[Lme4-commits] r1789 - in testing: . figures lme4 lme4/Meta lme4/R lme4/data lme4/doc lme4/help lme4/html old
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 3 16:03:38 CEST 2012
Author: bbolker
Date: 2012-10-03 16:03:37 +0200 (Wed, 03 Oct 2012)
New Revision: 1789
Added:
testing/Bacteria.Rnw
testing/Bacteria.Rnw~
testing/Bacteria.aux
testing/Bacteria.log
testing/Bacteria.pdf
testing/Bacteria.sed
testing/Bacteria.sed~
testing/Bacteria.tex
testing/Bacteria_glmmADMB.R
testing/Bacteria_glmmADMB.RData
testing/Bacteria_glmmML.R
testing/Bacteria_glmmML.RData
testing/Bacteria_glmmML.Rout
testing/Bacteria_glmmadmb.Rout
testing/Bacteria_lme4.0.R
testing/Bacteria_lme4.0.RData
testing/Bacteria_lme4.0.Rout
testing/Bacteria_lme4_NM.R
testing/Bacteria_lme4_NM.RData
testing/Bacteria_lme4_NM.Rout
testing/Bacteria_lme4_bobyqa.R
testing/Bacteria_lme4_bobyqa.RData
testing/Bacteria_lme4_bobyqa.Rout
testing/Cbpp.R
testing/Cbpp.Rnw
testing/Cbpp.Rnw~
testing/Cbpp.aux
testing/Cbpp.log
testing/Cbpp.pdf
testing/Cbpp.sed
testing/Cbpp.sed~
testing/Cbpp.tex
testing/CbppObs_lme4.R
testing/CbppObs_lme4.Rout
testing/CbppObs_lme4e_bobyqa.R
testing/CbppObs_lme4e_bobyqa.RData
testing/CbppObs_lme4e_bobyqa.Rout
testing/Cbpp_2012_02_02.pdf
testing/Cbpp_DEF.txt
testing/Cbpp_all.R
testing/Cbpp_all.Rnw
testing/Cbpp_glmmADMB.R
testing/Cbpp_glmmADMB.RData
testing/Cbpp_glmmADMB.Rout
testing/Cbpp_glmmML.R
testing/Cbpp_glmmML.RData
testing/Cbpp_glmmML.Rout
testing/Cbpp_lme4.0.R
testing/Cbpp_lme4.0.RData
testing/Cbpp_lme4.0.Rout
testing/Cbpp_lme4.R
testing/Cbpp_lme4.RData
testing/Cbpp_lme4.Rout
testing/Cbpp_lme4_NM.R
testing/Cbpp_lme4_NM.RData
testing/Cbpp_lme4_NM.Rout
testing/Cbpp_lme4_bobyqa.R
testing/Cbpp_lme4_bobyqa.RData
testing/Cbpp_lme4_bobyqa.Rout
testing/Cbpp_lme4e_NM.R
testing/Cbpp_lme4e_NM.RData
testing/Cbpp_lme4e_NM.Rout
testing/Cbpp_lme4e_bobyqa.R
testing/Cbpp_lme4e_bobyqa.RData
testing/Coalition_glmmADMB.R
testing/Coalition_glmmADMB.RData
testing/Coalition_lme4.R
testing/Coalition_lme4e_NM.R
testing/Coalition_lme4e_NM.RData
testing/Contraception-allplot.pdf
testing/Contraception-lme4eNM.pdf
testing/Contraception.Rnw
testing/Contraception.aux
testing/Contraception.log
testing/Contraception.pdf
testing/Contraception.tex
testing/Contraception_NM.R
testing/Contraception_NM.Rout
testing/Contraception_allpkg.R
testing/Contraception_analysis.R
testing/Contraception_bobyqa.R
testing/Contraception_bobyqa.Rout
testing/Contraception_glmmADMB.R
testing/Contraception_glmmADMB.RData
testing/Contraception_glmmADMB.Rout
testing/Contraception_glmmML.R
testing/Contraception_glmmML.RData
testing/Contraception_glmmML.Rout
testing/Contraception_junk.R
testing/Contraception_lme4.R
testing/Contraception_lme4.RData
testing/Contraception_lme4.Rout
testing/Contraception_lme4a.R
testing/Contraception_lme4a.RData
testing/Contraception_lme4a.Rout
testing/Contraception_lme4e_NM.R
testing/Contraception_lme4e_NM.RData
testing/Contraception_lme4e_NM.Rout
testing/Contraception_lme4e_bobyqa.R
testing/Contraception_lme4e_bobyqa.RData
testing/Contraception_lme4e_bobyqa.Rout
testing/Contraception_other.R
testing/GEN.Rnw
testing/GEN.Rnw~
testing/GEN_glmmADMB.R
testing/GEN_glmmML.R
testing/GEN_lme4.0.R
testing/GEN_lme4_NM.R
testing/GEN_lme4_bobyqa.R
testing/Generic_glmmADMB.R
testing/Generic_glmmML.R
testing/Generic_lme4.0.R
testing/Generic_lme4.R
testing/Generic_lme4_NM.R
testing/Generic_lme4a.R
testing/Generic_lme4e.R
testing/Generic_lme4e_NM.R
testing/InstEval_lme4e_NM.R
testing/Makefile
testing/NM_tolpwrss_vs_deviance.pdf
testing/RData
testing/README
testing/Rplots.pdf
testing/SNapply.R
testing/agqtest1.pdf
testing/agqtest2.pdf
testing/agqvec.R
testing/agqvec.Rout
testing/agqvec.R~
testing/anal1.R
testing/bobyqa1.R
testing/bobyqa1.RData
testing/bobyqa1_plot.pdf
testing/bobyqa1_prof.RData
testing/bobyqa_Contraception.R
testing/bobyqa_cbpp.R
testing/bobyqa_cbpp.RData
testing/bobyqa_cbpp.Rout
testing/bobyqa_coalition2.R
testing/bobyqa_coalition2.RData
testing/bobyqa_coalition2.Rout
testing/bobyqa_gen.R
testing/bobyqa_problem1.R
testing/bobyqa_prof.R
testing/coalition2.R
testing/delisle_forest.R
testing/donnesR_min.csv
testing/figures/
testing/figures/Bacteria-allplot.pdf
testing/figures/Bacteria-allplot2.pdf
testing/figures/Bacteria-lme4-NM.pdf
testing/figures/Bacteria-lme4-bobyqa.pdf
testing/figures/Cbpp-allplot.pdf
testing/figures/Cbpp-allplot2.pdf
testing/figures/Cbpp-lme4-NM.pdf
testing/figures/Cbpp-lme4-bobyqa.pdf
testing/figures/Cbpp-lme4e-NM.pdf
testing/figures/Cbpp-lme4e-bobyqa.pdf
testing/figures/Cbpp-unnamed-chunk-4.pdf
testing/figures/Cbpp-unnamed-chunk-5.pdf
testing/figures/Cbpp-unnamed-chunk-8.pdf
testing/figures/Contraception-Contraception-allplot.pdf
testing/figures/Contraception-Contraception-allplot2.pdf
testing/figures/Contraception-lme4e-NM.pdf
testing/figures/Contraception-lme4e-bobyqa.pdf
testing/genmake.R
testing/lme4/
testing/lme4/DESCRIPTION
testing/lme4/INDEX
testing/lme4/Meta/
testing/lme4/Meta/Rd.rds
testing/lme4/Meta/data.rds
testing/lme4/Meta/hsearch.rds
testing/lme4/Meta/links.rds
testing/lme4/Meta/nsInfo.rds
testing/lme4/Meta/package.rds
testing/lme4/Meta/vignette.rds
testing/lme4/NAMESPACE
testing/lme4/NEWS
testing/lme4/R/
testing/lme4/R/lme4
testing/lme4/R/lme4.rdb
testing/lme4/R/lme4.rdx
testing/lme4/data/
testing/lme4/data/Rdata.rdb
testing/lme4/data/Rdata.rds
testing/lme4/data/Rdata.rdx
testing/lme4/doc/
testing/lme4/doc/Doxyfile
testing/lme4/doc/Implementation.R
testing/lme4/doc/Implementation.Rnw
testing/lme4/doc/Implementation.pdf
testing/lme4/doc/PLSvGLS.R
testing/lme4/doc/PLSvGLS.Rnw
testing/lme4/doc/PLSvGLS.pdf
testing/lme4/doc/Theory.R
testing/lme4/doc/Theory.Rnw
testing/lme4/doc/Theory.pdf
testing/lme4/doc/index.html
testing/lme4/doc/lme4.bib
testing/lme4/help/
testing/lme4/help/AnIndex
testing/lme4/help/aliases.rds
testing/lme4/help/lme4.rdb
testing/lme4/help/lme4.rdx
testing/lme4/help/paths.rds
testing/lme4/html/
testing/lme4/html/00Index.html
testing/lme4/html/R.css
testing/lme4/libs/
testing/lme4Eigen_NM_out1.pdf
testing/methodtab.R
testing/miscfuns.R
testing/miscfuns_new.R
testing/mkgen
testing/old/
testing/old/Contraception.R
testing/old/Contraception1.RData
testing/old/Contraception_junk.R
testing/optimxcbpp.R
testing/profile.R
testing/search.csv
testing/slice.R
testing/testcbpp.R
testing/tmp1.pdf
testing/unnamed-chunk-4.pdf
testing/unnamed-chunk-5.pdf
testing/unnamed-chunk-8.pdf
testing/unnamed-chunk-9.pdf
testing/westfall.R
testing/westfall.RData
testing/westfall_splom.png
testing/xapply.R
Log:
dump!
Added: testing/Bacteria.Rnw
===================================================================
--- testing/Bacteria.Rnw (rev 0)
+++ testing/Bacteria.Rnw 2012-10-03 14:03:37 UTC (rev 1789)
@@ -0,0 +1,158 @@
+\documentclass{article}
+\newcommand{\code}[1]{{\tt #1}}
+
+\begin{document}
+%% Sweave/knitr options
+ %\textwidth,
+\SweaveOpts{
+ fig.width=8,fig.height=5,out.width="0.8\\textwidth",
+ fig.align="center",tidy=FALSE,echo=FALSE,
+ fig.path="figures/Bacteria-"}
+<<echo=FALSE,message=FALSE>>=
+## stuff for making pretty PDFs -- **ignore** if running
+## interactively ...
+if (require(knitr)) {
+ knit_hooks$set(fig=function(before, options, envir) {
+ if (before) {
+ par(bty="l",las=1)
+ } else { }
+ })}
+## messes up font metrics, too much trouble
+## olddev <- options(device = function(...) {
+## .Call("R_GD_nullDevice", PACKAGE = "grDevices")
+## })
+require(ggplot2)
+require(grid)
+zmargin <- opts(panel.margin=unit(0,"lines"))
+theme_update(theme_bw())
+@
+
+<<>>=
+prob <- "Bacteria"
+@
+
+<<>>=
+source("anal1.R")
+library(plyr)
+library(reshape2)
+library(ggplot2)
+@
+
+Get data:
+<<>>=
+dfiles <- list.files(pattern=paste(prob,"_.*.RData",sep=""))
+LL <- lapply(dfiles,getdat)
+names(LL) <- gsub(paste(prob,"_([^.]+)\\.RData",sep=""),
+ "\\1",dfiles)
+@
+
+\section{lme4}
+
+\subsection{Nelder-Mead}
+
+Performance as a function of \code{tolPwrss}, \code{nAGQ}:
+
+<<lme4-NM,echo=FALSE>>=
+dd2 <- LL$lme4_NM
+dd2$logtolpwrss <- log10(dd2$tolPwrss)
+dd2B <- ddply(dd2,.(nAGQ),
+ function(x) {
+ transform(x,scdeviance=(deviance-min(deviance))/diff(range(deviance)))
+ })
+dd2B$logtime <- log10(dd2B$time)
+mm <- melt(subset(dd2B,select=c(scdeviance,
+ deviance,logtolpwrss,logtime,nAGQ)),
+ id.var=c("logtolpwrss","nAGQ"))
+(gg1 <- ggplot(mm,aes(x=logtolpwrss,y=value,colour=factor(nAGQ)))+
+ geom_line(aes(group=nAGQ))+
+ facet_grid(variable~.,scale="free")+zmargin)
+@
+
+
+\subsection{bobyqa}
+
+Performance as a function of tolPwrss, rho-beg, rho-end:
+
+FIXME: better format!
+
+<<lme4-bobyqa>>=
+dd <- LL$lme4_bobyqa
+dd$logtolPwrss <- log10(dd$tolPwrss)
+g0 <- ggplot(dd,aes(x=factor(log10(rhobeg/2)),
+ y=factor(log10(rhoend/2)),colour=deviance))+
+ geom_point(aes(size=time),alpha=0.8)+
+ facet_wrap(~logtolPwrss)+
+ theme_bw()+zmargin+
+ ## scale_size_continuous(limits=c(0.01,20),to=c(0.5,6))+
+ labs(x=expression(paste("Start tol ",(log[10](rho/2)))),
+ y=expression(paste("End tol ",(log[10](rho/2)))))
+g0 %+% subset(dd,deviance<2384)
+@
+
+\section{Comparison of all approaches}
+
+\code{lme4} uses default settings here
+(\code{tolPwrss}=1e-11, \code{rhobeg}=2e-4, \code{rhoend=2e-7}).
+
+<<>>=
+## fix up Var-corr names
+## FIXME: works only for single-
+LL2 <- lapply(LL,function(x) {
+ names(x)[grep("^VarCorr",names(x))] <- "VarCorr"
+ x
+})
+@
+<<eval=FALSE>>=
+sapply(LL,ncol)
+lapply(LL2,colnames)
+@
+<<>>=
+allframe <- Rbind(LL2)
+## with(allframe,table(rhobeg,rhoend,tolPwrss))
+## want to get only DEFAULT tolPwrss/rhobeg/rhoend settings
+NMnondefault <- with(allframe,
+ pkg=="lme4" & method=="NelderMead" & tolPwrss!=1e-10)
+bobyqanondefault <- with(allframe,
+ pkg=="lme4" & method=="bobyqa" &
+ (tolPwrss!=1e-10 | rhobeg!=2e-4 | abs(rhoend/2e-7-1)>1e-3))
+t1 <- with(allframe,as.data.frame(table(nAGQ,pkg,method)))
+## t1[t1$Freq>0,]
+a2 <- subset(allframe,!(pkg=="lme4" & (tolPwrss!=1e-10 |
+ (!is.na(rhobeg) & rhobeg!=2e-4) |
+ (!is.na(rhoend) & abs(rhoend/2e-7-1)>1e-4))))
+## with(a2,table(method,pkg))
+a2$logtime <- log10(a2$time)
+m2 <- melt(subset(a2,
+ select=c(pkg,method,nAGQ,deviance,
+ logtime,
+ fixef..Intercept.,fixef.trtdrug,fixef.trtdrug.,fixef.I.week...2.TRUE,
+ VarCorr)),
+ id.var=c("pkg","method","nAGQ"))
+@
+
+<<eval=FALSE>>=
+## testing stuff for fig sizes
+pddev <- function(w=8,h=5) pdf("tmp1.pdf",width=w,height=h)
+pddev(10,5)
+gg2
+dev.off()
+@
+<<allplot,warning=FALSE>>=
+m2 <- transform(m2,Method=droplevels(interaction(pkg,method)))
+(gg2 <- ggplot(m2,aes(x=factor(nAGQ),y=value,
+ colour=Method,shape=Method))+
+ facet_wrap(~variable,scale="free")+
+ geom_point(alpha=0.5)+
+ geom_line(aes(x=as.numeric(factor(nAGQ)))))
+@
+
+Without \code{lme4.0}:
+<<allplot2,warning=FALSE>>=
+gg2 %+% subset(m2,pkg!="lme4.0")
+@
+
+<<>>=
+## options(device=olddev$device)
+@
+\end{document}
+
Added: testing/Bacteria.Rnw~
===================================================================
--- testing/Bacteria.Rnw~ (rev 0)
+++ testing/Bacteria.Rnw~ 2012-10-03 14:03:37 UTC (rev 1789)
@@ -0,0 +1,158 @@
+\documentclass{article}
+\newcommand{\code}[1]{{\tt #1}}
+
+\begin{document}
+%% Sweave/knitr options
+ %\textwidth,
+\SweaveOpts{
+ fig.width=8,fig.height=5,out.width="0.8\\textwidth",
+ fig.align="center",tidy=FALSE,echo=FALSE,
+ fig.path="figures/Bacteria-"}
+<<echo=FALSE,message=FALSE>>=
+## stuff for making pretty PDFs -- **ignore** if running
+## interactively ...
+if (require(knitr)) {
+ knit_hooks$set(fig=function(before, options, envir) {
+ if (before) {
+ par(bty="l",las=1)
+ } else { }
+ })}
+## messes up font metrics, too much trouble
+## olddev <- options(device = function(...) {
+## .Call("R_GD_nullDevice", PACKAGE = "grDevices")
+## })
+require(ggplot2)
+require(grid)
+zmargin <- opts(panel.margin=unit(0,"lines"))
+theme_update(theme_bw())
+@
+
+<<>>=
+prob <- "Bacteria"
+@
+
+<<>>=
+source("anal1.R")
+library(plyr)
+library(reshape2)
+library(ggplot2)
+@
+
+Get data:
+<<>>=
+dfiles <- list.files(pattern=paste(prob,"_.*.RData",sep=""))
+LL <- lapply(dfiles,getdat)
+names(LL) <- gsub(paste(prob,"_([^.]+)\\.RData",sep=""),
+ "\\1",dfiles)
+@
+
+\section{lme4}
+
+\subsection{Nelder-Mead}
+
+Performance as a function of \code{tolPwrss}, \code{nAGQ}:
+
+<<lme4-NM,echo=FALSE>>=
+dd2 <- LL$lme4_NM
+dd2$logtolpwrss <- log10(dd2$tolPwrss)
+dd2B <- ddply(dd2,.(nAGQ),
+ function(x) {
+ transform(x,scdeviance=(deviance-min(deviance))/diff(range(deviance)))
+ })
+dd2B$logtime <- log10(dd2B$time)
+mm <- melt(subset(dd2B,select=c(scdeviance,
+ deviance,logtolpwrss,logtime,nAGQ)),
+ id.var=c("logtolpwrss","nAGQ"))
+(gg1 <- ggplot(mm,aes(x=logtolpwrss,y=value,colour=factor(nAGQ)))+
+ geom_line(aes(group=nAGQ))+
+ facet_grid(variable~.,scale="free")+zmargin)
+@
+
+
+\subsection{bobyqa}
+
+Performance as a function of tolPwrss, rho-beg, rho-end:
+
+FIXME: better format!
+
+<<lme4-bobyqa>>=
+dd <- LL$lme4_bobyqa
+dd$logtolPwrss <- log10(dd$tolPwrss)
+g0 <- ggplot(dd,aes(x=factor(log10(rhobeg/2)),
+ y=factor(log10(rhoend/2)),colour=deviance))+
+ geom_point(aes(size=time),alpha=0.8)+
+ facet_wrap(~logtolPwrss)+
+ theme_bw()+zmargin+
+ ## scale_size_continuous(limits=c(0.01,20),to=c(0.5,6))+
+ labs(x=expression(paste("Start tol ",(log[10](rho/2)))),
+ y=expression(paste("End tol ",(log[10](rho/2)))))
+g0 %+% subset(dd,deviance<2384)
+@
+
+\section{Comparison of all approaches}
+
+\code{lme4} uses default settings here
+(\code{tolPwrss}=1e-11, \code{rhobeg}=2e-4, \code{rhoend=2e-7}).
+
+<<>>=
+## fix up Var-corr names
+## FIXME: works only for single-
+LL2 <- lapply(LL,function(x) {
+ names(x)[grep("^VarCorr",names(x))] <- "VarCorr"
+ x
+})
+@
+<<eval=FALSE>>=
+sapply(LL,ncol)
+lapply(LL2,colnames)
+@
+<<>>=
+allframe <- Rbind(LL2)
+## with(allframe,table(rhobeg,rhoend,tolPwrss))
+## want to get only DEFAULT tolPwrss/rhobeg/rhoend settings
+NMnondefault <- with(allframe,
+ pkg=="lme4" & method=="NelderMead" & tolPwrss!=1e-10)
+bobyqanondefault <- with(allframe,
+ pkg=="lme4" & method=="bobyqa" &
+ (tolPwrss!=1e-10 | rhobeg!=2e-4 | abs(rhoend/2e-7-1)>1e-3))
+t1 <- with(allframe,as.data.frame(table(nAGQ,pkg,method)))
+## t1[t1$Freq>0,]
+a2 <- subset(allframe,!(pkg=="lme4" & (tolPwrss!=1e-10 |
+ (!is.na(rhobeg) & rhobeg!=2e-4) |
+ (!is.na(rhoend) & abs(rhoend/2e-7-1)>1e-4))))
+## with(a2,table(method,pkg))
+a2$logtime <- log10(a2$time)
+m2 <- melt(subset(a2,
+ select=c(pkg,method,nAGQ,deviance,
+ logtime,
+ fixef..Intercept.,fixef.trtdrug,fixef.trtdrug.,fixef.I.week...2.TRUE,
+ VarCorr)),
+ id.var=c("pkg","method","nAGQ"))
+@
+
+<<eval=FALSE>>=
+## testing stuff for fig sizes
+pddev <- function(w=8,h=5) pdf("tmp1.pdf",width=w,height=h)
+pddev(10,5)
+gg2
+dev.off()
+@
+<<allplot,warning=FALSE>>=
+m2 <- transform(m2,Method=droplevels(interaction(pkg,method)))
+(gg2 <- ggplot(m2,aes(x=factor(nAGQ),y=value,
+ colour=Method,shape=Method)+
+ facet_wrap(~variable,scale="free")+
+ geom_point(alpha=0.5)+
+ geom_line(aes(x=as.numeric(factor(nAGQ)))))
+@
+
+Without \code{lme4.0}:
+<<allplot2,warning=FALSE>>=
+gg2 %+% subset(m2,pkg!="lme4.0")
+@
+
+<<>>=
+## options(device=olddev$device)
+@
+\end{document}
+
Added: testing/Bacteria.aux
===================================================================
--- testing/Bacteria.aux (rev 0)
+++ testing/Bacteria.aux 2012-10-03 14:03:37 UTC (rev 1789)
@@ -0,0 +1,5 @@
+\relax
+\@writefile{toc}{\contentsline {section}{\numberline {1}lme4}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Nelder-Mead}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}bobyqa}{1}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Comparison of all approaches}{1}}
Added: testing/Bacteria.log
===================================================================
--- testing/Bacteria.log (rev 0)
+++ testing/Bacteria.log 2012-10-03 14:03:37 UTC (rev 1789)
@@ -0,0 +1,278 @@
+This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2011.4.5) 11 APR 2012 12:52
+entering extended mode
+ %&-line parsing enabled.
+**Bacteria
+(./Bacteria.tex
+LaTeX2e <2009/09/24>
+Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
+yphenation, loaded.
+(/usr/share/texmf-texlive/tex/latex/base/article.cls
+Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
+(/usr/share/texmf-texlive/tex/latex/base/size10.clo
+File: size10.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
+)
+\c at part=\count79
+\c at section=\count80
+\c at subsection=\count81
+\c at subsubsection=\count82
+\c at paragraph=\count83
+\c at subparagraph=\count84
+\c at figure=\count85
+\c at table=\count86
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+)
+(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
+Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV at toks@=\toks14
+)
+(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
+Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
+
+(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty
+Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
+)
+(/etc/texmf/tex/latex/config/graphics.cfg
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+s/FAMILY/"binomial"/g
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+s/RESPONSE/y/g
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Added: testing/Bacteria.sed~
===================================================================
--- testing/Bacteria.sed~ (rev 0)
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@@ -0,0 +1,13 @@
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+## substitute DATNAME before NAME, FIXFORM/RANFORM before FORM, ..
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+s/FIXNAMES/ /g
+s/NAME/Bacteria/g
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+\setbox\hlLargeboxopenbrace=\hbox{\begin{Large}\verb.{.\end{Large}}%
+\setbox\hlLargeboxclosebrace=\hbox{\begin{Large}\verb.}.\end{Large}}%
+\setbox\hlLargeboxlessthan=\hbox{\begin{Large}\verb.<.\end{Large}}%
+\setbox\hlLargeboxdollar=\hbox{\begin{Large}\verb.$.\end{Large}}%
+\setbox\hlLargeboxunderscore=\hbox{\begin{Large}\verb._.\end{Large}}%
+\setbox\hlLargeboxand=\hbox{\begin{Large}\verb.&.\end{Large}}%
+\setbox\hlLargeboxhash=\hbox{\begin{Large}\verb.#.\end{Large}}%
+\setbox\hlLargeboxat=\hbox{\begin{Large}\verb. at .\end{Large}}%
+\setbox\hlLargeboxbackslash=\hbox{\begin{Large}\verb.\.\end{Large}}%
+\setbox\hlLargeboxgreaterthan=\hbox{\begin{Large}\verb.>.\end{Large}}%
+\setbox\hlLargeboxpercent=\hbox{\begin{Large}\verb.%.\end{Large}}%
+\setbox\hlLargeboxhat=\hbox{\begin{Large}\verb.^.\end{Large}}%
+\setbox\hlLargeboxsinglequote=\hbox{\begin{Large}\verb.'.\end{Large}}%
+\setbox\hlLargeboxbacktick=\hbox{\begin{Large}\verb.`.\end{Large}}%
+\setbox\hlLargeboxhat=\hbox{\begin{Large}\verb.^.\end{Large}}%
+
+
+
+\newsavebox{\hlLARGEboxclosebrace}%
+\newsavebox{\hlLARGEboxopenbrace}%
+\newsavebox{\hlLARGEboxbackslash}%
+\newsavebox{\hlLARGEboxlessthan}%
+\newsavebox{\hlLARGEboxgreaterthan}%
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/lme4 -r 1789
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