Merge branch 'master' into knitr

Bring the knitr branch fully in sync with master: pulls in the memo
template, the article-class letter template, the README and script
updates (assignment -> memo), the embed-fonts pass on the poster
figure PDFs, and the wiki_page.wiki deletion.

Two small conflicts resolved by hand:

- paper_template/text.Rtex: git detected the rename text.tex ->
  text.Rtex and conflicted only around the knitr <<init>>= chunk,
  which is absent on master. Keep the chunk.
- paper_template/Makefile: whitespace-only conflict on the
  '%.pdf: %.tex' rule (master's version had a trailing space).
  Keep the trimmed version.

Built paper_template (with knitr) and letter_template; both are
UA-2 compliant under the merged state.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

README

@@ -47,8 +47,8 @@ On other systems, installing a full TeX Live distribution should provide
 everything needed.
 
 All four templates build with LuaLaTeX (via latexmk -lualatex). The text
-fonts are Libertinus Serif and TeX Gyre Heros, both provided by
+fonts are EB Garamond (provided by texlive-fonts-extra) and TeX Gyre
-texlive-fonts-extra.
+Heros.
 
 ================================
 === Accessibility ==============

letter_template/text.tex

@@ -10,15 +10,7 @@
 % (-- => en-dash, --- => em-dash, `` and '' => curly quotes), so
 % re-enable them globally for every font loaded below.
 \defaultfontfeatures{Ligatures=TeX}
-\setmainfont{Libertinus Serif}
+\setmainfont{EB Garamond}
-% Mako prefers Adobe Garamond Premier Pro
-% (https://fonts.adobe.com/fonts/garamond-premier-pro). It is a
-% commercial font and is not redistributable, so the templates default
-% to the free Libertinus Serif above. If you have the font installed
-% (e.g., dropped into ~/.fonts/), comment the line above and uncomment
-% the next one. CDSC members can contact Mako (mako@atdot.cc) for the
-% font files.
-% \setmainfont{Garamond Premier Pro}
 \setsansfont{TeX Gyre Heros}
 
 \usepackage[letterpaper,left=1.3in,right=1.3in,top=0.8in,bottom=0.8in]{geometry}

memo_template/text.tex

@@ -18,15 +18,7 @@
 % (-- => en-dash, --- => em-dash, `` and '' => curly quotes), so
 % re-enable them globally for every font loaded below.
 \defaultfontfeatures{Ligatures=TeX}
-\setmainfont{Libertinus Serif}
+\setmainfont{EB Garamond}
-% Mako prefers Adobe Garamond Premier Pro
-% (https://fonts.adobe.com/fonts/garamond-premier-pro). It is a
-% commercial font and is not redistributable, so the templates default
-% to the free Libertinus Serif above. If you have the font installed
-% (e.g., dropped into ~/.fonts/), comment the line above and uncomment
-% the next one. CDSC members can contact Mako (mako@atdot.cc) for the
-% font files.
-% \setmainfont{Garamond Premier Pro}
 \setsansfont{TeX Gyre Heros}
 
 \usepackage[letterpaper,left=1.65in,right=1.65in,top=1.3in,bottom=1.2in]{geometry}

paper_template/.gitignore

@@ -13,3 +13,5 @@
 /*.ttt
 /*.bcf
 /*.run.xml
+/figures/*
+/*.tex

paper_template/Makefile

@@ -1,13 +1,11 @@
 #!/usr/bin/make
 
-all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
+all: $(patsubst %.Rtex,%.pdf,$(wildcard *.Rtex)) 
 
-# use the following section for Rnw/knitr documents
+%.tex: %.Rtex
-# all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
+	Rscript -e "library(knitr); knit('$<')"
-# %.tex: %.Rnw
-#	Rscript -e "library(knitr); knit('$<')"
 
-%.pdf: %.tex 
+%.pdf: %.tex
 	latexmk -f -lualatex $<
 
 clean: 
@@ -15,9 +13,9 @@ clean:
 	rm -f *.tmp *.run.xml
 	rm -f vc
 	rm -f *.bbl
-	# the following lines are useful for Rnw/knitr
+	# the following lines are useful for Rtex/knitr
-	# rm -rf cache/ figure/
+	rm -rf cache/ figure/
-	# rm -f *.tex
+	rm -f *.tex
 
 viewpdf: all
 	evince *.pdf
@@ -27,4 +25,4 @@ vc:	resources/vc-git
 pdf: all
 
 .PHONY: clean all
-# .PRECIOUS: %.tex
+.PRECIOUS: %.tex

paper_template/resources/preamble.R

@@ -0,0 +1,50 @@
+bold <- function(x) {paste('{\\textbf{',x,'}}', sep ='')}
+gray <- function(x) {paste('{\\textcolor{gray}{',x,'}}', sep ='')}
+wrapify <- function (x) {paste("{", x, "}", sep="")}
+
+# load("knitr_data.RData"); now broken up into small files so we'll bring 'em all in together
+r <- do.call("c", lapply(paste("knitr_rdata/", list.files("knitr_rdata"), sep=""),
+                         function (x) {load(x); return(r)}))
+
+attach(r)
+
+f <- function (x) {formatC(x, format="d", big.mark=',')}
+
+format.percent <- function(x) {paste(f(x*100),"\\%",sep='')}
+
+format.day.ordinal <- function(x) {
+    day <- format(x,format="%d")
+    daylast <- substr(day,nchar(day),nchar(day))
+    dayfirst <- substr(day,1,1)
+    if(dayfirst == '0')
+        day = daylast
+
+    if( daylast == "1")
+        day <- paste0(day,"st")
+    else if(daylast == "2")
+        day <- paste0(day,"nd")
+    else if (daylast == "3")
+        day <- paste0(day,"rd")
+    else
+        day <- paste0(day,"th")
+        
+    return(day)
+}
+
+format.month <- function(x){
+    return( format(x,format='%B %Y'))
+}
+
+format.date <- function(x) {
+    return(paste(format(x,format = '%B'),format.day.ordinal(x),format(x,format='%Y'),sep=' '))
+}
+
+format.pvalue <- function (x, digits=3) {
+    threshold <- 1*10^(-1*digits)
+    x <- round(x, digits)
+    if (x < threshold) {
+        return(paste("p<", threshold, sep=""))
+    } else {
+        return(paste("p=", x, sep=""))
+    }
+}

paper_template/text.Rtex

@@ -13,20 +13,23 @@
 \usepackage{tagpdf}
 \tagpdfsetup{activate-all}
 
+<<init, echo=FALSE>>=
+knit_hooks$set(document = function(x) {
+  x <- sub('\\usepackage[]{xcolor}',
+           '\\usepackage[dvipsnames]{xcolor}', x, fixed = TRUE)
+  x
+})
+opts_chunk$set(fig.path="figures/knitr-")
+
+source("resources/preamble.R")
+@
+
 \usepackage{fontspec}
 % fontspec disables the classic TeX input ligatures by default
 % (-- => en-dash, --- => em-dash, `` and '' => curly quotes), so
 % re-enable them globally for every font loaded below.
 \defaultfontfeatures{Ligatures=TeX}
-\setmainfont{Libertinus Serif}
+\setmainfont{EB Garamond}
-% Mako prefers Adobe Garamond Premier Pro
-% (https://fonts.adobe.com/fonts/garamond-premier-pro). It is a
-% commercial font and is not redistributable, so the templates default
-% to the free Libertinus Serif above. If you have the font installed
-% (e.g., dropped into ~/.fonts/), comment the line above and uncomment
-% the next one. CDSC members can contact Mako (mako@atdot.cc) for the
-% font files.
-% \setmainfont{Garamond Premier Pro}
 \setsansfont{TeX Gyre Heros}
 \usepackage{wrapfig}
 
@@ -62,7 +65,7 @@
 \makeatother
 \newcommand*\samethanks[1][\value{footnote}]{\footnotemark[#1]}
 
-% add bibliographic stuff 
+% add bibliographic stuff
 \usepackage[american]{babel}
 \usepackage{csquotes}
 \usepackage[natbib=true, style=apa, backend=biber]{biblatex}
@@ -125,7 +128,7 @@ fox jumps over the lazy dog.
 % between 45-90 characters and a rule of thumb for typesetting is that you
 % should be able to fit between 2-3 alphabets on one line.  Generally speaking,
 % the shorter the line length, the better -- and the smaller the linespacing
-% can become.  The following line is 3 alphabets (73 characters). 
+% can become.  The following line is 3 alphabets (73 characters).
 
 abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyz
 
@@ -145,45 +148,14 @@ brown fox jumps over the lazy dog.  The quick brown fox jumps over the
 lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
 fox jumps over the lazy dog \citep{989866}.
 
-The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
+\begin{table}
-over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
+  \centering
-quick brown fox jumps over the lazy dog.  The quick brown fox jumps over
+<<test_table, echo=FALSE>>=
-the lazy dog.  The quick brown fox jumps over the lazy dog.  The quick
+kable(form.copy, format="latex")
-brown fox jumps over the lazy dog.  The quick brown fox jumps over the
+@
-lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
+\caption{This is a test table. There are \Sexpr{f(nrow(form.copy))} rows in the table.}
-fox jumps over the lazy dog \citep{989866}.
+\label{tab:test}
-
+\end{table}
-The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
-over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
-quick brown fox jumps over the lazy dog.  The quick brown fox jumps over
-the lazy dog.  The quick brown fox jumps over the lazy dog.  The quick
-brown fox jumps over the lazy dog.  The quick brown fox jumps over the
-lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
-fox jumps over the lazy dog \citep{989866}.
-
-The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
-over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
-quick brown fox jumps over the lazy dog.  The quick brown fox jumps over
-the lazy dog.  The quick brown fox jumps over the lazy dog.  The quick
-brown fox jumps over the lazy dog.  The quick brown fox jumps over the
-lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
-fox jumps over the lazy dog \citep{989866}.
-
-The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
-over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
-quick brown fox jumps over the lazy dog.  The quick brown fox jumps over
-the lazy dog.  The quick brown fox jumps over the lazy dog.  The quick
-brown fox jumps over the lazy dog.  The quick brown fox jumps over the
-lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
-fox jumps over the lazy dog \citep{989866}.
-
-The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
-over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
-quick brown fox jumps over the lazy dog.  The quick brown fox jumps over
-the lazy dog.  The quick brown fox jumps over the lazy dog.  The quick
-brown fox jumps over the lazy dog.  The quick brown fox jumps over the
-lazy dog.  The quick brown fox jumps over the lazy dog.  The quick brown
-fox jumps over the lazy dog \citep{989866}.
 
 The quick brown fox jumps over the lazy dog.  The quick brown fox jumps
 over the lazy dog.  The quick brown fox jumps over the lazy dog.  The
@@ -208,4 +180,4 @@ fox jumps over the lazy dog \citep{989866}.
 
 \end{document}
 
-%  LocalWords:  
+%  LocalWords: