[R] lattice: clipping data, not plot margins

of achieving both correct margin line widths and clipping of outlying data? Thanks, Dan Bebber info: Windows XP, R 2.4.1., lattice 0.14-16 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] lmer, p-values and all that

Pinheiro Bates been in vain? Is there a publication on this issue? Thanks, Dan Bebber Department of Plant Sciences University of Oxford __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] tick label rotation in xyplot (lattice)

Is there any way of rotating tick labels in xyplot? Perhaps some command in scales? My y-values are high (1000s) leading to a lot of white space in the plots. Thanks, Dan Bebber Department of Plant Sciences University of Oxford __ R-help

Re: [R] Colour-coded Editor for R Code

Jon, are you using Windows? If so, try WinEdt with library(RWinEdt). It has all the features you want and need. For Linux/Unix use EMACS. There is a section on CRAN about editors. Cheers, Dan Bebber Department of Plant Sciences University of Oxford

[R] Likelihood of multiple random processes

normal distribution should be fitted? If so, then I suppose that the AIC of the two models could be calculated. Many thanks, Dan Bebber Department of Plant Sciences University of Oxford __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] Likelihood of multiple random processes

of the book fitdistr() supports as well as in several CRAN packages. Many thanks- I didn't know they were called mixture models. Page 437 is in front of me now. On Thu, 2 Nov 2006, Dan Bebber wrote: Is there a method in R for estimating the likelihood that two (or more) random variables

Re: [R] Statitics Textbook - any recommendation?

MJ Crawley Statistics: An Introduction Using R, received a good review in Journal of the Royal Statistical Society, Vol 169. Dan Bebber Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK [[alternative HTML version deleted

[R] Greedy triangulation

Hello, does anyone have code that will generate a greedy triangulation (triangulation that uses shortest non-overlapping edges) for a set of points in Euclidean space? Thanks, Dan Bebber ___ Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks

Re: [R] Greedy triangulation

,...){ plot(xy,asp=1,xlab=x,ylab=y,...) segments(gr$x1,gr$y1,gr$x2,gr$y2)} # #Test it # xy-matrix(runif(40,0,1),nc=2) gr-greedy(xy) plot.greedy(xy,gr,main=Greedy Triangulation) #END - Original Message - From: Greg Snow [EMAIL PROTECTED] To: Dan Bebber [EMAIL PROTECTED]; r-help

[R] glm cannot find valid starting values

glm(S ~ -1 + I(Mdif + 1),... i.e. (Mdif + 1) is a vector similar to Mdif. The error appears to occur when some values of Mdif are negative, though I have not had this problem with simulated datasets. Any solutions greatly appreciated (full details and data below). Dan Bebber Department of Plant

Re: [R] glm cannot find valid starting values

Brian Ripley wrote: BTW, your example cannot be pasted in as 'sdat' self-references. It could be fixed, but I gave up at that point. Oh dear, I'm very sorry. I forgot to run rm(list=ls(all=TRUE)) before testing. The corrected code is: #Data: S - c(0, 0, 0, 0, 28, 0, 1, 7, 0, 0, 39, 2, 0, 0,

[R] Force coefficients in glm()

Hello, I have a model glm(Y ~ X, family = quasipoisson(link = identity)) I would like to vary the coefficient for X and observe the effect on the deviance. Is this possible? Many thanks, Dan Bebber Department of Plant Sciences University of Oxford

Re: [R] How to test for significance of random effects?

. Dan Bebber Department of Plant Sciences University of Oxford Message: 12 Date: Sun, 07 May 2006 14:25:44 -0700 From: Spencer Graves [EMAIL PROTECTED] Subject: Re: [R] How to test for significance of random effects? To: Jon Olav Vik [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Message-ID

[R] nlme for groupedData with inner and outer factors

, with xmid and scal affected by bait and weight. There is also a random effect of subject on xmid and scal. Any help with formulating the correct model would be greatly appreciated. Many thanks, Dan Bebber Department of Plant Sciences University of Oxford p.s. Part of my data are shown below

[R] par(mfrow, fin) incompatibility?

incompatible? I am basing my code on Fig. 4.6 in MASS4. Running R 2.2.1 WinXP. Thanks Dan Bebber Department of Plant Sciences University of Oxford __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] bubble.plot() - standardize size of unit circle

Thanks Martin- I didn't know about the sunflowerplot function. Somehow I prefer the look of bubbles, but I guess you're right about the visual perception. Will have to read up on it. Dan --- Martin Maechler [EMAIL PROTECTED] wrote: Hi, Dan == Dan Bebber [EMAIL PROTECTED] on Thu, 21

[R] bubble.plot() - standardize size of unit circle

Hello, I wrote a wrapper for symbols() that produces a bivariate bubble plot, for use when plot(x,y) hides multiple occurrences of the same x,y combination (e.g. if x,y are integers). Circle area ~ counts per bin, and circle size is controlled by 'scale'. Question: how can I automatically make

Re: [R] bubble.plot() - standardize size of unit circle

Thanks- 'sizeplot' didn't come up in any of my searches. Dan --- Jim Lemon [EMAIL PROTECTED] wrote: Dan Bebber wrote: Hello, I wrote a wrapper for symbols() that produces a bivariate bubble plot, for use when plot(x,y) hides multiple occurrences of the same x,y combination (e.g

[R] plot(cox.zph()): customize xlab ylab

Hello, plot(cox.zph(my.ph),var=1,xlab=Year) gives the error: Error in plot.default(range(xx), yr, type = n, xlab = Time, ylab = ylab[i], : formal argument xlab matched by multiple actual arguments How can I customize the xlab and ylab for plots of cox.zph? Thanks, Dan Bebber Department

Re: [R] plot(cox.zph()): customize xlab ylab

Dear all, I've modified the plot.cox.zph function to allow customized xlab and ylab (see below). Someone might like to confirm that it works. Thanks for all the assistance. Dan ___ plot.cox.zph - function (x, resid = TRUE, se = TRUE, df = 4, nsmo = 40, var,

[R] R crashes when spherical autocorrelation specified in nlme

2.0.1 Windows XP SP2 Dual Intel Xeon 2.8GHz 2Gb RAM Thanks, Dan Bebber Department of Plant Sciences University of Oxford UK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

[R] predict.coxph fitted values for failure times

? Thanks, Dan Bebber Department of Plant Sciences University of Oxford ___ How much free photo storage do you get? Store your holiday __ R-help@stat.math.ethz.ch mailing list https

Re: [R] Dead wood code

will put a reprint in the post, and will forward the R code in a separate message. Please cite the article and acknowledge the original code in any publications. Cheers, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Date: Tue, 5 Apr 2005 10:07:00

[R] logistic regression

Helene, you should read up about AIC, deviance, and deviance residuals, then look at the summary() for your model. Dan Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford OX1 3RB UK Message: 78 Date: Tue, 8 Feb 2005 11:15:35 +0100 From:

[R] R package classification

. I would attempt such a classification, but my knowledge of statistical methods isn't good enough. Dan Bebber Department of Plant Sciences University of Oxford UK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

RE: [R] summary.lme() vs. anova.lme()

-1327.240 693.0919 mconc.lme2 2 16 -1363.095 -1300.785 697.5475 1 vs 2 8.91124 0.1786 I can't reject the null hypothesis of no effect of treatment. Many thanks. Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000

[R] summary.lme() vs. anova.lme()

0.0920 Pinheiro Bates (2000) only discusses anova() for single arguments briefly on p.90. I would like to know whether these results indicate that the significant effect found in summary(mconc.lme) is spurious (perhaps due to multiplicity). Many thanks, Dan Bebber Department of Plant Sciences

[R] Error with package update

this? Many thanks, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

RE: [R] sample variogram construction

times? Any help would be appreciated Quoting Dan Bebber [EMAIL PROTECTED]: Hi Matt, there are several R packages that will compute the sample variogram for you. Check out GeoR, sgeostat, nlme, spatial. There's no point in recoding the whole lot yourself, unless as a learning

RE: [R] sample variogram construction

Hi Matt, there are several R packages that will compute the sample variogram for you. Check out GeoR, sgeostat, nlme, spatial. There's no point in recoding the whole lot yourself, unless as a learning excercise. D p.s. For time series autocorrelations, you could use acf in package stats.

[R] spatial autcorrelation in glmmPQL

I am unable to specify error spatial autocorrelation structure in glmmPQL: DATA x and y coordinates for sample points at which presence/absence of seedlings and canopy openness were recorded in different forest stands. QUESTION Does seedling density increase with canopy openness? ANALYSIS

[R] Multiple logistic curves

, scal1=30, Asym2=25, xmid2=60, scal2=25)) THE RESULT I get the error message: Error in nls(size ~ SSlogis(Time, Asym1, xmid1, scal1) + SSlogis(Time, : step factor 0.000488281 reduced below `minFactor' of 0.000976563 Any hints in making this analysis work would be greatly appreciated. Dan

[R] Modelling compound logistic growth curves

(Time, : step factor 0.000488281 reduced below `minFactor' of 0.000976563 Assistance in doing this analysis would be much appreciated. Dan Bebber Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB Tel. 01865

Re: [R] Random intercept model with time-dependent covariates, results different from SAS

, so I guess that balance is not a requirement (assuming Fox is correct). However, the sample sizes are large compared to yours (and mine), which may make a difference. Dan Bebber Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road

[R] Error with arima()

Could someone please give a brief explanation, or pointer to an explanation, of the following error: arima(ts.growth, order = c(1,0,0),include.mean=T) Error in arima(ts.growth, order = c(1, 0, 0), include.mean = T) : non-stationary AR part from CSS and why it does not arise with

[R] Error() term in glm model formula

model, perhaps with Poisson error. However, the glm function does not seem to support adding an Error() term to the model. My question is: is there any way of modelling the experimental design in glm, or should I transform the data as best as I can and stick with aov? Many thanks, Dan Bebber

[R] Error() term in glm model formula

Hello, with regards to my recent question, the design is more a 'repeated measures in space' design than split plot. Dan Bebber *Original message follows** My data are numbers of trees in plots sampled in a number of forest stands. Some stands were subjected to a treatment, others

[R] Circular statistics with (direction,size) data

a better solution to this problem? Many thanks, Dan Bebber Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB Tel. 01865 275060 Web. http://www.forestecology.co.uk/ Data, data, data! he cried impatiently. I can't make