Brew and knit one PDF report split by variable with special characters (å æ ø) - encoding issue

I try to produce one PDF report split on sections based on a grouping variable, using `brew` and `knitr`. My grouping variable may contain special characters (umlauts), such as å æ ø. Umlauts in the document title only are handled fine with `\usepackage[utf8]{inputenc}` (see examples below). However, umlauts in the grouping variable generate an error with `\usepackage[utf8]{inputenc}`. On the other hand, when I tried `\usepackage[T1]{fontenc}`, umlauts in the grouping variable are handled properly. But now the title is not correctly encoded. I am struggling to get encoding right in both title and grouping variable. Here is an example where I try to produce one PDF report with subsections of summary statistics per species in the iris dataset. I hope it may illustrate my problem. R code to prepare data without umlauts ``` library(plyr) library(xtable) library(knitr) library(brew) library(stringr) ``` Create a summary table for each species in the built-in `iris` dataset. First, use the original `Species` names, without umlauts. Umlaut in document `\title` only (see code for the `.rnw` template file). Store summary tables in a list. ``` data(iris) iris_tbl <- dlply(.data = iris, .variables = .(Species), function(x) xtable(summary(x))) ``` Define function `brew_knit_pdf`. The function brews a template latex file `xxx.rnw` to a new `.rnw` file `xxx_out.rnw`, which has one section for each item/group that is looped over. The `xxx_out.rnw` from `brew` is then used as an input file in `knit2pdf` and is converted to a PDF. ``` brew_knit_pdf <- function(template, ...){ brew_out <- str_replace(string = template, pattern = ".rnw", replacement = "_out.rnw") brew(file = template, output = brew_out) knit2pdf(input = brew_out, ...) } brew_knit_pdf("iris_umlaut_tbl.rnw") ``` Code for the .rnw template file In my example, I have named the template file for the following code `iris_umlaut_tbl.rnw`. This file is used as input in the `brew_knit_pdf` function in the R script. ``` \documentclass{article} % \usepackage[T1]{fontenc} \usepackage[utf8]{inputenc} \usepackage{geometry} \geometry{tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm} \begin{document} \begin{titlepage} \title{Using brew and knitr to produce one PDF report split by a grouping variable.\\Problem with å æ ø in grouping variable} \clearpage\maketitle \thispagestyle{empty} \tableofcontents \end{titlepage} \newpage \section{Summary statistics for each species} % R code loop wrapped in brew syntax, which brews the template file xxx.rnw to a new .rnw file xxx_out.rnw, which has one section for each group that is looped over, i.e. the names of the list iris_tbl produced in the R script. <% for (Sp in names(iris_tbl)) { -%> \subsection{<%= Sp %>} <<sum-<%= Sp %>, echo=FALSE, results='asis'>>= print(iris_tbl[["<%= Sp %>"]]) @ \newpage <% } %> \end{document} ``` R code to prepare data with umlauts To mimic my real data, I replace Species names in the iris data with (non-sensical) names than contains umlauts. ``` data(iris) iris$Species <- as.character(iris$Species) iris$Species[iris$Species == "setosa"] <- "åsetosa" iris$Species[iris$Species == "versicolor"] <- "æversicolor" iris$Species[iris$Species == "virginica"] <- "øvirginica" # create a summary table for each species iris_tbl <- dlply(.data = iris, .variables = .(Species), function(x) xtable(summary(x))) ``` When the 'umlaut version' of iris_tbl has been prepared, I run the brew_knit_pdf function on the same .rnw file as above, except that I use different encoding packages (inputenc and/or fontenc). Result Here is a summary of four attempts so far; using datasets without or with umlauts, and using different encoding packages in the .rnw file. - The R data: iris_tbl prepared with non-umlaut Species - The .rnw file: umlauts in `\title{ }`, `\usepackage[utf8]{inputenc}` Output umlauts in title OK - The R data: iris_tbl prepared with umlaut version of Species - The .rnw file: umlauts in `\title{ }`, `\usepackage[utf8]{inputenc}` Output Error: running 'texi2dvi' on 'iris_umlaut_tbl_out.tex' failed LaTeX errors: ...Package inputenc Error: Unicode char \u8:æve not set up for use with LaTeX. - The R data: iris_tbl prepared with umlaut version of Species - The .rnw file: `umlauts in \title{ }`, `\usepackage[T1]{fontenc}`, `\usepackage[utf8]{inputenc}` Output Error: running 'texi2dvi' on 'iris_umlaut_tbl_out.tex' failed LaTeX errors: ...Package inputenc Error: Unicode char \u8:æve not set up for use with LaTeX. - The R data: iris_tbl prepared with umlaut version of Species - The .rnw file: umlauts in `\title{ }`, `\usepackage[T1]{fontenc}` Output umlauts in title not OK, umlauts in grouping variable OK Can anyone point me in the right direction to get the encoding right in both title and grouping variable? Thanks a lot in advance for taking your time. Session info Default text encoding in my R Studio 0.97.336: UTF-8 ``` > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252 LC_CTYPE=Norwegian (Bokmål)_Norway.1252 [3] LC_MONETARY=Norwegian (Bokmål)_Norway.1252 LC_NUMERIC=C [5] LC_TIME=Norwegian (Bokmål)_Norway.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] Hmisc_3.10-1 survival_2.37-4 pastecs_1.3-13 boot_1.3-9 [5] pspline_1.0-15 ggplot2_0.9.3.1 lubridate_1.2.0 stringr_0.6.2 [9] brew_1.0-6 knitr_1.1 xtable_1.7-1 plyr_1.8 [13] PerformanceAnalytics_1.1.0 xts_0.9-3 zoo_1.7-9 gdata_2.12.0.2 loaded via a namespace (and not attached): [1] cluster_1.14.4 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 evaluate_0.4.3 formatR_0.7 [7] grid_3.0.0 gtable_0.1.2 gtools_2.7.1 labeling_0.1 lattice_0.20-15 MASS_7.3-26 [13] memoise_0.1 munsell_0.4 proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3 [19] tools_3.0.0 > getOption("encoding") [1] "native.enc" ``` Update: I am very grateful for an 'off-SO' input from the brew package maintainer Jeffrey Horner. He had no encoding problems when running my script with Ubuntu and command-line R. This gave me some renewed hope. I have no opportunity to run Ubuntu myself, but today I updated RStudio (0.97.449) and set the default encoding to ISO8859-1 (thanks Yihui!). Now the special characters are encoded correctly both in the title and in the grouping variable with `\usepackage[latin1]{inputenc}` in the .rnw file. Also `\usepackage[ansinew]{inputenc}` works. I am not sure what went wrong in my original attempt. Possibly RStudio did not apply the default encoding set in Options, which I changed following Yihui's advice, to the script files when I re-opened them. But that's just a speculation.