[R] mgcv::gam() scale parameter estimates for quasibinomial error models

2021-04-14 Thread John Maindonald
.bib file: https://www.dropbox.com/s/r1yjqx0sni2pzjy/quasi.bib?dl=0 John Maindonald email: john.maindon...@anu.edu.au __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE d

Re: [R] R-help Digest, Vol 217, Issue 20

2021-03-20 Thread John Maindonald
No, it is not distribution free. Independent random sampling is assumed. That is a non-trivial assumption, and one that is very often not true or not strictly true. John Maindonald email: john.maindon...@anu.edu.au<mailto:john.maindon...@anu.edu.au> On 21/03/2021, at 00:

Re: [R] Regarding R licensing usage guidance

2019-07-23 Thread John Maindonald
. I do not know what Anamika’s position is, but he may well be trying to build a business from a much less privileged starting point than others of us may have enjoyed. In any case, the comment strikes a tone that is out of place in respectful discourse. John Maindonald email

Re: [R] p values from GLM

2016-04-03 Thread John Maindonald
dom number generator), small P-values shift the weight of evidence. An alternative that is apriori highly unlikely takes a lot of shifting. John Maindonald email: john.maindon...@anu.edu.au<mailto:john.maindon...@anu.edu.au> On 3/04/2016, at 22:00, r-help-requ...@r-pr

Re: [R] SWEAVE - a gentle introduction

2015-11-18 Thread John Maindonald
What’s more, for pdf output one can use R Markdown and judiciously sneak in html and/or LaTeX (consider however what the processing steps might do to such markup). John Maindonald email: john.maindon...@anu.edu.au<mailto:john.maindon...@anu.edu.au> On 19/11/2015, at 00:00,

Re: [R] R wont accept my zero count values in the GLM with quasi_poisson dsitribution

2015-07-28 Thread John Maindonald
estimated proportions for binomial data. For the poisson or quasipoisson family, use of the sqrt link avoids this problem. John Maindonald email: john.maindon...@anu.edu.aumailto:john.maindon...@anu.edu.au On 28/07/2015, at 22:00, r-help-requ...@r-project.orgmailto:r-help-requ...@r

[R] R: Re: Differences in output of lme() when introducing interactions

2015-07-23 Thread John Maindonald
. John Maindonald email: john.maindon...@anu.edu.aumailto:john.maindon...@anu.edu.au On 22/07/2015, at 22:00, r-help-requ...@r-project.orgmailto:r-help-requ...@r-project.org wrote: Da: li...@dewey.myzen.co.ukmailto:li...@dewey.myzen.co.uk Data: 21-lug-2015 11.58 A: angelo.arc

Re: [R] Error in lm() with very small (close to zero) regressor

2015-03-29 Thread John Maindonald
! ## cf also as.vector(pseudoinverse(t(Xcs0) %*% Xcs0) %*% t(Xcs0) %*% y) ## [1] -1.65842037 0.03797342 John Maindonald email: john.maindon...@anu.edu.aumailto:john.maindon...@anu.edu.au Centre for Mathematics Its Applications, Australian National University, Canberra ACT 0200

Re: [R] the making of _R_ eBooks

2015-03-24 Thread John Maindonald
Thanks for that. Useful to have that question asked and to get that information. John Maindonald email: john.maindon...@anu.edu.aumailto:john.maindon...@anu.edu.au On 25/03/2015, at 0:00, r-help-requ...@r-project.orgmailto:r-help-requ...@r-project.org wrote: From: John McKown

Re: [R] rpart and randomforest results

2014-04-08 Thread John Maindonald
monotonically with the number of splits). The ‘rel error’ column from printcp() can be hopelessly optimistic. John Maindonald email: john.maindon...@anu.edu.aumailto:john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications

Re: [R] Drawing a line in xyplot

2012-04-09 Thread John Maindonald
argument. The following is an alternative way to calculate one4all: one4all - layer(data=xdat, avy - median(mortality), panel.segments(0.1, avy, 0.3, avy, col=red,lwd=4), panel.segments(0.7, avy, 1, avy, col=red, lwd=4)) John Maindonald. This can be simplified by using the layering

Re: [R] Drawing a line in xyplot

2012-04-08 Thread John Maindonald
that produces the object gph would also be simpler and easier to follow if some relevant part was separated out into a separate layer. See also my notices on layering of lattice objects at: http://www.maths.anu.edu.au/%7Ejohnm/r-book/add-graphics.html John Maindonald email

[R] RC33 8th Int Conf on Social Science Methodology -- The R System ...

2011-11-02 Thread John Maindonald
researchers and users of research. The title for the planned session is: The R System as a Platform for Analysis and Development of Analysis Methodology http://conference.acspri.org.au/index.php/rc33/2012/schedConf/trackPolicies John Maindonald email: john.maindon...@anu.edu.au

Re: [R] R-help Digest, Vol 97, Issue 11

2011-03-09 Thread John Maindonald
You might look at the function confusion() in the DAAGxtras package. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27

Re: [R] cv.lm syntax error

2011-03-09 Thread John Maindonald
It means that dat$v1, dat$v2, . . . are not columns in the data frame df Specify the formula as v1 ~ v2+v2+v3+v4+v5+factor Then (assuming that factor is a column object of the right length) you should be fine. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473

Re: [R] \Sweaveopts error

2010-11-27 Thread John Maindonald
in the second line of code in output .tex file test2.tex John. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian

Re: [R] \Sweaveopts error

2010-11-27 Thread John Maindonald
and test.tex, irrespective of the 1 line or 2 issue. The first of the \SweaveOpts lines had an effect, unless I am missing something. John. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications

[R] \Sweaveopts error

2010-11-25 Thread John Maindonald
proto_0.3-8 loaded via a namespace (and not attached): [1] ggplot2_0.8.8 latticeExtra_0.6-14 Is there a workaround? John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John

Re: [R] \Sweaveopts error

2010-11-25 Thread John Maindonald
Yes, that has fixed the problem. (2010-11-24 r53659) Thanks. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian

[R] L-shaped boxes with lattice graphs?

2010-11-14 Thread John Maindonald
(x=0, y=0.5, lab = as.expression(levlist[which.panel[which.given]]), adj=0) } e.g. levlist - list(A, B) xyplot(11:14 ~ 1:4 | rep(1:2,2), scales=list(x=list(alternating=c(1,1), relation=sliced)), strip=stripfun, layout=c(1,2)) John Maindonald email: john.maindon

[R] Why software fails in scientific research

2010-02-28 Thread John Maindonald
of knowledge on animals and their environments for zoos, aquariums and related organizationsvalues the use of objective data to benefit conservation, science, animal welfare, education, and collection management. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473

Re: [R] parsing pdf files

2010-01-10 Thread John Maindonald
], ({\\em , availfun[nmatch,1], }), sep=) funentries - paste(\\indexentry , {, entrymat[,1],}{, entrymat[,2], },sep=) write(funentries, fdxfile) system(paste(makeindex -o, fndfile, fdxfile)) } John Maindonald

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?

2009-10-06 Thread John Maindonald
I had a large job time ago that ran fine under MacOS X. I'd expect the same to be true under Linux. It would run under Windows XP only if XP had been freshly rebooted. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre

[R] Use of R in Schools

2009-09-18 Thread John Maindonald
I am looking for information on experimentation with the use of R in the teaching of statistics and science in schools. Any leads would be very welcome. I am certain that there is such experimentation. I've made this inquiry on r-sig-teaching, with no response. John. John Maindonald

Re: [R] R User Group in Canberra

2009-07-31 Thread John Maindonald
Please add AUSTRALIA Canberra: Canberra R Users Group (CANRUG) http://canrug.togaware.com/ Cheers john. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical

[R] Strip labels: use xyplot() to plot columns in parallel with outer=TRUE

2009-05-09 Thread John Maindonald
in each panel, and the variable names are added: xyplot(form, data=df, outer=TRUE, strip=strip.custom(strip.names=TRUE, var.name=as.expression(lab2))) John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its

Re: [R] Accuracy of R and other platforms

2009-03-23 Thread John Maindonald
of accuracy really has then to be tuned to that application. Results in cases where the accuracy beyond (optimistically) the sixth digit is of no consequence are unlikely to give much clue on performance in such specialist applications. John Maindonald email: john.maindon

Re: [R] using a noisy variable in regression (not an R question)

2009-03-08 Thread John Maindonald
://www.maths.anu.edu.au/%7Ejohnm/r-book/2edn/xtras/xtras.pdf have brief comments, and code that can be used to illustrate the point. I support Stephen Kolassa's suggestions re using simulation for sensitivity analysis, though I think this can also be done analytically. John Maindonald email: john.maindon

[R] The Origins of R

2009-02-03 Thread John Maindonald
through the preface! There's an excellent brief summary of the history of R, and its connections with S, in Section 1.4 of John Chambers' Software for Data Analysis.Appendix A has further details on the development of S, a kind of pre-history of R. John Maindonald email

[R] Sweave style file

2008-12-26 Thread John Maindonald
It would, I consider, be useful to note, on the help pages for Sweave and RweaveLatex, that the path to Sweave.sty in the R installation can be extracted as paste(R.home(),share/texmf/, sep=/) or its equivalent. John Maindonald email: john.maindon...@anu.edu.au phone : +61 2

Re: [R] R] adding a new dataset to the default R distribution

2008-12-04 Thread John Maindonald
such datasets can be submitted? All it would require is for someone to offer to act as Keeper of the Miscellaneous Data. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman

[R] Congratulations, Ross!

2008-11-11 Thread John Maindonald
/uoa/about/news/articles/2008/11/rsnz_honours.cfm 12 November 2008. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National

Re: [R] R seven years ago

2008-10-09 Thread John Maindonald
, 2007 = 2015, 2008=1644) These will not be all that accurate; there will be omissions and duplications. Growth is close to exponential. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194

[R] R Citation rates

2008-08-12 Thread John Maindonald
deal more summary information that might be extracted. What is a good way, with readily available data, to standardize the country data. Environmental Science no doubt comes up tops because it is a coarser grouping than many other areas. John Maindonald email: [EMAIL PROTECTED] phone

Re: [R] Dividing by 0

2008-07-26 Thread John Maindonald
not do some smoothing at the start? John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200

[R] predict lmer

2008-05-10 Thread John Maindonald
=) rug(x) lines(x[ord], lower[ord]) lines(x[ord], upper[ord]) ploc - c(0.01, 0.05, 0.1, 0.2, 0.5, 0.8, 0.9) axis(2, at=log(ploc/(1-ploc)), labels=paste(ploc), las=2) } ## Usage glmm2 - lmer(rcr ~ litter + (1 | Farm), family=binomial, data=data.site) ciplot(obj=glmm2) John

[R] REvolution

2008-01-26 Thread John Maindonald
At present though, unless you have better success than me, all you will get from the Revolution Computing site is a revolutionary song! John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194

Re: [R] Symbolic substitution in parallel; use infinity symbol?

2008-01-01 Thread John Maindonald
[-length(zz)], zz[-1], SIMPLIFY=FALSE) y - rnorm(40) x0 - cut(y, breaks=breaks) plot(x0, y, xaxt=n) axis(1, at=1:3, labels=as.expression(lbl)) Thanks, Peter. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its

[R] Symbolic substitution in parallel; use infinity symbol?

2007-12-30 Thread John Maindonald
'. Is there is some relatively straightforward way to do this? The issue is of course more general than this specific example. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman

[R] Reminiscing on 20 years using S

2007-12-27 Thread John Maindonald
an answer. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 27 Dec 2007

Re: [R] Packages - a great resource, but hard to find the right one

2007-11-23 Thread John Maindonald
paper. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 23 Nov 2007, at 10:00

Re: [R] [R-sig-ME] mixed model testing

2007-11-07 Thread John Maindonald
whether conditions are sufficiently calm for an ocean liner to leave port. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27

Re: [R] postscript(), used from a pre R-2.6.0 workspace

2007-10-30 Thread John Maindonald
pedigree, and source the dumped file. I do not want to have to directly run the function that creates the database each time I start a session. Has anyone else hit this? John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its