[R] Poisson regression in R
I have these questions: (1) Use Poisson regression to estimate the main effects of car, age, and dist (each treated as categorical and modelled using indicator variables) and interaction terms. (2) It was determined by one study that all the interactions were unimportant and decided that age and car could be treated as though they were continuous variables. Fit a model incorporating these features and compare it with the best model obtained in (1). n is the number of insurance policies y is the number of claims car is the car in an insurance category age is the age of policy holder dist is the district where the policy holder lived (1 for London and other major cities, and 0 otherwise) Data: car age disty n 1 1 0 65 317 1 2 0 65 476 1 3 0 52 486 1 4 0 310 3259 2 1 0 98 486 2 2 0 159 1004 2 3 0 175 1355 2 4 0 877 7660 3 1 0 41 223 3 2 0 117 539 3 3 0 137 697 3 4 0 477 3442 4 1 0 11 40 4 2 0 35 148 4 3 0 39 214 4 4 0 167 1019 1 1 1 2 20 1 2 1 5 33 1 3 1 4 40 1 4 1 36 316 2 1 1 7 31 2 2 1 10 81 2 3 1 22 122 2 4 1 102 724 3 1 1 5 18 3 2 1 7 39 3 3 1 16 68 3 4 1 63 344 4 1 1 0 3 4 2 1 6 16 4 3 1 8 25 4 4 1 33 114 I need help finding the correct R code to construct models. According to the previous study, the model in (2) "is simpler than (1), fits well (deviance = 53.11, d.f. = 60, p-value = 0.72) and gives coefficients (standard errors): AGE, – 0.177 (0.018); CAR, 0.198 (0.021); DIST, 0.210 (0.059)." As of the first model, I think that I should use this code, but not sure: > firstmodel<-glm(y~factor(age)*factor(car)*factor(dist),family=poisson) As of the second model, I used this code, but it produces results that contradict what the previous study says (and deleting intercept does not help): > secondmodel<-glm(y~age+car+factor(dist),family=poisson) > summary(secondmodel) Call: glm(formula = y ~ age + car + factor(dist), family = poisson) Deviance Residuals: Min1QMedian3Q Max -14.0258 -3.3200 -0.62962.0575 18.1442 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept)3.082220.08127 37.92 <2e-16 *** age0.836640.02067 40.48 <2e-16 *** car -0.167230.01612 -10.37 <2e-16 *** factor(dist)1 -2.159370.05849 -36.92 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for poisson family taken to be 1) Null deviance: 5660.6 on 31 degrees of freedom Residual deviance: 1154.5 on 28 degrees of freedom AIC: 1330.8 Number of Fisher Scoring iterations: 5 -- View this message in context: http://www.nabble.com/Poisson-regression-in-R-tp15784126p15784126.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] One quick question concerning R
?lines -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Elizabeth Purdom Sent: Sunday, March 02, 2008 10:30 AM To: Marc Diamond Cc: R-help@r-project.org Subject: Re: [R] One quick question concerning R Hi, Not sure about what you want your plot to look like, but you should also look at 'matplot'. Best, Elizabeth Marc Diamond wrote: > Just started using 'R'. Nice system. Once quick question: Is it possible to > put plot more than one series against a common 'x variable on the same plot? > In otherwords, I may want a stacked bar chart of line chart containing more > than one series. Could not figure out how to do this. > > Thanks for your help. > > Marc Diamond > Aviation-Software, Inc. > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] One quick question concerning R
Hi, Not sure about what you want your plot to look like, but you should also look at 'matplot'. Best, Elizabeth Marc Diamond wrote: > Just started using 'R'. Nice system. Once quick question: Is it possible to > put plot more than one series against a common 'x variable on the same plot? > In otherwords, I may want a stacked bar chart of line chart containing more > than one series. Could not figure out how to do this. > > Thanks for your help. > > Marc Diamond > Aviation-Software, Inc. > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] difference between lrm's "Model L.R." and anova's "Chi-Square"
[EMAIL PROTECTED] wrote:
> I am running lrm() with a single factor. I then run anova() on the fitted
> model to obtain a p-value associated with having that factor in the model.
>
> I am noticing that the "Model L.R." in the lrm results is almost the same
> as the "Chi-Square" in the anova results, but not quite; the latter value
> is always slightly smaller.
>
> anova() calculates the p-value based on "Chi-Square", but I have
> independent evidence that "Model L.R." is the actual -2*log(LR), so should
> I be using that?
>
> Why are the values different?
anova (anova.Design) computes Wald statistics. When the log-likelihood
is very quadratic, these statistics will be very close to log-likelihood
ratio chi-square statistics. In general LR chi-square tests are better;
we use Wald tests for speed. It's best to take the time and do
lrtest(fit1,fit2) in Design, where one of the two fits is a subset of
the other.
Frank Harrell
>
> prob_a <- inv.logit(rnorm(1,0,1))
> prob_b <- inv.logit(rnorm(1,0,1))
> data <- data.frame(
> factor=c(rep("a",500),rep("b",500)),
> outcome=c(sample(c(1,0),100,replace=T,prob=c(prob_a,1-prob_a)),
> sample(c(1,0),100,replace=T,prob=c(prob_b,1-prob_b
> fit <- lrm(outcome~factor,data)
>
> fit # gives "Model L.R." e.g. 8.23, 11.76, 6.89...
> anova(fit)# gives "Chi-Square" e.g. 8.19, 11.69, 6.85...
>
> Previous Next| Save| Delete | Reply |
>
> __
> R-help@r-project.org mailing list
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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.
>
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] Could not install aroma.affymetrix
I don't know if this is the correct forum to ask the following question;
however, when I search the aroma.affymetrix discussion group, it suggested
that I should posted the question to r-help. Here it goes.
I followed the instructions on aroma.affymetrix trying to install the
packages; following are the steps:
> install.packages(c("R.oo", "R.utils"),
contriburl="http://www.braju.com/R/repos/";)
trying URL 'http://www.braju.com/R/repos//R.oo_1.4.1.zip'
Content type 'application/zip' length 889981 bytes (869 Kb)
opened URL
downloaded 869 Kb
trying URL 'http://www.braju.com/R/repos//R.utils_1.0.0.zip'
Content type 'application/zip' length 893989 bytes (873 Kb)
opened URL
downloaded 873 Kb
package 'R.oo' successfully unpacked and MD5 sums checked
package 'R.utils' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\mcoyne\Local
Settings\Temp\Rtmpjhahhp\downloaded_packages
updating HTML package descriptions
However, when I tried to load the package aroma.affymetrix I got the
following error:
> library (aroma.affymetrix)
Error in library(aroma.affymetrix) :
there is no package called 'aroma.affymetrix'
Any help is greatly appreciated.
My D. Coyne
[[alternative HTML version deleted]]
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[R] difference between lrm's "Model L.R." and anova's "Chi-Square"
I am running lrm() with a single factor. I then run anova() on the fitted
model to obtain a p-value associated with having that factor in the model.
I am noticing that the "Model L.R." in the lrm results is almost the same
as the "Chi-Square" in the anova results, but not quite; the latter value
is always slightly smaller.
anova() calculates the p-value based on "Chi-Square", but I have
independent evidence that "Model L.R." is the actual -2*log(LR), so should
I be using that?
Why are the values different?
prob_a <- inv.logit(rnorm(1,0,1))
prob_b <- inv.logit(rnorm(1,0,1))
data <- data.frame(
factor=c(rep("a",500),rep("b",500)),
outcome=c(sample(c(1,0),100,replace=T,prob=c(prob_a,1-prob_a)),
sample(c(1,0),100,replace=T,prob=c(prob_b,1-prob_b
fit <- lrm(outcome~factor,data)
fit # gives "Model L.R." e.g. 8.23, 11.76, 6.89...
anova(fit)# gives "Chi-Square" e.g. 8.19, 11.69, 6.85...
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[R] Predictive Analytics for Business, Marketing and Web (April 3-4, May 8-9, June 5-6)
http://www.nabble.com/file/p15782617/logo-300-pix-72-dpi-no-sub.jpg Predictive Analytics for Business, Marketing and Web is a concentrated training program that includes interactive breakout sessions. Dates: April 3-4, May 8-9, and June 5-6, 2008 Locations: Toronto (April), San Francisco (May), New York City (June) Sponsor: Prediction Impact, Inc. Instructor: http://predictionimpact.com/predictive-analytics-training.html#instructor Eric Siegel, Ph.D. 100% of October 2007 attendees rated this program Excellent or Very Good ( http://www.predictionimpact.com/predictive-analytics-seminar.html details ). **Early-bird special: Sign up one month ahead for $100 off the registration fee** (This seminar is offered in conjunction with the eMetrics Marketing Optimization Summit.) Business metrics do a great job summarizing the past. But if you want to predict how customers will respond in the future, there is one place to turn—predictive analytics. By learning from your abundant historical data, predictive analytics provides the marketer something beyond standard business reports and sales forecasts: actionable predictions for each customer. These predictions encompass all channels, both online and off, foreseeing which customers will buy, click, respond, convert or cancel. If you predict it, you own it. The customer predictions generated by predictive analytics deliver more relevant content to each customer, improving response rates, click rates, buying behavior, retention and overall profit. For online applications such as e-marketing and customer care recommendations, predictive analytics acts in real-time, dynamically selecting the ad, web content or cross-sell product each visitor is most likely to click on or respond to, according to that visitor's profile. This is AB selection, rather than just AB testing. In two days we cover: The techniques, tips and pointers you need in order to run a successful predictive analytics and data mining initiative How to strategically position and tactically deploy predictive analytics and data mining at your company How to bridge the prevalent gap between technical understanding and practical use How a predictive model works, how it's created and how much revenue it generates Several detailed case studies that demonstrate predictive analytics in action and make the concepts concrete No background in statistics or modeling is required. The only specific knowledge assumed for this training program is moderate experience with Excel. For more information, visit http://predictionimpact.com/predictive-analytics-training.html Predictive Analytics for Business, Marketing and Web , e-mail us at mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] or call (415) 683-1146. -- View this message in context: http://www.nabble.com/Predictive-Analytics-for-Business%2C-Marketing-and-Web-%28April-3-4%2C-May-8-9%2C-June-5-6%29-tp15782617p15782617.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Make plots with GNUplot. Have anyone tried that?
Another option to get graphs in LaTeX using the same fonts as the rest of the document is to export from R as an eps file, then use eps2pgf (http://sourceforge.net/projects/eps2pgf) to convert to a pgf file. Then in the LaTeX file just use \input with the created .pgf file. This creates the graph inside of the LaTeX document using the default font(s) within the document. Hope this helps, From: [EMAIL PROTECTED] on behalf of Henrik Bengtsson Sent: Sat 3/1/2008 4:58 PM To: Louise Hoffman Cc: r-help@r-project.org Subject: Re: [R] Make plots with GNUplot. Have anyone tried that? On Fri, Feb 29, 2008 at 2:12 PM, Louise Hoffman <[EMAIL PROTECTED]> wrote: > [snip] > > > Seriously. Be specific if you have a problem. (read the posting guide). R > > can > > also plot. If you don't like R's plots (which I could not understand) you > can > > export data and import them to gnuplot. So what? > > Okay, my post was not very good. > > The reason (I think) I need GNUplot, is that I would like to include > the plots from R in a Latex report, where I would like to have all the > text and equations in the plots with the same font as used in Latex. FYI, the LaTeX 'psfrag' package was designed for the purpose of having LaTeX replace the text in EPS figures with text specified in LaTeX. That should give you the same font as in your main document. I haven't used it in a while but it normally does what you want. My $0.02 Henrik > > So when I read about opening and closing "dev" for making a pdf I > figured that the plots that R produces are like the once Matlab makes; > shows what they ought to, nothing more, nothing less. > > So I was wondering if anyone know of an GNUplot friendly format and > the code that would produce that text file. > > I am new to both R and GNUplot, so I am pure ears if someone knows how > to make such plots in R. > > > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] coxpath() in package glmpath
Hi, I am new to model selection by coefficient shrinkage method such as lasso. And I became particularly interested in variable selection in Cox regression by lasso. I became aware of the coxpath() in R package glmpath does lasso on Cox model. I have tried the sample script on the help page of coxpath(), but I have difficult time understanding the output. Therefore, I would greatly appreciate if anyone can help me understand how to use the function. > data(lung.data) > attach(lung.data) > fit.a <- coxpath(lung.data) > print(fit.a) Call: coxpath(data = lung.data) Step 1 : karno Step 2 : celltype Step 5 : trt Step 6 : prior Step 7 : age Step 8 : diagtime > summary(fit.a) Call: coxpath(data = lung.data) Df Log.p.lik AIC BIC Step 1 0 -505.8840 1011.7679 1011.7679 Step 2 1 -486.0691 974.1382 977.0581 Step 5 2 -484.8520 973.7040 979.5440 Step 6 3 -483.4018 972.8036 981.5636 Step 7 4 -483.3801 974.7602 986.4401 Step 8 5 -483.2287 976.4573 991.0572 Step 9 6 -483.1112 978.2224 995.7423 first of all, why the number of steps between the above 2 outputs are different? I confirmed with coxph() that the numbers (log.p.lik, AIC, BIC) on the 1st row of summary(fit.a) are from a NULL Cox model, i.e. a model with only an intercept. Then how Step 1 in the output of summary(fit.a) is corresponding to "Step 1" in the output of print(fit.a) where it seems to mean a model with the variable "karno"? >predict(fit.a) trt celltype karno diagtime age prior 1 0. 0. 0. 0.000e+00 0.000e+00 0.000e+00 2 0. 0.0076 -0.0256 0.000e+00 0.000e+00 0.000e+00 5 0. 0.0450 -0.0286 0.000e+00 0.000e+00 0.000e+00 6 0.1428 0.1033 -0.0330 0.000e+00 0.000e+00 -4.326e-05 7 0.1468 0.1048 -0.0332 0.000e+00 -1.043e-07 -3.506e-04 8 0.1755 0.1139 -0.0340 5.642e-06 -1.404e-03 -2.367e-03 attr(,"s") [1] 1 2 5 6 7 8 attr(,"fraction") [1] 0.000 0.125 0.500 0.625 0.750 0.875 attr(,"mode") [1] "step" Second, if we compare the output of print(fit.a) and predict(fit.a), I can see some discrepancies. For example, "Step 1" of print(fit.a) was variable "karno", however, predict(fit.a) showed that the coefficient of "karno" was still 0. The same went with variable "trt" in "Step 5". What is the meaning of the discrepancies? I think I probably misunderstand the whole meaning of coefficient shrinkage in the first place. So I would appreciate if anyone can shed some lights. I would also like to have any opinion on how I should do variable selection from these output? Should I rely on the table (log.p.lik, aic, bic) from summary fit.a) , or should I rely on the coefficients table from print(fit.a) to eliminate those variables with 0 coefficients at certain step? Thank you very much for your time. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Re: How to create following chart for visualizing multivariate time series
If you want color, then a slight addition to Henrique's solution will do it:
x <- y <- seq(-4*pi, 4*pi, len=27)
r <- sqrt(outer(x^2, y^2, "+"))
library(lattice)
colkey <- colorRampPalette(c('red','yellow','green'))(32)
levelplot(r, colorkey=list(col=colkey),
col.regions=(col=colkey))
On Sat, Mar 1, 2008 at 6:08 PM, Henrique Dallazuanna <[EMAIL PROTECTED]> wrote:
> This works for me:
>
> x <- y <- seq(-4*pi, 4*pi, len=27)
> r <- sqrt(outer(x^2, y^2, "+"))
> library(lattice)
> levelplot(r, colorkey=list(col=gray((0:32)/32)),
>col.regions=(col=gray((0:32)/32)))
>
> 'r' is a matrix for you?
>
> On 01/03/2008, David Winsemius <[EMAIL PROTECTED]> wrote:
> > "Henrique Dallazuanna" <[EMAIL PROTECTED]> wrote in
> > news:[EMAIL PROTECTED]:
> >
> > library(lattice)
> > levelplot(r, colorkey=list(col=gray((0:32)/32)),
> > col.regions=(col=gray((0:32)/32)))
> >
> > When I try that example, I get an error, even after updating lattice.
> >
> > > levelplot(r, colorkey=list(col=gray((0:32)/32)),
> > + col.regions=(col=gray((0:32)/32)))
> > Error in UseMethod("levelplot") : no applicable method for "levelplot"
> >
> > If I simply change colorkey=FALSE to colorkey=TRUE in the first levelplot
> > help page example, I have what looks to me as "success".
> >
> > levelplot(z~x*y, grid, cuts = 50, scales=list(log="e"), xlab="",
> > ylab="", main="Weird Function", sub="with log scales",
> > colorkey = TRUE,
> > region = TRUE)
> >
> > --
> > David Winsemius
> >
> > >
> > > On 29/02/2008, Megh Dal <[EMAIL PROTECTED]> wrote:
> > >> Hi Jim, i think you could not get my point. I did not want to put
> > >> red-blue color there. I want to put a pallet which will describe
> > >> the values of r. please have a look on following :
> > > http://bp0.blogger.com/_k3l6qPzizGs/RvDVglPknRI/AKo/itlWOvuuO
> > > tI/s1600-h/pairwise_kl_window60.png. Please see how a color pallate
> > > is added on the right side of this plot describing the value of red
> > > color, value of blue color etc.
> > >>
> > >> Is there any solution?
> > >>
> > >> Regards,
> > >>
> > >>
> > >> jim holtman <[EMAIL PROTECTED]> wrote:
> > >> Try something like this:
> > >>
> > >> require(grDevices) # for colours
> > >> x <- y <- seq(-4*pi, 4*pi, len=27)
> > >> r <- sqrt(outer(x^2, y^2, "+"))
> > >> image(x, y, r, col=gray((0:32)/32))
> > >> colors <- colorRampPalette(c('red', 'yellow', 'blue')) # create
> > >> you color spectrum
> > >> image(x,y,r, col=colors(100))
> > >>
> > >>
> > >>
> > >> On Thu, Feb 28, 2008 at 9:28 PM, Megh Dal wrote:
> > >> > I used ?image function to do that, like below :
> > >> >
> > >> > require(grDevices) # for colours
> > >> > x <- y <- seq(-4*pi, 4*pi, len=27)
> > >> > r <- sqrt(outer(x^2, y^2, "+"))
> > >> > image(x, y, r, col=gray((0:32)/32))
> > >> >
> > >> > However my next problem to add a color pallet for color
> > >> > description [as shown in following link]. If anyone here tell
> > me how to do that, it will be good for me.
> > >> >
> > >>
> > >> > Megh Dal wrote: Hi all,
> > >>
> > >> >
> > >> > Can anyone here please tell me whether is it possible to produce
> > >> > a chart displayed in http://www.datawolf.blogspot.com/ in R for
> > > visualizing multivariate time series? If possible how?
> > >> >
> > >> >
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
> --
> Henrique Dallazuanna
> Curitiba-Paraná-Brasil
> 25° 25' 40" S 49° 16' 22" O
>
> __
> R-help@r-project.org mailing list
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>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve? Tell me what you want to
do, not how you want to do it.
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[R] inverse fourier transform
y<-ts(x, frequency=1/15) spec.pgram(y, log="no") There is high power in the very low frequency range for the data set of continuous dissolved oxygen on which I am preforming this analysis. This is the seasonal trend due to temperature (and all things that are associated- photosynthesis, respiration, and anything else on which the doubling of a reaction rate ever ten degrees celcius would act). I would like to make this low frequency spike zero and then inverse fourier transform to get the "filtered" signal. spec.pgram spits out a matrix z<-spec.pgram(y, log="no") print(z) spec, frequency, and phase are returned. They are not matched up and I would like to take out the frequency and its associated spectrum in the range of 0-6.53*10^6. Any suggestions? thanks Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Make plots with GNUplot. Have anyone tried that?
On Fri, Feb 29, 2008 at 2:12 PM, Louise Hoffman <[EMAIL PROTECTED]> wrote: > [snip] > > > Seriously. Be specific if you have a problem. (read the posting guide). R > > can > > also plot. If you don't like R's plots (which I could not understand) you > can > > export data and import them to gnuplot. So what? > > Okay, my post was not very good. > > The reason (I think) I need GNUplot, is that I would like to include > the plots from R in a Latex report, where I would like to have all the > text and equations in the plots with the same font as used in Latex. FYI, the LaTeX 'psfrag' package was designed for the purpose of having LaTeX replace the text in EPS figures with text specified in LaTeX. That should give you the same font as in your main document. I haven't used it in a while but it normally does what you want. My $0.02 Henrik > > So when I read about opening and closing "dev" for making a pdf I > figured that the plots that R produces are like the once Matlab makes; > shows what they ought to, nothing more, nothing less. > > So I was wondering if anyone know of an GNUplot friendly format and > the code that would produce that text file. > > I am new to both R and GNUplot, so I am pure ears if someone knows how > to make such plots in R. > > > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Re: How to create following chart for visualizing multivariate time series
"Henrique Dallazuanna" <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:
> This works for me:
>
> x <- y <- seq(-4*pi, 4*pi, len=27)
> r <- sqrt(outer(x^2, y^2, "+"))
> library(lattice)
> levelplot(r, colorkey=list(col=gray((0:32)/32)),
> col.regions=(col=gray((0:32)/32)))
Works for me as well.
> 'r' is a matrix for you?
It was the vector created by the first levelplot() example. I had not
run the code of Megh Dal.
When I hastily looked at the help page and saw that "colorkey" was
supposed to be a logical, I assumed that the list argument was throwing
the error. If I had read the full text I would have seen that a list
argument was also valid. This gives what appears to me to be identical
success, but maybe it has risks that I don't understand:
levelplot(r, colorkey=TRUE,
col.regions=(col=gray((0:32)/32)))
Thanks;
David Winsemius
>
> On 01/03/2008, David Winsemius <[EMAIL PROTECTED]> wrote:
>> "Henrique Dallazuanna" <[EMAIL PROTECTED]> wrote in
>> news:[EMAIL PROTECTED]:
>>
>> library(lattice)
>> levelplot(r, colorkey=list(col=gray((0:32)/32)),
>> col.regions=(col=gray((0:32)/32)))
>>
>> When I try that example, I get an error, even after updating
>> lattice.
>>
>> > levelplot(r, colorkey=list(col=gray((0:32)/32)),
>> + col.regions=(col=gray((0:32)/32)))
>> Error in UseMethod("levelplot") : no applicable method for
>> "levelplot"
>>
>> If I simply change colorkey=FALSE to colorkey=TRUE in the first
>> level
> plot
>> help page example, I have what looks to me as "success".
>>
>> levelplot(z~x*y, grid, cuts = 50, scales=list(log="e"), xlab="",
>> ylab="", main="Weird Function", sub="with log scales",
>> colorkey = TRUE,
>> region = TRUE)
>>
>> --
>> David Winsemius
>>
>> >
>> > On 29/02/2008, Megh Dal <[EMAIL PROTECTED]> wrote:
>> >> Hi Jim, i think you could not get my point. I did not want to
>> >> put red-blue color there. I want to put a pallet which will
>> >> describe the values of r. please have a look on following :
>> > http://bp0.blogger.com/_k3l6qPzizGs/RvDVglPknRI/AKo/itlWOv
>> > uuO tI/s1600-h/pairwise_kl_window60.png. Please see how a color
>> > pallate is added on the right side of this plot describing the
>> > value of red color, value of blue color etc.
>> >>
>> >> Is there any solution?
>> >>
>> >> Regards,
>> >>
>> >>
>> >> jim holtman <[EMAIL PROTECTED]> wrote:
>> >> Try something like this:
>> >>
>> >> require(grDevices) # for colours
>> >> x <- y <- seq(-4*pi, 4*pi, len=27)
>> >> r <- sqrt(outer(x^2, y^2, "+"))
>> >> image(x, y, r, col=gray((0:32)/32))
>> >> colors <- colorRampPalette(c('red', 'yellow', 'blue')) # create
>> >> you color spectrum
>> >> image(x,y,r, col=colors(100))
>> >>
>> >>
>> >>
>> >> On Thu, Feb 28, 2008 at 9:28 PM, Megh Dal wrote:
>> >> > I used ?image function to do that, like below :
>> >> >
>> >> > require(grDevices) # for colours
>> >> > x <- y <- seq(-4*pi, 4*pi, len=27)
>> >> > r <- sqrt(outer(x^2, y^2, "+"))
>> >> > image(x, y, r, col=gray((0:32)/32))
>> >> >
>> >> > However my next problem to add a color pallet for color
>> >> > description [as shown in following link]. If anyone here tell
>> me how to do that, it will be good for me.
>> >> >
>> >>
>> >> > Megh Dal wrote: Hi all,
>> >>
>> >> >
>> >> > Can anyone here please tell me whether is it possible to
>> >> > produce a chart displayed in
>> >> > http://www.datawolf.blogspot.com/ in R for
>> > visualizing multivariate time series? If possible how?
>> >> >
>> >> >
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.h
> tml
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] One quick question concerning R
x <- rnorm(10) y <- runif(10) z <- 1:10 plot(x~z, ylim=range(x, y), type='l') lines(y, col='red') On 01/03/2008, Marc Diamond <[EMAIL PROTECTED]> wrote: > Just started using 'R'. Nice system. Once quick question: Is it possible to > put plot more than one series against a common 'x variable on the same plot? > In otherwords, I may want a stacked bar chart of line chart containing more > than one series. Could not figure out how to do this. > > Thanks for your help. > > Marc Diamond > Aviation-Software, Inc. > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] COMPAR.GEE Output
Hello, I am running the program COMPAR.GEE within the package APE. My dependent variable is binomial, while my independent variable is a multi-state categorical variable. The output reports an estimate for each state of the independent variable except the first one. For example, for the variable X with 3 states, the output is: intercept (estimate) X2 (estimate) X3 (estimate) I have two questions: 1) Why does it not give me an intercept for the first variable and how do i get it; 2) can a get a general estimate of correlation, like a wald's statistic for the variable? Thank you! Charlie ~~ Charles G. Willis Department of Organismic and Evolutionary Biology 22 Divinity Ave Cambridge MA 02139 HP (857) 488-2506 WP (617) 496-3890 [EMAIL PROTECTED] http://www.people.fas.harvard.edu/%7Ecgwillis/ ~~ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] One quick question concerning R
Just started using 'R'. Nice system. Once quick question: Is it possible to put plot more than one series against a common 'x variable on the same plot? In otherwords, I may want a stacked bar chart of line chart containing more than one series. Could not figure out how to do this. Thanks for your help. Marc Diamond Aviation-Software, Inc. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Re: How to create following chart for visualizing multivariate time series
This works for me:
x <- y <- seq(-4*pi, 4*pi, len=27)
r <- sqrt(outer(x^2, y^2, "+"))
library(lattice)
levelplot(r, colorkey=list(col=gray((0:32)/32)),
col.regions=(col=gray((0:32)/32)))
'r' is a matrix for you?
On 01/03/2008, David Winsemius <[EMAIL PROTECTED]> wrote:
> "Henrique Dallazuanna" <[EMAIL PROTECTED]> wrote in
> news:[EMAIL PROTECTED]:
>
> library(lattice)
> levelplot(r, colorkey=list(col=gray((0:32)/32)),
> col.regions=(col=gray((0:32)/32)))
>
> When I try that example, I get an error, even after updating lattice.
>
> > levelplot(r, colorkey=list(col=gray((0:32)/32)),
> + col.regions=(col=gray((0:32)/32)))
> Error in UseMethod("levelplot") : no applicable method for "levelplot"
>
> If I simply change colorkey=FALSE to colorkey=TRUE in the first levelplot
> help page example, I have what looks to me as "success".
>
> levelplot(z~x*y, grid, cuts = 50, scales=list(log="e"), xlab="",
> ylab="", main="Weird Function", sub="with log scales",
> colorkey = TRUE,
> region = TRUE)
>
> --
> David Winsemius
>
> >
> > On 29/02/2008, Megh Dal <[EMAIL PROTECTED]> wrote:
> >> Hi Jim, i think you could not get my point. I did not want to put
> >> red-blue color there. I want to put a pallet which will describe
> >> the values of r. please have a look on following :
> > http://bp0.blogger.com/_k3l6qPzizGs/RvDVglPknRI/AKo/itlWOvuuO
> > tI/s1600-h/pairwise_kl_window60.png. Please see how a color pallate
> > is added on the right side of this plot describing the value of red
> > color, value of blue color etc.
> >>
> >> Is there any solution?
> >>
> >> Regards,
> >>
> >>
> >> jim holtman <[EMAIL PROTECTED]> wrote:
> >> Try something like this:
> >>
> >> require(grDevices) # for colours
> >> x <- y <- seq(-4*pi, 4*pi, len=27)
> >> r <- sqrt(outer(x^2, y^2, "+"))
> >> image(x, y, r, col=gray((0:32)/32))
> >> colors <- colorRampPalette(c('red', 'yellow', 'blue')) # create
> >> you color spectrum
> >> image(x,y,r, col=colors(100))
> >>
> >>
> >>
> >> On Thu, Feb 28, 2008 at 9:28 PM, Megh Dal wrote:
> >> > I used ?image function to do that, like below :
> >> >
> >> > require(grDevices) # for colours
> >> > x <- y <- seq(-4*pi, 4*pi, len=27)
> >> > r <- sqrt(outer(x^2, y^2, "+"))
> >> > image(x, y, r, col=gray((0:32)/32))
> >> >
> >> > However my next problem to add a color pallet for color
> >> > description [as shown in following link]. If anyone here tell
> me how to do that, it will be good for me.
> >> >
> >>
> >> > Megh Dal wrote: Hi all,
> >>
> >> >
> >> > Can anyone here please tell me whether is it possible to produce
> >> > a chart displayed in http://www.datawolf.blogspot.com/ in R for
> > visualizing multivariate time series? If possible how?
> >> >
> >> >
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help needed in R
Try this:
data <- as.data.frame(data)
names(data) <- c('Data', 'Indicator')
a)
sort(unique(subset(data, Indicator == 1))[,1])
b) with(subset(data, Indicator == 1),
tapply(Indicator, Data, sum))
On 01/03/2008, AbouEl-Makarim Aboueissa <[EMAIL PROTECTED]> wrote:
> Dear ALL:
>
> I have two quick questions about how to perform some steps in R. Could you
> please see the attached MS file if the data not clean enough in this email.
>
> Thank you so much for all your helps.
>
>
> Abou
>
>
>
> Here it is:
> =
>
> Consider the following matrix:
>
> data<-matrix(c(2,2,12,2,1,10,10,4,10,1,1,2,2,1,2,10,3,1,1,1,3,5,17,23,9,9,3,3,15,5,
> 4,5,5,5,4,8,1,15,3,3,1,6,3,6,3,4,5,14,4,
>
> 0,0,0,0,0,1,1,0,1,1,0,1,1,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,1,1,0,1,1,1,0,
> 0,0,0,0,0,0,0,0,0,0,0,0,0,0),49,2)
>
>
> [,1] [,2]
> [1,]20
> [2,]20
> [3,] 120
> [4,]20
> [5,]10
> [6,] 101
> [7,] 101
> [8,]40
> [9,] 101
> [10,]11
> [11,]10
> [12,]21
> [13,]21
> [14,]10
> [15,]20
> [16,] 101
> [17,]30
> [18,]11
> [19,]10
> [20,]10
> [21,]30
> [22,]51
> [23,] 170
> [24,] 230
> [25,]90
> [26,]90
> [27,]30
> [28,]30
> [29,] 151
> [30,]51
> [31,]40
> [32,]51
> [33,]51
> [34,]51
> [35,]40
> [36,]80
> [37,]10
> [38,] 150
> [39,]30
> [40,]30
> [41,]10
> [42,]60
> [43,]30
> [44,]60
> [45,]30
> [46,]40
> [47,]50
> [48,] 140
> [49,]40
>
>
>
>
>
> Q1. Column one is the data set, and column two is an indicator of 1 and 0.
> Some values
> in column one corresponding to indicator 1 in column two are
> different, and some
> are the same. There are 5 different groups of values in column one
> with indicator 1
> in column two.
>
> (a) How I can choose only one value (only one observation) from each of
> these groups to
> develop a vector of length 5 as: (1 25 10 15).
>
>
>
>
> (b) How I can find number of observations in each of these groups as a
> vector as:
> (2 254 1).
>
>
>
>
>
>
>
>
>
>
>
> These are the values with indicator 1.
>
> [,1] [,2]
> [1,]11
> [2,]11
> [3,]21
> [4,]21
> [5,]51
> [6,]51
> [7,]51
> [8,]51
> [9,]51
> [10,] 101
> [11,] 101
> [12,] 101
> [13,] 101
> [14,] 151
>
> =
>
>
>
>
>
> ==
> AbouEl-Makarim Aboueissa, Ph.D.
> Assistant Professor of Statistics
> Department of Mathematics & Statistics
> University of Southern Maine
> 96 Falmouth Street
> P.O. Box 9300
> Portland, ME 04104-9300
>
> Tel: (207) 228-8389
> Fax: (207) 780-5607
> Email: [EMAIL PROTECTED]
> [EMAIL PROTECTED]
> Office: 301C Payson Smith
>
>
>
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help needed in R
At 23:07 01.03.2008, AbouEl-Makarim Aboueissa wrote: >Dear ALL: > >I have two quick questions about how to perform some steps in R. >Could you please see the attached MS file if the data not clean >enough in this email. > >Thank you so much for all your helps. > > >Abou > > > >Here it is: >= > >Consider the following matrix: > >data<-matrix(c(2,2,12,2,1,10,10,4,10,1,1,2,2,1,2,10,3,1,1,1,3,5,17,23,9,9,3,3,15,5, > 4,5,5,5,4,8,1,15,3,3,1,6,3,6,3,4,5,14,4, > >0,0,0,0,0,1,1,0,1,1,0,1,1,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,1,1,0,1,1,1,0, > 0,0,0,0,0,0,0,0,0,0,0,0,0,0),49,2) > > > [,1] [,2] > [1,]20 > [2,]20 > [3,] 120 > [4,]20 > [5,]10 > [6,] 101 > [7,] 101 > [8,]40 > [9,] 101 >[10,]11 >[11,]10 >[12,]21 >[13,]21 >[14,]10 >[15,]20 >[16,] 101 >[17,]30 >[18,]11 >[19,]10 >[20,]10 >[21,]30 >[22,]51 >[23,] 170 >[24,] 230 >[25,]90 >[26,]90 >[27,]30 >[28,]30 >[29,] 151 >[30,]51 >[31,]40 >[32,]51 >[33,]51 >[34,]51 >[35,]40 >[36,]80 >[37,]10 >[38,] 150 >[39,]30 >[40,]30 >[41,]10 >[42,]60 >[43,]30 >[44,]60 >[45,]30 >[46,]40 >[47,]50 >[48,] 140 >[49,]40 > > > > > >Q1. Column one is the data set, and column two is an indicator of 1 >and 0. Some values > in column one corresponding to indicator 1 in column two > are different, and some > are the same. There are 5 different groups of values in > column one with indicator 1 > in column two. > >(a) How I can choose only one value (only one observation) from each >of these groups to > develop a vector of length 5 as: (1 25 10 15). > table1 <- table(data[data[, 2]==1, 1]) as.numeric(dimnames(table1)[[1]]) [1] 1 2 5 10 15 >(b) How I can find number of observations in each of these groups as >a vector as: > (2 254 1). > as.vector(table1) [1] 2 2 5 4 1 greetings Heinz >These are the values with indicator 1. > > [,1] [,2] > [1,]11 > [2,]11 > [3,]21 > [4,]21 > [5,]51 > [6,]51 > [7,]51 > [8,]51 > [9,]51 >[10,] 101 >[11,] 101 >[12,] 101 >[13,] 101 >[14,] 151 > >= > > > > > >== >AbouEl-Makarim Aboueissa, Ph.D. >Assistant Professor of Statistics >Department of Mathematics & Statistics >University of Southern Maine >96 Falmouth Street >P.O. Box 9300 >Portland, ME 04104-9300 > >Tel: (207) 228-8389 >Fax: (207) 780-5607 >Email: [EMAIL PROTECTED] > [EMAIL PROTECTED] >Office: 301C Payson Smith > > > >__ >R-help@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help needed in R
Dear ALL: I have two quick questions about how to perform some steps in R. Could you please see the attached MS file if the data not clean enough in this email. Thank you so much for all your helps. Abou Here it is: = Consider the following matrix: data<-matrix(c(2,2,12,2,1,10,10,4,10,1,1,2,2,1,2,10,3,1,1,1,3,5,17,23,9,9,3,3,15,5, 4,5,5,5,4,8,1,15,3,3,1,6,3,6,3,4,5,14,4, 0,0,0,0,0,1,1,0,1,1,0,1,1,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,1,1,0,1,1,1,0, 0,0,0,0,0,0,0,0,0,0,0,0,0,0),49,2) [,1] [,2] [1,]20 [2,]20 [3,] 120 [4,]20 [5,]10 [6,] 101 [7,] 101 [8,]40 [9,] 101 [10,]11 [11,]10 [12,]21 [13,]21 [14,]10 [15,]20 [16,] 101 [17,]30 [18,]11 [19,]10 [20,]10 [21,]30 [22,]51 [23,] 170 [24,] 230 [25,]90 [26,]90 [27,]30 [28,]30 [29,] 151 [30,]51 [31,]40 [32,]51 [33,]51 [34,]51 [35,]40 [36,]80 [37,]10 [38,] 150 [39,]30 [40,]30 [41,]10 [42,]60 [43,]30 [44,]60 [45,]30 [46,]40 [47,]50 [48,] 140 [49,]40 Q1. Column one is the data set, and column two is an indicator of 1 and 0. Some values in column one corresponding to indicator 1 in column two are different, and some are the same. There are 5 different groups of values in column one with indicator 1 in column two. (a) How I can choose only one value (only one observation) from each of these groups to develop a vector of length 5 as: (1 25 10 15). (b) How I can find number of observations in each of these groups as a vector as: (2 254 1). These are the values with indicator 1. [,1] [,2] [1,]11 [2,]11 [3,]21 [4,]21 [5,]51 [6,]51 [7,]51 [8,]51 [9,]51 [10,] 101 [11,] 101 [12,] 101 [13,] 101 [14,] 151 = == AbouEl-Makarim Aboueissa, Ph.D. Assistant Professor of Statistics Department of Mathematics & Statistics University of Southern Maine 96 Falmouth Street P.O. Box 9300 Portland, ME 04104-9300 Tel: (207) 228-8389 Fax: (207) 780-5607 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] Office: 301C Payson Smith __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question on getting all possible combinations
library("R.utils")
intToBin(0:63)
Best wishes
Wolfgang
--
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Benilton Carvalho scripsit:
> target = c("u", "d")
> apply(expand.grid(rep(list(target), 6)), 1, paste, sep="", collapse="")
>
> b
>
> On Mar 1, 2008, at 9:13 AM, Megh Dal wrote:
>
>> Hi all,
>>
>> Suppose I have to letters 'u' and 'd'. Now I want to find all
>> combinations like that :
>>
>> uu
>> ud
>> du
>> .
>>
>> dd
>>
>> This type of combination generally required for Option Pricing in
>> financial/derivative market. Here generally 'u' means: up-move and 'd'
>> means down move of price like Stock price etc.
>>
>> Is there any easy way in R for doing that?
>>
>> Regards,
>>
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Newbie: Incorrect number of dimensions
It would be helpful if you provided commented, minimal, self-contained, reproducible code. What does str(all_differ) say? That will tell you the structure of the object that you are trying to work with. On Sat, Mar 1, 2008 at 3:35 AM, Keizer_71 <[EMAIL PROTECTED]> wrote: > > > dim(data.sub) > [1] 1 140 > > #extracting all differentially express genes## > library(multtest) > two_side<- (1-pt(abs(data.sub),50))*2 > diff<- mt.rawp2adjp(two_side) > all_differ<-diff[[1]][37211:1,] > all_differ > > #list of differentially expressed genes## > > probe.names<- > + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] > > Error in all_differ[[1]][, "BY"] : incorrect number of dimensions > > Hi, > > I am pretty new with R. What i am trying to do is to find all differentially > express genes and list of differentially expressed genes. Am i doing > something wrong? > > I keep getting incorrect number of dimensions. How do i find out the correct > dimensions? > > thanks, > Keizer > > -- > View this message in context: > http://www.nabble.com/Newbie%3A-Incorrect-number-of-dimensions-tp15773090p15773090.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? Tell me what you want to do, not how you want to do it. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Make plots with GNUplot. Have anyone tried that?
There is a very basic interface between R and gnuplot in the TeachingDemos package. Look at the help for gp.plot. gp.open will run gnuplot and link it to R, gp.plot will send data to gnuplot and create a scatterplot. (gp.send will send extra commands to gnuplot and gp.close will clean up). Feel free to extend this to fit your needs, From: [EMAIL PROTECTED] on behalf of Louise Hoffman Sent: Fri 2/29/2008 4:54 PM To: Gabor Csardi Cc: r-help@r-project.org Subject: Re: [R] Make plots with GNUplot. Have anyone tried that? > If you still want to then read ?write.table, that can export your data > into a spreadsheet-like ascii format which can be used from GNUplot > easily. Very interesting. So if I e.g. write: ts.sim <- arima.sim(list(order = c(1,1,0), ar = 0.7), n = 200) ts.plot(ts.sim) How do I know the names of the rows to put in the data.frame() command? > Btw, comparing the graphics capabilities of GNUplot and R, it is > something like a three-wheel bicycle and a spaceship. Guess > which is which. =) I know that I will most likely spend a lot of time on just making the plots, but I atleast (for now =) ) think it could be fun to try. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to set up multiple spawns of R?
You may want to look at the nws package (there are others that also help with parallel versions, but on windows, nws seems to work the best (at least in my experiance so far)). From: [EMAIL PROTECTED] on behalf of Guy Perry Sent: Sat 3/1/2008 7:19 AM To: r-help@r-project.org Subject: [R] How to set up multiple spawns of R? Sorry: resending this; didn't have a title on it. Trying to set up multiple spawns of R --- Hi. I'm new to the list but I have a small problem with R. I'm trying to set up multiple spawns of R active at the same time on an AMD with a dual core in Vista so that I can cut down my permutation processing time. I've installed R in multiple places, which I thought was the correct way to do it but whether I use installs at "C:\Program Files\R1" and "C\...\R2", or even separately on the C: and D: drive, whenever I try to load my package (qtl), it gives me the error message: Error in library(qtl) : there is no package called 'qtl' The thing is, I've installed the packagen in both places (C\...\R1 and C\...\R2, or both the C: and D: drives) and it still gives me the message. Does anyone know how to set up a simultaneous R spawn? Clearly I'm wrong about how to get it started. Thanks, G Perry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to set up multiple spawns of R?
On 1 March 2008 at 09:19, Guy Perry wrote: | Sorry: resending this; didn't have a title on it. | | Trying to set up multiple spawns of R | --- | | Hi. I'm new to the list but I have a small problem with R. I'm trying to | set up multiple spawns of R active at the same time on an AMD with a dual | core in Vista so that I can cut down my permutation processing time. | | I've installed R in multiple places, which I thought was the correct way to | do it but whether I use installs at "C:\Program Files\R1" and "C\...\R2", or | even separately on the C: and D: drive, whenever I try to load my package | (qtl), it gives me the error message: | | Error in library(qtl) : there is no package called 'qtl' | | The thing is, I've installed the packagen in both places (C\...\R1 and | C\...\R2, or both the C: and D: drives) and it still gives me the message. | Does anyone know how to set up a simultaneous R spawn? Clearly I'm wrong | about how to get it started. Afraid so. What made you think you needed to _install R multiple times_ in order to _run R multiple times_ ? In short, you don't. R's core engine is single-threaded, so there is no obvious shortcut. That said, yopu can of course use parallel coding toolkits like Rmpi to spawn multiple R session -- which may be beneficial even if you don't have multiple cores. These things have been discussed a few times, so some focused Google queries (or RSiteSearch() queries) may help. Hth, Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] jpeg and margin text
Hi guys,
I use R 2.6.2 and Windows XP.
Ive got the following question: I wrote a lot of text into the margin of a
plot. When I use the jpeg-function, only a little part of the margin text
is displayed in the final jpeg? Any ideas to change it?
Source-Code:
datenbankdaten<-data.frame(LETTERS[1:20],
c(8,4.8,3.8,2.7,2.6,2.1,2,1.9,1.6,1,0.99,0.98,0.98,0.97,0.96,.96,0.8,0.8,0.7
,0.6),
c(8,4.8,3.8,0,2.6,2.1,2,1.9,1.6,1.1,0.99,0.98,0.97,0.97,0.96,.95,0.8,0.8,0,0
.6))
Zugehoerigkeit<-LETTERS[1:20]
Bezeichnung<-letters[1:20]
colnames(datenbankdaten)<-c("Bezeichnung","A","B")
# par = Setzt die Grafikparameter, die durch plot automatisch verwendet
werden
# mar = Anzahl der Textzeilen von den inneren Achsen des Schaubild zum Rand
# Zeilenvektor: c(bottom, left, top, right)
par(mar=c(3,4,4,25),family="serif")
Fontparameter<-1
today<-Sys.Date()
Vormonat<-Sys.Date()-20
Stand_aktuell<-format(today, "%B %Y")
Stand_Vormonat<-format(Vormonat, "%B %Y")
jpeg(paste("C:\\TOP-20.jpeg",sep=""),quality=100,width=1024, height=768)
plot(datenbankdaten[,2],ylim=c(0,max(datenbankdaten[,2],datenbankdaten[,3]))
,
xlab="", ylab="",
font.axis=Fontparameter,font.lab=Fontparameter,font.main=Fontparameter,font.
sub=Fontparameter,
bty="n",axes=F)
axis(1,at=1:20,label=rep("",20))
axis(1,at=1:9,label=sprintf("0%.0f",1:9))
axis(1,at=10:20,label=10:20)
Maximum<-max(datenbankdaten[,2],datenbankdaten[,3])
axis(2,at=0:Maximum,label=sprintf("%.2f",0:Maximum))
for(i in 1:(length(datenbankdaten[,2])+2)){
abline(h=i-1)
}
for(i in 1:20){
if(datenbankdaten[i,2]>=datenbankdaten[i,3]) farbe="red" else
farbe="green"
arrows(i,datenbankdaten[i,2],i,datenbankdaten[i,3],col=farbe,length=0,lwd=1.
5)
points(i,datenbankdaten[i,2],pch=22,col="light blue",bg="light
blue",cex=1.7)
points(i,datenbankdaten[i,3],pch=21,col="grey",bg="grey",cex=1.5)
}
for(i in 1:20){
if(datenbankdaten[i,2]>datenbankdaten[i,3])
#dreieck nach oben
points(i,datenbankdaten[i,2]-0.1,pch=24,col="red",bg="red")
if(datenbankdaten[i,2]__
R-help@r-project.org mailing list
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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] How to chain user mouse handlers in rgl
On 01/03/2008 5:41 AM, Dieter Menne wrote:
> Dear Rglers,
>
> With rgl, I would like to set marker when a button is pressed, but leave the
> standard trackball handling otherwise. Thanks to Duncan and Oleg for helping
> me handling key down.
I don't think there's currently an easy way to do that. What you would
have to do is to replicate the trackball handler in yours. (You can see
what it does in the src/rglview.cpp in the rgl source.)
If you want to write the R code (and docs for it) to fix this, I'll put
it into rgl.
Duncan Murdoch
> How do I say in a custom mouse handler "after having done your work, forward
> to standard trackball once only"? The example below shows the idea, but it
> works only once, then reverts to standard trackball handling.
>
> Dieter
>
> #--
> library(rgl)
> r3dDefaults
> open3d()
> shade3d(cube3d(color=rep(rainbow(6),rep(4,6
>
>
> btn3d <- function() {
> begin <- function(x, y) {
> # Add checking for key down later
> cat(x,y,"\n")
> # Forward to trackball (no easier way?)
> newhandler <- par3d("mouseMode")
> newhandler[1] <- "trackball"
> par3d(mouseMode = newhandler)
>}
>rgl.setMouseCallbacks(1, begin)
> }
>
> btn3d()
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
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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] Fwd: Re: How to create following chart for visualizing multivariate time series
"Henrique Dallazuanna" <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:
library(lattice)
levelplot(r, colorkey=list(col=gray((0:32)/32)),
col.regions=(col=gray((0:32)/32)))
When I try that example, I get an error, even after updating lattice.
> levelplot(r, colorkey=list(col=gray((0:32)/32)),
+ col.regions=(col=gray((0:32)/32)))
Error in UseMethod("levelplot") : no applicable method for "levelplot"
If I simply change colorkey=FALSE to colorkey=TRUE in the first levelplot
help page example, I have what looks to me as "success".
levelplot(z~x*y, grid, cuts = 50, scales=list(log="e"), xlab="",
ylab="", main="Weird Function", sub="with log scales",
colorkey = TRUE,
region = TRUE)
--
David Winsemius
>
> On 29/02/2008, Megh Dal <[EMAIL PROTECTED]> wrote:
>> Hi Jim, i think you could not get my point. I did not want to put
>> red-blue color there. I want to put a pallet which will describe
>> the values of r. please have a look on following :
> http://bp0.blogger.com/_k3l6qPzizGs/RvDVglPknRI/AKo/itlWOvuuO
> tI/s1600-h/pairwise_kl_window60.png. Please see how a color pallate
> is added on the right side of this plot describing the value of red
> color, value of blue color etc.
>>
>> Is there any solution?
>>
>> Regards,
>>
>>
>> jim holtman <[EMAIL PROTECTED]> wrote:
>> Try something like this:
>>
>> require(grDevices) # for colours
>> x <- y <- seq(-4*pi, 4*pi, len=27)
>> r <- sqrt(outer(x^2, y^2, "+"))
>> image(x, y, r, col=gray((0:32)/32))
>> colors <- colorRampPalette(c('red', 'yellow', 'blue')) # create
>> you color spectrum
>> image(x,y,r, col=colors(100))
>>
>>
>>
>> On Thu, Feb 28, 2008 at 9:28 PM, Megh Dal wrote:
>> > I used ?image function to do that, like below :
>> >
>> > require(grDevices) # for colours
>> > x <- y <- seq(-4*pi, 4*pi, len=27)
>> > r <- sqrt(outer(x^2, y^2, "+"))
>> > image(x, y, r, col=gray((0:32)/32))
>> >
>> > However my next problem to add a color pallet for color
>> > description [as shown in following link]. If anyone here tell
me how to do that, it will be good for me.
>> >
>>
>> > Megh Dal wrote: Hi all,
>>
>> >
>> > Can anyone here please tell me whether is it possible to produce
>> > a chart displayed in http://www.datawolf.blogspot.com/ in R for
> visualizing multivariate time series? If possible how?
>> >
>> >
__
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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] multiple boxplots using boxplot
Hi Marek, use a list instead of a data.frame; e.g. boxplot(list(x = rnorm(10), y = rnorm(20))) hth, Matthias Marek Bartkuhn wrote: > Hi, > > I have data in 3 vectors a,b and c looking like > > eg a:1.2 3.4 1.4 .. > > > I like to have the data from each vector as a boxplot, but the 3 > boxplots within one graph. > > One example is the first graph at > > http://www.statmethods.net/graphs/boxplot.html > > Unfortunately I do not really understand the corresponding > description. The vectors are of different length, therefore R > complains when I try to build a data.frame of the 3 vectors: > > arguments imply differing number of rows: 6175, 20, 190 > > What do I have to do? > > Marek > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Dr. Matthias Kohl www.stamats.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question on getting all possible combinations
target = c("u", "d")
apply(expand.grid(rep(list(target), 6)), 1, paste, sep="", collapse="")
b
On Mar 1, 2008, at 9:13 AM, Megh Dal wrote:
Hi all,
Suppose I have to letters 'u' and 'd'. Now I want to find all
combinations like that :
uu
ud
du
.
dd
This type of combination generally required for Option Pricing in
financial/derivative market. Here generally 'u' means: up-move and
'd' means down move of price like Stock price etc.
Is there any easy way in R for doing that?
Regards,
-
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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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.
[R] multiple boxplots using boxplot
Hi, I have data in 3 vectors a,b and c looking like eg a: 1.2 3.4 1.4 .. I like to have the data from each vector as a boxplot, but the 3 boxplots within one graph. One example is the first graph at http://www.statmethods.net/graphs/boxplot.html Unfortunately I do not really understand the corresponding description. The vectors are of different length, therefore R complains when I try to build a data.frame of the 3 vectors: arguments imply differing number of rows: 6175, 20, 190 What do I have to do? Marek __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting long names in boxplot
On Fri, Feb 29, 2008 at 4:40 PM, Alex Reynolds <[EMAIL PROTECTED]> wrote: > I have the following code: > > subsetTimeDataPlot <- boxplot(subsetTimeData$time ~ > subsetTimeData$build, horizontal=True, col="lightblue", ...) > > The 'names' component consists of strings that can be up to 20-30 > characters long. > > How would I go about drawing the names vertically (not the boxplot) or > shrinking the names text (I tried cex.names=0.7 but this didn't help). You might try: library(ggplot2) qplot(build, time, data=subsetTimeData, geom="boxplot") + coord_flip() which will automatically allocate enough space for the names. You can find out more about ggplot2 at http://had.co.nz/ggplot2. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to set up multiple spawns of R?
Sorry: resending this; didn't have a title on it. Trying to set up multiple spawns of R --- Hi. I'm new to the list but I have a small problem with R. I'm trying to set up multiple spawns of R active at the same time on an AMD with a dual core in Vista so that I can cut down my permutation processing time. I've installed R in multiple places, which I thought was the correct way to do it but whether I use installs at "C:\Program Files\R1" and "C\...\R2", or even separately on the C: and D: drive, whenever I try to load my package (qtl), it gives me the error message: Error in library(qtl) : there is no package called 'qtl' The thing is, I've installed the packagen in both places (C\...\R1 and C\...\R2, or both the C: and D: drives) and it still gives me the message. Does anyone know how to set up a simultaneous R spawn? Clearly I'm wrong about how to get it started. Thanks, G Perry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Grouping 30 arrays (geographical) of 1000 rows (individuals) by 20 columns (time-series data)
Hi, I have 30 arrays (geographical) of 1000 rows (individuals) by 20 columns (time-series data), and need to group arrays that are most similar. What packages and functions will be useful for this task ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question on getting all possible combinations
Hi all, Suppose I have to letters 'u' and 'd'. Now I want to find all combinations like that : uu ud du . dd This type of combination generally required for Option Pricing in financial/derivative market. Here generally 'u' means: up-move and 'd' means down move of price like Stock price etc. Is there any easy way in R for doing that? Regards, - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] inheritence in S4
Hi Christophe --
I don't know whether there's a particularly elegant way. This works
setClass("A", representation(x="numeric"))
setClass("B", representation(y="numeric"))
setClass("C", contains=c("A", "B"))
setMethod("show", "A", function(object) cat("A\n"))
setMethod("show", "B", function(object) cat("B\n"))
setMethod("show", "C", function(object) {
callGeneric(as(object, "A"))
callGeneric(as(object, "B"))
cat("C\n")
})
> new("C")
A
B
C
but obviously involves the developer in making explicit decisions
about method dispatch when there is multiple inheritance.
Martin
[EMAIL PROTECTED] writes:
> Hi the list
>
> I define a class A (slot a and b), a class C (slot c and d) and a class
> E that inherit from A and B.
> I define print(A) and print(B). For print(C), I would like to use both
> of them, but I do not see how...
>
> Thanks for your help...
>
> Christophe
>
>
> Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
__
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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.
[R] (no subject)
Trying to set up multiple spawns of R --- Hi. I'm new to the list but I have a small problem with R. I'm trying to set up multiple spawns of R active at the same time on an AMD with a dual core in Vista so that I can cut down my permutation processing time. I've installed R in multiple places, which I thought was the correct way to do it but whether I use installs at "C:\Program Files\R1" and "C\...\R2", or even separately on the C: and D: drive, whenever I try to load my package (qtl), it gives me the error message: Error in library(qtl) : there is no package called 'qtl' The thing is, I've installed the packagen in both places (C\...\R1 and C\...\R2, or both the C: and D: drives) and it still gives me the message. Does anyone know how to set up a simultaneous R spawn? Clearly I'm wrong about how to get it started. Thanks, G Perry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running LaTeX dvi previewer on MacOS X
Charilaos Skiadas wrote: > On Feb 29, 2008, at 5:39 PM, Michael wrote: > >> On 29 Feb 2008, Charilaos Skiadas wrote: >> >>> On Feb 29, 2008, at 12:38 PM, Michael wrote: On 29 Feb 2008, Frank E. Harrell, Jr. wrote: > Several people have given great advice on how to successfully use > X11 on > Mac to so we can use the dvi previewer to view latex() output from > Hmisc. Now after a version upgrade of X11 and X11sdk we are > getting > lots of crashes. I noticed a Mac dvi previewer with an executable > stored as /Applications/TeX/TeXShop.app/Contents/MacOS/TeXShop > > Can we bypass X11 problems and point Hmisc to this executable > for dvi > viewing? I think TeXshop converts dvi to pdf (something like dvips -> ps2pdf) for viewing. Why not just use pdf for Mac? Preview.app on Leopard does do live updating. >>> And Skim.app does updating on Tiger, and is IMHO much better to >>> Preview.app in other ways (works with pdfsync for instance, allows >>> syncing back and forth between the pdf file and the corresponding tex >>> source) >> We were not talking about using TeXshop to edit LaTeX files. >> Rather the >> latex() function Hmisc generates a dvi file and the question is how >> to view >> it since Mac does not have native dvi viewer (other than xdvi). >> The pdfsync >> function of Skim or TeXshop is irrelevant. > > Why is it important that the output file be a dvi file? Would it be a > problem to have the latex() function produce a pdf file on mac systems? > I thought the latex() command was just producing tex code. This discussion is about previewing the result of latex(), and Hmisc has several dvi-related functions. One could write a similar pdf conversion or pdf viewer functions taking as input the result of dvi(latex()). Also, I'm trying to just make the mechanisms in Hmisc for latex() that work fine on Linux/Unix/Windows work well for Mac users. Frank > >> Michael > > Haris Skiadas > Department of Mathematics and Computer Science > Hanover College > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bifurcation countings in a cluster dendrogram
Dear R helpers, I am quite new working with R, and that might be a very easy question for some of you. So I hope you can help me!! I used a hirarchical cluster analysis to create dendrograms, like that: hc <- hclust(dist(USArrests), "ave") plot(hc) plot(hc, hang = -1) Here I want to compare the number of bifurcations for each species, but therefor I need this numbers first. There should be an elegant way to get this- instead of counting everything. I would be happy if you could tell me the solution Thanks a lot in advance!!! Yvonne Fabian -- View this message in context: http://www.nabble.com/bifurcation-countings-in-a-cluster-dendrogram-tp15773122p15773122.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to chain user mouse handlers in rgl
Dear Rglers,
With rgl, I would like to set marker when a button is pressed, but leave the
standard trackball handling otherwise. Thanks to Duncan and Oleg for helping
me handling key down.
How do I say in a custom mouse handler "after having done your work, forward
to standard trackball once only"? The example below shows the idea, but it
works only once, then reverts to standard trackball handling.
Dieter
#--
library(rgl)
r3dDefaults
open3d()
shade3d(cube3d(color=rep(rainbow(6),rep(4,6
btn3d <- function() {
begin <- function(x, y) {
# Add checking for key down later
cat(x,y,"\n")
# Forward to trackball (no easier way?)
newhandler <- par3d("mouseMode")
newhandler[1] <- "trackball"
par3d(mouseMode = newhandler)
}
rgl.setMouseCallbacks(1, begin)
}
btn3d()
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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] Fitting long names in boxplot
On Fri, 2008-02-29 at 14:40 -0800, Alex Reynolds wrote:
> I have the following code:
>
> subsetTimeDataPlot <- boxplot(subsetTimeData$time ~
> subsetTimeData$build, horizontal=True, col="lightblue", ...)
>
> The 'names' component consists of strings that can be up to 20-30
> characters long.
>
> How would I go about drawing the names vertically (not the boxplot) or
> shrinking the names text (I tried cex.names=0.7 but this didn't help).
>
> Thanks for any advice, I apologize if these are stupid questions,
Look at ?par and argument/parameter 'las', which controls the
orientation of axis tick labels.
You'll also need to increase the margin size on the side of the plot
holding the labels if they are very long. For this, see ?par again and
parameters 'mar' or 'mai' depending on how you wish to define the margin
size.
## Example
dat <- data.frame(values = rnorm(100), group = gl(2, 50))
levels(dat$group) <- c("reallyreallylonglabel",
"anevenlongerlabel")
## las = 1 gets y-axis labels horizontal, but note note enough room
boxplot(values ~ group, data = dat, horizontal = TRUE, las = 1)
## so change the margin on the left (no. 2)
## default is c(5, 4, 4, 2) + 0.1
## and shrink text size so we don't need a huge margin
op <- par(mar = c(5, 10, 4, 2) + 0.1)
boxplot(values ~ group, data = dat, horizontal = TRUE, las = 1,
cex.axis = 0.7)
## reset the plotting parameters
par(op)
HTH
G
>
> -Alex
>
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Re: [R] Make plots with GNUplot. Have anyone tried that?
On Sat, Mar 01, 2008 at 12:54:56AM +0100, Louise Hoffman wrote: > > If you still want to then read ?write.table, that can export your data > > into a spreadsheet-like ascii format which can be used from GNUplot > > easily. > > Very interesting. > > So if I e.g. write: > ts.sim <- arima.sim(list(order = c(1,1,0), ar = 0.7), n = 200) > ts.plot(ts.sim) > > How do I know the names of the rows to put in the data.frame() command? ??? Which data.frame() command? (Btw. now you're trying to plot from R?) > > Btw, comparing the graphics capabilities of GNUplot and R, it is > > something like a three-wheel bicycle and a spaceship. Guess > > which is which. > > =) I know that I will most likely spend a lot of time on just making > the plots, but I atleast (for now =) ) think it could be fun to try. For you maybe, not for me. I'm lost, and I apologize, but I'll quit the discussion here. G. ps. i take back half of what i've said about GNUplot. It's a nice tool. Still, IMHO, (in most cases) it makes no sense to export data from R and plot it with GNUplot. -- Csardi Gabor <[EMAIL PROTECTED]>UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] "Raw" histogram plots
Why not use the interactive histogram in iplots? ihist(x) Then you can vary the binwidth interactively and get a very quick idea of the structure of your data by looking at a range of plots with different binwidths. Relying on a single plot to reveal everything about a variable's distribution is not a good idea. A couple of people suggested estimating the density. That may miss roundings, discretisation or other odd structures. We should never underestimate what Peter Huber called "the rawness of raw data". Antony Unwin Professor of Computer-Oriented Statistics and Data Analysis, Mathematics Institute, University of Augsburg, Germany [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Newbie: Incorrect number of dimensions
> dim(data.sub) [1] 1 140 #extracting all differentially express genes## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:1,] all_differ #list of differentially expressed genes## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in all_differ[[1]][, "BY"] : incorrect number of dimensions Hi, I am pretty new with R. What i am trying to do is to find all differentially express genes and list of differentially expressed genes. Am i doing something wrong? I keep getting incorrect number of dimensions. How do i find out the correct dimensions? thanks, Keizer -- View this message in context: http://www.nabble.com/Newbie%3A-Incorrect-number-of-dimensions-tp15773090p15773090.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting Dendrogram Help Getting Plot to Display Neatly
[EMAIL PROTECTED] wrote: > I have done a cluster analysis doing: > > 1-clusNorth <-hclust(dist(Artorious)^2, method="ward") > 2-clusNorth$labels <-Artorious$Name ## to show the case names and not > numbers > 3-dend1 <- as.dendrogram(clusNorth) > 4-plot(dend1) > > My Dendrogram is now showing the names of my cases in the dataframe on > the x axis > > 1OMNICELL INC COM > 2GETTY IMAGES INC COM > 3 INTERCONTINENTALEXCHANGE IN COM > 4 OPTIONSXPRESS HLDGS INC COM > 5 SUPERIOR WELL SVCS INC COM > 6 HCP INC COM > 7 SENIOR HSG PPTYS TR SH BEN INT > 8 NATIONWIDE HEALTH PPTYS INC COM > 9DUKE REALTY CORP COM NEW > 10 HEALTH CARE REIT INC COM > 11 POWERSHARES QQQ TRUST UNIT SER 1 > 12 FLEXTRONICS INTL LTD ORD > 13 VENTAS INC COM > > > However with 60 cases the names above are not fitting neatly into plot. > Can someone advice on plot > Parameters to fix the size of dendrogram and see the full names on X > axis? > Hi Neil, If the names are not too crowded, staxlab in the plotrix package might do it. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
