financial Time Series, 2nd ed. (Wiley) includes an
example on p. 103 that could be used for a reference.
Hope this helps.
Spencer Graves
tom soyer wrote:
Hi,
Does anyone know if R has a Lagrange multiplier (LM) test for ARCH
effects for univariant time series?
Thanks!
--
Tom
[[alternative HTML version deleted]]
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Re: [R] multiple functions with three dots
John Lande wrote:
Dear all,
I am creating functions with the three dot strategy. I wold like to have
suggestion when writing multiple functions that calls multiple functions
with
I will give you a couple of example:
a=1:5
b=6:10
d=3:7
example=function(x,y, z, ...){
plot(x,y, ...)
points(x,z, ...)
}
example(a,b,d)
how can I set different parameters for points and plot functions? for
example in plot I want to have bigger dots (lwd=3), while in the points I
want to have green dots.
any suggestion?
Hi John,
There are probably better solutions to this problem, but I usually add
explicit arguments like this:
example-function(x,y,z,y.lwd,z.col,...) {
...
plot(x,y,lwd=y.lwd,...)
points(x,z,col=z.col)
...
}
Jim
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Re: [R] (no subject)
bgchen wrote: r-help c(2.43, 3.22, 6.9, 3.03, 5.36, 6.9, 2.29, 6.13, 6.11, 4.25, 3.85, 5.09, 7.44, 2.86, 2.82, 3.64, 3.22, 7, 2.65, 4.5, 3.73, 5.09, 5.8, 7.87, 2.87, 2.9, 6.63, 6.8, 2.45, 7.68, 2.56, 2.54, 7.35, 4.61, 2.58, 3.27, 5.8, 3.13, 3.29, 2.56, 5.79, 2.67, 7.55, 7.13, 8.4, 6.16, 3.34, 6.49, 1.85, 7.4, 7.89, 3.3, 6.28, 6.52, 6.07, 4.26, 4.4, 3.1, 5.97, 6.69, 3.69, 4.62, 5.79, 2.54, 8.91, 3.48, 2.35, 7.28, 6.75, 6.97, 7.29, 2.28, 3.36, 4.79, 2.41, 7.93, 6.17, 2.19, 4.27, 7.17, 2.12, 3.05, 4.4, 5.35, 2.96, 3.54, 3.31, 7.28, 2.47, 2.27, 7.43, 3.69, 3.32, 2.61, 2.19, 5.67, 5.03, 7.58, 5.27, 2.25, 2.59, 4.16, 1.71, 3.64, 2.93, 7.2, 5.99, 7.68, 4.14, 5.83, 3.87, 7.29, 5.95, 3.4, 2.45, 2.85, 6.77, 3.58, 4.31, 5.83, 6.19, 2.56, 6.69, 7.2, 5.04, 4.34, 2.66, 7.68, 6.8, 2.5, 1.95, 7.12, 3.02, 2.58, 3.39, 3.78, 3.53, 4.42, 6.64, 2.19, 4.79, 5.75, 5.55, 5.57, 3.94, 7.27, 3.39, 6.64, 6.13, 4.55, 6.75, 3.79, 1.82, 5.95, 5.88, 2.64, 5.43, 7.9, 3.14, 5.38, 7.97, 5.83, 3.18, 2.47, 3.33, 6.98, 6.35, 6.1, 7.11, 7.34, 5.08, 2, 3.13, 2.96, 2.43, 2.12, 3.24, 3.13, 2.6, 5.15, 3.34, 7.07, 5.42, 3.1, 2.66, 2.42, 7.3, 3.28, 4.68, 5.9, 6.64, 4.79, 1.84, 6.78, 6.1, 3.29, 2.35, 2.16, 6.36, 6.41, 5.39, 2.48, 7.35, 5.87, 6.77, 5.66, 2.81, 5.27, 2.95, 7.01, 2.55, 3.4, 2.84, 2.35, 6.36, 4.31, 7.44, 3.35, 6.42, 5.86, 3.14, 6.95, 5.27, 2.05, 4.85, 3.37, 2.28, 7.59, 6.99, 5.68, 4.5, 2.81, 6.07, 5.27, 6.32, 5.25, 3.69, 3.89, 3.23, 3.5, 6.2, 6.78, 2.51, 5.87, 7, 6.99, 7.27, 7.62, 6.87, 2.38, 6.78, 3.11, 4.28, 7.57, 5.65, 3.32, 2.53, 3.09, 4.99, 2.19, 6.37, 2.68, 7.22, 2.47, 3.05, 4.92, 2.82, 7.72, 3.67, 6.76, 6.38, 3.18, 3.02, 6.2, 3.47, 3.02, 7.22, 2.21, 7.33, 7.58, 6.58, 2.98, 6.7, 2.64, 6, 2.72, 2, 6.35, 5.36, 6.74, 5.29, 6.22, 3.14, 7.15, 4.45, 2.34, 2.63, 4.62, 7.51, 7.4, 3.16, 5.99, 7.07, 4.85, 3.11, 4.6, 6.55, 2.63, 3.15, 5.16, 5.81, 3.99, 6.12, 4.08, 3.69, 3.32, 3.13, 2.41, 2.95, 2.88, 5.79, 5.83, 2.49, 3.8, 4.62, 3.71, 3.18, 7.41, 7.3, 6.51, 2.27, 7.15, 6.04, 8.11, 7.74, 7.09, 7.21, 2.54, 6.74, 3.48, 7.8, 6.41, 5.64, 5.11, 4.91, 2.25, 3.31, 3.95, 6.58, 5.38, 5.45, 3.46, 2.4, 5.79, 3.34, 3.32, 1.97, 2.49, 3.29, 5.69, 1.75, 4.57, 7.04, 5.29, 7.79, 7.84, 3.02, 4.36, 6.87, 2.14, 5.43, 4.11, 7.51, 2.13, 5.33, 2.91, 2.87, 5.95, 2.29, 2.08, 7.78, 3.96, 4.55, 2.82, 2.63, 3.13, 3.43, 5.96, 2.39, 4.98, 3.51, 6.26, 4.03, 2.41, 6.8, 7.64, 3.3, 2.66, 6.51, 3.33, 5.64, 2.5, 6.09, 2.63, 2.55, 2.52, 4.15, 5.3, 6.11, 5.13, 3.42, 7.42, 1.87, 6.64, 4.63, 3.25, 1.97, 5.44, 7.96, 6.67, 7.14, 5.12, 5.27, 7.48, 7.25, 2.51, 4.5, 2.87, 6.7, 2.09, 6.85, 2.16, 6.37, 3.01, 3.55, 4.5, 2.69, 3.52, 5.7, 3.02, 5.94, 7.38, 6.45, 5.33, 2.8, 4.83, 3.01, 6.34, 2.99, 1.98, 3.02, 3.11, 8.65, 6.38, 7.08, 7.74, 6.19, 7.97, 2.7, 5.05, 6.61, 3.75, 5.24, 6.59, 5.91, 2.02, 6.95, 3.05, 2.89, 5.09, 4.9, 6.78, 5.79, 5.42, 3.13, 3.97, 2.24, 5.91, 6.28, 3.44, 6.14, 2.41, 8.03, 3.39, 3.33, 3.21, 2.04, 4.49, 4.94, 3, 7.59, 6.84, 2.11, 6.36, 2.63, 2.01, 2.73, 4.94, 2.7, 2.65) 42 Jim __ 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.
