Re: [R] odesolve/lsoda differences on Windows and Mac UPDATE

2005-07-28 Thread Martin Henry H. Stevens
answer. Thank you for the time and interest, and I apologize for troubling you. I will get back to the list if I can ever repeat the problem or if I can figure out what I did wrong. Best Regards, Hank On Jul 27, 2005, at 12:36 PM, Martin Henry H. Stevens wrote: Hi - I am getting different

Re: [R] Graphics on MacOSX

2005-08-04 Thread Martin Henry H. Stevens
read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot

[R] user defined panel function

2005-08-29 Thread Martin Henry H. Stevens
) } ) Any thoughts? Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu

Re: [R] user defined panel function - Solved

2005-08-29 Thread Martin Henry H. Stevens
Problem Solved (see below) - Many thanks to Sundar Dorai-Raj! Hank Stevens On Aug 29, 2005, at 3:44 PM, Sundar Dorai-Raj wrote: Martin Henry H. Stevens wrote: Mac OS 10.3.9 R framework v. 2.1.1 I am attempting to put a fitted curve into each panel of a lattice graph, but am failing to do

Re: [R] anova on binomial LMER objects

2005-09-26 Thread Martin Henry H. Stevens
Hello all, 1. Does Matrix 0.98-7 fix any of this? 2. Assuming no, how does one acquire Matrix 0.95-13? Cheers, and thank you kindly in advance, Hank On Sep 26, 2005, at 9:05 AM, Douglas Bates wrote: On 9/25/05, Horacio Montenegro [EMAIL PROTECTED] wrote: Hi Spencer and Robert, I

Re: [R] Bug in lmer?

2005-09-30 Thread Martin Henry H. Stevens
To All: Mark and Martin's code ran fine on R : Version 2.1.1 (2005-06-20) on a Macintosh Dual 2 GHz G5 with 1.5 GB DDR SDRAM. Hank On Sep 30, 2005, at 3:21 AM, Martin Maechler wrote: source(ftp://stat.ethz.ch/U/maechler/R/mltloc-ex.R;, echo = TRUE) Dr. Martin Henry H. Stevens, Assistant

Re: [R] Bug in lmer?

2005-09-30 Thread Martin Henry H. Stevens
I forgot to mention the OS - Mac OS 10.4.2 (Tiger with the latest update). {:-) Hank On Sep 30, 2005, at 3:40 AM, Martin Henry H. Stevens wrote: To All: Mark and Martin's code ran fine on R : Version 2.1.1 (2005-06-20) on a Macintosh Dual 2 GHz G5 with 1.5 GB DDR SDRAM. Hank On Sep 30

[R] Repeated crashes on Mac

2005-10-04 Thread Martin Henry H. Stevens
: Hub in Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 500 mA USB Device: Apple Pro Keyboard, Mitsumi Electric, Up to 12 Mb/sec, 250 mA USB Device: Apple Optical USB Mouse, Logitech, Up to 1.5 Mb/sec, 500 mA Any thoughts? Thanks, Hank Stevens Dr. Martin Henry H. Stevens, Assistant

[R] R Cocoa GUI syntax color bug?

2005-10-06 Thread Martin Henry H. Stevens
you, Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E

[R] Under-dispersion - a stats question?

2005-10-10 Thread Martin Henry H. Stevens
stand to gain a much-reduced standard error if I let the procedure estimate my dispersion factor (which is what I assume the quasi- distributions do). Thank you for any input at all. Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford

Re: [R] Under-dispersion - a stats question?

2005-10-12 Thread Martin Henry H. Stevens
wrote: On Tue, 2005-10-11 at 17:16 -0400, Kjetil Holuerson wrote: Martin Henry H. Stevens wrote: Hello all: I frequently have glm models in which the residual variance is much lower than the residual degrees of freedom (e.g. Res.Dev=30.5, Res.DF = 82). Is it appropriate for me to use

[R] lattice with predicted values

2005-10-14 Thread Martin Henry H. Stevens
) varies by factor level. Cheers, Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http

[R] Citations relevant to lmer methods

2006-07-25 Thread Martin Henry H. Stevens
Hi Mixed Modelers, I was wondering if there are citations relevant to the concerns that Bates and others have regarding the inappropriateness of significance tests in mixed models that use comparison F-ratios to theoretical F distributions. It would just make my life a little easier

[R] Conservative ANOVA tables in lmer

2006-09-07 Thread Martin Henry H. Stevens
Dear lmer-ers, My thanks for all of you who are sharing your trials and tribulations publicly. I was hoping to elicit some feedback on my thoughts on denominator degrees of freedom for F ratios in mixed models. These thoughts and practices result from my reading of previous postings by Doug

Re: [R] Conservative ANOVA tables in lmer

2006-09-11 Thread Martin Henry H. Stevens
: DB == Douglas Bates [EMAIL PROTECTED] on Thu, 7 Sep 2006 07:59:58 -0500 writes: DB Thanks for your summary, Hank. DB On 9/7/06, Martin Henry H. Stevens [EMAIL PROTECTED] wrote: Dear lmer-ers, My thanks for all of you who are sharing your trials and tribulations

[R] geoR/variog4() not returning all directions

2004-09-16 Thread Martin Henry H. Stevens
. Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology/ http://www.muohio.edu

[R] glmmPQL correlation structure

2004-09-22 Thread Martin Henry H. Stevens
or chapter in Venables and Ripley 2002). Cheers, Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http

Re: [R] R glm

2004-09-23 Thread Martin Henry H. Stevens
PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513

Re: [R] R glm

2004-09-23 Thread Martin Henry H. Stevens
__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office

Re: [R] Re: tseries Package for R

2004-09-28 Thread Martin Henry H. Stevens
-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology/ http

[R] nlme model specification

2006-05-17 Thread Martin Henry H. Stevens
Hi folks, I am tearing my hair out on this one. I am using an example from Pinheiro and Bates. ### this works data(Orange) mod.lis - nlsList(circumference ~ SSlogis(age, Asymp, xmid, scal), data=Orange ) ### This works mod - nlme(circumference ~ SSlogis(age, Asymp, xmid, scal),

Re: [R] how to get correct coefficients from lm model

2006-05-18 Thread Martin Henry H. Stevens
On May 18, 2006, at 10:37 AM, Kum-Hoe Hwang wrote: Howdy I apologize for duplicated posting. But I decided to correct my previous posting. I had the regression results using r - lm(Y ~ nemp + as.factor(devt), data=d). Can you tell us how many levels of devt there are? Do

Re: [R] Incomplete Output from lmer{lme4}

2006-05-18 Thread Martin Henry H. Stevens
You may find it helpful to read the posting guide (http://www.R- project.org/posting-guide.html) On May 18, 2006, at 11:40 AM, Lusk, Jeffrey J wrote: I'm still relatively new to R, so my apologies if this is covered somewhere. I've been running some mixed-effect models in R using lme{nlme},

Re: [R] iraq statistics - OT

2006-05-19 Thread Martin Henry H. Stevens
Though I agree that the violent death rate in US cities is sad, I would also guess that the estimates are relatively accurate. I would also say that the experimental design assumed in the article is potentially badly flawed, with tremendous underreporting in Iraq and meticulous reporting

Re: [R] is possible to use update with lmer models

2006-05-25 Thread Martin Henry H. Stevens
Hi Ronaldo, I have no problem with update(). What versions of R, lmer, and Matrix are you using? Hanbk On May 25, 2006, at 8:08 AM, Ronaldo Reis-Jr. wrote: Hi, the question on subject is possible? example: m1 - lmer(y~1+(1|subject)) m2 - update(m1,.~.+x) I try but dont work, exist any

[R] binomial lmer and fixed effects

2006-06-09 Thread Martin Henry H. Stevens
Hi Folks, I think I have searched exhaustively, including, of course R-help (D. Bates, S. Graves, and others) and but I remain uncertain about testing fixed effects with lmer(..., family=binomial). I gather that mcmcsamp does not work with Do we rely exclusively on z values of model

[R] lmer binomial model overestimating data?

2006-06-14 Thread Martin Henry H. Stevens
Hi folks, Warning: I don't know if the result I am getting makes sense, so this may be a statistics question. The fitted values from my binomial lmer mixed model seem to consistently overestimate the cell means, and I don't know why. I assume I am doing something stupid. Below I include

Re: [R] appending

2006-06-14 Thread Martin Henry H. Stevens
Hi David, It would be helpful if you supply a little data, upon which this would operate. Hank On Jun 14, 2006, at 12:31 PM, Afshartous, David wrote: All, In the function below I have 24 individuals and 6 calculations per individual. The 6 calculations are collected each time in a 1:24

Re: [R] appending

2006-06-15 Thread Martin Henry H. Stevens
be deleted since it currently isn't used. The other arguments can be set as: delta.0.Y.0 = 50 gamma = 40. cheers, dave -Original Message- From: Martin Henry H. Stevens [mailto:[EMAIL PROTECTED] Sent: Wednesday, June 14, 2006 1:23 PM To: Afshartous, David Cc: r-help

Re: [R] Repost: Estimation when interaction is present: How do I get get the parameters from nlme?

2006-06-15 Thread Martin Henry H. Stevens
Hi John, I think a solution is to 1. recode A and B as a single factor, AB, with four levels, 2. define each fixed effect as a function of AB minus the intercept (e.g. ed50 ~ as.factor(AB)-1). 3. extract the tTable as a data.frame with summary(model)$tTable. I will be interested to see what

Re: [R] workspace question

2006-02-04 Thread Martin Henry H. Stevens
Hi Dave, Look at save in Help. R automatically loads the workspace called .Rdata at the beginning of a session. You could rename workspace, and load or save whatever you like. Hank On Feb 3, 2006, at 11:20 AM, Afshartous, David wrote: All, When starting R, how does one prevent the loading

Re: [R] Glossay of available R functions

2006-02-04 Thread Martin Henry H. Stevens
Hi Patricia and Alexandre, Start R help, and select the Search Engine Keywords link. This will take you to a page where keywords (including functions) are arranged by topic. It includes base and recommended packages. Also not that on the CRAN website (and mirrors) is a link for Task Views.

Re: [R] R and packages

2006-02-21 Thread Martin Henry H. Stevens
Agreed. Hank On Feb 21, 2006, at 2:40 AM, J Dougherty wrote: You want to take the sysad by the hairy of his chinny-chin-chin and explain the issue in short sentences. He or she ought to be able produce a solution without difficulty, and should not have any problems about doing so.

[R] Work around for TukeyHSD names

2004-05-14 Thread Martin Henry H. Stevens
differences , but provides differences that, I think, are slightly inaccurate. rowames(a) - rownames(b) # Provides rownames for the correct differences par(mar=c(5,10,4,2)+0.1) plot(a, las=1) # Puts correct labels on differences. Thanks for any comments, Hank Stevens Dr. Martin Henry H

Re: [R] IE5 and the html help function

2004-05-06 Thread Martin Henry H. Stevens
? Thanks! Kerstin Gross __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall

Re: [R] IE5 and the html help function RESEND

2004-05-06 Thread Martin Henry H. Stevens
read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html

[R] degrees of freedom in lm() treatment contrasts

2004-05-04 Thread Martin Henry H. Stevens
Does anyone have a good (and specific) reference for an explanation for the calculation of degrees of freedom in treatment contrasts? I checked the indexes of Venables and Ripley 2002, Crawley 2002, and Neter et al. (Applied Linear Statistical Models, 4th ed.), as well as the lm code. I would

Re: [R] Parametric Curves

2004-06-02 Thread Martin Henry H. Stevens
/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http

[R] lsoda with arbitrary zero thresholds

2004-06-09 Thread Martin Henry H. Stevens
as it reached 0.4 Any thoughts would be appreciated. Thanks! Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html

Re: [R] lsoda with arbitrary zero thresholds (with psuedo-solution)

2004-06-09 Thread Martin Henry H. Stevens
enough? Thank you kindly, as ever. Sincerely, Hank On Jun 9, 2004, at 12:45 PM, Martin Henry H. Stevens wrote: using R 2.0.0 I am trying to do some population modeling with lsoda, where I set arbitrary zero population sizes when values get close to zero, but am having no luck. As an example of what

Re: [R] Need for advise for Correspondence Analysis

2004-06-22 Thread Martin Henry H. Stevens
-guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E

[R] Simple indexing conundrum

2005-07-01 Thread Martin Henry H. Stevens
to subset airquality, retaining only the rows, containing the maximum Solar.R for each month. Any solution would be greatly appreciated. Regards, Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab

Re: [R] Simple indexing conundrum

2005-07-01 Thread Martin Henry H. Stevens
28 273 11.5 82 8 13 13324 259 9.7 73 9 10 13521 259 15.5 76 9 12 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy Sent: July 1, 2005 8:31 AM To: 'Martin Henry H. Stevens'; R-Help Subject: Re: [R

[R] Sample size and stepAIC, step, or AIC

2003-03-04 Thread Martin Henry H. Stevens
Do any R functions incorporate a sample sample size correction (e.g., Burnham and Anderson 1998). Thanks, Hank Stevens Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243

[R] citing a package?

2004-02-09 Thread Martin Henry H. Stevens
How do I cite a package (not R itself - I know how to do that)? Any thoughts or links? Many thanks in advance? Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513

Re: [R] citing a package?

2004-02-09 Thread Martin Henry H. Stevens
a download date, or an explicit statement that it is software (eg to make searching easier). -thomas Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http

[R] Spatial Voter Model

2004-04-16 Thread Martin Henry H. Stevens
( (table(Lat0)/sum(table(Lat0)))^2) 1 - sum( (table(Lat)/sum(table(Lat)))^2) layout(matrix(1:2, nrow=1)) # plot arenas plot(rep(1:L,each=L),rep(1:L,L),col=c(Lat0),pch=20) plot(rep(1:L,each=L),rep(1:L,L),col=c(Lat),pch=20) Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department

Re: [R] Dunn's post hoc test

2005-10-17 Thread Martin Henry H. Stevens
PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh

Re: [R] Help with lattice, regressions and respective lines

2005-10-17 Thread Martin Henry H. Stevens
__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford

Re: [R] Help with lattice, regressions and respective lines - Correction

2005-10-17 Thread Martin Henry H. Stevens
Hi Jose, I need to make a small correction in my code - mod$data$B works for glm objects, but not lm or aov objects. For those use, mod$model$B. On Oct 17, 2005, at 6:26 AM, Martin Henry H. Stevens wrote: Hi Jose, I am just beginning to plumb the depths of lattice, but perhaps my recent

Re: [R] Repeating lines in a data frame

2005-10-18 Thread Martin Henry H. Stevens
://www.R-project.org/posting- guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http

Re: [R] sample size determination

2005-10-18 Thread Martin Henry H. Stevens
- guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ E

Re: [R] creating a derived variable in a data frame

2005-10-20 Thread Martin Henry H. Stevens
://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529

[R] changing memory limits to speed up lsoda

2005-10-26 Thread Martin Henry H. Stevens
out how to change the appropriate memory allocation and have search R help and Introductory information and the archives, but connot figure out how to allocate more to the right place. I would greatly appreciate any pointers or tips or leads. Thank you, Hank Stevens Dr. Martin Henry H. Stevens

[R] panel function

2005-12-20 Thread Martin Henry H. Stevens
. }) Any and all thoughts are appreciated. Thank you kindly, Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http

Re: [R] panel function SOLVED

2005-12-20 Thread Martin Henry H. Stevens
: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Henry H. Stevens Sent: Tuesday, December 20, 2005 10:30 AM To: r-help@stat.math.ethz.ch Subject: [R] panel function R v. 2.2.0 on Mac OS 10.4.3 lattice v. 0.12-11 I am trying to add a horizontal panel mean line to a series

[R] Can't load Matrix 0.995-1 for lme4

2006-01-19 Thread Martin Henry H. Stevens
or assistance. Cheers, Hank Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany

Re: [R] How to write a two-way interaction as a random effect in a lmer model?

2006-12-20 Thread Martin Henry H. Stevens
Hi Eva, A couple questions: Are repeated measurements taken on rnr? Is rnr subject? Is stress a continuous variable? See below. On Dec 11, 2006, at 11:04 AM, Fucikova, Eva wrote: Dear All, I am working with linear mixed-effects models using the lme4 package in R. I created a model with

[R] lme4 mcmcsamp matrix not PD

2006-12-20 Thread Martin Henry H. Stevens
Hi folks, I am not providing a small replicable example, because I assume the problem is related to my quirky data (~650 obs.). I am using the latest lme4, matrix and coda, and R 2.4.0. I frequently get the following error message for this particular lmer model. I do not get this message for

Re: [R] lme4 mcmcsamp matrix not PD

2006-12-21 Thread Martin Henry H. Stevens
On Dec 20, 2006, at 4:20 PM, Martin Henry H. Stevens wrote: Hi folks, I am not providing a small replicable example, because I assume the problem is related to my quirky data (~650 obs.). I am using the latest lme4, matrix and coda, and R 2.4.0. I frequently get the following error message

[R] mcmcsamp and variance ratios

2007-01-03 Thread Martin Henry H. Stevens
Hi folks, I have assumed that ratios of variance components (Fst and Qst in population genetics) could be estimated using the output of mcmcsamp (the series on mcmc sample estimates of variance components). What I have started to do is to use the matrix output that included the

Re: [R] mcmcsamp and variance ratios

2007-01-04 Thread Martin Henry H. Stevens
On Jan 4, 2007, at 11:18 AM, Douglas Bates wrote: On 1/3/07, Martin Henry H. Stevens [EMAIL PROTECTED] wrote: Hi folks, I have assumed that ratios of variance components (Fst and Qst in population genetics) could be estimated using the output of mcmcsamp (the series on mcmc sample estimates

Re: [R] aov - glm - lmer

2007-01-05 Thread Martin Henry H. Stevens
, self-contained, reproducible code. Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http

[R] Wiki for Graphics tips for MacOS X

2007-01-31 Thread Martin Henry H. Stevens
Hi Folks, I just finished (the first draft of) a Wiki document to explains options for producing graphics to incorporate in MS Word. Thanks to all those who provided input, and who provided the wiki space. Here is the direct link. http://wiki.r-project.org/rwiki/doku.php?id=tips:using-

Re: [R] Repeated Measures design using lme

2007-04-24 Thread Martin Henry H. Stevens
Have you seen Pinheiro and Bates (2000) that lays out the nlme package? It is very helpful. Hank On Apr 14, 2007, at 8:02 PM, Kyle. wrote: You probably can do this with lme function, but I don't know that for sure. aov (included in the stats package), with a call to the Error function how I

Re: [R] R^2 from lme function

2007-05-14 Thread Martin Henry H. Stevens
Hi Cleber, I have been using this function I wrote for lmer output. It should be easy to convert to lme. As with everything, buyer beware. Note that it requires (full) maximum likelihood estimates. Rsq - function(reml.mod) { ## Based on ## N. J. D. Nagelkerke. A note on a general

Re: [R] R^2 from lme function

2007-05-14 Thread Martin Henry H. Stevens
Hi Cleber, By full I simply meant not REML. the function assumes that the fixed effects were estimated using REML criteria, and using update() simply changes that to ML. If the model was fit originally with ML, it shouldn't make any difference. I am reasonably sure that it should not matter

Re: [R] exemples, tutorial on lmer

2007-05-29 Thread Martin Henry H. Stevens
Hi Oliver, You could start with R News 2005, no. 1. Also the PDF associated with lme4, Implementation.pdf. Hnak On May 29, 2007, at 10:35 AM, Olivier MARTIN wrote: Hi all, I have some difficulties to work with the function lmer from lme4 Does somebody have a tutorial or different examples

[R] Different fonts on different axes

2007-05-31 Thread Martin Henry H. Stevens
Hi Folks, How do I get red bold font on my y axis and black standard font on my x axis? plot(runif(10), ylab=Red, Bold?, xlab=Black, standard?) Any pointers or examples would be great. Thanks! Hank Dr. Hank Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University

Re: [R] Different fonts on different axes

2007-05-31 Thread Martin Henry H. Stevens
: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Henry H. Stevens Sent: Thursday, May 31, 2007 11:00 AM To: R-Help Subject: [R] Different fonts on different axes Hi Folks, How do I get red bold font on my y axis and black standard font on my x axis? plot(runif

Re: [R] Aggregate to find majority level of a factor

2007-05-31 Thread Martin Henry H. Stevens
How about tapply? plot - gl(2,3); plot type - letters[c(1,2,2,1,1,1)]; type tapply(type, list(plot), function(x) {tabl - table(x) names(tabl[tabl==max (tabl)])}) Hank On May 31, 2007, at 3:25 PM, Thompson, Jonathan wrote: I want to use the

Re: [R] Interaction term in lmer

2007-06-01 Thread Martin Henry H. Stevens
HI Emine, The parentheses specify a variable as random or fixed. You are using center for random intercepts, but fixed for interactions. You may want mer(cbind( yvect, nvect-yvect) ~ trt + ( 1 | center) + (1 | trt:center), family = binomial, niter = 25, method = Laplace, control = list

Re: [R] Tools For Preparing Data For Analysis

2007-06-08 Thread Martin Henry H. Stevens
Is there an example available of this sort of problematic data that requires this kind of data screening and filtering? For many of us, this issue would be nice to learn about, and deal with within R. If a package could be created, that would be optimal for some of us. I would like to

Re: [R] {spam?} Nonlinear Regression

2007-06-11 Thread Martin Henry H. Stevens
Hi tronter, PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Hank On Jun 7, 2007, at 5:50 PM, tronter wrote: Hello I followed the example in page 59, chapter 11 of the 'Introduction to R'

Re: [R] Fwd: Using odesolve to produce non-negative solutions

2007-06-11 Thread Martin Henry H. Stevens
Hi Jeremy, First, setting hmax to a small number could prevent a large step, if you think that is a problem. Second, however, I don't see how you can get a negative population size when using the log trick. I would think that that would prevent completely any negative values of N (i.e.

Re: [R] Fwd: Using odesolve to produce non-negative solutions

2007-06-11 Thread Martin Henry H. Stevens
Hi Spencer, I have copied Woody Setzer. I have no idea whether lsoda can estimate parameters that could take imaginary values. Hank On Jun 11, 2007, at 12:52 PM, Spencer Graves wrote: in line Martin Henry H. Stevens wrote: Hi Jeremy, First, setting hmax to a small number could prevent

[R] Package update announcements

2007-06-11 Thread Martin Henry H. Stevens
Hi Folks, I was wondering what everyone thought about adding a sentence to each package update announcement that described what the package did. R extensions are so numerous that it is difficult to keep up with them. Would it be appropriate to ask package developers to add a brief sentence

Re: [R] Package update announcements

2007-06-12 Thread Martin Henry H. Stevens
wrote: MHHS == Martin Henry H Stevens [EMAIL PROTECTED] on Mon, 11 Jun 2007 17:23:46 -0400 writes: MHHS Hi Folks, I was wondering what everyone thought about MHHS adding a sentence to each package update announcement MHHS that described what the package did. R extensions

[R] lme or gls prediction intervals

2007-07-24 Thread Martin Henry H. Stevens
Hi folks, I am trying to generate 95% confidence intervals for a gls model using predict.nlme with R version 2.5.1 (2007-06-27) . nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-83. I have looked in help, and I can do it for lm and glm models, and I can generate

Re: [R] lme or gls prediction intervals

2007-07-25 Thread Martin Henry H. Stevens
starting point to me. Joris Martin Henry H. Stevens [EMAIL PROTECTED] To edu R-Help r- [EMAIL PROTECTED] Sent

Re: [R] Is Rwiki down?

2007-07-25 Thread Martin Henry H. Stevens
Me too. Hank On Jul 25, 2007, at 7:50 AM, Jin Lo wrote: Dear R-friends, is Rwiki down? I've been trying to login for the past couple of days with no success. Yours sincerely, Jin __ __ wherever

[R] italic greek symbols

2007-07-31 Thread Martin Henry H. Stevens
Hi Folks, I am using R 2.5.1 on a Mac OS X 10.4.9, via ESS. I would like to try to get an italic mu onto a plot axis label. I note that in a previous email, (Thu, 4 May 2006 19:41:41 +0100 (BST)), Brian Ripley wrote, There is no italic symbol font available on most devices. So unless you try to

Re: [R] italic greek symbols

2007-07-31 Thread Martin Henry H. Stevens
message: OS reports request to set locale to greek cannot be honored in: Sys.setlocale(LC_CTYPE, greek) Cheers, Hank On Jul 31, 2007, at 3:00 PM, Prof Brian Ripley wrote: On Tue, 31 Jul 2007, Martin Henry H. Stevens wrote: Hi Folks, I am using R 2.5.1 on a Mac OS X 10.4.9, via ESS. I would

Re: [R] residual plots for lmer in lme4 package

2007-08-16 Thread Martin Henry H. Stevens
Hi Margaret, Have a look at qqmath in the lattice package. ?qqmath Hank On Aug 16, 2007, at 2:45 AM, Margaret Gardiner-Garden wrote: Hi, I was wondering if I might be able to ask some advice about doing residual plots for the lmer function in the lme4 package. Our group's aim is to