Re: [Rd] Creating package Vignette

2011-07-14 Thread steven mosher
Also useful if you want to do an FAQ On Thu, Jul 14, 2011 at 10:12 AM, Melissa Jane Hubisz wrote: > Another workaround is to create a "dummy" vignette which does nothing > but include the pdf file. Something like this: > vignette.Rnw: > > % \VignetteIndexEntry{vignette} > % \VignetteKeywords{k

Re: [Rd] Creating package Vignette

2011-07-14 Thread Prof Brian Ripley
On Thu, 14 Jul 2011, Melissa Jane Hubisz wrote: Another workaround is to create a "dummy" vignette which does nothing but include the pdf file. Something like this: vignette.Rnw: % \VignetteIndexEntry{vignette} % \VignetteKeywords{keywords here} % \VignettePackage{package name} \documentclass

Re: [Rd] Creating package Vignette

2011-07-14 Thread Melissa Jane Hubisz
Another workaround is to create a "dummy" vignette which does nothing but include the pdf file. Something like this: vignette.Rnw: % \VignetteIndexEntry{vignette} % \VignetteKeywords{keywords here} % \VignettePackage{package name} \documentclass[a4paper]{article} \usepackage{hyperref} \usepackag

Re: [Rd] Creating package Vignette

2011-07-14 Thread Ben Bolker
Prof Brian Ripley stats.ox.ac.uk> writes: > > It depends what you mean by 'vignette': the R docs have been unclear > (but R >= 2.13.0 are more consistent). In most cases a 'vignette' is > an Sweave document, the vignette source being the .Rnw file, and the > vignette PDF the processed .pdf f

Re: [Rd] Creating package Vignette

2011-07-14 Thread Prof Brian Ripley
It depends what you mean by 'vignette': the R docs have been unclear (but R >= 2.13.0 are more consistent). In most cases a 'vignette' is an Sweave document, the vignette source being the .Rnw file, and the vignette PDF the processed .pdf file. At present vignette() means Sweave documents, as

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-14 Thread Alireza Mahani
You are absolutely right Gabe! I removed the line 'dim(A) <- dim(A)[1] * dim(A)[2]' and my code still executes properly. As you said, matrices are internally stored as one-dimensional arrays (column-major by default), it's just that R exposes them differently by assigning different attributes to th

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-14 Thread Gabriel Becker
On Thu, Jul 14, 2011 at 8:21 AM, Alireza Mahani wrote: > (I am using a LINUX machine) > > Jeff, > > In creating reproducible results, I 'partially' answered my question. I > have > attached two scripts, 'mvMultiply.r' and 'mvMultiply.cc'. Please copy both > files into your chosen directory, then r

[Rd] Creating package Vignette

2011-07-14 Thread Nipesh Bajaj
Hi all, I was trying to create some vignette files for my newly developed package, however wondering whether there could be any simpler way to do so. In writing R extension it is advised to go through Sweave route, however I have already got a big pdf file and want to use this as package vignette.

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-14 Thread Alireza Mahani
(I am using a LINUX machine) Jeff, In creating reproducible results, I 'partially' answered my question. I have attached two scripts, 'mvMultiply.r' and 'mvMultiply.cc'. Please copy both files into your chosen directory, then run 'Rscript mvMultiply.r' in that directory while changing the two boo

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-14 Thread Jeff Ryan
The .Call overhead isn't the issue. If you'd like some insight into what you are doing wrong (and right), you need to provide code for the list to reproduce your timings with. This is outlined in the posting guide as well. Best, Jeff On Jul 13, 2011, at 8:28 AM, asmahani wrote: > Hello, >

Re: [Rd] save.image compression_level argument

2011-07-14 Thread Andreas Eckner
> On Mon, 11 Jul 2011, andr...@eckner.com wrote: > >> Hi, >> >> in "save.image", it would be nice if there was a "compression_level" >> argument that is passed along to "save". >> >> Or is there a reason for disabling the "compression_level" option for >> saving workspaces, but enabling it for ma

[Rd] Performance of .C and .Call functions vs. native R code

2011-07-14 Thread asmahani
Hello, I am in the process of writing an R extension for parallelized MCMC, with heavy use of compiled code (C++). I have been getting my feet wet by implementing a simple matrix-vector multiplication function in C++ (which calls a BLAS level 2 function dgemv), and comparing it to the '%*%' operat

[Rd] image adds lines

2011-07-14 Thread Robert J. Hijmans
There seems to be a bug in "image" in R 13.1 (on windows 32 & 64 bits) and on R-devel that is not present in R 13.0 and before. The below creates a plot with many white lines, horizontal and vertical, more or less regularly spaced. The effect is particularly dramatic when the plotting window is ma