similar to: Using a function from splines.c in our package

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

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

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 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

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

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

Should R CMD check consider it an error to define a new method using setMethod for a class which is not currently defined? It seems to me that it would be best not to consider this an error. What currently happens in that setMethod issues a warning, quite correctly. This warning produces an object 'last.warning'. Then R CMD check issues a WARNING that 'last.warning' is an

I've noticed a curious interpretation of escaped characters in \examples{} in .Rd files. For example, if I type files <- dir(pattern="\\.txt") at the R prompt, I will get a vector containing all file names in the current directory containing the string ".txt". If I put \examples{ files <- dir(pattern="\\.txt") } in an .Rd file of a package,

>[Rd] boxplot() defaults {was "boxplot in extreme cases"} >Martin Maechler maechler at stat.math.ethz.ch >Mon Nov 8 10:36:42 CET 2004 > > AndyL> Try: > > AndyL> x <- list(x1=rep(c(0,1,2),c(10,20,40)), > x2=rep(c(0,1,2),c(10,40,20))) > AndyL> boxplot(x, pars=list(medpch=20, medcex=3)) > > AndyL> (Cf ?bxp, pointed to from

The R Journal home page doesn't make any promises about how frequently the journal will be published. Historically, though, there have been issues in June and December of each year. The June issue has always appeared by this time (6 August) in previous years. Has there been a change in the publication schedule? Are there still plans for a June 2016 issue? Thanks Gordon

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, I've been learning how to use R TclTk in Windows over the last few months. I have recently put together a collection of examples of some common widgets and their corresponding R code, at http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/ I would be interested in any feedback - Is it useful? Does it contain any significant errors or bad coding style? Does anyone else want to

I am not sure if what I am asking below should be discussed under r-help or r-devel, so please feel free to move over to r-devel. This is a spin off from Gordon Smyth's question about generic functions and Robert Gentleman's reply. I have tried to raise the question before and I am sure this has been discussed by others, but never on the r-help list what I can see. My concern is that

I am not sure if what I am asking below should be discussed under r-help or r-devel, so please feel free to move over to r-devel. This is a spin off from Gordon Smyth's question about generic functions and Robert Gentleman's reply. I have tried to raise the question before and I am sure this has been discussed by others, but never on the r-help list what I can see. My concern is that

Hi, I am trying to create a drop-down combobox in R TclTk. The following works fine for a ListBox but fails for a combobox: ################# THIS WORKS FINE - CREATES AN EMPTY LISTBOX ## tt<-tktoplevel() win <- .Tk.subwin(tt) .Tcl(paste("listbox",.Tk.ID(win),.Tcl.args())) tkpack(win) ################## THIS FAILS - ATTEMPTS TO CREATE A COMBOBOX ## tt<-tktoplevel() win

Hi, I have successfully installed R 1.7.0 and ActiveTcl 8.4.2.0 in Windows 2000. Yes, I know that Tcl is already bundled with R 1.7.0, but I want to use the iwidgets package to create a drop-down listbox, and I don't think iwidgets is included in the bundled R 1.7.0/TclTk installation package. I have set the environment variables TCL_LIBRARY and MY_TCLTK to the directory where I

Thanks Peter, I've started a new R session (in Windows) and managed to get both ways working now : ### THIS WORKS !!! ### library(tcltk) tclRequire("IWidgets") tt<-tktoplevel() combo <- tkwidget(tt,"iwidgets::combobox") tkpack(combo) ### AND THIS WORKS TOO !!! ### tt<-tktoplevel() win <- .Tk.subwin(tt)

Dear R-devel, I am experiencing issues with running GAM models using mclapply, it fails to return any values if the data input becomes large. For example here the code runs fine with a df of 100 rows, but fails at 1000. library(mgcv) library(parallel) > df <- data.frame( + x = 1:100, + y = 1:100 + ) > > mclapply(1:2, function(i, df) { + fit <- gam(y ~ s(x, bs =

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