similar to: address of Gordon Smyth ?

Hi Peter and others, If it helps, I wrote a small function glm.scoretest() for the statmod package on CRAN to compute score tests from glm fits. The score test for adding a covariate, or any set of covariates, can be extracted very neatly from the standard glm output, although you probably already know that. Regards Gordon --------------------------------------------- Professor Gordon K

Probably a simple question, but I can't find the answer to it ... In the 'ppinit' code it describes how it takes a 'file in standard format' and creates a point process object with it. Can anyone enlighten me as to what this 'standard format' is? The example given doesn't allow me to view the '.dat' file that apparently is in this format. Thanks, Suzie

SuppDists is orphaned on CRAN (and has been since 2013). https://cran.r-project.org/web/checks/check_results_.html Oddly, the simulate method for the inverse.gaussian family [inverse.gaussian()$simulate] depends (in a loose sense) on SuppDists (it fails if the SuppDists namespace is not available: if (!requireNamespace("SuppDists", quietly = TRUE)) stop("need CRAN

On 2019-09-25 3:26 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Tue, 24 Sep 2019 20:09:55 -0400 writes: > > > SuppDists is orphaned on CRAN (and has been since 2013). > > https://cran.r-project.org/web/checks/check_results_.html > > > Oddly, the simulate method for the inverse.gaussian family > >

Dear Catarina, I prefer to leave the AIC value as NA for the tweedie GLM family because it takes extra time to compute and is only occasionally wanted. It's easy to compute the AIC yourself using the dtweedie() function of the tweedie package. Best wishes Gordon At 03:05 AM 14/08/2007, Catarina Miranda wrote: >Dear Gordon; > >I have also sent this email to R help mailing list,

Ah, I spoke too soon. I started putting the demo code into a test suite and ran one check with valgrind and ? sure enough ? there's def more issues (a cpl functions) than the overt/easy ones (and, I went back to the check results page and, also sure enough, they're there, too). They look to be fairly straightforward to resolve but it's going to take a bit longer than "this

In R 2.1.1, the default behaviour of scan() was changed to process all C-style escapes, even when a delimiter was specified using the 'sep' argument. A new argument 'allowEscapes' was introduced to turn this processing off. Because read.table() calls scan(), read.table() inherits the new default behaviour of scan() but without a way to turn it off. For example, reading a file

This is just a suggestion/wish that it would be nice for the F-distribution functions to recognize limiting cases for infinite degrees of freedom, as the t-distribution functions already do. The t-distribution functions recognize that df=Inf is equivalent to the standard normal distribution: > pt(1,df=Inf) [1] 0.8413447 > pnorm(1) [1] 0.8413447 On the other hand, pf() will accept Inf

Dear all, I am trying to write a package using formal methods and classes from the methods package. I have not been able to get the package to pass rcmd check without warnings, because rcmd check does not recognize my generic functions as code objects and therefore queries why they have documentation entries. I have isolated the problem in a very small trivial example which I give below. I

Martin Maechler has suggested that I post this comment to r-devel. It was originally posted to bioconductor. --------------------------------- I'd like to raise the issue of a capitalization convention for naming objects in R. Almost everything in R used to be lowercase but recently there is increasing use of mixed upper/lower case to define names. There is potential for using the

>>>>> "GS" == Gordon K Smyth <smyth@wehi.edu.au> >>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.............> GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing

I am another person who has had trouble documenting S4 classes and (particularly) methods. The methods package itself is pretty cool by the way, but it is a pity that there are as yet no guidelines on S4 in the "Writing R Extensions" document. I have actually put together a guide on S4 documentation myself for the use of my own lab which is at

On page 165 of Mixed-Effects Models in S and S-Plus by Pinheiro and Bates there is an example of using lme() in the nlme package to fit a model with crossed random factors. The example assumes though that the data is grouped. Is it possible to use lme() to fit crossed random factors when the data is not grouped? E.g., y <- rnorm(12); a=gl(4,1,12); b=gl(3,4,12). Can I fit an additive model

1. I'm putting together my first package that uses S4 classes and objects. I'd like to document them, but I'm not sure what the documentation should look like, and package.skeleton doesn't produce any at all for the classes or methods. Are there any good examples to follow? 2. How do I do the equivalent of debug(foo), when foo is an anonymous function being used as a method?

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

I'm writing functions that need to behave differently for GLMs like binomial and Poisson with fixed deviance, and those like normal or gamma or quasi where the deviance is estimated from the data. Given a glm object, is there a simple way to tell this directly, or do I have to look at the name of the family? Duncan Murdoch

Hi. This will hopefully be readily understood but if not, bear with me. I have to do a repeated analysis (in spatstat) and want to batch file it. For each of my 'runs' certain variables change. At present I am manually specifying these changes and want to automate it if possible. Ok, I am creating an object which is comprised of 'levels' that are 'characters'. Further

Hi; How do I make it so that it's impossible to SSH into the server directly as root? That is, make it necessary to SSH in as an ordinary user and then su to root? TIA, Suzie -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.centos.org/pipermail/centos/attachments/20100105/9d567d47/attachment-0002.html>

Hi; I don't want sendmail. What's a good secure email server that I can yum? I really only need smtp right now, but who knows what the future will bring? TIA, Suzie -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.centos.org/pipermail/centos/attachments/20091123/1ef8c879/attachment-0003.html>

Dear all, I am running a logistic regression and this is the output: glm(formula = educationUniv ~ brncntr, family = binomial) Deviance Residuals: Min 1Q Median 3Q Max # ???? ????? ?? ???????? -0.8825 -0.7684 -0.7684 1.5044 1.6516 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -1.06869 0.01155 -92.487 <2e-16 *** brncntrNo