search for: bebber

Dear list, If anyone knows how to assign dimnames to matrices or arrays I would be most grateful for help. I've tried various permutations of likely-looking code but get error messages every time. I could find no example in the documentation. Many thanks, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000

I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e. including a corSpatial correlation in the model specification. In this case the distance metric should be calculated on the sphere, therefore metric = "euclidean" in (for example) corSpher would be incorrect. I would be grateful for help on how to

.../, but rgeos will not run with this either 3. I then install GEOS 3.2.3, and now rgeos works fine! It seems therefore that there is a mismatch between the GEOS version that is available on Synaptic, and the rgeos version on Cran (just in case anyone else comes across this issue). Best wishes, Dan Bebber

...ized linear 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 ____________________________ Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB Tel. 01865 275060 [[alternative HTML version deleted]]

...ccording to what they do (e.g. classification, graphics, spatial statistics), to assist the user in finding the appropriate package for their problem? Or perhaps the search facility is enough. 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

...values into a new vector W of length n. At present I am doing this with a for.... loop, but I imagine there is a faster way that doesn?t involve loops. If anyone knows the way I would be most grateful. Below is the code I am using at present- for (i in 1:n){ W[i]<-P[V[i],i]} Many thanks, Dan Bebber ____________________________ Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275060 Fax. 01865 275074

...reedom in mixed models. The take-home message appears to be: don't trust the p-values from lme. Questions: Should I give up hypothesis testing for fixed effects terms in mixed models? Has my time spent reading Pinheiro & Bates been in vain? Is there a publication on this issue? Thanks, Dan Bebber Department of Plant Sciences University of Oxford

...hs of the plot are thin, due to clipping. If I include > trellis.par.set(clip=list(panel = "off")) then the outer margin line widths are fine, but the outlying data is visible. Is there any way 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

...are misshapen, e.g. the diamond pch = 23 is not symmetrical. There is no problem using postscript(), although Microsoft Word does not do a good job of importing postscript graphics (text comes out too large). Is there a way to make the plotting symbols in metafiles appear as vectors? Thanks, Dan Bebber Using: R 2.11.1, Windows Vista Business

...a coxph model in library(survival). However, none of the prediction options ("lp", "risk", "expected", "terms") seem to bear any relationship to failure time. Perhaps I am asking the wrong question, but can coxph provide predicted failure times? Thanks, Dan Bebber Department of Plant Sciences University of Oxford ___________________________________________________________ How much free photo storage do you get? Store your holiday

...r in createPolygonsComment(p) : #rgeos_PolyCreateComment: orphaned hole, cannot find containing polygon for hole at index 2 #Code ends I don't know my way around SpatialPolygonsDataFrame objects very well, and have no idea how to fix the errant hole. Any help greatly appreciated. Thanks Dan Bebber

...cts. The relationship ppath ~ cut for each subject and weight appear to follow a logistic curve, 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: sublcut ppath bait weight 1 pv1_ 0.0 1.000000000 1 0 2 pv1_ 0.1 0.827773821 1 0 3 pv1_ 0.2 0.380102502 1 0 4 pv1_ 0.3 0.209151878 1 0 5 pv1_ 0.4 0.076...

...poly(d, 2) 4 315 2.01592 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 University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000

Do any of you know any simple programming editors for R scripts which offer basic colour-coding and bracket-matching facilities? Dregging through scripts to find a missing comma or parentheses is something I'd rather do less of... Jon Minton [[alternative HTML version deleted]]

...o be no facility for weighting observations by vector size. My solution would be to create a data set of angles in which my observations are repeated in proportion to the vector size, but this would lead to very large data sets. Does anyone have 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 bricks without clay" - Sherloc...

...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 > arima0(ts.growth, order = c(1,0,0)) Many thanks ____________________________ Dr. Daniel P. Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB [[alternative HTML version deleted]]

...15, scal1=30, Asym2=25, xmid2=67, 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 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 275060 Web. http://www.forestecology.co.uk/ "Data, data, data!" he cried impatiently. "I can't make bricks without clay" - Sherlock...

...1=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 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/

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

...roken in: packageDescription(i, fields = "Title", lib.loc = lib) 6: DESCRIPTION file of package 'file7460' missing or broken in: packageDescription(i, fields = "Title", lib.loc = lib) I am running R 2.0 on Windows XP. Any ideas what caused this? Many thanks, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000