[R] Regarding Bivariate normal distribution.
Dear all R gurus, My question is related to statistics rather directly to R. Suppose (X,Y) has a bivariate normal distrubution. I want to find two values of X and Y say x, and y respectively, such that: P[Xx, Yy] = 0.05 My questions are : 1. Can x and y be uniquely found? 2. If it is, how I can find them using R Your help will be highly appreciated. Thanks and regards, __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lme or gls prediction intervals
Martin, Have you checked ?intervals.gls This intervals are approximate, but this would be the obvious starting point to me. Joris Martin Henry H. Stevens [EMAIL PROTECTED] To edu R-Help r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] lme or gls prediction intervals 24/07/2007 19:22 Hi folks, I am trying to generate 95% confidence intervals for a gls model using predict.nlme with R version 2.5.1 (2007-06-27) . nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-83. I have looked in help, and I can do it for lm and glm models, and I can generate simple predictions for lme models with various levels -- I am familiar with the basics. Is there a way to get prediction intervals for gls models? My best model uses varPower(), so I am reluctant to fall back on lm predictions. Thank you, Hank Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] values from a linear model
On Tuesday 24 July 2007 12:02:58 Manuele Pesenti wrote: Dear R users, how can I extrapolate values listed in the summary of an lm model but not directly available between object values such as the the standard errors of the calculated parameters? thank you very much for all interesting answer :) Manuele -- Manuele Pesenti [EMAIL PROTECTED] [EMAIL PROTECTED] http://mpesenti.polito.it __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to use replace for efficiency
Hi
I think I have been struggling to use replace correctly, I usually
work my way around this using a loop, but I think this is in fact
inefficient.
I have a dataset with runoff from three plots and associated rainfall.
However either the datarecording was sloppy, or the rainfall very
patchy. So I am trying to remove data from my dataset for which the
runoff is larger than the rainfall on the same day. (Don't worry, the
rainfall data is in fact the rainfall associated to the three days
around the runoff event). On days that no runoff was recorded the data
includes NA
The dataset is called wheat2
I use the following:
for (i in 1:nrow(wheat2)) {
# Insert NA's if runoff data rainfall data
if (is.na(wheat2[i,5:7])==FALSE any(wheat2[i,5:7]wheat2[i,8])) {
wheat2[i,5:7] - NA
}
}
I tried this:
wheat1 - replace(wheat2[,5:7],is.na(wheat2[i,5:7])==FALSE
any(wheat2[i,5:7]wheat2[i,8]),NA)
wheat3 - cbind(wheat2[1:4],wheat1,wheat2[,8])
wheat3[5539,] # the culprit row
DateRain Rain StartDate EndDate RO.A RO.B RO.C filtered.Rain
5539 28-Feb-580 27-Feb-58 28-Feb-5861.588.7
65 0
Not sure what I am doing wrong, any help is appreciated
Willem
Here is a data sample and note the very high value for runoff (RO) and
no rainfall on 28 Feb 1958
DateRain Rain StartDate EndDate RO.A RO.B RO.C filtered.Rain
14-Feb-58 0 NA NA NA 0
15-Feb-58 0 NA NA NA 0
16-Feb-58 0 NA NA NA 0
17-Feb-58 0 NA NA NA 0
18-Feb-58 0 18-Feb-58 18-Feb-58 0 0 0 23.6
19-Feb-58 23.6 NA NA NA 23.6
20-Feb-58 0 NA NA NA 23.6
21-Feb-58 0 NA NA NA 0
22-Feb-58 0 NA NA NA 0
23-Feb-58 0 NA NA NA 0
24-Feb-58 0 NA NA NA 0
25-Feb-58 0 NA NA NA 0
26-Feb-58 0 NA NA NA 0
27-Feb-58 0 NA NA NA 0
28-Feb-58 0 27-Feb-58 28-Feb-58 61.5 88.7 65 0
01-Mar-58 0 NA NA NA 0
02-Mar-58 0 NA NA NA 0
03-Mar-58 0 NA NA NA 0
04-Mar-58 0 NA NA NA 1.5
05-Mar-58 1.5 NA NA NA 1.5
06-Mar-58 0 NA NA NA 1.5
07-Mar-58 0 NA NA NA 0.5
08-Mar-58 0.5 NA NA NA 0.5
09-Mar-58 0 NA NA NA 7.6
10-Mar-58 7.1 NA NA NA 9.1
11-Mar-58 2 NA NA NA 57.4
12-Mar-58 48.3 09-Mar-58 12-Mar-58 0.1 1.5 0 51.1
13-Mar-58 0.8 NA NA NA 49.9
14-Mar-58 0.8 NA NA NA 1.6
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] how to use replace for efficiency
You don't need to use 'replace', just use indexing in the assignment:
isCrap - apply((wheat2[,5:7] wheat2[,8]), 1, any)
wheat2[isCrap,5:7] - NA
Felix
On 7/25/07, willem vervoort [EMAIL PROTECTED] wrote:
Hi
I think I have been struggling to use replace correctly, I usually
work my way around this using a loop, but I think this is in fact
inefficient.
I have a dataset with runoff from three plots and associated rainfall.
However either the datarecording was sloppy, or the rainfall very
patchy. So I am trying to remove data from my dataset for which the
runoff is larger than the rainfall on the same day. (Don't worry, the
rainfall data is in fact the rainfall associated to the three days
around the runoff event). On days that no runoff was recorded the data
includes NA
The dataset is called wheat2
I use the following:
for (i in 1:nrow(wheat2)) {
# Insert NA's if runoff data rainfall data
if (is.na(wheat2[i,5:7])==FALSE any(wheat2[i,5:7]wheat2[i,8])) {
wheat2[i,5:7] - NA
}
}
I tried this:
wheat1 - replace(wheat2[,5:7],is.na(wheat2[i,5:7])==FALSE
any(wheat2[i,5:7]wheat2[i,8]),NA)
wheat3 - cbind(wheat2[1:4],wheat1,wheat2[,8])
wheat3[5539,] # the culprit row
DateRain Rain StartDate EndDate RO.A RO.B RO.C filtered.Rain
5539 28-Feb-580 27-Feb-58 28-Feb-5861.588.7
65 0
Not sure what I am doing wrong, any help is appreciated
Willem
Here is a data sample and note the very high value for runoff (RO) and
no rainfall on 28 Feb 1958
DateRain Rain StartDate EndDate RO.A RO.B RO.C filtered.Rain
14-Feb-58 0 NA NA NA 0
15-Feb-58 0 NA NA NA 0
16-Feb-58 0 NA NA NA 0
17-Feb-58 0 NA NA NA 0
18-Feb-58 0 18-Feb-58 18-Feb-58 0 0 0 23.6
19-Feb-58 23.6 NA NA NA 23.6
20-Feb-58 0 NA NA NA 23.6
21-Feb-58 0 NA NA NA 0
22-Feb-58 0 NA NA NA 0
23-Feb-58 0 NA NA NA 0
24-Feb-58 0 NA NA NA 0
25-Feb-58 0 NA NA NA 0
26-Feb-58 0 NA NA NA 0
27-Feb-58 0 NA NA NA 0
28-Feb-58 0 27-Feb-58 28-Feb-58 61.5 88.7 65 0
01-Mar-58 0 NA NA NA 0
02-Mar-58 0 NA NA NA 0
03-Mar-58 0 NA NA NA 0
04-Mar-58 0 NA NA NA 1.5
05-Mar-58 1.5 NA NA NA 1.5
06-Mar-58 0 NA NA NA 1.5
07-Mar-58 0 NA NA NA 0.5
08-Mar-58 0.5 NA NA NA 0.5
09-Mar-58 0 NA NA NA 7.6
10-Mar-58 7.1 NA NA NA 9.1
11-Mar-58 2 NA NA NA 57.4
12-Mar-58 48.3 09-Mar-58 12-Mar-58 0.1 1.5 0 51.1
13-Mar-58 0.8 NA NA NA 49.9
14-Mar-58 0.8 NA NA NA 1.6
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--
Felix Andrews / 安福立
PhD candidate
Integrated Catchment Assessment and Management Centre
The Fenner School of Environment and Society
The Australian National University (Building 48A), ACT 0200
Beijing Bag, Locked Bag 40, Kingston ACT 2604
http://www.neurofractal.org/felix/
voice:+86_1051404394 (in China)
mobile:+86_13522529265 (in China)
mobile:+61_410400963 (in Australia)
xmpp:[EMAIL PROTECTED]
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Re: [R] Regarding Bivariate normal distribution.
No, x and y are not unique. In fact, there is an infinite number of x and y pairs that are roots to the equation P[Xx, Yy] = 0.05. -- Wolfgang Viechtbauer Department of Methodology and Statistics University of Maastricht, The Netherlands http://www.wvbauer.com/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Arun Kumar Saha Sent: Wednesday, July 25, 2007 08:58 To: r-help@stat.math.ethz.ch Subject: [R] Regarding Bivariate normal distribution. Dear all R gurus, My question is related to statistics rather directly to R. Suppose (X,Y) has a bivariate normal distrubution. I want to find two values of X and Y say x, and y respectively, such that: P[Xx, Yy] = 0.05 My questions are : 1. Can x and y be uniquely found? 2. If it is, how I can find them using R Your help will be highly appreciated. Thanks and regards, __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regarding Bivariate normal distribution.
Hi Arun
i hope you will fin this document useful :)
http://www.geocities.com/~mikemclaughlin/math_stat/Dists/Compendium.pdf
no they cannot be found uniquely. as rightly pointed by Mr. Wolfgang, that
there will be infinite pairs for each x you can get correspoinding y
above document will be of use :)
Regards,
Gaurav Yadav
+++
Assistant Manager, CCIL, Mumbai (India)
Mob: +919821286118 Email: [EMAIL PROTECTED]
Bhagavad Gita: Man is made by his Belief, as He believes, so He is
Arun Kumar Saha [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
07/25/2007 12:27 PM
To
r-help@stat.math.ethz.ch R-help@stat.math.ethz.ch
cc
Subject
[R] Regarding Bivariate normal distribution.
Dear all R gurus,
My question is related to statistics rather directly to R. Suppose
(X,Y) has a bivariate normal distrubution. I want to find two values
of X and Y say x, and y respectively, such that:
P[Xx, Yy] = 0.05
My questions are :
1. Can x and y be uniquely found?
2. If it is, how I can find them using R
Your help will be highly appreciated.
Thanks and regards,
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
DISCLAIMER AND CONFIDENTIALITY CAUTION:\ \ This message and ...{{dropped}}
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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] Strange warning in summary.lm
Dear Peter, Uwe and Brian, I've found some more problems with options(OutDec = ,). 1) as.numeric yields NA where it shouldn't z - c(12, 12,34, 12.34) options(OutDec = ,) as.numeric(z) [1] 12,00NA 12,34 Warning message: NAs introduced by coercion in: as.double.default(z) # should result in c(12, 12.34, NA) options(OutDec = .) as.numeric(z) [1] 12.00NA 12.34 Warning message: NAs introduced by coercion in: as.double.default(z) 2) anova yields the same warning as summary x - runif(100) y - rnorm(100) options(OutDec = ,) summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: Min 1Q Median 3Q Max -2,81744 -0,61680 0,02107 0,66309 2,20599 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -0,073531 0,195880 -0,3750,708 x0,007519 0,318159 0,0240,981 Residual standard error: 0,9795 on 98 degrees of freedom Multiple R-Squared: 5.699e-06, Adjusted R-squared: -0.0102 F-statistic: 0.0005585 on 1 and 98 DF, p-value: 0,9812 Warning message: NAs introduced by coercion in: as.double.default(Cf[okP]) anova(lm(y~x)) Analysis of Variance Table Response: y Df Sum Sq Mean Sq F value Pr(F) x 1 0,001 0,001 6e-04 0,9812 Residuals 98 94,031 0,960 Warning message: NAs introduced by coercion in: as.double.default(Cf[okP]) Cheers, 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 ONKELINX, Thierry Verzonden: donderdag 19 juli 2007 13:56 Aan: Peter Dalgaard CC: r-help@stat.math.ethz.ch; Uwe Ligges Onderwerp: Re: [R] Strange warning in summary.lm Dear Peter, Here's an example. Notice the warning in the last two lines of the summary with options(OutDec = ,). It's not present with options(OutDec = .). Cheers, Thierry x - runif(100) y - rnorm(100) options(OutDec = ,) summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: Min1QMedian3Q Max -2,389749 -0,607002 0,006969 0,689535 1,713197 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0,033970,17774 0,1910,849 x -0,092190,29518 -0,3120,755 Residual standard error: 0,868 on 98 degrees of freedom Multiple R-Squared: 0.0009943, Adjusted R-squared: -0.0092 F-statistic: 0.09754 on 1 and 98 DF, p-value: 0,7555 Warning message: NAs introduced by coercion in: as.double.default(Cf[okP]) options(OutDec = .) summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: Min1QMedian3Q Max -2.389749 -0.607002 0.006969 0.689535 1.713197 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0.033970.17774 0.1910.849 x -0.092190.29518 -0.3120.755 Residual standard error: 0.868 on 98 degrees of freedom Multiple R-Squared: 0.0009943, Adjusted R-squared: -0.0092 F-statistic: 0.09754 on 1 and 98 DF, p-value: 0.7555 -- -- 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: Peter Dalgaard [mailto:[EMAIL PROTECTED] Verzonden: donderdag 19 juli 2007 13:37 Aan: ONKELINX, Thierry CC: Uwe Ligges; r-help@stat.math.ethz.ch Onderwerp: Re: [R] Strange warning in summary.lm ONKELINX, Thierry wrote: The problem also exists in a clean workspace. But I've found the troublemaker. I had set options(OutDec = ,). Resetting this to options(OutDec = .) solved the problem. Thanks, Thierry Oups. That sounds like there's a bug somewhere. Can you cook up a minimal example which shows the behaviour? -- O__ Peter Dalgaard Øster Farimagsgade 5,
[R] A problem with anova()
I fitted tree growth data with Chapman-Richards growth function using nls. summary(CR) Formula: HEIGHT ~ A * (1 - exp(-B * AGE))^C Parameters: Estimate Std. Error t value Pr(|t|) A 29.007627 0.270485 107.24 2e-16 *** B 0.030813 0.001095 28.13 2e-16 *** C 1.849405 0.068659 26.94 2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 1.879 on 713 degrees of freedom Algorithm port, convergence message: relative convergence (4) When I try to run the anova90 function I get this: anova(CR) Error in anova.nls(CR) : anova is only defined for sequences of nls objects Could you tell me what the problem is? Thanks Michael [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Ggplot2 equivalent of axis and problem with log scale
Dear useRs, Recently I've discorved ggplot2 and I must say that I really like it, although the documentation still is a working in progress. My first question: How can I change the position of the labels and the text of the labels? With a basic plot I would use axis(2, at = position.of.the.ticks, labels = text.at.the.ticks). Could someone provide me with an example of how to do this with ggplot2? The second question is probably a little bug. If I plot the y-axis in log10 scale then geom_errorbar still plot the values in the original scale. See the example below. The second plot is what I would suspect when plotting the first graph. library(ggplot2) df - data.frame(x = rep(1:10, 10), y = rnorm(100)) df$y - 10 ^ (df$x + df$y) df - cbind(df, predict(lm(I(log10(y)) ~ x, data = df), interval = c)) df[, 3:5] - 10 ^ df[, 3:5] ggplot(data = df, aes(x = x, y = y)) + geom_point() + scale_y_log10() + geom_line(aes(y = fit)) + geom_errorbar(aes(min = lwr, max = upr)) ggplot(data = df, aes(x = x, y = y)) + geom_point() + scale_y_log10() + geom_line(aes(y = fit)) + geom_errorbar(aes(min = log10(lwr), max = log10(upr))) Thanks, 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] options(OutDec) etc {was Strange warning in summary.lm}
Without going into your details, I think options() should NEVER influence what as.numeric() does (which I think you are indirectly suggesting it should). In my eyes, using a decimal comma instead of decimal point in scientific computing is an abomination in itself. Providing an option for *output* is one thing, but having it influence basic R engine functions like as.numeric(), format(), ... is an absolute NO!_NO! for me. So I am strongly opposed to an 'InDec' option as was mentioned earlier in this thread. We could consider adding a 'dec' (or 'decimal.sep') *argument* to some R functions, but such an argument must default to . rather than yet another option. R should remain as *functional* as possible. == options() should be used sparingly. They should only influence printed output at most, not computations per se. Of course I know that this is not strictly possible since the computations can use textConnection() etc.. Martin Maechler, ETH Zurich OT == ONKELINX, Thierry [EMAIL PROTECTED] on Wed, 25 Jul 2007 11:04:43 +0200 writes: OT Dear Peter, Uwe and Brian, OT I've found some more problems with options(OutDec = ,). OT 1) as.numeric yields NA where it shouldn't z - c(12, 12,34, 12.34) options(OutDec = ,) as.numeric(z) OT [1] 12,00NA 12,34 OT Warning message: OT NAs introduced by coercion in: as.double.default(z) OT # should result in c(12, 12.34, NA) options(OutDec = .) as.numeric(z) OT [1] 12.00NA 12.34 OT Warning message: OT NAs introduced by coercion in: as.double.default(z) OT 2) anova yields the same warning as summary x - runif(100) y - rnorm(100) options(OutDec = ,) summary(lm(y~x)) OT Call: OT lm(formula = y ~ x) OT Residuals: OT Min 1Q Median 3Q Max OT -2,81744 -0,61680 0,02107 0,66309 2,20599 OT Coefficients: OT Estimate Std. Error t value Pr(|t|) OT (Intercept) -0,073531 0,195880 -0,3750,708 OT x0,007519 0,318159 0,0240,981 OT Residual standard error: 0,9795 on 98 degrees of freedom OT Multiple R-Squared: 5.699e-06, Adjusted R-squared: -0.0102 OT F-statistic: 0.0005585 on 1 and 98 DF, p-value: 0,9812 OT Warning message: OT NAs introduced by coercion in: as.double.default(Cf[okP]) anova(lm(y~x)) OT Analysis of Variance Table OT Response: y OT Df Sum Sq Mean Sq F value Pr(F) OT x 1 0,001 0,001 6e-04 0,9812 OT Residuals 98 94,031 0,960 OT Warning message: OT NAs introduced by coercion in: as.double.default(Cf[okP]) OT Cheers, OT Thierry OT OT ir. Thierry Onkelinx OT Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest OT Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance OT Gaverstraat 4 OT 9500 Geraardsbergen OT Belgium OT tel. + 32 54/436 185 OT [EMAIL PROTECTED] OT www.inbo.be OT Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt OT 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 ONKELINX, Thierry Verzonden: donderdag 19 juli 2007 13:56 Aan: Peter Dalgaard CC: r-help@stat.math.ethz.ch; Uwe Ligges Onderwerp: Re: [R] Strange warning in summary.lm Dear Peter, Here's an example. Notice the warning in the last two lines of the summary with options(OutDec = ,). It's not present with options(OutDec = .). Cheers, Thierry x - runif(100) y - rnorm(100) options(OutDec = ,) summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: Min1QMedian3Q Max -2,389749 -0,607002 0,006969 0,689535 1,713197 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0,033970,17774 0,1910,849 x -0,092190,29518 -0,3120,755 Residual standard error: 0,868 on 98 degrees of freedom Multiple R-Squared: 0.0009943, Adjusted R-squared: -0.0092 F-statistic: 0.09754 on 1 and 98 DF, p-value: 0,7555 Warning message: NAs introduced by coercion in: as.double.default(Cf[okP]) options(OutDec = .) summary(lm(y~x)) Call: lm(formula = y ~ x) Residuals: Min1QMedian3Q Max -2.389749 -0.607002 0.006969 0.689535 1.713197 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 0.03397
[R] plots
Hi Sir I did not find any function of graph which plot one variable on x-axis and 2 or more than 2 variables on y-axis. Moreover, how can I change the labels of L-moments diagram obtained by plotlmrdia(lmrdia()) Thank you -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange warning in summary.lm
On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: Dear Peter, Uwe and Brian, I've found some more problems with options(OutDec = ,). 1) as.numeric yields NA where it shouldn't It should: where does it say otherwise? OutDec affects output, only. z - c(12, 12,34, 12.34) options(OutDec = ,) as.numeric(z) [1] 12,00NA 12,34 Warning message: NAs introduced by coercion in: as.double.default(z) # should result in c(12, 12.34, NA) options(OutDec = .) as.numeric(z) [1] 12.00NA 12.34 Warning message: NAs introduced by coercion in: as.double.default(z) 2) anova yields the same warning as summary It does not in current R: try any fairly recent version of R-devel. Please don't keep reporting a problem we have already fixed, as the FAQ and the posting guide explicitly ask of you. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.
A subset of the data looks as follows df[1:10,14:20] PR10 PR11 PR12 PR13 PR14 PR15 PR16 1 VTIKVGD 2 VSIKVGG 3 VTIRVGG 4 VSIKIGG 5 VSIKVGG 6 VSIRVGG 7 VTIKIGG 8 VSIKVEG 9 VSIKVGG 10VSIKVGG The result I would like is as follows PR10PR11 PR12 ... [V:10][S:7,T:3][I:10] The result can be in a matrix or a vector and each variablename, value and frequency should be accessible so as to be used for comparisons with another dataset later. The frequency can be a count or a percentage. Allan. - Original Message From: Adaikalavan Ramasamy [EMAIL PROTECTED] To: Allan Kamau [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, July 24, 2007 10:21:51 PM Subject: Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset. The name of the table should give you the value. And if you have a matrix, you just need to convert it into a vector first. m - matrix( LETTERS[ c(1:3, 3:5, 2:4) ], nc=3 ) m [,1] [,2] [,3] [1,] A C B [2,] B D C [3,] C E D tb - table( as.vector(m) ) tb A B C D E 1 2 3 2 1 paste( names(tb), :, tb, sep= ) [1] A:1 B:2 C:3 D:2 E:1 If this is not what you want, then please give a simple example. Regards, Adai Allan Kamau wrote: Hi all, If the question below as been answered before I apologize for the posting. I would like to get the frequencies of occurrence of all values in a given variable in a multivariate dataset. In short for each variable (or field) a summary of values contained with in a value:frequency pair, there can be many such pairs for a given variable. I would like to do the same for several such variables. I have used table() but am unable to extract the individual value and frequency values. Please advise. Allan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting gam models
Hi again, I have found a post in R.help archives made from someone who had the same problem when exporting the smooth function estimate got from a GAM, to plot it into another graphic software (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/23136.html) However, I haven't found any reply to this post. She suggested the function preplot() and I have hound that function in gam package, but not in mgcv package. Is it possible to do this in mgcv package or do I have to move to gam package? Thank you very much Lucía zarauz _ AZTI - TecnaliaLucia Zarauz AZTI - Tecnalia / Unidad de Investigación Marina Herrera kaia portualdea z/g 20110 Pasaia (Gipuzkoa) Tel: 943 004 800 - Fax: 943 004 801 e-mail: [EMAIL PROTECTED] www.azti.es ; www.tecnalia.info _ LEGE OHARRA AVISO LEGAL DISCLAIMER Mezu hau pertsonala eta isilpekoa da eta baimenik gabeko erabilera debekatua dago legalki. Jasotzailea ez bazara ezabatu mezua, bidali eta kontserbatu gabe. Este mensaje es personal y confidencial y su uso no autorizado está prohibido legalmente. Si usted no es el destinatario, proceda a borrarlo, sin reenviarlo ni conservarlo. This message is personal and confidential, unauthorised use is legally prohibited. If you are not the intended recipient, delete it without resending or backing it. -Mensaje original- De: Lucia Zarauz Enviado el: martes, 24 de julio de 2007 13:53 Para: 'Henrique Dallazuanna' CC: r-help@stat.math.ethz.ch Asunto: RE: [R] plotting gam models Hi Henrique, Thank you for your suggestion. Actually, I have already tried it, but I am confused because the plot I get is not the same as the output of plot(model) or plot.gam(model). The yaxis is different On the other hand, if I build a more complex model, as for example: model- gam(x ~ s(lat,long) + s(temperature)) I would like to extract the information to build the effects for each explanatory factor (one graph for s(lat,long) and another for s(temperature)), as R does when you use 'plot(model)' and you press return for subsequent pages. My final aim is to plot the influence of s(lat,long) as a contourplot superposed on a geographical map. Maybe there is an easier way to do it... Thank you very much lucía _ Lucia Zarauz AZTI - Tecnalia / Unidad de Investigación Marina Herrera kaia portualdea z/g 20110 Pasaia (Gipuzkoa) Tel: 943 004 800 - Fax: 943 004 801 e-mail: [EMAIL PROTECTED] www.azti.es ; www.tecnalia.info _ LEGE OHARRA AVISO LEGAL DISCLAIMER Mezu hau pertsonala eta isilpekoa da eta baimenik gabeko erabilera debekatua dago legalki. Jasotzailea ez bazara ezabatu mezua, bidali eta kontserbatu gabe. Este mensaje es personal y confidencial y su uso no autorizado está prohibido legalmente. Si usted no es el destinatario, proceda a borrarlo, sin reenviarlo ni conservarlo. This message is personal and confidential, unauthorised use is legally prohibited. If you are not the intended recipient, delete it without resending or backing it. De: Henrique Dallazuanna [mailto:[EMAIL PROTECTED] Enviado el: martes, 24 de julio de 2007 13:36 Para: Lucia Zarauz CC: r-help@stat.math.ethz.ch Asunto: Re: [R] plotting gam models see ?predict.gam -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O On 24/07/07, Lucia Zarauz [EMAIL PROTECTED] wrote: Hi everybody, I am working with gams and I have found some questions when plotting gams models. I am using mgcv, and my model looks something like this: model- gam(x ~ s(lat,long)) I can plot the output of the model using plot(model) or plot.gam(model) and I get a surface plot. That is ok, but what I want to do now is to extract the data used to perform the surface plot. Like that I would be able to superpose them to a geographical map, and to plot these data using other programs. Thank you very much in advance Lucía _ Lucia Zarauz AZTI - Tecnalia / Unidad de Investigación Marina Herrera kaia portualdea z/g 20110 Pasaia (Gipuzkoa) Tel: 943 004 800 - Fax: 943 004 801 e-mail: [EMAIL PROTECTED] www.azti.es ; www.tecnalia.info _ LEGE OHARRA AVISO LEGAL DISCLAIMER Mezu hau pertsonala eta isilpekoa da eta baimenik gabeko erabilera debekatua dago legalki. Jasotzailea ez bazara ezabatu mezua, bidali eta kontserbatu gabe. Este mensaje es personal y confidencial y su uso no autorizado está prohibido legalmente. Si usted no es el destinatario, proceda a borrarlo, sin reenviarlo ni conservarlo. This message is personal and confidential,
Re: [R] plots
amna khan wrote: I did not find any function of graph which plot one variable on x-axis and 2 or more than 2 variables on y-axis. You can use xyplot() from the package lattice. library(lattice) xyplot(y1+y2+y3~x) I suspect, the problem is, that plot() erases everything that was plotted earlier and establishes a new coordinate system in the plotting window. In case of basic graphics, you can set par(new=TRUE) and call plot() several times. points(), lines() and other functions from the basic graphics will add new curves to the existing plot. Initially, you must set axis ranges large enough to fit everything you want to plot. -- View this message in context: http://www.nabble.com/plots-tf4141246.html#a11780013 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange warning in summary.lm
-Oorspronkelijk bericht- Van: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Verzonden: woensdag 25 juli 2007 12:20 Aan: ONKELINX, Thierry CC: r-help@stat.math.ethz.ch Onderwerp: Re: [R] Strange warning in summary.lm On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: Dear Peter, Uwe and Brian, I've found some more problems with options(OutDec = ,). 1) as.numeric yields NA where it shouldn't It should: where does it say otherwise? OutDec affects output, only. I was doing something like options(OutDec = ,) df - data.frame(var = rep(1:8/4, 10), x = rnorm(80)) df.a - aggregate(df$x, by = list(var = df$var), FUN = sum) as.numeric(df.a$var) [1] NA NA NA 1 NA NA NA 2 Warning message: NAs introduced by coercion in: as.double.default(df.a$var) because I needed df.a$var as numeric again. 2) anova yields the same warning as summary It does not in current R: try any fairly recent version of R-devel. Please don't keep reporting a problem we have already fixed, as the FAQ and the posting guide explicitly ask of you. Sorry about that. I wasn't aware that the error was in a fixed subroutine that is used by summary and anova. I'm hestating to use a R-devel version because I haven't tried installing R from a tar.gz (I'm one of those lazy windows users that prefer the .exe version). For now I think I'll return to the good old option(OutDec = .). [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: plots
Hi [EMAIL PROTECTED] napsal dne 25.07.2007 12:17:54: Hi Sir I did not find any function of graph which plot one variable on x-axis and 2 or more than 2 variables on y-axis. ?matplot or you can do plot(x,y, ylim=range(all.your.y), type=n) and add lines/points by lines(x, one.of.your.y) points(x, other.of.your.y) Regards Petr Moreover, how can I change the labels of L-moments diagram obtained by plotlmrdia(lmrdia()) Thank you -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with sub !
Dear all, I am trying to use sub to replace patterns in a character array that contains german names with german special characters. I have the following problem: sub(\\xdf,ss,Wei\xdferitzkreis) Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : input string 1 is invalid in this locale sub(\xdf,ss,Wei\xdferitzkreis) Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : 'pattern' is invalid in this locale Does anybody know how to tackle this problem ? thanks a lot!! Marco [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting gam models
What's wrong with the predict.gam(...,type=terms) suggestion (see yesterday)? Here's example code: ## example data from ?gam n-400;sig-2 x - runif(n, 0, 1);z - runif(n, 0, 1) x2 - runif(n, 0, 1);x3 - runif(n, 0, 1) f0 - function(x) 2 * sin(pi * x) f1 - function(x) exp(2 * x) f2 - function(x) 0.2*x^11*(10*(1-x))^6+10*(10*x)^3*(1-x)^10 f3 - function(x) 0*x f - f0(x) + f1(z) + f2(x2) e - rnorm(n, 0, sig) y - f + e b-gam(y~s(x,z)+s(x2)+s(x3)) ## make a grid of data over which to predict zm - xm - seq(0,1,length=40) pd - data.frame(x=rep(xm,40),z=rep(zm,rep(40,40)), x2=rep(.5,40^2),x3=rep(.5,40^2)) ## predict, termwise pv - predict(b,newdata=pd,type=terms) colnames(pv) ## plot result contour(zm,xm,matrix(pv[,1],40,40)) On Wednesday 25 July 2007 11:43, Lucia Zarauz wrote: Hi again, I have found a post in R.help archives made from someone who had the same problem when exporting the smooth function estimate got from a GAM, to plot it into another graphic software (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/23136.html) However, I haven't found any reply to this post. She suggested the function preplot() and I have hound that function in gam package, but not in mgcv package. Is it possible to do this in mgcv package or do I have to move to gam package? Thank you very much Lucía zarauz _ AZTI - TecnaliaLucia Zarauz AZTI - Tecnalia / Unidad de Investigación Marina Herrera kaia portualdea z/g 20110 Pasaia (Gipuzkoa) Tel: 943 004 800 - Fax: 943 004 801 e-mail: [EMAIL PROTECTED] www.azti.es ; www.tecnalia.info _ LEGE OHARRA AVISO LEGAL DISCLAIMER Mezu hau pertsonala eta isilpekoa da eta baimenik gabeko erabilera debekatua dago legalki. Jasotzailea ez bazara ezabatu mezua, bidali eta kontserbatu gabe. Este mensaje es personal y confidencial y su uso no autorizado está prohibido legalmente. Si usted no es el destinatario, proceda a borrarlo, sin reenviarlo ni conservarlo. This message is personal and confidential, unauthorised use is legally prohibited. If you are not the intended recipient, delete it without resending or backing it. -Mensaje original- De: Lucia Zarauz Enviado el: martes, 24 de julio de 2007 13:53 Para: 'Henrique Dallazuanna' CC: r-help@stat.math.ethz.ch Asunto: RE: [R] plotting gam models Hi Henrique, Thank you for your suggestion. Actually, I have already tried it, but I am confused because the plot I get is not the same as the output of plot(model) or plot.gam(model). The yaxis is different On the other hand, if I build a more complex model, as for example: model- gam(x ~ s(lat,long) + s(temperature)) I would like to extract the information to build the effects for each explanatory factor (one graph for s(lat,long) and another for s(temperature)), as R does when you use 'plot(model)' and you press return for subsequent pages. My final aim is to plot the influence of s(lat,long) as a contourplot superposed on a geographical map. Maybe there is an easier way to do it... Thank you very much lucía _ Lucia Zarauz AZTI - Tecnalia / Unidad de Investigación Marina Herrera kaia portualdea z/g 20110 Pasaia (Gipuzkoa) Tel: 943 004 800 - Fax: 943 004 801 e-mail: [EMAIL PROTECTED] www.azti.es ; www.tecnalia.info _ LEGE OHARRA AVISO LEGAL DISCLAIMER Mezu hau pertsonala eta isilpekoa da eta baimenik gabeko erabilera debekatua dago legalki. Jasotzailea ez bazara ezabatu mezua, bidali eta kontserbatu gabe. Este mensaje es personal y confidencial y su uso no autorizado está prohibido legalmente. Si usted no es el destinatario, proceda a borrarlo, sin reenviarlo ni conservarlo. This message is personal and confidential, unauthorised use is legally prohibited. If you are not the intended recipient, delete it without resending or backing it. De: Henrique Dallazuanna [mailto:[EMAIL PROTECTED] Enviado el: martes, 24 de julio de 2007 13:36 Para: Lucia Zarauz CC: r-help@stat.math.ethz.ch Asunto: Re: [R] plotting gam models see ?predict.gam -- Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange warning in summary.lm
On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: -Oorspronkelijk bericht- Van: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Verzonden: woensdag 25 juli 2007 12:20 Aan: ONKELINX, Thierry CC: r-help@stat.math.ethz.ch Onderwerp: Re: [R] Strange warning in summary.lm On Wed, 25 Jul 2007, ONKELINX, Thierry wrote: Dear Peter, Uwe and Brian, I've found some more problems with options(OutDec = ,). 1) as.numeric yields NA where it shouldn't It should: where does it say otherwise? OutDec affects output, only. I was doing something like options(OutDec = ,) df - data.frame(var = rep(1:8/4, 10), x = rnorm(80)) df.a - aggregate(df$x, by = list(var = df$var), FUN = sum) as.numeric(df.a$var) [1] NA NA NA 1 NA NA NA 2 Warning message: NAs introduced by coercion in: as.double.default(df.a$var) because I needed df.a$var as numeric again. And as Martin maechler has pointed out, we don't (and can't because ',' is used for other things) support that. 2) anova yields the same warning as summary It does not in current R: try any fairly recent version of R-devel. Please don't keep reporting a problem we have already fixed, as the FAQ and the posting guide explicitly ask of you. Sorry about that. I wasn't aware that the error was in a fixed subroutine that is used by summary and anova. I'm hestating to use a R-devel version because I haven't tried installing R from a tar.gz (I'm one of those lazy windows users that prefer the .exe version). For now I think I'll return to the good old option(OutDec = .). Binary versions are available on CRAN. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Function polr and discrete ordinal scale
Dear all,
To modelize the abundance of fish (4 classes) with a set of environmental
variables, I used the polr and predict.polr functions. I would like to know how
to bring the cumulated probabilities back to a discrete ordinal scale.
For the moment I used the predict.polr function with the argument class. Is
there an other way?
polrf - polrf - polr_mod(formula = acipenser_gueldenstaedtii ~ Long +
poly(Surf, 2, raw = TRUE) + poly(TempSum, 2, raw = TRUE) , data = mydata,
method = logistic, Hess = TRUE, na.action = na.omit)
pred1 - predict.polr(polrf, newdata = mydata2, type = class)
predict.polr - function(object, newdata, type=c(class,probs), ...)
{
if(!inherits(object, polr)) stop(Not a polr fit)
type - match.arg(type)
if(missing(newdata)) Y - object$fitted
else {
newdata - as.data.frame(newdata)
Terms - delete.response(object$terms)
m - model.frame(Terms, newdata, na.action = function(x) x)
X - model.matrix(Terms, m, contrasts = object$contrasts)
xint - match((Intercept), dimnames(X)[[2]], nomatch=0)
if(xint 0) X - X[, -xint, drop=F]
n - nrow(X)
q - length(object$zeta)
eta - drop(X %*% object$coef)
cumpr - matrix(plogis(matrix(object$zeta, n, q, byrow=T) - eta), , q)
Y - t(apply(cumpr, 1, function(x) diff(c(0, x, 1
dimnames(Y) - list(dimnames(X)[[1]], object$lev)
}
if(!is.null(object$na.action)) Y - napredict(object$na.action, Y)
switch(type, class={
Y - factor(max.col(Y), levels=seq(along=object$lev),
labels=object$lev)
}, probs={})
drop(Y)
}
Thank you.
Géraldine LASSALLE
Cemagref
Unité Ecosystèmes estuariens et
Poissons migrateurs amphihalins
50 avenue de Verdun
33612 Gazinet-Cestas
Tel: 05.57.89.09.98
Fax: 05.57.89.08.01
[EMAIL PROTECTED]
http://haddock.bordeaux.cemagref.fr:8080/ocms1/opencms/estuaires/Poissons_migrateurs_et_changement_global.html
[[alternative HTML version deleted]]
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[R] Best-fit linear model for the two matrices plotted.
Hi all.. I am so far successful in plotting the matrices containing r-values and evol.distances using R. But I am facing a problem to fit a line to it. I tried using lm function but no success..!! Can you please help me for that? I am giving the functions, I tried, to get a plot here: dismat - read.table(M:\dreb5.txt,sep=\t) cormat - read.table(M:\cordreb5.txt,sep=\t) plot(as.vector(as.matrix(cormat)), as.vector(as.matrix(dismat))) linmod - lm(cormat~dismat, data=??) - I am not sure what should be given for the data as two matrices are ploted against each other! Thanking you. Urmi - Get the freedom to save as many mails as you wish. Click here to know how. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to add circular text for a graph with concentric circles
[EMAIL PROTECTED] wrote:
Dear R experts,
I am plotting the population of students who live in a city, and in
successive circular bands made of the contiguous districts that surround
the city. This is a stylized figure, where I specify the area of each
successive circle based on the cumulative population of students. I want
to compare two sets of concentric circles across different populations -
such as 'All students' and 'Private students' (those attending private
school) by using the same colours and the same dimension of the outer
circle. I have attached the .pdf file with the output, and the R code to
generate the first set of circles.
I would appreciate any tips about how to rotate the text label that marks
each concentric circle (except the central circle) to be curved around the
circle, located in the middle of each band, thus following the circle
instead of being horizontal, as I have it now.
Hi Suhas,
This is kind of rough, being rejigged from an old piece of Postscript
code that I wrote to get text in an arc. You specify the text and
whatever else is needed as in the following example:
arctext-function(x,center=c(0,0),radius=1,
midangle=pi/2,stretch=1.1,cex=1,...) {
oldcex-par(cex)
par(cex=cex)
xwidth-strwidth(x)*stretch
startpos-midangle+xwidth/(radius*2)
xvec-strsplit(x,)[[1]]
xwidths-rep(mean(stretch*strwidth(xvec)),length(xvec))
arcpos-startpos-cumsum(xwidths)
for(i in 1:length(arcpos))
text(center[1]+radius*cos(arcpos[i]),center[2]+radius*sin(arcpos[i]),
xvec[i],adj=c(0.5,0.5),srt=(arcpos[i]-midangle)*180/pi)
par(cex=oldcex)
}
plot((1:5)
arctext(bendy as a bloody piece of spaghetti,center=c(3,3))
radius is obviously the radius of the arc,
midangle is where you want the center of the text,
stretch is how much to stretch the text to make it look nice
and cex is the expansion factor.
You will probably notice that I kludged the spacing by making
it monospaced. I'll have a try at getting proportionally spaced
text to work right when I get a chance.
Jim
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.
Also if you want to access the individual values, you can just leave it as a list: x.val - apply(x, 2, table) # access each value x.val$PR14[V] V 8 On 7/25/07, Allan Kamau [EMAIL PROTECTED] wrote: A subset of the data looks as follows df[1:10,14:20] PR10 PR11 PR12 PR13 PR14 PR15 PR16 1 VTIKVGD 2 VSIKVGG 3 VTIRVGG 4 VSIKIGG 5 VSIKVGG 6 VSIRVGG 7 VTIKIGG 8 VSIKVEG 9 VSIKVGG 10VSIKVGG The result I would like is as follows PR10PR11 PR12 ... [V:10][S:7,T:3][I:10] The result can be in a matrix or a vector and each variablename, value and frequency should be accessible so as to be used for comparisons with another dataset later. The frequency can be a count or a percentage. Allan. - Original Message From: Adaikalavan Ramasamy [EMAIL PROTECTED] To: Allan Kamau [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, July 24, 2007 10:21:51 PM Subject: Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset. The name of the table should give you the value. And if you have a matrix, you just need to convert it into a vector first. m - matrix( LETTERS[ c(1:3, 3:5, 2:4) ], nc=3 ) m [,1] [,2] [,3] [1,] A C B [2,] B D C [3,] C E D tb - table( as.vector(m) ) tb A B C D E 1 2 3 2 1 paste( names(tb), :, tb, sep= ) [1] A:1 B:2 C:3 D:2 E:1 If this is not what you want, then please give a simple example. Regards, Adai Allan Kamau wrote: Hi all, If the question below as been answered before I apologize for the posting. I would like to get the frequencies of occurrence of all values in a given variable in a multivariate dataset. In short for each variable (or field) a summary of values contained with in a value:frequency pair, there can be many such pairs for a given variable. I would like to do the same for several such variables. I have used table() but am unable to extract the individual value and frequency values. Please advise. Allan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.
Try summary: summary(x) PR10 PR11 PR12 PR13 PR14 PR15 PR16 V:10 S:7 I:10 K:8 I:2 E:1 D:1 T:3 R:2 V:8 G:9 G:9 On 7/25/07, Allan Kamau [EMAIL PROTECTED] wrote: A subset of the data looks as follows df[1:10,14:20] PR10 PR11 PR12 PR13 PR14 PR15 PR16 1 VTIKVGD 2 VSIKVGG 3 VTIRVGG 4 VSIKIGG 5 VSIKVGG 6 VSIRVGG 7 VTIKIGG 8 VSIKVEG 9 VSIKVGG 10VSIKVGG The result I would like is as follows PR10PR11 PR12 ... [V:10][S:7,T:3][I:10] The result can be in a matrix or a vector and each variablename, value and frequency should be accessible so as to be used for comparisons with another dataset later. The frequency can be a count or a percentage. Allan. - Original Message From: Adaikalavan Ramasamy [EMAIL PROTECTED] To: Allan Kamau [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Tuesday, July 24, 2007 10:21:51 PM Subject: Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset. The name of the table should give you the value. And if you have a matrix, you just need to convert it into a vector first. m - matrix( LETTERS[ c(1:3, 3:5, 2:4) ], nc=3 ) m [,1] [,2] [,3] [1,] A C B [2,] B D C [3,] C E D tb - table( as.vector(m) ) tb A B C D E 1 2 3 2 1 paste( names(tb), :, tb, sep= ) [1] A:1 B:2 C:3 D:2 E:1 If this is not what you want, then please give a simple example. Regards, Adai Allan Kamau wrote: Hi all, If the question below as been answered before I apologize for the posting. I would like to get the frequencies of occurrence of all values in a given variable in a multivariate dataset. In short for each variable (or field) a summary of values contained with in a value:frequency pair, there can be many such pairs for a given variable. I would like to do the same for several such variables. I have used table() but am unable to extract the individual value and frequency values. Please advise. Allan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining summary of frequencies of value occurrences for a variable in a multivariate dataset.
Is this what you want:
x - read.table(textConnection( PR10 PR11 PR12 PR13 PR14 PR15 PR16
+ 1 VTIKVGD
+ 2 VSIKVGG
+ 3 VTIRVGG
+ 4 VSIKIGG
+ 5 VSIKVGG
+ 6 VSIRVGG
+ 7 VTIKIGG
+ 8 VSIKVEG
+ 9 VSIKVGG
+ 10VSIKVGG), header=TRUE)
x.t - apply(x, 2, function(.col){
+ .tab - table(.col)
+ paste('[', paste(names(.tab), .tab, sep=:, collapse=','), ']', sep='')
+ })
x.t
PR10PR11PR12PR13PR14PR15
[V:10] [S:7,T:3][I:10] [K:8,R:2] [I:2,V:8] [E:1,G:9]
PR16
[D:1,G:9]
On 7/25/07, Allan Kamau [EMAIL PROTECTED] wrote:
A subset of the data looks as follows
df[1:10,14:20]
PR10 PR11 PR12 PR13 PR14 PR15 PR16
1 VTIKVGD
2 VSIKVGG
3 VTIRVGG
4 VSIKIGG
5 VSIKVGG
6 VSIRVGG
7 VTIKIGG
8 VSIKVEG
9 VSIKVGG
10VSIKVGG
The result I would like is as follows
PR10PR11 PR12 ...
[V:10][S:7,T:3][I:10]
The result can be in a matrix or a vector and each variablename, value and
frequency should be accessible so as to be used for comparisons with another
dataset later.
The frequency can be a count or a percentage.
Allan.
- Original Message
From: Adaikalavan Ramasamy [EMAIL PROTECTED]
To: Allan Kamau [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Sent: Tuesday, July 24, 2007 10:21:51 PM
Subject: Re: [R] Obtaining summary of frequencies of value occurrences for a
variable in a multivariate dataset.
The name of the table should give you the value. And if you have a
matrix, you just need to convert it into a vector first.
m - matrix( LETTERS[ c(1:3, 3:5, 2:4) ], nc=3 )
m
[,1] [,2] [,3]
[1,] A C B
[2,] B D C
[3,] C E D
tb - table( as.vector(m) )
tb
A B C D E
1 2 3 2 1
paste( names(tb), :, tb, sep= )
[1] A:1 B:2 C:3 D:2 E:1
If this is not what you want, then please give a simple example.
Regards, Adai
Allan Kamau wrote:
Hi all,
If the question below as been answered before I
apologize for the posting.
I would like to get the frequencies of occurrence of
all values in a given variable in a multivariate
dataset. In short for each variable (or field) a
summary of values contained with in a value:frequency
pair, there can be many such pairs for a given
variable. I would like to do the same for several such
variables.
I have used table() but am unable to extract the
individual value and frequency values.
Please advise.
Allan.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with sub !
Try Sys.setlocale(). marco.R.help marco.R.help wrote: I am trying to use sub to replace patterns in a character array that contains german names with german special characters. I have the following problem: sub(\\xdf,ss,Wei\xdferitzkreis) Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : input string 1 is invalid in this locale sub(\xdf,ss,Wei\xdferitzkreis) Error in sub(pattern, replacement, x, ignore.case, extended, fixed, useBytes) : 'pattern' is invalid in this locale Does anybody know how to tackle this problem ? -- View this message in context: http://www.nabble.com/problem-with-sub-%21-tf4141431.html#a11781512 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Operator and
Yann Mauon wrote: Hello, I'am new to the R world and have a lot of question but the first is : How to deal with opertor in table objects? (Or how to deal with in general...) I explain my problem. I read a file with the read.table expression. I then obtain a matrix. I read the first line for example with the commande data[,1]. Then I would like to select only the element in this line that are greater than 2. Is there an elegant way to achieve that ? Thanks by advance... Note that read.table() returns a data frame, not a matrix. To subset, try this: subset(data, data[,1] 2) OR subset(data, data[,1] 2, select=1) Of course, it is always nice if each column in your data frame has a meaningful name, so it can be referred to by name rather than number. ?subset ?names -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Operator and
mm - matrix(1:9, nrow=3) ; mm subset(mm[,1],mm[,1] 3) # Note I used 3 not 2 here. Have a look at some of the introductory documents on the R site ( Contributed documents under OTHER in the documentation). They should answer a lot of your basic questions like this. Documents by Lemon, Maindonald and Verzani are good places to start. Also the Introduction to R is useful. --- Yann Mauon [EMAIL PROTECTED] wrote: Hello, I'am new to the R world and have a lot of question but the first is : How to deal with opertor in table objects? (Or how to deal with in general...) I explain my problem. I read a file with the read.table expression. I then obtain a matrix. I read the first line for example with the commande data[,1]. Then I would like to select only the element in this line that are greater than 2. Is there an elegant way to achieve that ? Thanks by advance... -- View this message in context: http://www.nabble.com/Operator-%3E-and-%3C-tf4141869.html#a11781567 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Operator and
Hello, I'am new to the R world and have a lot of question but the first is : How to deal with opertor in table objects? (Or how to deal with in general...) I explain my problem. I read a file with the read.table expression. I then obtain a matrix. I read the first line for example with the commande data[,1]. Then I would like to select only the element in this line that are greater than 2. Is there an elegant way to achieve that ? Thanks by advance... -- View this message in context: http://www.nabble.com/Operator-%3E-and-%3C-tf4141869.html#a11781567 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Operator and
Hi you definitely shall make a quick glance to some documentation which comes with R e.g. R intro manual. Or look at CRAN where is quite impressive amount of literature from basic stuff to advanced papers. To your question: [EMAIL PROTECTED] napsal dne 25.07.2007 14:23:58: Hello, I'am new to the R world and have a lot of question but the first is : How to deal with opertor in table objects? (Or how to deal with in general...) I explain my problem. I read a file with the read.table expression. I then obtain a matrix. I read the first line for example with the commande data[,1]. Then I would like to You did not select line but column. data[,1] 2 will give you logical vector which you can use for selection of rows from data. data[data[,1] 2,] Regards. Petr select only the element in this line that are greater than 2. Is there an elegant way to achieve that ? Thanks by advance... -- View this message in context: http://www.nabble.com/Operator-%3E-and-%3C- tf4141869.html#a11781567 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Minitab Parametric Distribution Analysis in R
Minitab can perform a Parametric Distribution Analysis - Arbitrary Censoring with one of eight distributions (e.g., weibull), giving the maximum likelihood estimates of the parameters in the distribution for a given dataset. Does R have a package that provides equivalent functionality? Thanks for any advice you can offer. Tom La Bone [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Is Rwiki down?
Dear R-friends, is Rwiki down? I've been trying to login for the past couple of days with no success. Yours sincerely, Jin wherever you're surfing. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plots
--- amna khan [EMAIL PROTECTED] wrote: Hi Sir I did not find any function of graph which plot one variable on x-axis and 2 or more than 2 variables on y-axis. I think ?points or ?lines may be what you want. Moreover, how can I change the labels of L-moments diagram obtained by plotlmrdia(lmrdia()) Cannot help here. Thank you -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rgraphviz and R 2.5.1 entry point Rf_allocString could not be located
Dear R-Helpers In R 2.5.1, the command library(Rgraphviz) fails on my Windows (XP SP2) system with error popup The procedure entry point Rf_allocString could not be located in the dynamic link library R.dll. Thanks in advance for any suggestion in solving the error. My D. Coyne Imagination is more important than knowledge... (Albert Einstein) [EMAIL PROTECTED] BioInformatics Enthusiast Office: 301-865-0243 Cell:301-399-6351 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rgraphviz and R 2.5.1 entry point Rf_allocString could not be located
On Wed, 25 Jul 2007, My Coyne wrote: Dear R-Helpers In R 2.5.1, the command library(Rgraphviz) fails on my Windows (XP SP2) system with error popup The procedure entry point Rf_allocString could not be located in the dynamic link library R.dll. Thanks in advance for any suggestion in solving the error. Use a version of the package compiled for R 2.5.1. That currently picked up by using the menus in R 2.5.1 works for me. Also, this is not the right list for questions about Bioconductor packages, and please send properly formatted plain text only. My D. Coyne Imagination is more important than knowledge... (Albert Einstein) [EMAIL PROTECTED] BioInformatics Enthusiast Office: 301-865-0243 Cell:301-399-6351 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lme or gls prediction intervals
Hi Joris, Thank you for the reply. I also realize that I meant confidence intervals, not prediction intervals! I am trying to do something analogous to predict(model.gls, newdata, interval=confidence) but predict.gls does not have an interval argument. I am guessing that this is because it is subtle and complicated to figure out what the appropriate hypothesis is, but I was hoping to get some feedback. Cheers, Hank On Jul 25, 2007, at 3:21 AM, [EMAIL PROTECTED] wrote: Martin, Have you checked ?intervals.gls This intervals are approximate, but this would be the obvious starting point to me. Joris Martin Henry H. Stevens [EMAIL PROTECTED] To edu R-Help r- [EMAIL PROTECTED] Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] lme or gls prediction intervals 24/07/2007 19:22 Hi folks, I am trying to generate 95% confidence intervals for a gls model using predict.nlme with R version 2.5.1 (2007-06-27) . nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-83. I have looked in help, and I can do it for lm and glm models, and I can generate simple predictions for lme models with various levels -- I am familiar with the basics. Is there a way to get prediction intervals for gls models? My best model uses varPower(), so I am reluctant to fall back on lm predictions. Thank you, Hank Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum If you send an attachment, please try to send it in a format anyone can read, such as PDF, text, Open Document Format, HTML, or RTF. Please try not to send me MS Word or PowerPoint attachments- Why? See: http://www.gnu.org/philosophy/no-word-attachments.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is Rwiki down?
Me too. Hank On Jul 25, 2007, at 7:50 AM, Jin Lo wrote: Dear R-friends, is Rwiki down? I've been trying to login for the past couple of days with no success. Yours sincerely, Jin __ __ wherever you're surfing. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Dr. Hank Stevens, Associate Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E Pluribus Unum If you send an attachment, please try to send it in a format anyone can read, such as PDF, text, Open Document Format, HTML, or RTF. Please try not to send me MS Word or PowerPoint attachments- Why? See: http://www.gnu.org/philosophy/no-word-attachments.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Open two graphic devices at a time
Hello, I would like to export my plots to harddisk (jpeg or pdf). I know that could be done with pdf(...) and jpeg(...). But my problem is that if I open e.g. the pdf device my plot does not appear on the screen. If I plot to the x11 device and try to export later the outputfile is damaged. How can I manage that problem? I want to see my plots on screen and want to export them. Is there a chance to open two different devices, or is the only way printing twice. One time to x11() and one time to pdf()? Thanks a lot for any idea -- View this message in context: http://www.nabble.com/Open-two-graphic-devices-at-a-time-tf4142321.html#a11783029 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Time when object was created
Dear ComRades, Last night I left an Intel Core Duo Windows Vista system running an extensive mixed glm with lmer. This morning I found that R-lmer had finished the job successfully. I would like to know at what time the object containing the results (call it lme_1) was finished. I guess there is some simple function that when applied to the object would give me the time stamp? Thanks Rubén __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to add circular text for a graph with concentric circles
Thanks, Jim. I tried to implement this but the text swings all over the place. I
had thought that there could be a function where I could specify the circle's
origin, radius and angle of the location of the starting letter, then, based on
a specified font size and letter spacing, the arc could be plotted out. But
clearly, the problem is not as small as I thought, and it appears that I need to
spend some time learning more of the basics before attempting something this
complicated. Thanks for your help anyways.
best regards,
Suhas
Jim Lemon
[EMAIL PROTECTED]
m.au To
[EMAIL PROTECTED]
07/25/2007 cc
07:38 AMr-help@stat.math.ethz.ch
Subject
Re: [R] How to add circular text for a
graph with concentric circles
[EMAIL PROTECTED] wrote:
Dear R experts,
I am plotting the population of students who live in a city, and in
successive circular bands made of the contiguous districts that surround
the city. This is a stylized figure, where I specify the area of each
successive circle based on the cumulative population of students. I want
to compare two sets of concentric circles across different populations -
such as 'All students' and 'Private students' (those attending private
school) by using the same colours and the same dimension of the outer
circle. I have attached the .pdf file with the output, and the R code to
generate the first set of circles.
I would appreciate any tips about how to rotate the text label that marks
each concentric circle (except the central circle) to be curved around the
circle, located in the middle of each band, thus following the circle
instead of being horizontal, as I have it now.
Hi Suhas,
This is kind of rough, being rejigged from an old piece of Postscript
code that I wrote to get text in an arc. You specify the text and
whatever else is needed as in the following example:
arctext-function(x,center=c(0,0),radius=1,
midangle=pi/2,stretch=1.1,cex=1,...) {
oldcex-par(cex)
par(cex=cex)
xwidth-strwidth(x)*stretch
startpos-midangle+xwidth/(radius*2)
xvec-strsplit(x,)[[1]]
xwidths-rep(mean(stretch*strwidth(xvec)),length(xvec))
arcpos-startpos-cumsum(xwidths)
for(i in 1:length(arcpos))
text(center[1]+radius*cos(arcpos[i]),center[2]+radius*sin(arcpos[i]),
xvec[i],adj=c(0.5,0.5),srt=(arcpos[i]-midangle)*180/pi)
par(cex=oldcex)
}
plot((1:5)
arctext(bendy as a bloody piece of spaghetti,center=c(3,3))
radius is obviously the radius of the arc,
midangle is where you want the center of the text,
stretch is how much to stretch the text to make it look nice
and cex is the expansion factor.
You will probably notice that I kludged the spacing by making
it monospaced. I'll have a try at getting proportionally spaced
text to work right when I get a chance.
Jim
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[R] Odp: Open two graphic devices at a time
Hi far from beeing an expert in graphic devices AFAIK you can either see your graph on screen (x11 device) or to open other device (pdf, png, ...) and to issue plotting commands to that device. Do not forget dev.off() after your plot is finished. Or you can save your plot by menu command File/Save as... (on Windows), which you did not specify. Regards Petr [EMAIL PROTECTED] napsal dne 25.07.2007 15:55:12: Hello, I would like to export my plots to harddisk (jpeg or pdf). I know that could be done with pdf(...) and jpeg(...). But my problem is that if I open e.g. the pdf device my plot does not appear on the screen. If I plot to the x11 device and try to export later the outputfile is damaged. How can I manage that problem? I want to see my plots on screen and want to export them. Is there a chance to open two different devices, or is the only way printing twice. One time to x11() and one time to pdf()? Thanks a lot for any idea -- View this message in context: http://www.nabble.com/Open-two-graphic-devices- at-a-time-tf4142321.html#a11783029 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odp: Open two graphic devices at a time
@Petr Hello, now I tried it with savePlot(). This is a very easy way. Now I don't need two devices. Thanks a lot MatzeK Petr Pikal wrote: Hi far from beeing an expert in graphic devices AFAIK you can either see your graph on screen (x11 device) or to open other device (pdf, png, ...) and to issue plotting commands to that device. Do not forget dev.off() after your plot is finished. Or you can save your plot by menu command File/Save as... (on Windows), which you did not specify. Regards Petr [EMAIL PROTECTED] napsal dne 25.07.2007 15:55:12: Hello, I would like to export my plots to harddisk (jpeg or pdf). I know that could be done with pdf(...) and jpeg(...). But my problem is that if I open e.g. the pdf device my plot does not appear on the screen. If I plot to the x11 device and try to export later the outputfile is damaged. How can I manage that problem? I want to see my plots on screen and want to export them. Is there a chance to open two different devices, or is the only way printing twice. One time to x11() and one time to pdf()? Thanks a lot for any idea -- View this message in context: http://www.nabble.com/Open-two-graphic-devices- at-a-time-tf4142321.html#a11783029 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Open-two-graphic-devices-at-a-time-tf4142321.html#a11783905 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Constructing bar charts with standard error bars
I am new to R. I want to graph group data using a Traditional Bar Chart with Standard Error Bar, like the kind shown here: http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html Is there a simple way to do this? So far, I have only figured out how to plot the bars using barplot. testdata - scan(, list(group=0,xbar=0,se=0)) 400 0.36038 0.02154 200 0.35927 0.02167 100 0.35925 0.02341 50 0.35712 0.01968 25 0.35396 0.01931 barplot(testdata$xbar, names.arg=as.character(testdata$group), main=a=4.0, xlab=Group, ylab=xbar) xvalues - c(0.7, 1.9, 3.1, 4.3, 5.5) arrows(xvalues, testdata$xbar, xvalues, testdata$xbar+testdata$se, length= 0.4, angle=90, code=3) The best clue I have so far is Rtips #5.9: http://pj.freefaculty.org/R/Rtips.html#5.9 which is what I based my present solution off of. However, I do not understand how this works. It seems like there is no concrete way to determine the arrow drawing parameters x0 and x1 for a barplot. Moreover, the bars seem to be cut off. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ggplot2 equivalent of axis and problem with log scale
On 7/25/07, ONKELINX, Thierry [EMAIL PROTECTED] wrote: Dear useRs, Recently I've discorved ggplot2 and I must say that I really like it, although the documentation still is a working in progress. My first question: How can I change the position of the labels and the text of the labels? With a basic plot I would use axis(2, at = position.of.the.ticks, labels = text.at.the.ticks). Could someone provide me with an example of how to do this with ggplot2? Have a look at scale_continous - in particular the breaks and labels arguments (although I haven´t tested them much yet). You need + scale_x_continuous() and + scale_y_continuous() as appropriate. The second question is probably a little bug. If I plot the y-axis in log10 scale then geom_errorbar still plot the values in the original scale. See the example below. The second plot is what I would suspect when plotting the first graph. Yes, that's a bug - I`ll try and get it fixed in the next version. Thanks, Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Minitab Parametric Distribution Analysis in R
The survival package (survreg() function) will fit quite a few parametric models under censoring. If you aren't doing regression, but just one-sample fitting, you can feed the appropriate censored or truncated likelihood to mle() in the stat4 package. Both packages should be part of your R distribution. -thomas On Wed, 25 Jul 2007, Tom La Bone wrote: Minitab can perform a Parametric Distribution Analysis - Arbitrary Censoring with one of eight distributions (e.g., weibull), giving the maximum likelihood estimates of the parameters in the distribution for a given dataset. Does R have a package that provides equivalent functionality? Thanks for any advice you can offer. Tom La Bone [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] qda(MASS) function error
Dear R user, I'm using qda (quadratic discriminant analysis) function (package MASS) to classify 58 explanatory variables (numeric type with different ranges) using a grouping variable (factor 2 levels 0 1). I'm using the qda method for class 'data.frame' (in this way I don't need to specify a formula). Using the function: result.qda-qda(explanatory.variables, grouping.variable, method=moment) I obtain the following error message: Error in qda.default(x, grouping, ...) : rank deficiency in group 0 I run the script excluding some variables and I've individuated 2 explanatory variables that give problems, but I don't understand why they give them. The two excluded variables are numeric with two possible values: 0 and 1, but in the rest of group of variables, some similar variables are considered. I don't have this problem using lda function for linear discriminant analysis. What does this error message mean? What types of variables does qda function consider? Thank in advance, Mauro Rossi -- Mauro Rossi Istituto di Ricerca per la Protezione Idrogeologica Consiglio Nazionale delle Ricerche Via della Madonna Alta, 126 06128 Perugia Italia Tel. +39 075 5014421 Fax +39 075 5014420 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing bar charts with standard error bars
John Zabroski wrote: I am new to R. I want to graph group data using a Traditional Bar Chart with Standard Error Bar, like the kind shown here: http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html There are severe problems with dynamite plots such as these. See http://biostat.mc.vanderbilt.edu/DynamitePlots for a list of problems and solutions. Frank Is there a simple way to do this? So far, I have only figured out how to plot the bars using barplot. testdata - scan(, list(group=0,xbar=0,se=0)) 400 0.36038 0.02154 200 0.35927 0.02167 100 0.35925 0.02341 50 0.35712 0.01968 25 0.35396 0.01931 barplot(testdata$xbar, names.arg=as.character(testdata$group), main=a=4.0, xlab=Group, ylab=xbar) xvalues - c(0.7, 1.9, 3.1, 4.3, 5.5) arrows(xvalues, testdata$xbar, xvalues, testdata$xbar+testdata$se, length= 0.4, angle=90, code=3) The best clue I have so far is Rtips #5.9: http://pj.freefaculty.org/R/Rtips.html#5.9 which is what I based my present solution off of. However, I do not understand how this works. It seems like there is no concrete way to determine the arrow drawing parameters x0 and x1 for a barplot. Moreover, the bars seem to be cut off. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing bar charts with standard error bars
John Zabroski johnzabroski at gmail.com writes: I am new to R. I want to graph group data using a Traditional Bar Chart with Standard Error Bar, like the kind shown here: http://samiam.colorado.edu/~mcclella/ftep/twoGroups/twoGroupGraphs.html Is there a simple way to do this? [snip] The best clue I have so far is Rtips #5.9: http://pj.freefaculty.org/R/Rtips.html#5.9 which is what I based my present solution off of. However, I do not understand how this works. It seems like there is no concrete way to determine the arrow drawing parameters x0 and x1 for a barplot. Moreover, the bars seem to be cut off. barplot() returns the x values you need for x0 and x1. barplot(...,ylim=c(0,xbar+se)) will set the upper y limit so the bars don't get cut off. Here are three ways to create such a barplot (I will add this to the wiki once it's back on line): (n.b.: the with() command is just a shortcut to avoid having to type testdata$xbar, testdata$group, etc.) ## 1. tweaked version of what you did above testdata - data.frame(group=c(400,200,100,50,25), xbar= c(0.36038 , 0.35927 , 0.35925 , 0.35712 , 0.35396), se = c(0.02154,0.02167,0.02341,0.01968, 0.01931)) xvals = with(testdata, barplot(xbar, names.arg=group, main=a=4.0, xlab=Group, ylab=xbar,ylim=c(0,max(xbar+se with(testdata, arrows(xvals, xbar, xvals, xbar+se, length=0.4, angle=90, code=3)) ## 2. using the plotCI function from plotrix to draw the ##arrows instead library(plotrix) xvals = with(testdata, barplot(xbar, names.arg=group, main=a=4.0, xlab=Group, ylab=xbar,ylim=c(0,max(xbar+se with(testdata, plotCI(xvals, xbar, liw=0,uiw=se,add=TRUE,pch=NA,gap=FALSE)) ## 3. the most automatic way, using barplot2() from the ## gplots package library(gplots) with(testdata, barplot2(xbar,names.arg=group,main=a=4.0, xlab=Group,ylab=xbar,plot.ci=TRUE, ci.u=xbar+se,ci.l=xbar)) P.S. I hope you're not hoping to infer a statistically significant difference among these groups ... cheers Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initalizing and checking validity of S4 classes
Martin Morgan [EMAIL PROTECTED] writes:
Hi Michal --
Add validObject to your initialize method:
Actually, a call to valid object is part of the default initialization
method which has been masked. A different solution, which might have
some other benefits is to delegate back to the default method using
callNextMethod. So you could do:
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
callNextMethod(.Object=.Object, v=cv, l=cl)
} )
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject.
Yes. Anytime you specialize a method you must take responsibility for
any less specific methods. In this case, the default 'initialize'
does object validation. So if you want validation, you either need to
do it directly or invoke the default method.
(2) Responsibility for object
validity is ambiguous -- does it belong with 'new', 'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).
This is a good point. It suggests that, at least, one must initialize
all non-inherited slots to valid values _before_ calling the next
method.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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[R] if - else
Greetings, I have some confusion with the use of if - else. Let's say I have a four variables as follows: Condition DateFound DateFirstEvent DateSecondEvent NA10Jan2000 NA NA 0 05Jan2000 07Jan2000 10Jan2000 1 07Jan2000 07Jan2000 08Jan2000 2 09Jan2000 NA NA Now, what I need to do is make a new variable that is either the midpoint of the first and second event dates, or the date found (I will call Start). I tried an if - else condition as follows: Start - if (DateFirstEven DateSecondEvent) (DateFirstEvent+DateSecondEvent)/2 else DateFound I also tried Start - if (any(DateFirstEven DateSecondEvent)) (DateFirstEvent+DateSecondEvent)/2 else DateFound Only the first half of the expression was ever evaluated. I hope I have not been to brief, and will certainly appreciate any help. Thanks, Jim -- James J. Roper Population Dynamics and Conservation of Terrestrial Vertebrates Caixa Postal 19034 81531-990 Curitiba, Paraná, Brasil === E-mail: [EMAIL PROTECTED] Phone/Fone/Teléfono: 55 41 33611764 celular: 55 41 99870543 Casa: 55 41 33857249 === Ecologia e Conservação na UFPR http://www.bio.ufpr.br/ecologia/ --- http://jjroper.googlepages.com/ http://arsartium.googlepages.com/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reversing the x-axis terms on a boxplot
Hi, I am able to reverse the order of plotting on regular plots (i.e. with the plot() function) by manually setting the xlim variable. Is there some trick like this which will work for a boxplot? * for example: l - sample(letters, 500, replace=TRUE) n - runif(500) boxplot(n ~ l) this will produce a plot with the x-axis ranging from a-z ... i know that these are labels, associated with an integer index-- but is there someway to reverse the plotting order? Thanks in advance, Dylan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Updating packages in Ubuntu feisty for 2.5
Hi - I do have exactly the same problem with the same distribution (Ubuntu Feisty amd64) and am unable to upgrade to R 2.5.1. The r-base-core is version 2.4.1 in Ubuntu depositories while all others r-cran related packages are upgraded to R 2.5.1 (r-base-dev, r-base...). So far I have been unsuccessful at upgrading R. I posted on the Ubuntu forum but got no answer yet. Details: $ uname -a Linux bronski 2.6.20-16-generic #2 SMP Thu Jun 7 19:00:28 UTC 2007 x86_64 GNU/Linux R.version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) Christophe Colleen Doherty a écrit : Hi, I would like to run R2.5.1 in Ubuntu feisty on an AMD64 chip. I am a total newbie to Linux. I have successfully compiled 2.5 however, I am not able to figure out how to upgrade the packages. I am not able to find an R-base-core_2.5.1-1_amd64 or all on the CRAN mirrors. I can find one on the Ubuntu feisty site, however when I try to install it I get a warning that Dependency is not stisfiable: libc6 I am pretty convinced I have libc6 installed. When I reinstall it with apt-get It says the latest version is currently installed. I would appreciate any help or advice that y'all have. If this is more appropriate on another list, please let me know where and I will post it there. Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] initalizing and checking validity of S4 classes
Dear Martin and Seth,
Thanks a million for explanations and suggestions. I find myself still in the
process of learning S4 system. Can you possibly suggest some material that I
could use in this process?
Anything apart from Programming with data book? I also know the notes written
by John Chambers and I also have Fritz Leisch's slides from the first UseR!,
all three available on the Web. Do you have any suggestions in that matter?
Thanks a lot in advance!
Best, Michal
Martin Morgan mtmorgan at fhcrc.org writes:
Hi Michal --
Add validObject to your initialize method:
Actually, a call to valid object is part of the default initialization
method which has been masked. A different solution, which might have
some other benefits is to delegate back to the default method using
callNextMethod. So you could do:
setMethod(initialize, someclass,
function(.Object, v=numeric(0), l=character(0))
{
# strip the vector names
cv - v
cl - l
names(cv) - NULL
names(cl) - NULL
callNextMethod(.Object=.Object, v=cv, l=cl)
} )
Here are two interpretations of this. (1) using 'initialize' means
that you are taking control of the initialization process, and hence
know when you need to call validObject.
Yes. Anytime you specialize a method you must take responsibility for
any less specific methods. In this case, the default 'initialize'
does object validation. So if you want validation, you either need to
do it directly or invoke the default method.
(2) Responsibility for object
validity is ambiguous -- does it belong with 'new', 'initialize', or a
'constructor' that the programmer might write? This is particularly
problematic with R's copy semantics, where creating transiently
invalid objects seems to be almost necessary (e.g., callNextMethod()
in 'initialize' might initialize the inherited slots of the object,
but the object itself is of the derived class and could well be
invalid 'invalid' after the base class has finished with initialize).
This is a good point. It suggests that, at least, one must initialize
all non-inherited slots to valid values _before_ calling the next
method.
+ seth
:
::
::: Note that my e-mail address has changed to m.j.bojanowski at uu dot nl
::: Please update you address books accordingly. Thank you!
::
:
Michal Bojanowski
ICS / Department of Sociology
Utrecht University
Heidelberglaan 2; 3584 CS Utrecht
The Netherlands
m.j.bojanowski at uu dot nl
http://www.fss.uu.nl/soc/bojanowski/
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Subscript out of bounds when using datadist() from Design library
I am running R version 2.4.1 on Windows XP. I have a question regarding the datadist() function from the Design library. I have a data.frame (call it my.data) with 4 columns. When I submit the code datadist(data=my.data) I get the following error message: Error in X[[1]] : subscript out of bounds I suspect there may be something wrong with my data.frame (I'm certain there is nothing wrong with datadist()), but I don't know what. Has anyone experienced the mistake I seem to be making? Regards, Cody Hamilton Edwards Lifesciences __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subscript out of bounds when using datadist() from Design library
Cody Hamilton wrote: I am running R version 2.4.1 on Windows XP. I have a question regarding the datadist() function from the Design library. I have a data.frame (call it my.data) with 4 columns. When I submit the code datadist(data=my.data) I get the following error message: Error in X[[1]] : subscript out of bounds I suspect there may be something wrong with my data.frame (I'm certain there is nothing wrong with datadist()), but I don't know what. Has anyone experienced the mistake I seem to be making? If I follow the help page for datadist(), I think you want the following: datadist(my.data) Note the following in the description of the data argument: Unless the first argument is a fit object, data must be an integer. A data frame is not a fit object, so I think that was the reason it did not work for you. Regards, Cody Hamilton Edwards Lifesciences __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using contrasts on matrix regressions (using gmodels, perhaps)
Hi, I want to test for a contrast from a regression where I am regressing the columns of a matrix. In short, the following. X - matrix(rnorm(50),10,5) Y - matrix(rnorm(50),10,5) lm(Y~X) Call: lm(formula = Y ~ X) Coefficients: [,1] [,2] [,3] [,4] [,5] (Intercept) 0.3350 -0.1989 -0.1932 0.7528 0.0727 X10.2007 -0.8505 0.0520 0.1501 0.3248 X20.3212 0.7008 -0.0963 -0.2584 0.6711 X30.3781 -0.7321 0.1907 -0.1721 0.3073 X4 -0.1778 0.2822 -0.0644 -0.2649 -0.4140 X5 -0.1079 -0.0475 0.6047 -0.8369 -0.5928 I want to test for c'b = 0 where c is (lets say) the contrast (0, 0, 1, 0, -1). Is it possible to do so, in one shot, using gmodels or something else? Many thanks and best wishes, Ranjan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subscript out of bounds when using datadist() from Design library
Chuck, Quite right. Thank you. Regards, -Cody -Original Message- From: Chuck Cleland [mailto:[EMAIL PROTECTED] Sent: Wednesday, July 25, 2007 4:33 PM To: Cody Hamilton Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Subscript out of bounds when using datadist() from Design library Cody Hamilton wrote: I am running R version 2.4.1 on Windows XP. I have a question regarding the datadist() function from the Design library. I have a data.frame (call it my.data) with 4 columns. When I submit the code datadist(data=my.data) I get the following error message: Error in X[[1]] : subscript out of bounds I suspect there may be something wrong with my data.frame (I'm certain there is nothing wrong with datadist()), but I don't know what. Has anyone experienced the mistake I seem to be making? If I follow the help page for datadist(), I think you want the following: datadist(my.data) Note the following in the description of the data argument: Unless the first argument is a fit object, data must be an integer. A data frame is not a fit object, so I think that was the reason it did not work for you. Regards, Cody Hamilton Edwards Lifesciences __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using contrasts on matrix regressions (using gmodels, perhaps)
The doBy package has an esticon function which allows you to do that. Regards Søren Fra: [EMAIL PROTECTED] på vegne af Ranjan Maitra Sendt: to 26-07-2007 01:30 Til: R-help Emne: [R] using contrasts on matrix regressions (using gmodels, perhaps) Hi, I want to test for a contrast from a regression where I am regressing the columns of a matrix. In short, the following. X - matrix(rnorm(50),10,5) Y - matrix(rnorm(50),10,5) lm(Y~X) Call: lm(formula = Y ~ X) Coefficients: [,1] [,2] [,3] [,4] [,5] (Intercept) 0.3350 -0.1989 -0.1932 0.7528 0.0727 X10.2007 -0.8505 0.0520 0.1501 0.3248 X20.3212 0.7008 -0.0963 -0.2584 0.6711 X30.3781 -0.7321 0.1907 -0.1721 0.3073 X4 -0.1778 0.2822 -0.0644 -0.2649 -0.4140 X5 -0.1079 -0.0475 0.6047 -0.8369 -0.5928 I want to test for c'b = 0 where c is (lets say) the contrast (0, 0, 1, 0, -1). Is it possible to do so, in one shot, using gmodels or something else? Many thanks and best wishes, Ranjan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reversing the x-axis terms on a boxplot
Dylan Beaudette said the following on 7/25/2007 11:18 AM: Hi, I am able to reverse the order of plotting on regular plots (i.e. with the plot() function) by manually setting the xlim variable. Is there some trick like this which will work for a boxplot? * for example: l - sample(letters, 500, replace=TRUE) n - runif(500) boxplot(n ~ l) this will produce a plot with the x-axis ranging from a-z ... i know that these are labels, associated with an integer index-- but is there someway to reverse the plotting order? Thanks in advance, Dylan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Try this: set.seed(1) l - sample(letters, 500, replace=TRUE) n - runif(500) l - factor(l, levels = rev(letters)) boxplot(n ~ l) This is explained in the details section of ?boxplot. If multiple groups are supplied either as multiple arguments or via a formula, parallel boxplots will be plotted, in the order of the arguments or the order of the levels of the factor (see 'factor'). This means you can create any order you want by setting the factor levels explicitly. HTH, --sundar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subscript out of bounds when using datadist() from Design library
Cody Hamilton wrote: I am running R version 2.4.1 on Windows XP. I have a question regarding the datadist() function from the Design library. I have a data.frame (call it my.data) with 4 columns. When I submit the code datadist(data=my.data) You can just use dd - datadist(my.data); options(datadist='dd') If that doesn't fix it, generate a test dataset that fails or do save(..., compress=TRUE) and send me your dataset so I can debug. Frank I get the following error message: Error in X[[1]] : subscript out of bounds I suspect there may be something wrong with my data.frame (I'm certain there is nothing wrong with datadist()), but I don't know what. Has anyone experienced the mistake I seem to be making? Regards, Cody Hamilton Edwards Lifesciences __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] question on using gl1ce from lasso2 package
G'day Li, On Wed, 25 Jul 2007 00:50:43 -0400 Li Li [EMAIL PROTECTED] wrote: I tried several settings by using the family=gaussian in gl1ce, but none of them works. [...] gl1ce(Petal.Width~Sepal.Length+Sepal.Width+Petal.Length, data=iris,family=gaussian()) Error in eval(expr, envir, enclos) : object etastart not found Does anyone have experience with this function? Any help will be appreciated, Actually, gl1ce(Petal.Width~Sepal.Length+Sepal.Width+Petal.Length, data=iris, + family=gaussian) should work. No need to say `family=gaussian()'. However, omitting the brackets leads to an even more obscure error message and using traceback() makes me believe that the function `family()' must have been changed since this code was ported from S-Plus to R. The version with brackets does not seem to work since the function that tries to determine initial values for the iterative process of fitting a GLM tries to access an object called `etastart', which exist in the list of formal parameters of glm() but is not a formal parameter of gl1ce(). I am not sure whether this problem always existed or is also new due to changes in glm() and accompanying functions. (Time to re-work the whole lasso2 package, I guess.) A way to solve your problem is to issue the following commands: etastart - NULL gl1ce(Petal.Width~Sepal.Length+Sepal.Width+Petal.Length, data=iris, + family=gaussian()) However, since you are using the gaussian family, why not use l1ce() directly? The following command leads to the same output: l1ce(Petal.Width~Sepal.Length+Sepal.Width+Petal.Length, data=iris, + absolute=TRUE) Hope this helps. Cheers, Berwin === Full address = Berwin A TurlachTel.: +65 6515 4416 (secr) Dept of Statistics and Applied Probability+65 6515 6650 (self) Faculty of Science FAX : +65 6872 3919 National University of Singapore 6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED] Singapore 117546http://www.stat.nus.edu.sg/~statba __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] For loops
Hi,
is there a way of simplifying the following code:
G - rep(NA,n)
for(i in 1:n)
{
gj - 0
for(j in 1:n)
{
for(l in 1:n)
{
for(m in 1:n)
{
gj - gj+G.fun(XB[i]+p[3]*X[j,3]+p[4]*X[l,4]+p[5]*X[m,5],ff)
}
}
}
G[i] - gj/n^3
}
Thanks.
Joaquim Santos
__
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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] [BioC] Color Question about image function in graphics package
Hello Shiliang, please have a look a the manual page for image (access from R by typing ?image ). You can specify which colors to use and at which values to switch colors using the arguments breaks and colors. For example: image(matrix(rnorm(36),4,9)+20,col=c(red,blue),breaks=c(-1e5,20,1e5)) basically says: display every cell with a value below 20 in red (breaks[1:2] specify the interval for red) and every value above 20 in blue (breaks[2:3] specify the interval for blue). Regards, Joern swang wrote: Dear Lists: I had a matrix which has lrt score for my microarray data. I just wonder how to visualize them with score over 20 in particular color such as blue. I cannot understand the color relationship with the value in z matrix. For example, If I see a red color in my image generated by image function. I don't know what is the value of z in that spot. Example: aaa - matrix(rnorm(36),4,9) image(aaa) Can I paint the cells at which their values are higher than a certain value in image()? Or I have to use some other functions, best Shiliang [[alternative HTML version deleted]] ___ Bioconductor mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Updating packages in Ubuntu feisty for 2.5
On Wed, Jul 25, 2007 at 09:57:18PM +0200, Christophe Bonenfant wrote: Hi - I do have exactly the same problem with the same distribution (Ubuntu Feisty amd64) and am unable to upgrade to R 2.5.1. The r-base-core is version 2.4.1 in Ubuntu depositories while all others r-cran related packages are upgraded to R 2.5.1 (r-base-dev, r-base...). So far I have been unsuccessful at upgrading R. I posted on the Ubuntu forum but got no answer yet. Wrong place. Please subscribe to r-sig-debian, and ask there. Someone may just walk you through (locally) building the R 2.5.1 package for Debian. After all, there *are* R 2.5.1 packages for Ubuntu, though for 32-bit bit aka x86 intel. Dirk Details: $ uname -a Linux bronski 2.6.20-16-generic #2 SMP Thu Jun 7 19:00:28 UTC 2007 x86_64 GNU/Linux R.version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) Christophe Colleen Doherty a écrit : Hi, I would like to run R2.5.1 in Ubuntu feisty on an AMD64 chip. I am a total newbie to Linux. I have successfully compiled 2.5 however, I am not able to figure out how to upgrade the packages. I am not able to find an R-base-core_2.5.1-1_amd64 or all on the CRAN mirrors. I can find one on the Ubuntu feisty site, however when I try to install it I get a warning that Dependency is not stisfiable: libc6 I am pretty convinced I have libc6 installed. When I reinstall it with apt-get It says the latest version is currently installed. I would appreciate any help or advice that y'all have. If this is more appropriate on another list, please let me know where and I will post it there. Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] if - else
try: Start - ifelse (DateFirstEven DateSecondEvent, (DateFirstEvent+DateSecondEvent)/2, DateFound) On 7/25/07, James J. Roper [EMAIL PROTECTED] wrote: Greetings, I have some confusion with the use of if - else. Let's say I have a four variables as follows: Condition DateFound DateFirstEvent DateSecondEvent NA10Jan2000 NA NA 0 05Jan2000 07Jan2000 10Jan2000 1 07Jan2000 07Jan2000 08Jan2000 2 09Jan2000 NA NA Now, what I need to do is make a new variable that is either the midpoint of the first and second event dates, or the date found (I will call Start). I tried an if - else condition as follows: Start - if (DateFirstEven DateSecondEvent) (DateFirstEvent+DateSecondEvent)/2 else DateFound I also tried Start - if (any(DateFirstEven DateSecondEvent)) (DateFirstEvent+DateSecondEvent)/2 else DateFound Only the first half of the expression was ever evaluated. I hope I have not been to brief, and will certainly appreciate any help. Thanks, Jim -- James J. Roper Population Dynamics and Conservation of Terrestrial Vertebrates Caixa Postal 19034 81531-990 Curitiba, Paraná, Brasil === E-mail: [EMAIL PROTECTED] Phone/Fone/Teléfono: 55 41 33611764 celular: 55 41 99870543 Casa: 55 41 33857249 === Ecologia e Conservação na UFPR http://www.bio.ufpr.br/ecologia/ --- http://jjroper.googlepages.com/ http://arsartium.googlepages.com/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to auto-scale cex of y-axis labels in lattice dotplot?
When I create a dotplot in lattice, I frequently observe overplotting of the labels along the vertical axis. On my screen, this illustrates overplotting of the letters: windows() reps=6 dat=data.frame(let=rep(letters,each=reps), grp=rep(1:reps, 26), y=runif(26*reps)) dotplot(let~y|grp, dat) Is there a way to automatically scale the labels so that they are not over-plotted? I currently do something like this: Calculate or guess the number of panel rows: NumPanelRows cexLab - min(1, .9*par()$pin[2]/ (nlevels(dat$let)*NumPanelRows*strheight(A,units=in))) dotplot(..., scales=list(y=list(cex=cexLab)) Is there an easier way? Is there a function that I can call which calculates the layout of the panels that will be used in the dotplot? Any tips will be appreciated. K Wright __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Updating packages in Ubuntu feisty for 2.5
Hi, I would like to run R2.5.1 in Ubuntu feisty on an AMD64 chip. I am a total newbie to Linux. I have successfully compiled 2.5 however, I am not able to figure out how to upgrade the packages. I am not able to find an R-base-core_2.5.1-1_amd64 or all on the CRAN mirrors. I can find one on the Ubuntu feisty site, however when I try to install it I get a warning that Dependency is not stisfiable: libc6 I am pretty convinced I have libc6 installed. When I reinstall it with apt-get It says the latest version is currently installed. I would appreciate any help or advice that y'all have. If this is more appropriate on another list, please let me know where and I will post it there. Thanks! -- Colleen Doherty Thomashow Lab 310 Plant Biology Michigan State University East Lansing, MI 48824 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] DF and intercept term meaning for mixed (lme) models
Hi, I am using the lme package to fit mixed effects models to a set of data. I am having a difficult time understanding the *meaning* of the numDF (degrees of freedom in the numerator), denDF (DF in the denomenator), as well as the Intercept term in the output. For example: I have a groupedData object called 'Soil', and am fitting an lme model as follows: ## fit a simple model # errors partitioned among replicates fit1 - lme( log(ksat) ~ log(conc) + ordered(sar) + soil_id , random = ~ 1 | rep, data=Soil ) ## check significance of model terms anova(fit1) numDF denDF F-value p-value (Intercept) 1 1253 64313.21 .0001 log(conc) 1 597 173.34 .0001 ordered(sar) 2 597 13.87 .0001 soil_id 29 597 54.92 .0001 I am pretty sure that I am interpreting the p-values for the predictor terms to mean that these terms contribute significantly to the variation in the response variable, (?) . I am not sure what the significance of the Intercept term really means. Does it have something to do with the significance of the random effects in the model? Also, from a practical standpoint, how can I best describe / interpret the numDF and denDF terms to others... or do they even matter to a person who is looking to see if the 'treatment' predictor terms had any effect on the response term? Thanks in advance. Dylan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
