Re: [Rd] UTF8 markdown vignette

] Verzonden: vrijdag 19 december 2014 14:02 Aan: Yihui Xie CC: ONKELINX, Thierry; r-devel@r-project.org; Kurt Hornik Onderwerp: Re: [Rd] UTF8 markdown vignette On 18/12/2014, 12:17 AM, Yihui Xie wrote: For the record, I saw a change had been made in R-devel: https://github.com/wch/r-source/commit

Re: [Rd] UTF8 markdown vignette

- Van: xieyi...@gmail.com [mailto:xieyi...@gmail.com] Namens Yihui Xie Verzonden: woensdag 10 december 2014 4:37 Aan: Duncan Murdoch CC: ONKELINX, Thierry; r-devel@r-project.org; Kurt Hornik Onderwerp: Re: [Rd] UTF8 markdown vignette I took a look at the R source and I realized that the encoding

[Rd] UTF8 markdown vignette

Dear all, I'm trying to use a Markdown vignette with UTF-8 encoding. It compiles well when knitting the vignette in RStudio, but it fails to recognize the UTF-8 settings when building the source package. Can someone point out what I'm doing wrong? I tried to put the relevant information below.

Re: [Rd] UTF8 markdown vignette

desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Verzonden: dinsdag 9 december 2014 11:04 Aan: ONKELINX, Thierry; r-devel@r-project.org

Re: [Rd] UTF8 markdown vignette

Xie [x...@yihui.name] Verzonden: dinsdag 9 december 2014 17:13 Aan: ONKELINX, Thierry CC: r-devel@r-project.org; Duncan Murdoch; Kurt Hornik Onderwerp: Re: [Rd] UTF8 markdown vignette A few things to clarify: 1. You do not necessarily have to keep the \usepackage{} line if you use

Re: [Rd] How to test impact of candidate changes to package?

Dear Stephanie, Have a look at the testthat package and the related article in the R Journal. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat

Re: [Rd] Multiple versions of data in a package

Dear Chris, Add both snps_36 and genes_36 to the same rda file. Then you should both load with a single data() command. However make sure to document all functions well. Then it is up to the user to use the functions correctly. You can implement some controls to give a warning when incorrect

Re: [Rd] summary of lme4.0 model in package

[mailto:jorism...@gmail.com] Verzonden: donderdag 3 april 2014 15:18 Aan: ONKELINX, Thierry CC: Joshua Wiley; r-devel@r-project.org Onderwerp: Re: [Rd] summary of lme4.0 model in package Thierry, did you try to importFrom() in the namespace file? That way you know for sure you have the correct summary

[Rd] summary of lme4.0 model in package

Dear all, My package has Depends: lme4.0 in the DESCRIPTION. I need to extract the fixed effect of a model and their standard errors. I use coef(summary(model)) inside a function to do that. Model is the output of a call to glmer() from the lme4.0 package. coef(summary(model)) throws an

Re: [Rd] summary of lme4.0 model in package

be extracted from a given body of data. ~ John Tukey Van: Joshua Wiley [mailto:jwiley.ps...@gmail.com] Verzonden: donderdag 3 april 2014 12:36 Aan: ONKELINX, Thierry CC: r-devel@r-project.org Onderwerp: Re: [Rd] summary of lme4.0 model in package Dear Thierry, You have lme4.0_0.99-4 attached

Re: [Rd] summary of lme4.0 model in package

Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: ONKELINX, Thierry

[Rd] predictions in nlme without fixed covariantes

Dear all, predict.lme() throws an error when the fixed part consists of only an intercept and using newdata. See the reproducible example below. I've tracked the error down to asOneFormula() which returns in this case NULL instead of a formula. Changing NULL instead of ~1 in that function (see

Re: [Rd] Error from R CMD check

[mailto:murdoch.dun...@gmail.com] Verzonden: dinsdag 30 juli 2013 13:18 Aan: ONKELINX, Thierry CC: r-devel@r-project.org Onderwerp: Re: [Rd] Error from R CMD check On 13-07-30 6:34 AM, ONKELINX, Thierry wrote: Dear all, I'm puzzled by the error I get from R CMD check one of my packages. I'm running R CMD

[Rd] Error from R CMD check

Dear all, I'm puzzled by the error I get from R CMD check one of my packages. I'm running R CMD check with the --as-cran flag and it get the error both from running it from the command line as from within Rstudio. On the same machine R CMD check on my GRTS package

Re: [Rd] Non-vignette sweave file in package

and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Verzonden: donderdag 4 april 2013 19:04 Aan: ONKELINX, Thierry CC: r-devel@r

[Rd] Non-vignette sweave file in package

Dear all, I'm documenting an elaborate analysis as a private package. The package writes all required output to a database. I use a Sweave file to transform all the results from the database into a report. Now I would like to add this Sweave to my package. I'm a bit puzzled on how to do that.

[Rd] incorrect import?

Dear all, I'm not getting what I'm doing wrong. The line below from my read.fsa.bin function throws an error when just loading my AFLP package and disappears when I load the zoo package as well. #the line that throws the error Index - which(Peak == rollmax(Peak, k = 1 + 2 *

Re: [Rd] incorrect import?

of data. ~ John Tukey Van: Joris Meys [mailto:jorism...@gmail.com] Verzonden: maandag 28 januari 2013 11:27 Aan: ONKELINX, Thierry Onderwerp: Re: [Rd] incorrect import? 'rollmax' is a generic S3 method, and the point of that is to be visible to the user. If you only import the generic, it can't

Re: [Rd] There is pmin and pmax each taking na.rm, how about psum?

Why don't you make a matrix and use colSums or rowSums? x = c(1,3,NA,5) y = c(2,NA,4,1) colSums(rbind(x, y), na.rm = TRUE) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance

[Rd] Strange bug in my package

Dear all, I get a bug in the examples of my AFLP package on R-forge (https://r-forge.r-project.org/R/?group_id=1027) but only on the Linux version. The windows version compiles. The Mac version skips the examples and compiles. The strange thing is that the packages compiles on my Ubuntu 10.10

[Rd] Error message library()

Dear all, When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package

Re: [Rd] Problem with defining new method for residuals()

Tukey -Oorspronkelijk bericht- Van: Martin Morgan [mailto:mtmor...@fhcrc.org] Verzonden: vrijdag 11 maart 2011 7:36 Aan: ONKELINX, Thierry CC: r-devel@r-project.org; John Chambers Onderwerp: Re: [Rd] Problem with defining new method for residuals() On 03/10/2011 08:21 AM

[Rd] Problem with defining new method for residuals()

Dear all, I'm writing a package and I would like to reuse the residuals() function. When I use a function which calls the redefined residuals (for my custom class) I get an error (see below). It looks like the wrong method is used. The strange this is, that when it execute the code manually it

[Rd] Sweave choking on \\ in filename

Dear all, Sweave chokes when using \\ in the path to the Rnw file. Using / works fine. The problem is that Eclipse+StatET uses \\ in the filename. And example of the error, traceback and sessionInfo are given below. Best regards, Thierry

Re: [Rd] incorrect result (41/10-1/10)%%1 (PR#13863)

This is not a bug. It is a case of R FAQ 7.34: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-the se-numbers-are-equal_003f ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research

[Rd] Extend FAQ 7.22

Dear all, I suggest to extend FAQ 7.22 by mentioning ggplot2 graphics as well. 7.22 Why do lattice/trellis/ggplot2 graphics not work? The most likely reason is that you forgot to tell R to display the graph. Lattice functions such as xyplot() create a graph object, but do not display it (the

[Rd] Link to documentation in another package

Dear all, One of the functions that I wrote (ggsave.latex) extents the functionality of a function (ggsave) in another package (ggplot2). Instead of copying all the information I would like to create a link in the helpfile of ggsave.latex to the helpfile of ggsave. I tried \code{\link{ggsave}}

Re: [Rd] calculating means per group

Dear Luc, You should send this kind of questions to the general mailing list ([EMAIL PROTECTED]) instead of the developer list. To answer your question: have a look at ?by and ?aggregate HTH, Thierry ir. Thierry

[Rd] Take marginality into account in factor.scope

Dear devellopeRs, I've altered factor.scope() from the stats package so it can take marginality into account. Therefore I've added the argument marginal. When marginal is NULL, factor.scope() works like the original version. The marginality is to be specified as a named list. The name of the