[R] Dates and location for useR! 2024
Dear All, We are pleased to announce that useR! 2024 will be a hybrid conference, taking place 8-11 July in Salzburg, Austria. The conference website is yet to be set up. In the meantime, you can keep up-to-date the following ways: useR! LinkedIn Page: https://www.linkedin.com/company/user-conf useR! Twitter: https://twitter.com/_useRconf R Foundation Mastodon: https://fosstodon.org/@R_Foundation (we will likely set up a Mastodon account for useR! in due course) Best wishes, Heather On behalf of the R Foundation Conference Committee ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Call for proposals to organize a hybrid useR! in 2023 or 2024
Dear All, The R Foundation Conference Committee invites proposals to organize a hybrid useR! in 2023 or 2024: https://www.r-project.org/conferences/useR_2023_call.html The call is open to teams worldwide and the deadline for outline proposals is **Wednesday 30 November 2022**. Selected hosts will have support from the R Consortium to underwrite event management provided or managed by the Linux Foundation Events Team. Any queries should be sent to r-conferen...@r-project.org (after a careful read of the call!). Best wishes, Heather Turner on behalf of the R Foundation Conference Committee ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Call for proposals to organize useR! 2023 as a global online conference
Dear All, The R Foundation Conference Committee invites proposals to organize useR! 2023 as a global online conference: https://www.r-project.org/conferences/useR_2023_call.html The call is open to teams worldwide and the deadline for outline proposals is **Friday 22 April 2022**. Any queries should be sent to r-conferen...@r-project.org (after a careful read of the call!). Best wishes, Heather Turner on behalf of the R Foundation Conference Committee ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] useR! 2020 survey
Dear All, We hope you have been able to watch/attend some of the breakout sessions, keynotes, R core panel, contributed tutorials, or online tutorials that were part of the useR! 2020 program. We'd appreciate it you took 5 minutes to let us know a bit more about yourself and what you thought of useR! this year, by answering the useR! 2020 survey: bit.ly/useR2020survey. Many thanks, Heather [[alternative HTML version deleted]] ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] The R Journal Vol. 3/2 now published
Dear All, The second issue of the third volume of The R Journal is now available: http://journal.r-project.org/current.html. Thanks to everyone involved. Heather -- Editor in chief heather.tur...@r-project.org ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] The R Journal Vol. 3/1 now published
Dear All, The first issue of the third volume of The R Journal is now available at http://journal.r-project.org/current.html. Thanks to everyone involved. Heather -- Editor in chief heather.tur...@r-project.org ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] *REMINDER* useR! 2011 call for tutorials
As announced, the R user conference useR! 2011 is scheduled for August 16-18, 2011, and will take place at the University of Warwick, Coventry, UK. Before the official program, half-day tutorials will be offered on Monday, August 15. We invite R users to submit proposals for three hour tutorials on special topics regarding R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification of why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before October 29, 2010 to useR-2011_at_R-project.org. A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2011 We hope to see you in Coventry! The organizing committee: John Aston, Julia Brettschneider, David Firth, Ashley Ford, Ioannis Kosmidis, Tom Nichols, Elke Thönnes and Heather Turner __ 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] useR! 2011: announcement and call for tutorials
We are pleased to announce that the R user conference useR! 2011 is scheduled for August 16-18, 2011, and will take place at the University of Warwick, Coventry, UK. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online later this year). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before October 29, 2010, see below). INVITED SPEAKERS Adrian Bowman, Lee Edlefsen, Ulrike Grömping, Wolfgang Huber, Brian Ripley, Jonathan Rougier, Simon Urbanek, and Brandon Whitcher. USER-CONTRIBUTED SESSIONS The conference will feature both talks and posters illustrating the use of R in practice. Contributions are welcome that introduce recent developments in the R Project (including CRAN packages), demonstrate applications of R in areas of current interest, or otherwise engage and inspire participants in their use of R. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Monday, August 15. We invite R users to submit proposals for three hour tutorials on special topics regarding R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification of why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before October 29, 2010 to useR-2011_at_R-project.org. A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2011 We hope to see you in Coventry! The organizing committee: John Aston, Julia Brettschneider, David Firth, Ashley Ford, Ioannis Kosmidis, Tom Nichols, Elke Thönnes and Heather Turner ___ r-annou...@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] nls + quasi-poisson distribution
Dear Suresh, The gnm package for generalized nonlinear models might be what you want here. This allows you to specify nonlinear models with family=quasipoisson. For an introduction to the package see the article in R News: http://cran.r-project.org/doc/Rnews/Rnews_2007-2.pdf If your model requires a custom nonlin function and you get stuck on this, or you have any other queries about the package, I'm happy to be contacted directly. Best regards, Heather On 06/07/10 07:04, Suresh Krishna wrote: Hello R-helpers, I would like to fit a non-linear function to data (Discrete X axis, over-dispersed Poisson values on the Y axis). I found the functions gnlr in the gnlm package from Jim Lindsey: this can handle nonlinear regression equations for the parameters of Poisson and negative binomial distributions, among others. I also found the function nls2 in the software package accompanying the book Statistical tools for nonlinear regression by Huet et al: this can handle nonlinear regression with Poisson distributed Y-axis values. I was wondering if there was any other option: specifically, any option that handled nonlinear fitting with quasi-Poisson distributions (to handle the overdispersion). This is a very new area for me, and I am still trying to figure out the best way to do this, so I would appreciate any and all pointers. Thanks much, Suresh __ 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] Generating model formulas for all k-way terms
Hi Michael,
You need to substitute the value of i for the symbol i in your formula, i.e.
update(mod, substitute(.~.^i, list(i = i)))
So, with some other tidying up:
Kway - function(formula, family, data, ..., order=nt) {
models - list()
mod - glm(formula, family, data, ...)
mod$call$formula - formula
terms - terms(formula)
tl - attr(terms, term.labels)
nt - length(tl)
models[[1]] - mod
for(i in 2:order) {
models[[i]] - update(mod, substitute(.~.^p, list(p = i)))
} # null model
mod0 - update(mod, .~1)
models - c(list(mod0), models)
names(models) - paste(mod, 0:order, sep = .)
class(models) - glmlist
models
}
mods - Kway(Freq ~ A + B + C, data=df, family=poisson)
Best wishes,
Heather
Michael Friendly wrote:
For the vcdExtra package, I'm exploring methods to generate and fit
collections of glm models,
and handling lists of such model objects, of class glmlist. The
simplest example is fitting all
k-way models, from k=0 (null model) to the model with the highest-order
interaction. I'm
having trouble writing a function, Kway (below) to do what is done in
the example below
factors - expand.grid(A=1:3, B=1:2, C=1:3)
Freq - rpois(nrow(factors), lambda=40)
df - cbind(factors, Freq)
mod.0 - glm(Freq ~ 1, data=df, family=poisson)
mod.1 - update(mod.0, . ~ A + B + C)
mod.2 - update(mod.1, . ~ .^2)
mod.3 - update(mod.1, . ~ .^3)
library(vcdExtra)
summarize(glmlist(mod.0, mod.1, mod.2, mod.3))
Model Summary:
LR Chisq Df Pr(Chisq) AIC
mod.0 21.3310 17 0.2118 -12.6690
mod.1 21.1390 14 0.0981 -6.8610
mod.2 15.8044 11 0.1485 -6.1956
mod.3 14.7653 10 0.1409 -5.2347
# Generate and fit all 1-way, 2-way, ... k-way terms in a glm
Kway - function(formula, family, data, ..., order=nt) {
models - list()
mod - glm(formula, family, data, ...)
terms - terms(formula)
tl - attr(terms, term.labels)
nt - length(tl)
models[[1]] - mod for(i in 2:order) {
models[[i]] - update(mod, .~.^i)
} # null model
mod0 - update(mod, .~1)
models - c(mod0, models) class(models) - glmlist
models
}
mods - Kway(Freq ~ A + B + C, data=df, family=poisson)
Error in terms.formula(tmp, simplify = TRUE) : invalid power in formula
I still don't understand how to manipulate formulas in functions. Can
someone help?
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Re: [R] Statistic community?
When discussions do burst out on the allstat list, people are usually pointed to one of the following alternatives: http://groups.google.com/group/MedStats http://datashaping.ning.com/forum HTH Heather Peters Gj (PSYCHOLOGY) wrote: Hey Antje list, Antje wrote: I'm very glad to use the R-help mailing list for R-related question but more and more often I face general statistical problems. Does anyone know by chance a community (mailinglist, forum, ...) where I can ask these kind of questions? I myself have recently started lurking at the Allstat and Stat-L lists. Stat-L does not seem very active, and my impression of Allstat is that it's mostly used for distributing information about conferences and vacancies. In addition, Allstat does not encourage discussion on-list - their rules ask you to reply to people in person. I myself prefer on-list discussions, as I frequently learn from these (just by lurking). So you could also try out these two lists - and if you find anything else, I would love to hear about them :-) Kind regards, Gjalt-Jorn --- Gjalt-Jorn Peters Work Social Psychology, faculty of Psychology Neuroscience, Maastricht 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-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] R course in Scotland
Hello Peter, If you want to use R for bioinformatics, you probably want a course using Bioconductor (www.bioconductor.org). To combine with a introduction to R, the following should be good: http://www3.imperial.ac.uk/stathelp/courses/statisticalmicroarrayanalysisusingr but some time to wait till the next course. The following may provide a good alternative: http://www.ebi.ac.uk/training/handson/course_090119_transcriptomics.html Otherwise there are lots of materials from previous courses on http://www.bioconductor.org/workshops which you can use for self-teaching. Hope that helps, Heather -- Dr H Turner Senior Research Fellow Dept. of Statistics The University of Warwick Coventry CV4 7AL Tel: 024 76575870 Fax: 024 76524532 Url: www.warwick.ac.uk/go/heatherturner Gustavo Carvalho wrote: Hello, Take a look at this course: http://www.r4all.group.shef.ac.uk/index.html I don't think they teach tools for working with the genome, but it might be helpful anyway. On Thu, Nov 20, 2008 at 11:16 AM, Peter Saffrey [EMAIL PROTECTED] wrote: (apologies if this is the wrong list) I'm a bioinformatician looking for a course in using R, in particular the tools for working with the genome - I've heard they're lightning fast. I'm in Glasgow, but I've tried the Robertson centre for biostatistics and they use minitab. If anybody knows of a course, I would be grateful. Glasgow or Edinburgh would be preferable, but anywhere in the UK will do if it's a good course. Thanks, Peter __ 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] Citing R in journal articles (or the failure to)
Hi Achim,
Thanks for pointing us to the code from the colorspace package - a good
example of how to keep the citation information up-to-date
automatically, something I had not considered...
Heather
--
Dr H Turner
Senior Research Fellow
Dept. of Statistics
The University of Warwick
Coventry
CV4 7AL
Tel: 024 76575870
Fax: 024 76524532
Url: www.warwick.ac.uk/go/heatherturner
Achim Zeileis wrote:
On Wed, 12 Nov 2008, Michael Friendly wrote:
One could complement that by a
url = {http://CRAN.R-project.org/package=tweedie}
In two recent in press articles where I cited R packages,
I was asked by the copy-editor to add a location or url to the
references. Could I suggest that citation() be modified to include
the URL automatically?
That's a good suggestion and one that I discussed several times with
Kurt. The problem is that citation() only looks at the installed package
which doesn't know where it came from. Thus, I have AFAIK no simple
means of checking whether a particular package I'm using was obtained
from CRAN, Bioc, R-Forge, or some local source package. Hence, the URL
cannot be included automatically.
I agree that this would be nice to have. One idea would be that the CRAN
maintainer adds a line to the DESCRIPTION file upon release to CRAN.
There are a few ideas how to do this exactly and it's not yet implemented.
As a package maintainer, however, you can improve the situation for your
own packages by writing a CITATION file that has the CRAN URL in it. For
example, the first citEntry() in the colorspace package has:
## R = 2.8.0 passes package metadata to citation().
if(!exists(meta) || is.null(meta)) meta -
packageDescription(colorspace)
year - sub(-.*, , meta$Date)
note - sprintf(R package version %s, meta$Version)
citEntry(entry = Manual,
title = {colorspace}: Color Space Manipulation,
author = personList(as.person(Ross Ihaka),
as.person(Paul Murrell),
as.person(Kurt Hornik),
as.person(Achim Zeileis)),
year = year,
note = note,
url = http://CRAN.R-project.org/package=colorspace;,
textVersion =
paste(Ross Ihaka, Paul Murrell, Kurt Hornik, Achim Zeileis,
sprintf((%s)., year),
colorspace: Color Space Manipulation.,
paste(note, ., sep = ),
URL http://CRAN.R-project.org/package=colorspace;)
)
Best wishes,
Z
In the function, this would entail replacing the line
z$url - meta$URL
with something like
z$url - if (is.null(meta$URL)
paste(http://CRAN.R-project.org/package=;, package, sep=) else
meta$URL
I say something like because I'm not sure how to handle other
repositories.
Along similar lines, someone recently posted a script to generate
a .bib file for all packages installed. It would be useful if someone
were to implement that script for CRAN and make the resulting
R-packages.bib file available on the CRAN site.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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Re: [R] Understanding glm family documentation: dev.resids
Hi Peter, You are right, the dev.resids function does compute the square of the deviance residuals. Equivalently, dev.resids computes the d_i values, where d_i is the contribution of the $i$th observation to the deviance. The d_i can be defined directly and it is useful to have a function that returns these values rather than their signed square root (the deviance residuals), since they are used to compute the deviance in the glm algorithm and elsewhere, as sum(d_i). The name dev.resids may be a bit misleading, but it is essentially an internal function, so it's not unreasonable for it to have a loose interpretation (a function that returns a function of the deviance residuals). However, it is less reasonable for the documentation to say something misleading, so you could submit a bug report on that I guess. Best regards, Heather Dr H Turner Senior Research Fellow Dept. of Statistics The University of Warwick Coventry CV4 7AL Tel: 024 76575870 Fax: 024 76524532 Url: www.warwick.ac.uk/go/heatherturner Peter Dunn wrote: Hi all Consider the family function, as used by glm. The help page says the value of the family object is a list, one element of which is the following: dev.resids function giving the deviance residuals as a function of (y, mu, wt). But reading any of the family functions (eg poisson) shows that dev.resids is a function that computes the *square* of the deviance residuals (at least, by every definition I know of). Further, the deviance residuals returned by residuals.glm are essentially computed as the square root of dev.resids. Something seems amiss. The element dev.resids actually seems to compute the deviance residuals squared. I guess the help file could be changed to read: dev.resids function giving the square of the deviance residuals as a function of (y, mu, wt). ...but then, dev.resids still seems a misleading label, but that may so entrenched it will never changed. (By my definition, the square of the deviance residuals is not quite the unit deviance as the weights need to be incorporated differently, but others may disagree.) Of course, I could be way off track. I would appreciate enlightenment. P. Peter Dunn Biostatistician School of Health and Sport Science Faculty of Science, Health and Education University of the Sunshine Coast Tel: +61 7 5456 5085 Fax: +61 7 5430 2896 Email: [EMAIL PROTECTED] www.usc.edu.au CRICOS Provider Number: 01595D This communication is intended for the recipient only and should not be forwarded, distributed or otherwise read by others without express permission. The views expressed in this email are not necessarily those of the University of the Sunshine Coast. __ 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] nls: Fitting two models at once?
Dear Martin,
You can use the same idea of concatenating the data in R. The following
reproduces your example:
spec - c(asfe, dias)
n1 - length(asfe)
n2 - length(dias)
CYT - c(28 * CYTF, 24.6 * 2 * CYTB6)
B559HP - c(B559HP, numeric(n2))
B559LP - c(numeric(n1), B559LP)
C550 - c(numeric(n1), C550)
spec.fit -
nls(
spec ~ cyt.v*CYT + hp.v*B559HP + lp.v*B559LP + c550.v*C550,
start = list(cyt.v = 0.5, hp.v = 0.03, lp.v = 1,
c550.v = 1) # arbitrary
);
or more efficiently, using lm
spec.fit - lm(spec ~ 0 + CYT + B559HP + B559LP + C550)
# draw stuff
plot(
1, 2,
type=n,
xlim = c(540, 575),
ylim=c(-0.002, 0.008),
);
# first spectrum and fit
lines(wl, asfe, type=b, pch=19); # solid circles
lines(wl, fitted(spec.fit)[1:n1], col = red);
# second spectrum and fit
lines(wl, dias, type=b);
lines(wl, fitted(spec.fit)[(n1 + 1):(n1 + n2)], col = blue);
Best wishes,
Heather
Dr H Turner
Senior Research Fellow
Dept. of Statistics
The University of Warwick
Coventry
CV4 7AL
Tel: 024 76575870
Fax: 024 76524532
Url: www.warwick.ac.uk/go/heatherturner
Martin Ballaschk wrote:
Hello,
I'm still a newbie user and struggling to automate some analyses from
SigmaPlot using R. R is a great help for me so far!
But the following problem makes me go nuts.
I have two spectra, both have to be fitted to reference data. Problem: the
both spectra are connected in some way: the stoichiometry of coefficients
cytf.v/cytb.v is 1/2.
{{In the SigmaPlot workflow one has to copy the two spectra into one column
beneath each other and the two spectra are somehow treated as one curve -
like in http://home.arcor.de/ballaschk/cytbf-help/sigmaplot%20formula.png}}
Can anybody help? :(
I tried to condense everything to the minimum R script below to give an
impression of what I'm talking about.
Martin
# Minimal R script reading remote data for convenience
### READ IN DATA
# first spectrum
asfe - read.table(http://home.arcor.de/ballaschk/cytbf-help/asfe.csv;)[, 1];
# second spectrum
dias - read.table(http://home.arcor.de/ballaschk/cytbf-help/dias.csv;)[, 1];
# reference data for fit, wavelength = wl
ref - read.table(http://home.arcor.de/ballaschk/cytbf-help/reference.csv;,
sep=\t, dec=., header=T);
attach(ref);
### FITTING, problem: 2*cytf.v == cytb.v
# fit first spectrum to two reference spectra
asfe.fit -
nls(
asfe ~ (cytf.v * 28) * CYTF + hp.v * B559HP,
start = list(cytf.v = 0.5, hp.v = 0.03) # arbitrary
);
# fit second spectrum to three reference spectra
dias.fit -
nls(
dias ~ (cytb.v * 24.6 * 2) * CYTB6 + lp.v * B559LP + c550.v * C550,
start = list(cytb.v = 1, lp.v = 1, c550.v = 1) # arbitrary
);
# draw stuff
plot(
1, 2,
type=n,
xlim = c(540, 575),
ylim=c(-0.002, 0.008),
);
# first spectrum and fit
lines(wl, asfe, type=b, pch=19); # solid circles
lines(wl, fitted(asfe.fit), col = red);
# second spectrum and fit
lines(wl, dias, type=b);
lines(wl, fitted(dias.fit), col = blue);
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