Re: [Rd] issue with Rd2pdf and \Sexpr in Rd files

2012-03-19 Thread Dan Tenenbaum
Hello, Sorry to repeat myself, but I was wondering if anyone had taken a look at this. Because of this problem, reference manuals are not being created for many Bioconductor packages (any package where there is a \Sexpr in an .Rd file). Thanks in advance--we appreciate your help very much. Dan

[Rd] diff(time) vs. difftime?

2012-03-19 Thread Spencer Graves
I've just uncovered an infelicity in as.difftime: > as.difftime(diff(as.POSIXct(c('2012-12-12', '2012-12-13'))), units='hours') Time difference of 1 days Is this a bug in the code or in my understanding? Thanks again for all your hard work in making R the great produ

[Rd] diff(time) vs. difftime?

2012-03-19 Thread Spencer Graves
I just encountered another RTFM problem: With diff(as.POSIXct(...), ...) I was unable to control the units of the results. Examples: > (d.d <- diff(as.POSIXct(c('2012-12-12', '2012-12-13' Time difference of 1 days > (d.h <- diff(as.POSIXct(c('2012-12-12 08:00', '2012-12-12 09:00'))

[Rd] bzip2'ed data under data/

2012-03-19 Thread Sebastian P. Luque
Hi, R CMD check PACKAGE_VERSION_tar.gz gives warning: Files not of a type allowed in a ‘data’ directory: ‘tser1.csv.bz2’ ‘tser2.csv.bz2’ Please use e.g. ‘inst/extdata’ for non-R data files which I didn't expect, based on section 1.1.5 (Data in packages) of the Writing R Extensions manual: Tab

Re: [Rd] merge bug fix in R 2.15.0

2012-03-19 Thread Stephanie M. Gogarten
I would like to add a vote for keeping blank suffixes in merge(), as I routinely use this functionality. An example use case: # using R 2.14.1 # d1 is some data that I've been working on for a while d1 <- data.frame(a=letters[1:10], b=1:10) # d2 is some new data from a collaborator. I want to

[Rd] Problem with table

2012-03-19 Thread Terry Therneau
R version 2.14.0, started with --vanilla > table(c(1,2,3,4,NA), exclude=2, useNA='ifany') 134 1112 This came from a local user who wanted to remove one particular response from some tables, but also wants to have NA always reported for data checking purposes. I do

Re: [Rd] Converting expression to a function

2012-03-19 Thread Hadley Wickham
Hi John, Here's a somewhat streamlined version of the code: Form2resfun <- function(f, params) { stopifnot(inherits(f, "formula"), length(f) == 3) # Create function body body <- substitute( crossprod(rhs - lhs), list(lhs = f[[2]], rhs = f[[3]]) ) # Create argument list free_para

[Rd] Design choice of plot.design for formulas

2012-03-19 Thread Thaler,Thorn,LAUSANNE,Applied Mathematics
Dear all, Today I figured out that the formula interface of plot.design is kind of counter intuitive. Suppose the following setting ddf <- expand.grid(a=factor(1:3), b=factor(1:3)) ddf$y <- rnorm(9) plot.design(y ~ a + b, data=ddf) which does what it should do, basically printing the means for t