diff --git a/DESCRIPTION b/DESCRIPTION index c4fa6217c..3a867f600 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,6 +28,7 @@ Authors@R: c( person("Dominik", "Leutnant", role = c("aut", "cph"), email = "leutnant@fh-muenster.de"), person(family = "MDPI", role = c("aut", "cph")), person("Oğuzhan", "Öğreden", role = c("aut"), comment = c(ORCID = "0000-0002-9949-3348")), + person("Dalton", "Hance", role = c("aut"), email = "dhance@usgs.gov"), person("Daniel", "Nüst", role = c("aut", "cph"), email = "daniel.nuest@uni-muenster.de", comment = c(ORCID = "0000-0002-0024-5046")) ) Description: A suite of custom R Markdown formats and templates for diff --git a/NAMESPACE b/NAMESPACE index f771ceff0..8a5aca5df 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -6,6 +6,7 @@ export(aea_article) export(amq_article) export(ams_article) export(asa_article) +export(biometrics_article) export(copernicus_article) export(copernicus_journal_abbreviations) export(ctex) diff --git a/NEWS b/NEWS index 5516d9e4b..81685b3b7 100644 --- a/NEWS +++ b/NEWS @@ -3,6 +3,8 @@ rticles 0.6 (unreleased) - Added the template for the SAGE Journals (thanks, @oguzhanogreden, #181). +- Added the template for Biometrics (thanks, @daltonhance, #170). + - Added the template for Copernicus Publications journals (thanks, @nuest, #172). - Supports syntax highlighting in the `ieee_article()` and `acm_article()` formats (thanks, @rainer-rq-koelle, #182). diff --git a/R/biometrics_article.R b/R/biometrics_article.R new file mode 100644 index 000000000..38b49510c --- /dev/null +++ b/R/biometrics_article.R @@ -0,0 +1,21 @@ +#' Biometrics Journal format. +#' +#' This format was adapted from the Biometrics Macro package. +#' +#' +#' @inheritParams rmarkdown::pdf_document +#' @param ... Arguments to \code{rmarkdown::pdf_document} +#' @return R Markdown output format to pass to \code{\link[rmarkdown:render]{render}} +#' @examples +#' \dontrun{ +#' rmarkdown::draft("MyArticle.Rmd", template = "biometrics_article", package = "rticles") +#' } +#' +#' @export +biometrics_article <- function(..., keep_tex = TRUE, citation_package = 'natbib'){ + template <- find_resource("biometrics_article", "template.tex") + inherit_pdf_document(template = template, + keep_tex = keep_tex, + citation_package = citation_package, + ...) +} diff --git a/README.md b/README.md index 988e41d35..cc95abbb3 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,8 @@ The **rticles** package provides a suite of custom [R Markdown](http://rmarkdown - [AMS](https://www.ametsoc.org/) articles +- [Biometrics](http://www.biometrics.tibs.org/) articles + - [Bulletin de l'AMQ](https://www.amq.math.ca/bulletin/) journal submissions - [CTeX](http://ctex.org) documents diff --git a/inst/rmarkdown/templates/biometrics_article/resources/template.tex b/inst/rmarkdown/templates/biometrics_article/resources/template.tex new file mode 100644 index 000000000..b1d41afa6 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/resources/template.tex @@ -0,0 +1,101 @@ +\documentclass[useAMS,usenatbib$if(referee)$,referee$endif$]{biom} +%\documentclass[useAMS,usenatbib,referee]{biom} +% +% +% Papers submitted to Biometrics should ALWAYS be prepared +% using the referee option!!!! +% +% +% If your system does not have the AMS fonts version 2.0 installed, then +% remove the useAMS option. +% +% useAMS allows you to obtain upright Greek characters. +% e.g. \umu, \upi etc. See the section on "Upright Greek characters" in +% this guide for further information. +% +% If you are using AMS 2.0 fonts, bold math letters/symbols are available +% at a larger range of sizes for NFSS release 1 and 2 (using \boldmath or +% preferably \bmath). +% +% The usenatbib command allows the use of Patrick Daly's natbib package for +% cross-referencing. +% +% If you wish to typeset the paper in Times font (if you do not have the +% PostScript Type 1 Computer Modern fonts you will need to do this to get +% smoother fonts in a PDF file) then uncomment the next line +% \usepackage{Times} +%%%%% AUTHORS - PLACE YOUR OWN MACROS HERE %%%%% + +\usepackage[figuresright]{rotating} +\usepackage{tikz} +\usepackage{amsmath} +\usepackage[hyphens]{url} % not crucial - just used below for the URL +\usepackage{hyperref} +\usepackage[utf8]{inputenc} +\usepackage{graphicx} +\usepackage{longtable} +\usepackage{booktabs} +%% \raggedbottom % To avoid glue in typesetteing, sbs>> + +$if(highlighting-macros)$ +$highlighting-macros$ +$endif$ + +% tightlist command for lists without linebreak +\providecommand{\tightlist}{% + \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\setcounter{footnote}{2} + +\title[$header$]{$title$} + +\author{$for(author)$ $author.name$ \email{$author.email$} \\ $author.affiliation$ $sep$ \and + $endfor$ + } + +\begin{document} + +\date{{\it Received $month$} $year$} + +\pagerange{\pageref{firstpage}--\pageref{lastpage}} \pubyear{$year$} + +\volume{0} +\artmonth{January} +\doi{0000-0000-0000} + +% This label and the label ``lastpage'' are used by the \pagerange +% command above to give the page range for the article + +\label{firstpage} + +% pub the summary here + +\begin{abstract} +$abstract$ +\end{abstract} + +% +% Please place your key words in alphabetical order, separated +% by semicolons, with the first letter of the first word capitalized, +% and a period at the end of the list. +% + +\begin{keywords} +$keywords$. +\end{keywords} + +\maketitle + +$body$ + +$if(natbib)$ + +\bibliographystyle{biom} +\bibliography{$bibliography$} + +$endif$ + +\label{lastpage} + +\end{document} diff --git a/inst/rmarkdown/templates/biometrics_article/skeleton/bibliography.bib b/inst/rmarkdown/templates/biometrics_article/skeleton/bibliography.bib new file mode 100644 index 000000000..f302a8115 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/skeleton/bibliography.bib @@ -0,0 +1,66 @@ +%% This BibTeX bibliography file was created using BibDesk. +%% http://bibdesk.sourceforge.net/ + + +%% Created for Sachs, Michael (NIH/NCI) [E] at 2014-10-27 13:53:44 -0400 + + +%% Saved with string encoding Unicode (UTF-8) + + + +@book{pepe2003statistical, + Author = {Pepe, Margaret Sullivan}, + Date-Added = {2014-10-27 17:28:41 +0000}, + Date-Modified = {2014-10-27 17:53:38 +0000}, + Publisher = {Oxford University Press}, + Title = {The statistical evaluation of medical tests for classification and prediction}, + Year = {2003}} + +@article{hoerl1970ridge, + Author = {Hoerl, Arthur E and Kennard, Robert W}, + Date-Added = {2014-10-27 17:28:25 +0000}, + Date-Modified = {2014-10-27 17:28:25 +0000}, + Journal = {Technometrics}, + Number = {1}, + Pages = {55--67}, + Publisher = {Taylor \& Francis Group}, + Title = {Ridge regression: Biased estimation for nonorthogonal problems}, + Volume = {12}, + Year = {1970}} + +@article{zou2005regularization, + Author = {Zou, Hui and Hastie, Trevor}, + Date-Added = {2014-10-27 17:28:23 +0000}, + Date-Modified = {2014-10-27 17:28:23 +0000}, + Journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, + Number = {2}, + Pages = {301--320}, + Publisher = {Blackwell Publishing Ltd}, + Title = {Regularization and variable selection via the elastic net}, + Volume = {67}, + Year = {2005}} + +@article{schoenfeld1982partial, + Author = {Schoenfeld, David}, + Date-Added = {2014-10-27 17:28:09 +0000}, + Date-Modified = {2014-10-27 17:28:09 +0000}, + Journal = {Biometrika}, + Number = {1}, + Pages = {239--241}, + Publisher = {Oxford University Press}, + Title = {Partial residuals for the proportional hazards regression model}, + Volume = {69}, + Year = {1982}} + +@article{heagerty2000time, + Author = {Heagerty, Patrick J and Lumley, Thomas and Pepe, Margaret S}, + Date-Added = {2014-10-27 17:28:02 +0000}, + Date-Modified = {2014-10-27 17:28:02 +0000}, + Journal = {Biometrics}, + Number = {2}, + Pages = {337--344}, + Publisher = {Blackwell Publishing Ltd}, + Title = {Time-dependent ROC curves for censored survival data and a diagnostic marker}, + Volume = {56}, + Year = {2000}} diff --git a/inst/rmarkdown/templates/biometrics_article/skeleton/biom.bst b/inst/rmarkdown/templates/biometrics_article/skeleton/biom.bst new file mode 100644 index 000000000..c89f77a66 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/skeleton/biom.bst @@ -0,0 +1,1109 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% +%% Author : Aptara +%% Created On : Fri Apr 20 14:44:07 2007 +%% Last Modified By: +%% Last Modified On: +%% Version : 0.1 +%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%% +ENTRY + { address + author + booktitle + chapter + edition + editor + howpublished + institution + journal + key + note + number + organization + pages + publisher + school + series + title + type + volume + year + } + {} + { label extra.label sort.label } + +INTEGERS { output.state before.all mid.sentence after.sentence after.block } + +FUNCTION {init.state.consts} +{ #0 'before.all := + #1 'mid.sentence := + #2 'after.sentence := + #3 'after.block := +} + +STRINGS { s t } + +FUNCTION {output.nonnull} +{ + swap$ + output.state mid.sentence = + { ", " * write$ } + { output.state after.block = + { add.period$ write$ + newline$ + "\newblock " write$ + } + { output.state before.all = + 'write$ + { add.period$ " " * write$ } + if$ + } + if$ + mid.sentence 'output.state := + } + if$ +} + +FUNCTION {output} +{ duplicate$ empty$ + 'pop$ + 'output.nonnull + if$ +} + +FUNCTION {output.check} +{ 't := + duplicate$ empty$ + { pop$ "empty " t * " in " * cite$ * warning$ } + 'output.nonnull + if$ +} + +FUNCTION {output.year.check} +{ year empty$ + { "empty year in " cite$ * warning$ } + { write$ + " (" year * extra.label * ")" * + mid.sentence 'output.state := + } + if$ +} + +FUNCTION {output.bibitem} +{ newline$ + "\bibitem[" write$ + label write$ + "]{" write$ + cite$ write$ + "}" write$ + newline$ + "" + before.all 'output.state := +} + +FUNCTION {fin.entry} +{ add.period$ + write$ + newline$ +} + +FUNCTION {new.block} +{ output.state before.all = + 'skip$ + { after.block 'output.state := } + if$ +} + +FUNCTION {new.sentence} +{ output.state after.block = + 'skip$ + { output.state before.all = + 'skip$ + { after.sentence 'output.state := } + if$ + } + if$ +} + +FUNCTION {not} +{ { #0 } + { #1 } + if$ +} + +FUNCTION {and} +{ 'skip$ + { pop$ #0 } + if$ +} + +FUNCTION {or} +{ { pop$ #1 } + 'skip$ + if$ +} + +FUNCTION {new.block.checkb} +{ empty$ + swap$ empty$ + and + 'skip$ + 'new.block + if$ +} + +FUNCTION {field.or.null} +{ duplicate$ empty$ + { pop$ "" } + 'skip$ + if$ +} + +FUNCTION {emphasize} +{ duplicate$ empty$ + { pop$ "" } + { "{\em " swap$ * "}" * } + if$ +} + +FUNCTION {smallcapsify} +{ duplicate$ empty$ + { pop$ "" } + { "{\sc " swap$ * "}" * } + if$ +} + +FUNCTION {embolden} +{ duplicate$ empty$ + { pop$ "" } + { "{\bf " swap$ * ",}" * } + if$ +} + +INTEGERS { nameptr namesleft numnames } + +FUNCTION {format.names} +{ 's := + #1 'nameptr := + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't := + nameptr #1 > + { namesleft #1 > + { ", " * t * } + { numnames #2 > + { "," * } + 'skip$ + if$ + t "others" = + { " et~al." * } + { " and " * t * } + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ +} + +FUNCTION {format.lab.names2} +{ 's := + #1 'nameptr := + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { s nameptr "{vv~}{ll}{, jj.}" format.name$ 't := + nameptr #1 > + { namesleft #1 > + { ", " * t * } + { numnames #2 > + 'skip$ + 'skip$ + if$ + t "others" = + { " et~al." * } + { " and " * t * } + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ +} + +FUNCTION {format.authors} +{ author empty$ + { "" } + { author format.names } + if$ +} + +FUNCTION {format.key} +{ empty$ + { key field.or.null } + { "" } + if$ +} + +FUNCTION {format.editors} +{ editor empty$ + { "" } + { editor format.names + editor num.names$ #1 > + { ", editors" * } + { ", editor" * } + if$ + } + if$ +} + +FUNCTION {format.title} +{ title empty$ + { "" } + { title "t" change.case$ } + if$ +} + +FUNCTION {n.dashify} +{ 't := + "" + { t empty$ not } + { t #1 #1 substring$ "-" = + { t #1 #2 substring$ "--" = not + { "--" * + t #2 global.max$ substring$ 't := + } + { { t #1 #1 substring$ "-" = } + { "-" * + t #2 global.max$ substring$ 't := + } + while$ + } + if$ + } + { t #1 #1 substring$ * + t #2 global.max$ substring$ 't := + } + if$ + } + while$ +} + +FUNCTION {format.btitle} +{ title emphasize +} + +FUNCTION {tie.or.space.connect} +{ duplicate$ text.length$ #3 < + { "~" } + { " " } + if$ + swap$ * * +} + +FUNCTION {either.or.check} +{ empty$ + 'pop$ + { "can't use both " swap$ * " fields in " * cite$ * warning$ } + if$ +} + +FUNCTION {format.bvolume} +{ volume empty$ + { "" } + { "volume" volume tie.or.space.connect + series empty$ + 'skip$ + { " of " * series emphasize * } + if$ + "volume and number" number either.or.check + } + if$ +} + +FUNCTION {format.number.series} +{ volume empty$ + { number empty$ + { series field.or.null } + { output.state mid.sentence = + { "number" } + { "Number" } + if$ + number tie.or.space.connect + series empty$ + { "there's a number but no series in " cite$ * warning$ } + { " in " * series * } + if$ + } + if$ + } + { "" } + if$ +} + +FUNCTION {format.edition} +{ edition empty$ + { "" } + { output.state mid.sentence = + { edition "l" change.case$ " edition" * } + { edition "t" change.case$ " edition" * } + if$ + } + if$ +} + +INTEGERS { multiresult } + +FUNCTION {multi.page.check} +{ 't := + #0 'multiresult := + { multiresult not + t empty$ not + and + } + { t #1 #1 substring$ + duplicate$ "-" = + swap$ duplicate$ "," = + swap$ "+" = + or or + { #1 'multiresult := } + { t #2 global.max$ substring$ 't := } + if$ + } + while$ + multiresult +} + +FUNCTION {format.pages} +{ pages empty$ + { "" } + { pages multi.page.check + { "pages" pages n.dashify tie.or.space.connect } + { "page" pages tie.or.space.connect } + if$ + } + if$ +} + +FUNCTION {format.vol.num.pages} +{ volume field.or.null embolden + pages empty$ + 'skip$ + { duplicate$ empty$ + { pop$ format.pages } + { " " * pages n.dashify * } + if$ + } + if$ +} + +FUNCTION {format.chapter.pages} +{ chapter empty$ + 'format.pages + { type empty$ + { "chapter" } + { type "l" change.case$ } + if$ + chapter tie.or.space.connect + pages empty$ + 'skip$ + { ", " * format.pages * } + if$ + } + if$ +} + +FUNCTION {format.in.ed.booktitle} +{ booktitle empty$ + { "" } + { editor empty$ + { "In " booktitle emphasize * } + { "In " format.editors * ", " * booktitle emphasize * } + if$ + } + if$ +} + +FUNCTION {format.thesis.type} +{ type empty$ + 'skip$ + { pop$ + type "t" change.case$ + } + if$ +} + +FUNCTION {format.tr.number} +{ type empty$ + { "Technical Report" } + 'type + if$ + number empty$ + { "t" change.case$ } + { number tie.or.space.connect } + if$ +} + +FUNCTION {format.article.crossref} +{ "In" + " \cite{" * crossref * "}" * +} + +FUNCTION {format.book.crossref} +{ volume empty$ + { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ + "In " + } + { "Volume" volume tie.or.space.connect + " of " * + } + if$ + "\cite{" * crossref * "}" * +} + +FUNCTION {format.incoll.inproc.crossref} +{ "In" + " \cite{" * crossref * "}" * +} + +FUNCTION {article} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + crossref missing$ + { journal emphasize " " * "journal" output.check + format.vol.num.pages + before.all 'output.state := + output + } + { format.article.crossref output.nonnull + format.pages output + } + if$ + new.block + note output + fin.entry +} + +FUNCTION {book} +{ output.bibitem + author empty$ + { format.editors "author and editor" output.check + editor format.key output + } + { format.authors output.nonnull + crossref missing$ + { "author and editor" editor either.or.check } + 'skip$ + if$ + } + if$ + output.year.check + new.block + format.btitle "title" output.check + crossref missing$ + { format.bvolume output + new.block + format.number.series output + new.sentence + publisher "publisher" output.check + address output + } + { new.block + format.book.crossref output.nonnull + } + if$ + format.edition output + new.block + note output + fin.entry +} + +FUNCTION {booklet} +{ output.bibitem + format.authors output + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + howpublished output + address output + new.block + note output + fin.entry +} + +FUNCTION {inbook} +{ output.bibitem + author empty$ + { format.editors "author and editor" output.check + editor format.key output + } + { format.authors output.nonnull + crossref missing$ + { "author and editor" editor either.or.check } + 'skip$ + if$ + } + if$ + output.year.check + new.block + format.btitle "title" output.check + crossref missing$ + { format.bvolume output + format.chapter.pages "chapter and pages" output.check + new.block + format.number.series output + new.sentence + publisher "publisher" output.check + address output + } + { format.chapter.pages "chapter and pages" output.check + new.block + format.book.crossref output.nonnull + } + if$ + format.edition output + new.block + note output + fin.entry +} + +FUNCTION {incollection} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + crossref missing$ + { format.in.ed.booktitle "booktitle" output.check + format.bvolume output + format.number.series output + format.chapter.pages output + new.sentence + publisher "publisher" output.check + address output + format.edition output + } + { format.incoll.inproc.crossref output.nonnull + format.chapter.pages output + } + if$ + new.block + note output + fin.entry +} + +FUNCTION {inproceedings} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + crossref missing$ + { format.in.ed.booktitle "booktitle" output.check + format.bvolume output + format.number.series output + format.pages output + address output + new.sentence + organization output + publisher output + } + { format.incoll.inproc.crossref output.nonnull + format.pages output + } + if$ + new.block + note output + fin.entry +} + +FUNCTION {conference} { inproceedings } + +FUNCTION {manual} +{ output.bibitem + format.authors output + author format.key output + output.year.check + new.block + format.btitle "title" output.check + organization address new.block.checkb + organization output + address output + format.edition output + new.block + note output + fin.entry +} + +FUNCTION {mastersthesis} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + "Master's thesis" format.thesis.type output.nonnull + school "school" output.check + address output + new.block + note output + fin.entry +} + +FUNCTION {misc} +{ output.bibitem + format.authors output + author format.key output + output.year.check + new.block + format.title output + new.block + howpublished output + new.block + note output + fin.entry +} + +FUNCTION {phdthesis} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.btitle "title" output.check + new.block + "PhD thesis" format.thesis.type output.nonnull + school "school" output.check + address output + new.block + note output + fin.entry +} + +FUNCTION {proceedings} +{ output.bibitem + format.editors output + editor format.key output + output.year.check + new.block + format.btitle "title" output.check + format.bvolume output + format.number.series output + address output + new.sentence + organization output + publisher output + new.block + note output + fin.entry +} + +FUNCTION {techreport} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + format.tr.number output.nonnull + institution "institution" output.check + address output + new.block + note output + fin.entry +} + +FUNCTION {unpublished} +{ output.bibitem + format.authors "author" output.check + author format.key output + output.year.check + new.block + format.title "title" output.check + new.block + note "note" output.check + fin.entry +} + +FUNCTION {default.type} { misc } + +MACRO {ajs} {"Australian Journal of Statistics"} +MACRO {annpr} {"Annals of Probability"} +MACRO {annst} {"Annals of Statistics"} +MACRO {anzjs} {"Australian and New Zealand Journal of Statistics"} +MACRO {appst} {"Applied Statistics"} +MACRO {bcs} {"Biometrics"} +MACRO {bj} {"Biometrical Journal"} +MACRO {bka} {"Biometrika"} +MACRO {bs} {"Bayesian Statistics"} +MACRO {cjs} {"Canadian Journal of Statistics"} +MACRO {csa} {"Communications in Statistics, A"} +MACRO {csb} {"Communications in Statistics, B"} +MACRO {csc} {"Communications in Statistics, C"} +MACRO {econ} {"Econometrica"} +MACRO {isr} {"International Statistics Review"} +MACRO {jabes} {"Journal of Agricultural, Biological, and Environmental Statistics"} +MACRO {jasa} {"Journal of the American Statistical Association"} +MACRO {jma} {"Journal of Multivariate Analysis"} +MACRO {jqt} {"Journal of Quality Technology"} +MACRO {jrssa} {"Journal of the Royal Statistical Society, Series A"} +MACRO {jrssb} {"Journal of the Royal Statistical Society, Series B"} +MACRO {jscs} {"Journal of Statistical Computation and Simulation"} +MACRO {sim} {"Statistics in Medicine"} +MACRO {sjs} {"Scandinavian Journal of Statistics"} +MACRO {ss} {"Statistical Science"} +MACRO {stat} {"Statistics"} +MACRO {tas} {"The American Statistician"} +MACRO {tcs} {"Technometrics"} +MACRO {thestat} {"The Statistician"} +MACRO {risi} {"Review of the International Statistics Institute"} + +MACRO {jan} {"January"} +MACRO {feb} {"February"} +MACRO {mar} {"March"} +MACRO {apr} {"April"} +MACRO {may} {"May"} +MACRO {jun} {"June"} +MACRO {jul} {"July"} +MACRO {aug} {"August"} +MACRO {sep} {"September"} +MACRO {oct} {"October"} +MACRO {nov} {"November"} +MACRO {dec} {"December"} + +READ + +FUNCTION {sortify} +{ purify$ + "l" change.case$ +} + +INTEGERS { len } + +FUNCTION {chop.word} +{ 's := + 'len := + s #1 len substring$ = + { s len #1 + global.max$ substring$ } + 's + if$ +} + +FUNCTION {format.lab.names} +{ 's := + s #1 "{vv~}{ll}" format.name$ + s num.names$ duplicate$ + #2 > + { pop$ " et~al." * } + { #2 < + 'skip$ + { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = + { " et~al." * } + { " and " * s #2 "{vv~}{ll}" format.name$ * } + if$ + } + if$ + } + if$ +} + +FUNCTION {author.key.label} +{ author empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { author format.lab.names } + if$ +} + +FUNCTION {author.editor.key.label} +{ author empty$ + { editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.lab.names } + if$ + } + { author format.lab.names } + if$ +} + +FUNCTION {editor.key.label} +{ editor empty$ + { key empty$ + { cite$ #1 #3 substring$ } + 'key + if$ + } + { editor format.lab.names } + if$ +} + +FUNCTION {my.full.label} +{ 's := + #1 'nameptr := % nameptr = 1; + s num.names$ 'numnames := % numnames = num.name$(s); + numnames 'namesleft := + { namesleft #0 > } + + { s nameptr "{vv~}{ll}" format.name$ 't := % get the next name + nameptr #1 > + { namesleft #1 > + { ", " * t * } + { numnames #2 > + { "," * } + 'skip$ + if$ + t "others" = + { " et~al\mbox{.}" * } % jrh: avoid spacing problems + { " and " * t * } % from Chicago Manual of Style + if$ + } + if$ + } + 't + if$ + nameptr #1 + 'nameptr := % nameptr += 1; + namesleft #1 - 'namesleft := % namesleft =- 1; + } + while$ + +} + +FUNCTION {calc.label} +{ type$ "book" = + type$ "inbook" = + or + 'author.editor.key.label + { type$ "proceedings" = + 'editor.key.label + 'author.key.label + if$ + } + if$ + "\protect\citeauthoryear{" author my.full.label * "}{" * swap$ * "}{" +% "\protect\citeauthoryear{" author format.lab.names * "}{" * swap$ * "}{" +% "\protect\citeauthoryear{" format.authors * "}{" * swap$ * "}{" +% "\protect\citeauthoryear{" swap$ * "}{" + * + year field.or.null purify$ #-1 #4 substring$ + * + 'label := +} + +FUNCTION {sort.format.names} +{ 's := + #1 'nameptr := + "" + s num.names$ 'numnames := + numnames 'namesleft := + { namesleft #0 > } + { nameptr #1 > + { " " * } + 'skip$ + if$ + s nameptr "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" format.name$ 't := + nameptr numnames = t "others" = and + { "et al" * } + { t sortify * } + if$ + nameptr #1 + 'nameptr := + namesleft #1 - 'namesleft := + } + while$ +} + +FUNCTION {sort.format.title} +{ 't := + "A " #2 + "An " #3 + "The " #4 t chop.word + chop.word + chop.word + sortify + #1 global.max$ substring$ +} + +FUNCTION {author.sort} +{ author empty$ + { key empty$ + { "to sort, need author or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { author sort.format.names } + if$ +} + +FUNCTION {author.editor.sort} +{ author empty$ + { editor empty$ + { key empty$ + { "to sort, need author, editor, or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { editor sort.format.names } + if$ + } + { author sort.format.names } + if$ +} + +FUNCTION {editor.sort} +{ editor empty$ + { key empty$ + { "to sort, need editor or key in " cite$ * warning$ + "" + } + { key sortify } + if$ + } + { editor sort.format.names } + if$ +} + +FUNCTION {presort} +{ calc.label + label sortify + " " + * + type$ "book" = + type$ "inbook" = + or + 'author.editor.sort + { type$ "proceedings" = + 'editor.sort + 'author.sort + if$ + } + if$ + #1 entry.max$ substring$ + 'sort.label := + sort.label + * + " " + * + title field.or.null + sort.format.title + * + #1 entry.max$ substring$ + 'sort.key$ := +} + +ITERATE {presort} + +SORT + +STRINGS { last.label next.extra } + +INTEGERS { last.extra.num } + +FUNCTION {initialize.extra.label.stuff} +{ #0 int.to.chr$ 'last.label := + "" 'next.extra := + #0 'last.extra.num := +} + +FUNCTION {forward.pass} +{ last.label label = + { last.extra.num #1 + 'last.extra.num := + last.extra.num int.to.chr$ 'extra.label := + } + { "a" chr.to.int$ 'last.extra.num := + "" 'extra.label := + label 'last.label := + } + if$ +} + +FUNCTION {reverse.pass} +{ next.extra "b" = + { "a" 'extra.label := } + 'skip$ + if$ + label extra.label * "}" * 'label := + extra.label 'next.extra := +} + +EXECUTE {initialize.extra.label.stuff} + +ITERATE {forward.pass} + +REVERSE {reverse.pass} + +FUNCTION {bib.sort.order} +{ sort.label + " " + * + year field.or.null sortify + * + " " + * + title field.or.null + sort.format.title + * + #1 entry.max$ substring$ + 'sort.key$ := +} + +ITERATE {bib.sort.order} + +SORT + +FUNCTION {begin.bib} +{ preamble$ empty$ + 'skip$ + { preamble$ write$ newline$ } + if$ + "\begin{thebibliography}{}" write$ newline$ +} + +EXECUTE {begin.bib} + +EXECUTE {init.state.consts} + +ITERATE {call.type$} + +FUNCTION {end.bib} +{ newline$ + "\end{thebibliography}" write$ newline$ +} + +EXECUTE {end.bib} +%% +%% End of file `biom.bst'. +%% diff --git a/inst/rmarkdown/templates/biometrics_article/skeleton/biom.cls b/inst/rmarkdown/templates/biometrics_article/skeleton/biom.cls new file mode 100644 index 000000000..e03b4150a --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/skeleton/biom.cls @@ -0,0 +1,2080 @@ +% Biom journal document class file +% v1.0 for LaTeX 2e +% +% Copyright (C) The International Biometric Society 2006 +% for LaTeX version 2E, by Techbooks, India +% +% Change history + +% Modified by: Aptara +% Modification date: 27th Dec 2010 +% Modification: \@fptop, \@fpbot, to make compatible with latest rotating.sty + +% Preamble to this style file + +\NeedsTeXFormat{LaTeX2e} +\ProvidesClass{biom}[2006/12/12 v2.2 LaTeX2e Biom document class] + +\def\@version{1.0} +\typeout{Document Style `Biom' v\@version, released 2006 December 12} +% +% Journals use two-sided printing. +% +\@twosidetrue +\@twocolumntrue +\@mparswitchtrue +\def\ds@draft{\overfullrule 5pt} +\def\ds@twocolumn{\@twocolumntrue} +\def\ds@onecolumn{\@twocolumnfalse} + +% letters option +% +\newif\if@letters +\def\ds@letters{\@letterstrue} + +% landscape option +% +\newif\ifSFB@landscape +\def\ds@landscape{\SFB@landscapetrue} + +% galley option +% +\newif\ifSFB@galley +\def\ds@galley{\SFB@galleytrue} + +% usenatbib option +% +\newif\if@usenatbib +\def\ds@usenatbib{\@usenatbibtrue} + +% usedcolumn option +% +\newif\if@usedcolumn +\def\ds@usedcolumn{\@usedcolumntrue} + +% usegraphicx option +\newif\if@usegraphicx +\def\ds@usegraphicx{\@usegraphicxtrue\usepackage[dvips]{graphicx}} + +% referee option +% +\newif\ifSFB@referee +\def\ds@referee{% + \SFB@refereetrue + \@twocolumnfalse +} +\newif\ifdoublesp@cing +\def\ds@doublespacing{% + \doublesp@cingtrue +}% +%%% +%%% NHT: New AMS fonts option +%%% +\newif\ifNHT@useAMS +\def\ds@useAMS{\NHT@useAMStrue} +% +\ifSFB@referee +\ExecuteOptions{letterpaper,twoside,final} +\else +\ExecuteOptions{a4paper,twoside,final} +\fi +\ProcessOptions +% +% **************************************** +% * FONTS * +% **************************************** +% +\lineskip 1pt +\normallineskip 1pt +\ifSFB@referee + \def\baselinestretch{1.8}%1.5} +\else + \ifdoublesp@cing + \def\baselinestretch{2} +\else + \def\baselinestretch{1} +\fi\fi +\if@twocolumn + \renewcommand\normalsize{\@setfontsize\normalsize\@ixpt{11}% + \abovedisplayskip 6pt plus 2pt minus 2pt + \belowdisplayskip \abovedisplayskip + \abovedisplayshortskip 6pt plus 2pt + \belowdisplayshortskip \abovedisplayshortskip + \let\@listi\@listI} + \else + \ifSFB@referee + \renewcommand\normalsize{\@setfontsize\normalsize\@xiipt{14.5}% From size12.clo + \abovedisplayskip 4pt plus 1pt minus 1pt + \belowdisplayskip \abovedisplayskip + \abovedisplayshortskip 4pt plus 1pt + \belowdisplayshortskip \abovedisplayshortskip + \let\@listi\@listI} + \else + \renewcommand\normalsize{\@setfontsize\normalsize\@ixpt{11}% + \abovedisplayskip 4pt plus 1pt minus 1pt + \belowdisplayskip \abovedisplayskip + \abovedisplayshortskip 4pt plus 1pt + \belowdisplayshortskip \abovedisplayshortskip + \let\@listi\@listI} + \fi +\fi +\newcommand\small{\@setfontsize\small\@ixpt{10}% + \abovedisplayskip 4pt plus 1pt minus 1pt + \belowdisplayskip \abovedisplayskip + \abovedisplayshortskip 4pt plus 1pt + \belowdisplayshortskip \abovedisplayshortskip + \def\@listi{\leftmargin\leftmargini + \topsep 2pt plus 1pt minus 1pt + \parsep \z@ + \itemsep 2pt}} +\newcommand\footnotesize{\@setfontsize\footnotesize\@viiipt{9}% + \abovedisplayskip 4pt plus 1pt minus 1pt + \belowdisplayskip \abovedisplayskip + \abovedisplayshortskip 4pt plus 1pt + \belowdisplayshortskip \abovedisplayshortskip + \renewcommand\@listi{\leftmargin\leftmargini + \topsep 2pt plus 1pt minus 1pt + \parsep \z@ + \itemsep 2pt}} +\newcommand\scriptsize{\@setfontsize\scriptsize\@vipt{8}} +\newcommand\tiny{\@setfontsize\tiny\@vpt{6}} +% +\if@twocolumn + \newcommand\large{\@setfontsize\large\@xpt{11}} + \else + \newcommand\large{\@setfontsize\large\@xpt{12}} + \fi +\newcommand\Large{\@setfontsize\Large\@xiipt{14}} +\newcommand\LARGE{\@setfontsize\LARGE\@xivpt{17}} +\newcommand\huge{\@setfontsize\huge\@xviipt{20}} +\newcommand\Huge{\@setfontsize\Huge\@xxpt{25}} +% +\newcommand\sevensize{\@setfontsize\sevensize\@viipt{8}} +% +\normalsize + +%%%%%%%%%%%%%%%%%%%%%%%% Extra Math / Symbol code %%%%%%%%%%%%%%%%%%%%%%%% + + \newcommand{\rmn}[1]{{\mathrm{#1}}} + \newcommand{\itl}[1]{{\mathit{#1}}} + \newcommand{\bld}[1]{{\mathbf{#1}}} + +\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm} +\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf} +\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt} +\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf} +\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit} +\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl} +\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc} +%\DeclareRobustCommand\cal{\@fontswitch{\relax}{\mathcal}} +%\DeclareRobustCommand\mit{\@fontswitch{\relax}{\mathchoice}} +\DeclareRobustCommand*\cal{\@fontswitch\relax\mathcal} +\newcommand{\mit}{\protect\pmit} +\newcommand{\pmit}{\@fontswitch{\relax}{\mathnormal}} +% + +\def\hexnumber#1{\ifcase#1 0\or1\or2\or3\or4\or5\or6\or7% + \or8\or9\or A\or B\or C\or D\or E\or F\fi} + +\def\setboxz@h{\setbox\z@\hbox} +\def\wdz@{\wd\z@} +\def\boxz@{\box\z@} +\def\setbox@ne{\setbox\@ne} +\def\wd@ne{\wd\@ne} + +\def\math@atom#1#2{% + \binrel@{#1}\binrel@@{#2}} +\def\binrel@#1{\setboxz@h{\thinmuskip0mu + \medmuskip\m@ne mu\thickmuskip\@ne mu$#1\m@th$}% + \setbox@ne\hbox{\thinmuskip0mu\medmuskip\m@ne mu\thickmuskip + \@ne mu${}#1{}\m@th$}% + \setbox\tw@\hbox{\hskip\wd@ne\hskip-\wdz@}} +\def\binrel@@#1{\ifdim\wd2<\z@\mathbin{#1}\else\ifdim\wd\tw@>\z@ + \mathrel{#1}\else{#1}\fi\fi} + +% These must be here because \newif and \newtoks are defined \outer. +\newif\iffirstta +\newtoks\math@groups +\newif\ifd@f + + +% Make these do nothing (for backwards compatibility} +\let\loadboldmathitalic=\relax +\let\loadboldgreek=\relax + +% font definitions for NFSS release 2 + +\newcommand{\textbfit}[1]{\textbf{\textit{#1}}} +\newcommand{\mathbfit}[1]{\textbf{\textit{#1}}} +\newcommand{\textbfss}[1]{\textbf{\textsf{#1}}} +\newcommand{\mathbfss}[1]{\textbf{\textsf{#1}}} + + % + \def\mathch{\protect\p@mathch} + \def\p@mathch#1#2{% + \begingroup + \let\@nomath\@gobble \mathversion{#1}% + \math@atom{#2}{% + \mathchoice% + {\hbox{$\m@th\displaystyle#2$}}% + {\hbox{$\m@th\textstyle#2$}}% + {\hbox{$\m@th\scriptstyle#2$}}% + {\hbox{$\m@th\scriptscriptstyle#2$}}}% + \endgroup} + % + \def\bmath{\protect\p@boldm} + \def\p@boldm#1{\mathch{bold}{#1}} +% + + \let\mit=\mathnormal + % + % The following is needed because NFSS release 2 + % does not define the bold + % math symbol font to be available! + % +% + \SetSymbolFont{symbols}{bold}{OMS}{cmsy}{b}{n} + % +% \DeclareSymbolFont{bmisymbols}{OML}{cmm}{b}{it} +% \DeclareMathSymbol{\balpha}{0}{bmisymbols}{"0B} +% \DeclareMathSymbol{\bbeta}{0}{bmisymbols}{"0C} +% \DeclareMathSymbol{\bgamma}{0}{bmisymbols}{"0D} +% \DeclareMathSymbol{\bdelta}{0}{bmisymbols}{"0E} +% \DeclareMathSymbol{\bepsilon}{0}{bmisymbols}{"0F} +% \DeclareMathSymbol{\bzeta}{0}{bmisymbols}{"10} +% \DeclareMathSymbol{\boldeta}{0}{bmisymbols}{"11} +% \DeclareMathSymbol{\btheta}{0}{bmisymbols}{"12} +% \DeclareMathSymbol{\biota}{0}{bmisymbols}{"13} +% \DeclareMathSymbol{\bkappa}{0}{bmisymbols}{"14} +% \DeclareMathSymbol{\blambda}{0}{bmisymbols}{"15} +% \DeclareMathSymbol{\bmu}{0}{bmisymbols}{"16} +% \DeclareMathSymbol{\bnu}{0}{bmisymbols}{"17} +% \DeclareMathSymbol{\bxi}{0}{bmisymbols}{"18} +% \DeclareMathSymbol{\bpi}{0}{bmisymbols}{"19} +% \DeclareMathSymbol{\brho}{0}{bmisymbols}{"1A} +% \DeclareMathSymbol{\bsigma}{0}{bmisymbols}{"1B} +% \DeclareMathSymbol{\btau}{0}{bmisymbols}{"1C} +% \DeclareMathSymbol{\bupsilon}{0}{bmisymbols}{"1D} +% \DeclareMathSymbol{\bphi}{0}{bmisymbols}{"1E} +% \DeclareMathSymbol{\bchi}{0}{bmisymbols}{"1F} +% \DeclareMathSymbol{\bpsi}{0}{bmisymbols}{"20} +% \DeclareMathSymbol{\bomega}{0}{bmisymbols}{"21} +% \DeclareMathSymbol{\bvarepsilon}{0}{bmisymbols}{"22} +% \DeclareMathSymbol{\bvartheta}{0}{bmisymbols}{"23} +% \DeclareMathSymbol{\bvarpi}{0}{bmisymbols}{"24} +% \DeclareMathSymbol{\bvarrho}{0}{bmisymbols}{"25} +% \DeclareMathSymbol{\bvarsigma}{0}{bmisymbols}{"26} +% \DeclareMathSymbol{\bvarphi}{0}{bmisymbols}{"27} + % + +%% Define font shapes for Euler upright Math +\ifNHT@useAMS + \DeclareSymbolFont{UPM}{U}{eur}{m}{n} + \SetSymbolFont{UPM}{bold}{U}{eur}{b}{n} + \DeclareSymbolFont{AMSa}{U}{msa}{m}{n} + \DeclareMathSymbol{\upi}{0}{UPM}{"19} + \DeclareMathSymbol{\umu}{0}{UPM}{"16} + \DeclareMathSymbol{\upartial}{0}{UPM}{"40} + \DeclareMathSymbol{\leqslant}{3}{AMSa}{"36} + \DeclareMathSymbol{\geqslant}{3}{AMSa}{"3E} + \DeclareMathSymbol{\la}{3}{AMSa}{46} + \DeclareMathSymbol{\ga}{3}{AMSa}{38} + % + \let\oldle=\le \let\oldleq=\leq + \let\oldge=\ge \let\oldgeq=\geq + \let\leq=\leqslant \let\le=\leqslant + \let\geq=\geqslant \let\ge=\geqslant + +\else + \newcommand{\upi}{\pi} + \newcommand{\umu}{\mu} + \newcommand{\upartial}{\partial} + \newcommand{\la}{\,\rlap{\raise 0.5ex\hbox{$<$}}{\lower 1.0ex\hbox{$\sim$}}\,} + \newcommand{\ga}{\,\rlap{\raise 0.5ex\hbox{$>$}}{\lower 1.0ex\hbox{$\sim$}}\,} + +\fi + +% Astronomy and Astrophysics symbol macros + +%\newcommand\getsto{\mathrel{\mathchoice {\vcenter{\offinterlineskip +%\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr\gets\cr\to\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr\gets +%\cr\to\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr\gets +%\cr\to\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%\gets\cr\to\cr}}}}} + +%\newcommand\cor{\mathrel{\mathchoice {\hbox{$\widehat=$}}{\hbox{$\widehat=$}} +%{\hbox{$\reset@font\scriptstyle\hat=$}} +%{\hbox{$\reset@font\scriptscriptstyle\hat=$}}}} + +%\newcommand\lid{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr<\cr\noalign{\vskip1.2pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr<\cr +%\noalign{\vskip1.2pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr<\cr +%\noalign{\vskip1pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%<\cr +%\noalign{\vskip0.9pt}=\cr}}}}} + +%\newcommand\gid{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr>\cr\noalign{\vskip1.2pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr>\cr +%\noalign{\vskip1.2pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr>\cr +%\noalign{\vskip1pt}=\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%>\cr +%\noalign{\vskip0.9pt}=\cr}}}}} + +%\newcommand\sol{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr\sim\cr<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr\sim\cr +%<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr\sim\cr +%<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%\sim\cr<\cr}}}}} + +%\newcommand\sog{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr\sim\cr>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr\sim\cr +%>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%\sim\cr>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%\sim\cr>\cr}}}}} + +%\newcommand\lse{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr<\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%<\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%<\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%<\cr\simeq\cr}}}}} + +%\newcommand\gse{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr>\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%>\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%>\cr\simeq\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%>\cr\simeq\cr}}}}} + +%\newcommand\grole{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr>\cr\noalign{\vskip-1.5pt}<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%>\cr\noalign{\vskip-1.5pt}<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%>\cr\noalign{\vskip-1pt}<\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%>\cr\noalign{\vskip-0.5pt}<\cr}}}}} + +%\newcommand\leogr{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr<\cr\noalign{\vskip-1.5pt}>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%<\cr\noalign{\vskip-1.5pt}>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%<\cr\noalign{\vskip-1pt}>\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%<\cr\noalign{\vskip-0.5pt}>\cr}}}}} + +%\newcommand\loa{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr<\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%<\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%<\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%<\cr\approx\cr}}}}} + +%\newcommand\goa{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil +%$\reset@font\displaystyle##$\hfil\cr>\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\textstyle##$\hfil\cr +%>\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptstyle##$\hfil\cr +%>\cr\approx\cr}}} +%{\vcenter{\offinterlineskip\halign{\hfil$\reset@font\scriptscriptstyle##$\hfil\cr +%>\cr\approx\cr}}}}} + +%\newcommand\sun{\hbox{$\odot$}} +%\newcommand\earth{\hbox{$\oplus$}} +%\newcommand\degr{\hbox{$^\circ$}} +%\newcommand\diameter{{\ifmmode\mathchoice +%{\ooalign{\hfil\hbox{$\reset@font\displaystyle/$}\hfil\crcr +%{\hbox{$\reset@font\displaystyle\mathchar"20D$}}}} +%{\ooalign{\hfil\hbox{$\reset@font\textstyle/$}\hfil\crcr +%{\hbox{$\reset@font\textstyle\mathchar"20D$}}}} +%{\ooalign{\hfil\hbox{$\reset@font\scriptstyle/$}\hfil\crcr +%{\hbox{$\reset@font\scriptstyle\mathchar"20D$}}}} +%{\ooalign{\hfil\hbox{$\reset@font\scriptscriptstyle/$}\hfil\crcr +%{\hbox{$\reset@font\scriptscriptstyle\mathchar"20D$}}}} +%\else{\ooalign{\hfil/\hfil\crcr\mathhexbox20D}}% +%\fi}} + +%\newcommand\sq{\ifmmode\squareforqed\else{\unskip\nobreak\hfil +%\penalty50\hskip1em\null\nobreak\hfil\squareforqed +%\parfillskip=0pt\finalhyphendemerits=0\endgraf}\fi} +%\newcommand\squareforqed{\hbox{\rlap{$\sqcap$}$\sqcup$}} + +\newcommand{\romn}[1] {{\mathrm #1}} + +\newcommand\fd{\hbox{$.\!\!^{\reset@font\romn d}$}} +\newcommand\fh{\hbox{$.\!\!^{\reset@font\romn h}$}} +\newcommand\fm{\hbox{$.\!\!^{\reset@font\romn m}$}} +\newcommand\fs{\hbox{$.\!\!^{\reset@font\romn s}$}} +\newcommand\fdg{\hbox{$.\!\!^\circ$}} +\newcommand\farcm{\hbox{$.\mkern-4mu^\prime$}} +\newcommand\farcs{\hbox{$.\!\!^{\prime\prime}$}} +\newcommand\fp{\hbox{$.\!\!^{\reset@font\reset@font\scriptscriptstyle\romn p}$}} +\newcommand\arcmin{\hbox{$^\prime$}} +\newcommand\arcsec{\hbox{$^{\prime\prime}$}} + +\def\micron{\hbox{$\umu$m}} + +%%%Command to produce a box round selected text +%%%NB This is for use in the file mnguide only -- it is NOT +%%% to be used in the journal +\newcommand{\boxit}[1]{% + \noindent\fbox{% + \begin{minipage}[]{84mm}#1\end{minipage} + } +} + +%%%%%%%%%%%%%%%%%%%%% End of Extra Math / Symbol code %%%%%%%%%%%%%%%%%%%%% + +% **************************************** +% * PAGE LAYOUT * +% **************************************** +% +% SIDE MARGINS: +\if@twocolumn + \setlength\oddsidemargin{-2.5pc} + \setlength\evensidemargin{-2.5pc} +\else + \ifSFB@referee +%%%% marie change margins to center with 1 inch margins +% \setlength\oddsidemargin{-0in}%\z@} +% \setlength\evensidemargin{-0in} + \setlength\oddsidemargin{-0.125in}%\z@} + \setlength\evensidemargin{-0.125in} + \else + \setlength\oddsidemargin{-2pc} + \setlength\evensidemargin{-2pc} + \fi +\fi +\setlength\marginparwidth{4pc} +\setlength\marginparsep{0.5pc} + +% VERTICAL SPACING: +%\if@twocolumn +% \setlength\topmargin{-2pc} +%\else +\ifSFB@referee + \setlength\topmargin{-5.1pc}% +\else + \setlength\topmargin{-2.5pc}%\z@} +\fi +\setlength{\headheight}{14pt} +\setlength{\headsep} {21pt} +\setlength{\topskip} {9pt} +\setlength{\footskip} {22pt} %was 26 pt +% +% DIMENSION OF TEXT: % SFB 0.1.01 +% +\newdimen\SFB@measure +\SFB@measure 42pc +% +\setlength\textheight{660pt} +\setlength\textwidth{\SFB@measure} +% +\ifSFB@landscape + \setlength\textwidth{\textheight} + \setlength\textheight{\SFB@measure} +\fi +\ifSFB@referee +%%%% marie modification to get max width with 1 in margins +% \setlength\textwidth{36pc} + \setlength\textwidth{6.5in} +\fi +\setlength\columnsep{1pc} +\setlength\columnseprule{0pt} + +% FOOTNOTES: +\setlength\footnotesep{4pt} +\setlength\skip{\footins 19.5pt plus 12pt minus 1pt} + +% FLOATS: +\setlength\floatsep{ 12pt plus 5.5pt minus 1pt} +\setlength\textfloatsep{ 12pt plus 7.5pt} +\setlength\intextsep{ 12pt plus 5.5pt minus 2pt} +\setlength\dblfloatsep{ 12pt plus 5.5pt minus 2pt } +\setlength\dbltextfloatsep{ 15pt plus 4.5pt minus 3pt} +\setlength\@fptop{ 0pt plus 1fil}% Aptara +\setlength\@fpsep{ 12pt plus 0fil } +\setlength\@fpbot{ 0pt plus 1fil }% Aptara + +\setlength\@dblfptop{ 0pt plus 0fil} +\setlength\@dblfpsep{ 12pt plus 0fil} +\setlength\@dblfpbot{ 0pt plus 0fil} +\setlength\marginparpush{ 5pt } + +% **************************************** +% * PARAGRAPHING * +% **************************************** +% +\newlength{\realparindent} % needed for abstract +\setlength\parskip{ \z@}% plus .1pt } +\setlength\parindent{ 10pt } +\setlength{\realparindent}{\parindent} +\setlength\partopsep{ 0pt plus 1pt } +\@lowpenalty 51 +\@medpenalty 151 +\@highpenalty 301 +\@beginparpenalty -\@lowpenalty +\@endparpenalty -\@lowpenalty +\@itempenalty -\@lowpenalty +\hyphenpenalty=500 +\clubpenalty=0 +\widowpenalty=10000 + +% **************************************** +% * PARTS & SECTIONS NUMBERS * +% **************************************** +% +\newcounter {part} +\newcounter {section} +\newcounter {subsection}[section] +\newcounter {subsubsection}[subsection] +\newcounter {paragraph}[subsubsection] +\newcounter {subparagraph}[paragraph] +\def\thepart {\arabic{part}} +\def\thesection {\arabic{section}} +\def\thesubsection {\thesection.\arabic{subsection}} +\def\thesubsubsection {\thesubsection.\arabic{subsubsection}} +\def\theparagraph {\thesubsubsection.\arabic{paragraph}} +\def\thesubparagraph {\theparagraph.\arabic{subparagraph}} + +%%%Additional material below is from GJI class file +% Sometimes people want to number equations by section, rather than +% sequentially through the whole paper. + +\newcommand\eqsecnum{ + \@newctr{equation}[section] + \def\theequation{\normalsize\mbox{\arabic{section}.\arabic{equation}}}} + +\newcommand\eqsubsecnum{ + \@newctr{equation}[subsection] + \def\theequation{\normalsize% + \mbox{\arabic{section}.\arabic{subsection}.\arabic{equation}}}} + +% **************************************** +% * PARTS * +% **************************************** +% +\def\part{\par \addvspace{4ex}\@afterindentfalse + \secdef\@part\@spart} +\def\@part[#1]#2{\ifnum \c@secnumdepth >\m@ne + \refstepcounter{part} + \addcontentsline{toc}{part}{Part \thepart: #1} + \else \addcontentsline{toc}{part}{#1} + \fi + {\parindent 0pt \raggedright + \ifnum \c@secnumdepth >\m@ne + \reset@font\large\rm PART + \ifcase\thepart \or ONE \or TWO \or THREE \or FOUR \or FIVE + \or SIX \or SEVEN \or EIGHT \or NINE \or TEN \else \fi + \par \nobreak + \fi + \reset@font\LARGE \rm #2 \markboth{}{}\par } + \nobreak \vskip 3ex \@afterheading} +\def\@spart#1{{\parindent 0pt \raggedright + \reset@font\LARGE \rm #1\par} + \nobreak \vskip 3ex \@afterheading} + +% **************************************** +% * SECTIONS * +% **************************************** +% +% \@startsection modified to leave less space before \subsection +% if it immediately follows \section + +% \@startsection {NAME}{LEVEL}{INDENT}{BEFORESKIP}{AFTERSKIP}{STYLE} + +\newif\if@levelone + +\def\@startsection#1#2#3#4#5#6{\if@noskipsec \leavevmode \fi + \par \@tempskipa #4\relax + \@afterindenttrue + \ifnum #2=\@ne % if level=1 ie. section + \global\@levelonetrue + \else + \global\@levelonefalse + \fi + \ifdim \@tempskipa <\z@ \@tempskipa -\@tempskipa \@afterindentfalse\fi + \if@nobreak + \everypar{}\ifnum#2=2 \vskip 0pt plus1pt\fi % was 6pt + \else + \addpenalty{\@secpenalty}\addvspace{\@tempskipa} + \fi \@ifstar + {\@ssect{#3}{#4}{#5}{#6}}{\@dblarg{\@sect{#1}{#2}{#3}{#4}{#5}{#6}}}} + +\def\SFB@hangraggedright{\rightskip=\@flushglue \let\\=\@centercr \parindent=0pt} + +\newif\if@firstsection +\@firstsectiontrue +\def\section{% + \if@firstsection \fixfootnotes\@firstsectionfalse \fi% + \@startsection{section}{1}{\z@} + {-22pt plus -12pt minus -1pt}{\ifbackmatter5.5pt\else2pt\fi} + {\SFB@hangraggedright\reset@font\normalsize\ifbackmatter\fontsize{10}{12}\selectfont\sc\centering\else\bf\raggedright\fi}} +\def\subsection{\@startsection{subsection}{2}{\z@} + {-11pt plus -9pt minus -1pt}{2pt} + {\SFB@hangraggedright\reset@font\normalsize\it\ifbackmatter\centering\else\raggedright\fi}} +\def\subsubsection{\@startsection{subsubsection}{3}{10pt} + {-11pt plus -9pt minus -1pt}{0pt} + {\SFB@hangraggedright\reset@font\normalsize\it}} +\def\paragraph{\@startsection{paragraph}{4}{\parindent} + {0pt}{-0.01em}{\reset@font\normalsize\it}} + +\def\subparagraph{\@startsection{subparagraph}{5}{\parindent} + {12pt plus 2.25pt minus 1pt}{-0.5em}{\reset@font\normalsize\it}} +\setcounter{secnumdepth}{3} % SFB 0.1.01 +% +% \@sect{NAME}{LEVEL}{INDENT}{BEFORESKIP}{AFTERSKIP}{STYLE}[ARG1]{ARG2} +\def\@sect#1#2#3#4#5#6[#7]#8{% + \ifnum #2>\c@secnumdepth + \def\@svsec{}% + \else + \refstepcounter{#1}% + \if@levelone % is it a \section or \section* + \ifSFB@appendix + \edef\@svsec{}% + \else + \edef\@svsec{\csname the#1\endcsname.\hskip .5em}% + \fi + \else + \ifnum#2=1 + \edef\@svsec{\csname the#1\endcsname.\hskip .5em}% + \else + \edef\@svsec{\csname the#1\endcsname\hskip .5em}% + \fi + \fi + \fi + \@tempskipa #5\relax + \ifdim \@tempskipa>\z@ + \begingroup #6\relax + \if@levelone + \ifSFB@appendix + \@hangfrom{\hskip #3\relax\@svsec}{\interlinepenalty \@M + Appendix #8% \csname the#1\endcsname\ifx#8\empty\else:\hskip 0.5em{#8}\fi + \par}% + \else + \@hangfrom{\hskip #3\relax\@svsec}{\interlinepenalty \@M #8\par}% \uppercase + \fi + \else + \@hangfrom{\hskip #3\relax{\rm\@svsec}}{\interlinepenalty \@M #8\par}% + \fi + \endgroup + \csname #1mark\endcsname{#7}% + \addcontentsline{toc}{#1}{\ifnum #2>\c@secnumdepth \else %ajw + \protect\numberline{\csname the#1\endcsname}\fi #7}%ajw + \else + \def\@svsechd{#6\hskip #3{\rm\@svsec}\if@levelone \uppercase{#8}\else #8.\hskip1em\fi% + \csname #1mark\endcsname{#7}% + \addcontentsline{toc}{#1}{\ifnum #2>\c@secnumdepth \else %ajw + \protect\numberline{\csname the#1\endcsname}\fi#7}%ajw + }\fi + \@xsect{#5}} + +% from latex.tex +% \@ssect{INDENT}{BEFORESKIP}{AFTERSKIP}{STYLE}{ARG} +\def\@ssect#1#2#3#4#5{% + \@tempskipa #3\relax + \ifdim \@tempskipa>\z@ + \begingroup #4\@hangfrom{\hskip #1}{% + \interlinepenalty \@M + \if@levelone + {#5}% + \else {#5}% + \fi\par}% + \endgroup + \else + \def\@svsechd{#4\hskip #1\relax + \if@levelone + \uppercase{#5}% + \else {#5}% + \fi} + \fi + \@xsect{#3}% +} + +\newif\ifSFB@appendix +\def\appendix{\par + \if|\@date|\else\vskip10pt{\centering\@date\endgraf}\fi% + \gdef\@date{}% + \SFB@appendixtrue + \@addtoreset{equation}{section} + \@addtoreset{table}{section} + \@addtoreset{figure}{section} + \setcounter{secnumdepth}{0} + \setcounter{section}{0} + \setcounter{equation}{0} + \setcounter{figure}{0} + \setcounter{table}{0} + \def\thesection{\Alph{section}} + \renewcommand\thesubsection{\thesection\arabic{subsection}} + \renewcommand\theequation{A.\thesection\arabic{equation}} +%%% marie get rid of these as quick fix for the endfloat problem +% \renewcommand\thefigure{A.\thesection\@arabic\c@figure} +% \renewcommand\thetable{A.\thesection\@arabic\c@table} +} + +\newcounter{discounter} +\newenvironment{discussion}{\par\addvspace{30pt plus2pt minus1pt}% +\gdef\@email{}% +%%%% + \refstepcounter{discounter} + \setcounter{section}{0} + \setcounter{equation}{0} + \setcounter{figure}{0} + \setcounter{table}{0} +%%%% +}{\Verticalskip\z@\par\addvspace{12pt plus2pt minus1pt}} +% +\newdimen\@topalign\@topalign11pt +\def\topalign#1{\global\advance\@topalign#1} +\def\makediscussionhead{\let\break\endgraf% +\TwoColumn[\hrule width\textwidth height.5pt\vskip12pt% +\ifnum\c@discounter=1\vskip18pt\noindent{\LARGE\bf Discussions}\endgraf\vskip18pt\fi + {\reset@font\large\bf + \begin{tabular}[t]{@{\hskip24pt}p{\columnwidth}@{}}\let\\=\author@nextline\@author + \\ \vspace*{-9pt} \@email\endgraf + \end{tabular} + \endgraf} + \vskip 22pt +]\Verticalskip\@topalign +} +% +\def\@outputpage{% +\begingroup % the \endgroup is put in by \aftergroup + \let \protect \noexpand + \@resetactivechars + \global\let\@@if@newlist\if@newlist + \global\@newlistfalse + \@parboxrestore + \shipout \vbox{% + \set@typeset@protect + \aftergroup \endgroup + \aftergroup \set@typeset@protect + % correct? or just restore by ending + % the group? + \if@specialpage + \global\@specialpagefalse\@nameuse{ps@\@specialstyle}% + \fi + \if@twoside + \ifodd\count\z@ \let\@thehead\@oddhead \let\@thefoot\@oddfoot + \let\@themargin\oddsidemargin + \else \let\@thehead\@evenhead + \let\@thefoot\@evenfoot \let\@themargin\evensidemargin + \fi + \fi + \reset@font + \normalsize + \normalsfcodes + \let\label\@gobble + \let\index\@gobble + \let\glossary\@gobble + \baselineskip\z@skip \lineskip\z@skip \lineskiplimit\z@ + \@begindvi + \vskip \topmargin + \moveright\@themargin \vbox {% + \setbox\@tempboxa \vbox to\headheight{% + \vfil + \color@hbox + \normalcolor + \hb@xt@\textwidth{\@thehead}% + \color@endbox + }% %% 22 Feb 87 + \dp\@tempboxa \z@ + \box\@tempboxa + \vskip \headsep + \box\@outputbox + \baselineskip \footskip + \color@hbox + \normalcolor + \hb@xt@\textwidth{\@thefoot}% + \color@endbox + }% + }% + \global\let\if@newlist\@@if@newlist + \global \@colht \textheight + \stepcounter{page}% + \let\firstmark\botmark +} +% +\newdimen\Verticalskip\Verticalskip\z@ +\def\@outputdblcol{% + \if@firstcolumn + \global \@firstcolumnfalse + \global \setbox\@leftcolumn \box\@outputbox + \ifswitchcols\global\switchcolsfalse + \ifdim\@partialpageht>0pt\advance\@partialpageht\Verticalskip\fi + \vglue\@partialpageht + \fi + \else + \global \@firstcolumntrue + \setbox\@outputbox \vbox {% + \hbox to\textwidth {% + \hbox to\columnwidth {% + \box\@leftcolumn \hss}% + \hfil + \vrule \@width\columnseprule + \hfil + \hbox to\columnwidth {% + \box\@outputbox \hss}% + }% + }% + \@combinedblfloats + \@outputpage + \begingroup + \@dblfloatplacement + \@startdblcolumn + \@whilesw\if@fcolmade \fi + {\@outputpage + \@startdblcolumn}% + \endgroup + \fi +} +% +% +\let\save@clearpage\clearpage +\let\save@outputpage\@outputpage +\newdimen\@partialpageht\@partialpageht10pc +\newif\ifswitchcols +\newbox\store@outputbox +\newdimen\storedboxheight +% +\def\store@outputpage{% + \global\setbox\store@outputbox \vbox to \storedboxheight{% + \leftline{\box\@outputbox}\vss}% + \noindent%\fbox + {\box\store@outputbox}% + \par%\vrule width\textwidth height1pt + \global\let\@outputpage\save@outputpage} +% +\def\balancepage{\@ifnextchar[{\balancecolpagebreak}{\balancecolpagebreak[0pt]}} +\def\balancecolpagebreak[#1]{\ifvmode\vadjust\fi{\vskip-\baselineskip + \leftline{\vrule width\typewidth height\draftrule depth0pt}% + \expandafter\ifdim#1=0pt\vfill\else\vskip#1\fi}\pagebreak} +% +\def\balanceandcontinue{% + \par + \ifdim\pagegoal=\maxdimen + \else + \global\let\@outputpage\store@outputpage + \ifdim\@colht=\pagegoal + \global\storedboxheight\pagetotal + \else + \global\storedboxheight\@colht + \global\advance\storedboxheight-\pagegoal + \global\advance\storedboxheight\pagetotal + \fi + \fi + \onecolumn + \global\switchcolstrue} +% +\def\TwoColumn{\@ifnextchar[{\@TwoColumn}{\@TwoColumn[]}} +\def\@TwoColumn[#1]{% + \balanceandcontinue + \let\clearpage\relax + \def\@tempa{#1}% + \ifx\@tempa\@empty + \twocolumn + \else + #1\global\@partialpageht\pagetotal\twocolumn + \fi + \let\clearpage\save@clearpage +} + +% **************************************** +% * SKIPS * +% **************************************** +% +\newskip\@indentskip +\newskip\smallindent +\newskip\@footindent +\newskip\@leftskip +\@indentskip=18pt +\smallindent=1.5em +\@footindent=\smallindent +\@leftskip=\z@ + +% **************************************** +% * LISTS * +% **************************************** +% +\setlength\leftmargini{ \z@ } +\setlength\leftmarginii{ 1em } +\setlength\leftmarginiii{ 1em } +\setlength\leftmarginiv{ 1em } +\setlength\leftmarginv{ 1pc } +\setlength\leftmarginvi{ 1pc } +\setlength\leftmargin{\leftmargini} +\setlength\labelsep{ 0.5em} +\labelwidth\leftmargini\advance\labelwidth-\labelsep +% +% label macros for Range-Left and Range-Right labels +\def\makeRLlabel#1{\rlap{#1}\hss} +\def\makeRRlabel#1{\hss\llap{#1}} +\def\makenewlabel#1{#1} +% +\def\@listI{\leftmargin\leftmargini + \parsep \z@ + \topsep 6pt plus 1pt minus 1pt + \itemsep \z@ plus .1pt +} +\let\@listi\@listI +\@listi +\def\@listii{\leftmargin\leftmarginii + \topsep 6pt plus 1pt minus 1pt + \parsep \z@ + \itemsep \z@ plus .1pt +} +\def\@listiii{\leftmargin\leftmarginiii + \topsep 6pt plus 1pt minus 1pt + \parsep \z@ + \partopsep \z@ + \itemsep \topsep +} +\def\@listiv{\leftmargin\leftmarginiv +} +\def\@listv{\leftmargin\leftmarginv + \labelwidth\leftmarginv\advance\labelwidth-\labelsep +} +\def\@listvi{\leftmargin\leftmarginvi + \labelwidth\leftmarginvi\advance\labelwidth-\labelsep +} +% +% ITEMIZE +\def\itemize{% + \ifnum \@itemdepth >3 \@toodeep + \else \advance\@itemdepth \@ne + \edef\@itemitem{labelitem\romannumeral\the\@itemdepth}% + \list{\csname\@itemitem\endcsname}% + {\let\makelabel\makeRRlabel}% +% \parindent 1em% +% \leftmargin 3.5em\labelsep 0.5em\itemindent 2.0em\labelwidth 0.5em% + \labelwidth5pt + \labelsep5pt + \leftmargin\z@ + \advance\leftmargin\labelwidth + \advance\leftmargin\labelsep + \leftskip\leftmargin + \fi} +\def\labelitemi{$\bullet$} +\def\labelitemii{--} +\def\labelitemiii{$\cdot$} +\def\labelitemiv{*} +% +% ENUMERATE +% SFB -- enumerate with optional argument to set left margin... +\def\enumerate{\ifnum \@enumdepth >3 \@toodeep \else + \advance\@enumdepth \@ne + \edef\@enumctr{enum\romannumeral\the\@enumdepth}% + \fi + \@ifnextchar [{\@enumeratetwo}{\@enumerateone}% +} +\def\@enumeratetwo[#1]{% + \list{\csname label\@enumctr\endcsname}% + {\settowidth\labelwidth{[#1]} + \leftmargin\z@ + \advance\leftmargin\labelwidth + \advance\leftmargin\labelsep + \listparindent 1em + \usecounter{\@enumctr} + \let\makelabel\makenewlabel} +} +\def\@enumerateone{% + \list{\csname label\@enumctr\endcsname}% + {\usecounter{\@enumctr} + \settowidth\labelwidth{(9)} + \leftmargin\z@ + \advance\leftmargin\labelwidth + \advance\leftmargin\labelsep + \listparindent 1em + \let\makelabel\makenewlabel}} +% +\def\labelenumi{\theenumi} +\def\theenumi{(\arabic{enumi})}% \roman +\def\labelenumii{\theenumii} +\def\theenumii{(\alph{enumii})} +\def\p@enumii{\theenumi} +\def\labelenumiii{\theenumiii} +\def\theenumiii{(\arabic{enumiii})} +\def\p@enumiii{\theenumi(\theenumii)} +\def\labelenumiv{\theenumiv} +\def\theenumiv{(\Alph{enumiv})} +\def\p@enumiv{\p@enumiii\theenumiii} +% +% DESCRIPTION +\def\descriptionlabel#1{\reset@font\bf #1} +\def\description{\list{}{\labelwidth\z@ + \leftmargin 1em + \itemindent -1em +}} +\let\enddescription\endlist + +% **************************************** +% * DISPLAYED TEXT * +% **************************************** +% +% VERSE +\def\verse{\let\\=\@centercr + \list{}{\itemsep\z@ + \itemindent -\@indentskip + \listparindent \itemindent + \rightmargin\leftmargin + \advance\leftmargin \@indentskip}\item[]} +\let\endverse\endlist +% +% QUOTATION +\def\quotation{\list{}{\listparindent \smallindent +% \itemindent\listparindent + \leftmargin\z@\rightmargin\leftmargin + \parsep 0pt plus 1pt}\item[]\reset@font\small} +\let\endquotation=\endlist +% +% QUOTE +\def\quote{\list{}{\leftmargin\z@\rightmargin\leftmargin}\item[]% + \reset@font\small} +\let\endquote=\endlist +% +% BSL QUOTE +\newenvironment{lquote}{\begin{list}{}% + {\setlength{\leftmargin}{2em}} + \item[]} + {\end{list}} +% +% **************************************** +% * OTHER ENVIRONMENTS * +% **************************************** +% +% THEOREM +\def\@begintheorem#1#2{\reset@font\rm \trivlist \item[\hskip \labelsep + {\reset@font\bf #1\ #2.}]} +\def\@opargbegintheorem#1#2#3{\reset@font\rm \trivlist + \item[\hskip \parindent{\reset@font~\bf #1\ #2.\ (#3)}]}% \labelsep +\def\@endtheorem{\endtrivlist} +% +% PROOF +\def\proof{\reset@font\rm \trivlist \item[\hskip \parindent%labelsep + {\reset@font~~\it Proof.}]} +\def\endproof{\hspace*{1em}%{\begin{picture}(6.5,6.5)% +% \put(0,0){\framebox(6.5,6.5){}}\end{picture}} +\endtrivlist} +\@namedef{proof*}{\reset@font\rm \trivlist \item[\hskip \labelsep + {\reset@font\it Proof.}]} +\@namedef{endproof*}{\endtrivlist} +\def\proofbox{\begin{picture}(6.5,6.5)% + \put(0,0){\framebox(6.5,6.5){}}\end{picture}} +% +% TITLEPAGE +\def\titlepage{\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn + \else \newpage \fi \thispagestyle{empty}\c@page\z@} +\def\endtitlepage{\if@restonecol\twocolumn \else \newpage \fi} + +% ARRAY AND TABULAR +% +\arraycolsep 5pt +\tabcolsep 6pt +\arrayrulewidth .5pt +\doublerulesep 1.5pt + +\def\tabular{\def\@halignto{} + \def\Hline{\noalign{\ifnum0=`}\fi + \vskip 3pt + \hrule \@height \arrayrulewidth + \vskip 1.25pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\hline{\noalign{\ifnum0=`}\fi + \vskip 1pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\fullhline{\noalign{\ifnum0=`}\fi + \vskip 3pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\@xhline{\ifx\@tempa\hline + \vskip -6pt + \vskip \doublerulesep + \fi + \ifnum0=`{\fi}} + \def\@arrayrule{\@addtopreamble{\hskip -.5\arrayrulewidth +% \vrule \@width \arrayrulewidth + \hskip .5\arrayrulewidth}} +\centering\@tabular +} +\def\endtabular{\crcr\egroup\egroup $\egroup\par\vspace*{-20pt}} +\expandafter \let \csname endtabular*\endcsname = \endtabular +% TABBING +% +\@namedef{tabular*}#1{% + \def\Hline{\noalign{\ifnum0=`}\fi + \vskip 3pt + \hrule \@height \arrayrulewidth + \vskip 1.25pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\hline{\noalign{\ifnum0=`}\fi + \vskip 1pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\fullhline{\noalign{\ifnum0=`}\fi + \vskip 3pt + \hrule \@height \arrayrulewidth + \vskip 3pt + \futurelet \@tempa\@xhline} + \def\@xhline{\ifx\@tempa\hline + \vskip -6pt + \vskip \doublerulesep + \fi + \ifnum0=`{\fi}} + \def\@arrayrule{\@addtopreamble{\hskip -.5\arrayrulewidth +% \vrule \@width \arrayrulewidth + \hskip .5\arrayrulewidth}} +\centering + \setlength\dimen@{#1}% + \edef\@halignto{to\the\dimen@}\@tabular} +% +\tabbingsep \labelsep + +% MINIPAGE +% +\skip\@mpfootins = \skip\footins + +% FRAMEBOX +% +% Space left between box and text by \fbox and \framebox. +\fboxsep = 3pt +% Width of rules in box made by \fbox and \framebox. +\fboxrule = \arrayrulewidth + +% **************************************** +% * TITLE AND ABSTRACT * +% **************************************** +% +\def\maketitle{\par + \begingroup + \if@twocolumn + \twocolumn[\vspace*{17pt}\@maketitle] + \else + \newpage + \global\@topnum\z@ + \@maketitle + \fi + \thispagestyle{titlepage} + \endgroup + \@thanks + \ifSFB@referee \clearpage\setcounter{page}{1}\fi + \let\maketitle\relax + \let\@maketitle\relax + \gdef\@author{} + \gdef\@title{} + \let\thanks\relax +} +\def\newauthor{% DE's definitions + \ifnum\c@emailcnt=0\else + \printemails\\ + \setcounter{emailcnt}{0} + \fi + \ifnum\c@emailxcnt=0\else + \printemailxs\\ + \setcounter{emailxcnt}{0} + \fi + \end{tabular} + \vskip 24pt\par + \begin{tabular}[t]{@{}c@{}}\let\\=\author@nextline% +} +\def\and{% + \ifnum\c@emailcnt=0\else + \printemails\\ + \setcounter{emailcnt}{0} + \fi + \ifnum\c@emailxcnt=0\else + \printemailxs\\ + \setcounter{emailxcnt}{0} + \fi + \end{tabular} + \vskip 24pt \par{\bf and}\par\vskip 6pt + \begin{tabular}[t]{@{}c@{}}\let\\=\author@nextline% +} +\def\@maketitle{\newpage + \vspace*{23pt} + {\raggedright \sloppy + {\reset@font\Large\centering\bf \@title \par} + \vskip 25pt + {\reset@font\large\centering\bf\mathversion{bold} + \begin{tabular}[t]{@{}c@{}}\let\\=\author@nextline\@author + \ifnum\c@emailcnt=0\else + \printemails + \setcounter{emailcnt}{0} + \fi + \ifnum\c@emailxcnt=0\else + \printemailxs\\ + \setcounter{emailxcnt}{0} + \fi + \end{tabular} + \par} + \vskip 22pt + } %End of DE's definitions + %{\centering\@email\par} + \vskip 25pt + \unvbox\absbox + \vskip 6pt + \unvbox\keywdbox + \vskip 14pt + \par\noindent + \vskip 18pt +} + +\def\noaffil{yes} +\def\YES{yes} +\def\author@nextline{ %DE's definition +\ifx\noaffil\YES +\tabularnewline[4pt] +\gdef\noaffil{no}\else +\tabularnewline[0pt] +\fi\reset@font\ifbackmatter\it\fi\ignorespaces\mathversion{normal}% +\let\\=\author@nextline} %let command added by NT to bring + % subsequent lines into correct format + +\def\thanks#1{\vphantom{\footnotemark} + \protected@xdef\@thanks{\@thanks% + \protect\footnotetext[\the\c@footnote]{#1}}% +} + +% +%\def\abstract{\if@twocolumn +% \start@SFBbox\@abstract +% \else +% \@abstract +% \fi} +%\def\endabstract{\if@twocolumn +% \endlist\finish@SFBbox +% \else +% \endlist +% \fi} +%\def\@abstract{\list{}{% +% \listparindent\realparindent +% \itemindent\z@ +% \labelwidth\z@ \labelsep\z@ +% \leftmargin 11pc\rightmargin\z@ +% \parsep 0pt plus 1pt}\item[]% +% \reset@font\normalsize{\bf ABSTRACT}\\\reset@font\large +%} % SFB 0.1.01 +% + +% 12/28/2010 -- change to make margins of summary same as those of manuscript + +\newbox\absbox +\def\abstract{\global\setbox\absbox\vbox\bgroup\hsize\textwidth\small\leftskip0pc\rightskip\leftskip\noindent{\sc +Summary:\hskip1em}\ignorespaces} +\def\endabstract{\egroup} + +\newbox\keywdbox +\def\keywords{\global\setbox\keywdbox\vbox\bgroup\hsize\textwidth\small\leftskip0pc\rightskip\leftskip\noindent{\sc +Key words:\hskip1em}\ignorespaces} +\def\endkeywords{\egroup} + +%\newif\ifSFB@keywords +%\def\keywords{\if@twocolumn +% \start@SFBbox\@keywords +% \else +% \@keywords +% \fi +%} +%\def\@keywords{\list{}{% +% \labelwidth\z@ \labelsep\z@ +% \leftmargin 11pc\rightmargin\z@ % was 11pc\right.... +% \parsep 0pt plus 1pt}\item[]\reset@font\large{\bf Key words: }% +%} +%\def\endkeywords{\if@twocolumn +% \endlist\addvspace{37pt plus 0.5\baselineskip}\finish@SFBbox +% \else +% \endlist +% \fi +% \@thanks +% \gdef\@thanks{} +% \SFB@keywordstrue +%} +\def\nokeywords{\ifSFB@keywords\else % + \if@twocolumn \start@SFBbox\addvspace{37pt}\finish@SFBbox \fi + \@thanks + \gdef\@thanks{}\fi +} + +\def\author@tabular{\def\@halignto{}\@authortable} +\let\endauthor@tabular=\endtabular +% +\def\author@tabcrone{\vspace{2pt}{\ifnum0=`}\fi% + \@xtabularcr[-7pt]\reset@font\small\it + \let\\=\author@tabcrtwo\ignorespaces} +% +\def\author@tabcrtwo{{\ifnum0=`}\fi\@xtabularcr[-7pt]\reset@font\small\it + \let\\=\author@tabcrtwo\ignorespaces} +% +\def\@authortable{\leavevmode \hbox \bgroup $\let\@acol\@tabacol + \let\@classz\@tabclassz \let\@classiv\@tabclassiv + \let\\=\author@tabcrone\ignorespaces \@tabarray} + +\def\start@SFBbox{\@next\@currbox\@freelist{}{}% + \global\setbox\@currbox + \vbox\bgroup + \hsize \textwidth + \@parboxrestore +} +\def\finish@SFBbox{\par\vskip -\dbltextfloatsep + \egroup + \global\count\@currbox\tw@ + \global\@dbltopnum\@ne + \global\@dbltoproom\maxdimen\@addtodblcol + \global\vsize\@colht + \global\@colroom\@colht +} + +% **************************************** +% * PAGE STYLES * +% **************************************** +% +\mark{{}{}} +\gdef\@author{\mbox{}} +\def\author{\@ifnextchar [{\@authortwo}{\@authorone}} +\def\@authortwo[#1]#2{\gdef\@author{#2}\gdef\@shortauthor{\uppercase{#1}}} +\def\@authorone#1{\gdef\@author{#1}\gdef\@shortauthor{\uppercase{#1}}} +\gdef\@shortauthor{} +\gdef\@title{\mbox{}} +\def\title{\@ifnextchar [{\@titletwo}{\@titleone}} +\def\@titletwo[#1]#2{\gdef\@title{{#2}}\gdef\@shorttitle{{#1}}} +\def\@titleone#1{\gdef\@title{{#1}}\gdef\@shorttitle{{#1}}} +\gdef\@shorttitle{} +\def\@email{} +\def\@emailx{} +\newcounter{emailcnt} +\newcounter{emailxcnt} +\gdef\emailbreak{} +\newcount\tempcount +\def\printemails{ +\tempcount=0 +\@whilenum\c@emailcnt>0 +\do{% +\global\advance\tempcount 1 +\\ +\@emailsymbol{\the\tempcount}{\it email:}\ \csname @@email\romannumeral\the\tempcount\endcsname +\global\addtocounter{emailcnt}{-1}} +} +%% +\def\printemailxs{ +\tempcount=0 +\@whilenum\c@emailxcnt>0 +\do{% +\global\advance\tempcount 1 +\\ +{\it email:}\ \csname @@emailx\romannumeral\the\tempcount\endcsname +\global\addtocounter{emailxcnt}{-1}} +} + +\def\emailx#1{\global\addtocounter{emailxcnt}{1}% + \expandafter\gdef\csname @@emailx\romannumeral\theemailxcnt\endcsname{#1}% +} + +\def\email#1{\global\addtocounter{emailcnt}{1}% + \expandafter\gdef\csname @@email\romannumeral\theemailcnt\endcsname{#1}% +} + +\def\xemail#1{\refstepcounter{emailcnt}\ifx\@email\@empty% + \protected@xdef\@email{\ifbackmatter{\rm email:}\else\@emailsymbol{\c@emailcnt}{\it email:}\fi\ #1 }% + \else% + \protected@xdef\@email{\@email\ifbackmatter{\rm + email:}\else\@emailsymbol{\c@emailcnt}{\it email:}\fi\ #1 }% + \fi}% +\def\@doi{000} +\def\doi#1{\gdef\@doi{#1}} +\def\@date{} +\def\date#1{\gdef\@date{#1}} +\def\volume#1{\gdef\@volume{#1}} +\gdef\@volume{000} +\def\artmonth#1{\gdef\@month{#1}} +\gdef\@month{000} +\def\editor#1{\gdef\@editor{#1}} +\gdef\@editor{XxX} +\AtEndDocument{\if|\@date|\else\vskip10pt{\centering\@date\endgraf}\fi} +\def\tod@y{\today} +\def\microfiche#1{\gdef\@microfiche{#1}} +\gdef\@microfiche{} +\def\pubyear#1{\gdef\@pubyear{#1}} +\gdef\@pubyear{0000} +\def\pagerange#1{\gdef\@pagerange{#1}} +\gdef\@pagerange{000--000} +\def\journal#1{\gdef\@journal{#1}} +\def\plate#1{\gdef\pl@te{#1}} +\ifx\CUP@mtlplain@loaded\undefined + \def\@printed{\qquad Printed \tod@y\qquad + (MN \LaTeX\ style file v\@version)} +\else + \def\@printed{} +\fi +\gdef\@journal{\vbox{\fontsize{10}{10}\selectfont\vbox{\hsize\textwidth{\sc Biometrics} +{\@volume}, \@pagerange\hfill\ifx\@doi\@empty\else{DOI:}\ \@doi\fi}\par +\vbox{\@month\ \@pubyear}}} +% (\number\year) \@microfiche\@printed} +% +% \ps@empty and \ps@plain defined in LATEX.TEX +% +\def\@ddell{} +\if@letters + \def\@ddell{L} +\fi +\def\ps@headings{\let\@mkboth\markboth + \def\@oddhead{\Large\hfill{\small\it\@shorttitle}\hfill\hspace{1.5em}% + \rm\@ddell\hbox to 0pt{\small\thepage}} + \def\@oddfoot{}%\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, \@pagerange\hfil} + \def\@evenhead{\Large\@ddell\hbox to + 0pt{\small\thepage}\hspace{1.5em}\hfill\small{\it Biometrics, \@month}\ \@pubyear\hfill} + \def\@evenfoot{}%\hfil\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, \@pagerange} + \def\sectionmark##1{\markboth{##1}{}} + \def\subsectionmark##1{\markright{##1}}} + +\def\ps@myheadings{\let\@mkboth\@gobbletwo + \def\@oddhead{\Large\hfill\it\rightmark\hspace{1.5em}\rm\@ddell\thepage} + \def\@oddfoot{\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, \@pagerange\hfil} + \def\@evenhead{\Large\@ddell\thepage\hspace{1.5em}\it\leftmark\hfill} + \def\@evenfoot{\hfil\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, \@pagerange} + \def\sectionmark##1{} + \def\subsectionmark##1{}} + +\font\mycirc = lcircle10 at 6pt% cioptic% +\def\Copyright{\leavevmode\raise3pt\hbox{\reset@font\mycirc\char'151}\llap{\raise1.25pt\hbox +to 7.75pt{\tiny C}}} +\def\ps@titlepage{\let\@mkboth\@gobbletwo + \def\@oddhead{\footnotesize\@journal\hfill} + \def\@oddfoot{\hfill{\reset@font\ This paper has been submitted for consideration for publication in {\it Biometrics}}\hfill} +%\hfill{\reset@font\thepage}\hfill} + \def\@evenhead{\footnotesize\@journal\hfill} + %\def\@evenfoot{\hfil\small\copyright\ \@pubyear\ The Society for the Study + %of Evolution. All rights reserved.} + \def\sectionmark##1{} + \def\subsectionmark##1{}} + +\def\ps@plate{\let\@mkboth\@gobbletwo + \def\@oddhead{\footnotesize\pl@te\hfill} + \def\@oddfoot{\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, + \@pagerange\hfil} + \def\@evenhead{\footnotesize\pl@te\hfill} + \def\@evenfoot{\hfil\small\copyright\ \@pubyear\ RAS, MNRAS {\bf \@volume}, + \@pagerange} +} + +% **************************************** +% * TABLE OF CONTENTS, ETC. * +% **************************************** +% +\def\@pnumwidth{1.55em} +\def\@tocrmarg {2.55em} +\def\@dotsep{4.5} +\setcounter{tocdepth}{2} +\def\@undottedtocline#1#2#3#4#5{\ifnum #1>\c@tocdepth + \else + \vskip \z@ plus .2pt + {\hangindent #2\relax + \rightskip \@tocrmarg \parfillskip -\rightskip + \parindent #2\relax \@afterindenttrue + \interlinepenalty\@M \leavevmode + \@tempdima #3\relax #4\nobreak \hfill \nobreak + \hbox to\@pnumwidth{\hfil\reset@font\rm \ }\par}\fi} +\def\tableofcontents{\@restonecolfalse + \if@twocolumn\@restonecoltrue\onecolumn\fi + \section*{CONTENTS} \@starttoc{toc} + \if@restonecol\twocolumn\fi \par\vspace{12pt}} +\def\l@part#1#2{\addpenalty{-\@highpenalty} + \addvspace{2.25em plus 1pt} + \begingroup + \parindent \z@ \rightskip \@pnumwidth + \parfillskip -\@pnumwidth + {\reset@font\normalsize\rm + \leavevmode \hspace*{3pc} + #1\hfil \hbox to\@pnumwidth{\hss \ }}\par + \nobreak \global\@nobreaktrue + \everypar{\global\@nobreakfalse\everypar{}}\endgroup} +\def\l@section#1#2{\addpenalty{\@secpenalty} + \@tempdima 1.5em + \begingroup + \parindent \z@ \rightskip \@pnumwidth + \parfillskip -\@pnumwidth \reset@font\rm \leavevmode + \advance\leftskip\@tempdima \hskip -\leftskip + #1\nobreak\hfil \nobreak\hbox to\@pnumwidth{\hss \ }\par + \endgroup} +\def\l@subsection{\@undottedtocline{2}{1.5em}{2.3em}} +\def\l@subsubsection{\@undottedtocline{3}{3.8em}{3.2em}} +\def\l@paragraph{\@undottedtocline{4}{7.0em}{4.1em}} +\def\l@subparagraph{\@undottedtocline{5}{10em}{5em}} +\def\listoffigures{\@restonecolfalse + \if@twocolumn\@restonecoltrue\onecolumn\fi + \section*{LIST OF FIGURES\@mkboth{LIST OF FIGURES}{LIST OF FIGURES}} + \@starttoc{lof} \if@restonecol\twocolumn\fi} +\def\l@figure{\@undottedtocline{1}{1.5em}{2.3em}} +\def\listoftables{\@restonecolfalse + \if@twocolumn\@restonecoltrue\onecolumn\fi + \section*{LIST OF TABLES\@mkboth{LIST OF TABLES}{LIST OF TABLES}} + \@starttoc{lot} \if@restonecol\twocolumn\fi} +\let\l@table\l@figure + +% **************************************** +% * BIBLIOGRAPHY * +% **************************************** +% +\def\thebibliography#1{\section*{References} + \addcontentsline{toc}{section}{References} + \list{}{\usecounter{dummy}% + \labelwidth\z@ + \leftmargin 5em + \itemsep \z@ + \itemindent-\leftmargin + } + \reset@font + \parindent\z@ + \parskip\z@ plus .1pt\relax + \def\newblock{\hskip .11em plus .33em minus .07em} + \sloppy\clubpenalty4000\widowpenalty4000 + \sfcode`\.=1000\relax +} +\let\endthebibliography=\endlist +\def\@biblabel#1{\hspace*{\labelsep}[#1]} +% +\newcommand\refname{References} +\if@usenatbib% + \def\newblock{\hskip .11em plus .33em minus .07em} + \usepackage[authoryear]{natbib} + \bibpunct{(}{)}{;}{a}{,}{,} + % Re-define these in upper case as natbib.sty has them capitalised + \renewcommand\bibname{Bibliography} + \renewcommand\refname{References} +\fi +% +\def\eqnbreaktop#1{\break\vrule width\columnwidth height.5pt\par% +\vrule height#1 width0pt\par +\noindent\vrule width\columnwidth height.5pt\par\vskip6pt\noindent +\ignorespaces} +\def\aurepeat{\leavevmode\raise3pt\hbox{\vrule height.25pt width2.25pc}} +\newcounter{dummy} +\def\thebibliography#1{\section*{\refname} + \addcontentsline{toc}{section}{References} + \list{}{\usecounter{dummy}% + \labelwidth\z@ + \leftmargin 20pt + \itemsep \z@ + \itemindent-\leftmargin} + \reset@font + \parindent\z@ + \parskip\z@\relax% plus .1pt + \def\newblock{\hskip .11em plus .33em minus .07em} + \sloppy\clubpenalty4000\widowpenalty4000 + \sfcode`\.=1000\relax +} +\let\endthebibliography=\endlist +\def\@biblabel#1{\hspace*{\labelsep}[#1]} + +% new column specifiers to be used with dcolumn +\if@usedcolumn% + \usepackage{dcolumn} + \newcolumntype{d}[1]{D{.}{.}{#1}} + \newcolumntype{.}{D{.}{.}{-1}} + \newcolumntype{,}{D{,}{,}{2}} +\fi + +% **************************************** +% * THE INDEX * +% **************************************** +% +\newif\if@restonecol +\def\theindex{\section*{INDEX} + \addcontentsline{toc}{section}{INDEX} + \reset@font\footnotesize \parindent\z@ \parskip\z@ plus .1pt\relax + \let\item\@idxitem} +\def\@idxitem{\par\hangindent 1em} +\def\subitem {\par\hangindent 1em \hspace*{1em}} +\def\subsubitem{\par\hangindent 1em\hspace*{1em}} +\def\endtheindex{\if@restonecol\onecolumn\else\clearpage\fi} +\def\indexspace{\par\vskip\baselineskip \relax} + +% **************************************** +% * FOOTNOTES * +% **************************************** +% +\def\footnoterule{\kern-3\p@ \hrule width 3.5pc height .5\p@ \kern 5\p@} + +%\renewcommand{\thefootnote}{\mbox{{$\fnsymbol{footnote}$}}} +\renewcommand{\thempfootnote}{\mbox{{${\alph{mpfootnote}}$}}} + +\def\@fnsymbol#1{\ifcase#1\or \mbox{${^{\star}}$}\or + \dagger\or \ddagger\or + \S \or \P \or \|\or \mbox{$^{\star\star}$}\or \dagger\dagger + \or \ddagger\ddagger\or \S\S\or \P\P\or \|\|\else *** + \fi\relax} + +\def\@emailsymbol#1{\ifcase#1\or *\or **\or ***\or ****\or *****\or ******\or *******\or ********\or *********\or ********** + \fi\relax} + +\providecommand\@makefntext[1]{} + +\renewcommand{\@makefnmark}{$^{\@thefnmark}$} +\renewcommand\@makefntext[1]{\footnotesize\parindent 1em\noindent + $^{\@thefnmark}$\hspace{0pt}#1} + +\newcommand{\fixfootnotes}{% +\renewcommand{\@makefnmark}{$^{\@thefnmark}$}% +\renewcommand\@makefntext[1]{\parindent 1em\noindent\fontsize{8}{10}\selectfont% + \hskip1em$^{\@thefnmark}$\hskip0pt##1}% +\renewcommand{\thefootnote}{\arabic{footnote}}% +\setcounter{footnote}{0}% +} +%**************************************** +% * FIGURES AND TABLES * +% **************************************** +% +\setcounter{topnumber}{5} +\def\topfraction{.9} +\setcounter{bottomnumber}{5} +\def\bottomfraction{.9} +\setcounter{totalnumber}{10} +\def\textfraction{.1} +\def\floatpagefraction{.9} +\setcounter{dbltopnumber}{2} +\def\dbltopfraction{.9} +\def\dblfloatpagefraction{.9} + +\newif\ifst@rredfloat +\newcounter{table} +\def\thetable{\@arabic\c@table} +\def\fps@table{tbp} +\def\ftype@table{1} +\def\fstyle@table{\reset@font\fontsize{9}{10pt}\selectfont\rm} +\def\thead#1{\reset@font#1} +\def\ext@table{lot} +\def\fnum@table{Table \thetable} +%% +\def\FigName{figure} +% +\long\def\@makecaption#1#2{% + \ifx\FigName\@captype +% \vskip\abovecaptionskip + \SFB@makefigurecaption{#1}{#2}% +% \vskip\belowcaptionskip + \else + \SFB@maketablecaption{#1}{#2}% +% \vskip\belowcaptionskip + \fi +} +% +\newenvironment{table} + {\def\footnoterule{\kern-3\p@ \hrule width 3pc height \z@ \kern 5\p@}% + \centering\fstyle@table% + \@float{table}} + {\end@float} +%% +\newenvironment{table*} + {\def\footnoterule{\kern-3\p@ \hrule width 3pc height \z@ \kern 5\p@}% + \centering\fstyle@table% + \@dblfloat{table}} + {\end@dblfloat} + +%\def\table{\def\baselinestretch{1}% +% \let\@makecaption=\SFB@maketablecaption% +% \def\footnoterule{\kern-3\p@ \hrule width 3pc height \z@ \kern 5\p@}% +% \@float{table}\fstyle@table} +%\let\endtable\end@float +%\@namedef{table*}{\def\baselinestretch{1}\st@rredfloattrue% +%\def\footnoterule{\kern-3\p@ \hrule width 3pc height \z@ \kern 5\p@}% +% \@dblfloat{table}\centering\fstyle@table} +%\@namedef{endtable*}{\end@dblfloat\st@rredfloatfalse} + +\newcounter{figure} +\def\thefigure{\@arabic\c@figure} +\def\fps@figure{tbp} +\def\ftype@figure{2} +\def\fstyle@figure{\reset@font\small\rm} +\def\ext@figure{lof} +\def\fnum@figure{{\bf Figure \thefigure}} +%% +\newenvironment{figure} + {\@float{figure}} + {\end@float} +%% +\newenvironment{figure*} + {\@dblfloat{figure}} + {\end@dblfloat} +%% +%\@namedef{figure*}{\def\baselinestretch{1}\st@rredfloattrue +% \let\@makecaption=\SFB@makefigurecaption% +% \@dblfloat{figure}\centering\fstyle@figure} +%\@namedef{endfigure*}{\end@dblfloat\st@rredfloatfalse} + +\long\def\SFB@makefigurecaption#1#2{\vskip 6pt% + \setbox\@tempboxa\hbox{\reset@font{\bf #1}% + \if@cont \ -- {\it continued}\else{\bf.}\hskip1em\fi{\rm #2}\par}% + \ifdim \wd\@tempboxa >\hsize% + {\reset@font{\bf#1}% + \if@cont \ -- {\it continued}\else{\bf.}\hskip1em\fi{\rm #2}\par}% + \else% + \ifst@rredfloat% + \hbox to\hsize{\hfill\box\@tempboxa\hfill}%% + \else% + \hbox to\hsize{\hfill\box\@tempboxa\hfill}% + \fi% + \fi% +% \vskip 6pt% + \@contfalse% +}% + +\long\def\SFB@maketablecaption#1#2{\vskip 6pt + {\reset@font\centering\small{\bf #1}\par\vskip1pt + {\it #2}\par}% + \vskip 0pt + \@contfalse +} + +\newif\if@cont +\def\caption{\refstepcounter\@captype \@dblarg{\@caption\@captype}} +\def\contcaption{\@conttrue\SFB@caption\@captype} + +\long\def\SFB@caption#1#2{%\par + \begingroup + \@parboxrestore + \reset@font\normalsize + \@makecaption{\csname fnum@#1\endcsname}{\ignorespaces #2}\par + \endgroup} + +\voffset3pc +\hoffset1pc +% **************************************** +% * CUP specials * +% **************************************** +% +% +% The following code is taken from authordate.sty, by David Rhead, of +% the Cripps Computing Centre (February 1990), with some modifications +% by ggw. It is intended for documents +% that use the author-date citation system. When used in conjunction with +% authordate1.bst, ... , authordate4.bst, it allows citations of the +% form \shortcite{bloggs-60} as well as the usual \cite{bloggs-60}. +% When +% ... \cite{bloggs-60} ... \shortcite{bloggs-60} ... +% appears in the input file, +% ... (Bloggs, 1960) ... (1960) ... +% appears in the final document. +% +% Code taken from apalike.sty. +% +\def\@cite#1#2{(#1\if@tempswa , #2\fi)} +\def\@biblabel#1{} + +% Set length of hanging indentation for bibliography entries +% + +\if@usenatbib\relax\else% +\newlength{\bibhang} +\setlength{\bibhang}{2em} +\fi + +% Define default title and page-head text. +% +\def\bibtitle{References} +\def\bibheadtitle{REFERENCES} + +% Code taken from aaai.sty. +% +% don't box citations, add space between multiple citations, separate with ; +\def\@citex[#1]#2{% + \if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi + \def\@citea{}\@cite{\@for\@citeb:=#2\do + {\@citea\def\@citea{; }\@ifundefined + {b@\@citeb}{{\reset@font\bf ?}\@warning + {Citation `\@citeb' on page \thepage \space undefined}}% +{\csname b@\@citeb\endcsname}}}{#1}} +% Allow short (name-less) citations, when used in +% conjunction with a bibliography style that creates labels like +% \citename{, } +\let\@internalcite\cite +\def\cite{\def\citename##1{##1}\@internalcite} +\def\shortcite{\def\citename##1{}\@internalcite} + +% RM for BSP note at end of article +\def\bsp{\vspace{0.5cm}\reset@font\normalsize\noindent This paper +has been typeset from a \TeX / \LaTeX\ file prepared by the author.} + + +% **************************************** +% * FLEQN * +% **************************************** +% +% FLEQN DOCUMENT-STYLE OPTION - released 9 March 1987 +% for LaTeX version 2.09 +% Copyright (C) 1987 by Leslie Lamport +% +% The following commands make the displayed math environments flush left, +% with an indentation of \mathindent from the prevailing left margin. + +\def\[{\relax\ifmmode\@badmath\else\begin{trivlist}\item[]\leavevmode + \hbox to\linewidth\bgroup\hfil$ + \displaystyle + \hskip\mathindent\bgroup\fi} + +\def\]{\relax\ifmmode \egroup $\hfil + \egroup \end{trivlist}\else \@badmath \fi} + +\def\equation{\refstepcounter{equation}\trivlist \item[]\leavevmode + \hbox to\linewidth\bgroup\hfil $ + \displaystyle +\hskip\mathindent} + + +\def\endequation{$\hfil + \displaywidth\linewidth\@eqnnum\egroup \endtrivlist} + +\def\longequation{\refstepcounter{equation}\trivlist \item[]\leavevmode + \hbox to\textwidth\bgroup\hfil $ + \displaystyle +\hskip\mathindent} + + +\def\endlongequation{$\hfil + \displaywidth\linewidth\@eqnnum\egroup \endtrivlist} + +\def\eqnarray{\stepcounter{equation}\let\@currentlabel=\theequation +\global\@eqnswtrue +\global\@eqcnt\z@\tabskip\@centering\let\\=\@eqncr%mathindent +\abovedisplayskip\topsep\ifvmode\advance\abovedisplayskip\partopsep\fi +\belowdisplayskip\abovedisplayskip +\belowdisplayshortskip\abovedisplayskip +\abovedisplayshortskip\abovedisplayskip +$$\halign +to \linewidth\bgroup\@eqnsel\hskip\@centering$\displaystyle\tabskip\z@ + {##}$&\global\@eqcnt\@ne \hskip 2\arraycolsep \hfil${##}$\hfil + &\global\@eqcnt\tw@ \hskip 2\arraycolsep $\displaystyle{##}$\hfil + \tabskip\@centering&\llap{##}\tabskip\z@\cr} + +\def\endeqnarray{\@@eqncr\egroup + \global\advance\c@equation\m@ne$$\global\@ignoretrue} + +\newdimen\mathindent +\mathindent = \z@ + +% **************************************** +% * MISCELLANEOUS * +% **************************************** +% +% DATE +\def\today{\number\day\ \ifcase\month\or + January\or February\or March\or April\or May\or June\or + July\or August\or September\or October\or November\or December + \fi \ \number\year} + +% REVISED AUTHOR QUERY COMMAND +% Queries in text are printed in large bold font, in square brackets +% Queries in references are printed as bold number followed by text + \DeclareFixedFont{\largerm}{OT1}{cmss}{m}{n}{17} + \DeclareFixedFont{\largeital}{OT1}{cmss}{m}{sl}{17} + \newcommand{\aquery}[1]{\mbox{\largerm {[#1]}}} + \newcommand{\BSLquery}[1]{\aquery{#1}} + %For backwards compatibility with old query command + \newcommand{\tquery}[1]{\mbox{\largeital{[#1]}}} + %Typesetter query: same format + \newenvironment{query}{\vspace{5mm} \noindent {\bf Queries}\\}{} + \newcommand{\authorquery}[2]{\noindent{{\bf #1} #2}\\} + +% definition required for newarray.sty +\gdef\d@llar{} + +% **************************************** +% * INITIALIZATION * +% **************************************** +% +% +\newif\ifbackmatter +\def\backmatter{% + \global\backmattertrue + } +% +% +%%%NHT: this code needs fixed. +%%% At the moment the zif is always undefined, so it does nothing! +\newif\ifCUPmtlplainloaded +\ifx\CUP@mtlplain@loaded\undefined +\else + \global\CUPmtlplainloadedtrue + \input mnsym +\fi +% +\flushbottom +\ps@headings +\ifSFB@galley + \raggedbottom + \ps@empty +\fi +%\ifSFB@referee +% \raggedbottom +%\fi +\pagenumbering{arabic} +\if@twocolumn + \twocolumn + \sloppy +\else + \onecolumn +\fi +\frenchspacing +%%%% +\usepackage{theorem} +\newcounter{theorem} +\renewcommand\thetheorem{\arbic{theorem}} +\newtheorem{theorem}{Theorem}%[theorem] +%\newtheorem{algorithm}{Algorithm}%[theorem] +\newtheorem{corollary}{Corollary}%[section]%[theorem] +\newtheorem{fact}{Fact}%[section] +\newtheorem{property}{Property}%[section] +\newtheorem{result}{Result}%[section] +\newtheorem{lemma}{Lemma}%[section] +%\newtheorem{proof}{Proof} +%%% +\newtheorem{assumption}{Assumption}%[section] +\newtheorem{case}{Case}%[section] +\newtheorem{axiom}{Axiom}%[section] +\newtheorem{change}{Change}%[section] +\newtheorem{claim}{Claim}%[section] +\newtheorem{conjecture}{Conjecture}%[section] +\newtheorem{definition}{Definition}%[section] +\newtheorem{example}{Example}%[section] +\newtheorem{formula}{Formula}%[section] +\newtheorem{hypothesis}{Hypothesis}%[section] +\newtheorem{method}{Method}%[section] +\newtheorem{model}{Model}%[section] +\newtheorem{notation}{Notation}%[section] +\newtheorem{note}{Note}%[section] +\newtheorem{objective}{Objective}%[section] +\newtheorem{observation}{Observation}%[section] +\newtheorem{principle}{Principle}%[section] +\newtheorem{problem}{Problem}%[section] +\newtheorem{procedure}{Procedure}%[section] +\newtheorem{remark}{Remark}%[section] +\newtheorem{step}{Step}%[section] + +\gdef\PROOF{Proof} +%\gdef\ALGO{Algorithm} +\gdef\CORO{Corollary} +\gdef\FACT{Fact} +\gdef\PROPRT{Property} +\gdef\RESULT{Result} +\gdef\LEMMA{Lemma} +\gdef\THRM{Theorem} +\gdef\TRUE{true} +\def\thname{} +\gdef\@thm#1#2{\refstepcounter{#1}% + \trivlist + \@topsep \theorempreskipamount % used by first \item + \@topsepadd \theorempostskipamount % used by \@endparenv + \@ifnextchar [% + {\@ythm{#1}{#2}}% + {\xdef\thname{#2} +\@begintheorem{#2}{\ifx\thname\PROOF\unskip:\else\csname the#1\endcsname:\fi}\ignorespaces\ifx\Boldhead\TRUE\reset@font\itshape\fi}}%fci +\global\let\@xthm\relax +\newskip\theorempreskipamount +\newskip\theorempostskipamount +\global\setlength\theorempreskipamount{12pt plus 5pt minus 3pt} +\global\setlength\theorempostskipamount{8pt plus 3pt minus 1.5pt} +%%%% +\font\sqbox=msam10 +\def\endnewtrivlist{% + \if@inlabel + \leavevmode + \global \@inlabelfalse + \fi + \if@newlist + \@noitemerr + \global \@newlistfalse + \fi + \ifx\thname\PROOF\qquad \hfill {\sqbox\char'003}\else\fi\ifhmode\unskip \par\fi + \if@noparlist \else + \ifdim\lastskip >\z@ + \@tempskipa\lastskip \vskip -\lastskip + \advance\@tempskipa\parskip \advance\@tempskipa -\@outerparskip + \vskip\@tempskipa + \fi + \@endparenv + \fi +} +%%%% +\global\let\@endtheorem=\endnewtrivlist +\@onlypreamble\@xnthm +\@onlypreamble\@ynthm +\@onlypreamble\@othm +\@onlypreamble\newtheorem +\@onlypreamble\theoremstyle +\@onlypreamble\theorembodyfont +\@onlypreamble\theoremheaderfont +\theoremstyle{plain} +%% +\ifx\upshape\undefined +\gdef\theorem@headerfont{\sc} +\else \gdef\theorem@headerfont{\normalfont\sc}\fi%bfseries +%\FACT \PROPRT \RESULT \LEMMA \THRM + +\gdef\th@plain{\normalfont%\itshape + \def\@begintheorem##1##2{% + \xdef\Check{##1}% + \ifx\Check\ALGO\gdef\Boldhead{true}\else% + \ifx\Check\CORO\gdef\Boldhead{true}\else% + \ifx\Check\FACT\gdef\Boldhead{true}\else% + \ifx\Check\PROPRT\gdef\Boldhead{true}\else% + \ifx\Check\RESULT\gdef\Boldhead{true}\else% + \ifx\Check\LEMMA\gdef\Boldhead{true}\else% + \ifx\Check\THRM\gdef\Boldhead{true}\else% + \gdef\Boldhead{false}\fi\fi\fi\fi\fi\fi\fi% + \item[\hskip\parindent \theorem@headerfont\def\checkhead{##1}% \labelsep + \ifx\Boldhead\TRUE{\reset@font\normalfont~~\sc##1\ ##2}\enspace\else% + \ifx\thname\PROOF{\reset@font\sc##1:}\enspace\else##1\ ##2\enspace\fi\fi]}% +\def\@opargbegintheorem##1##2##3{% + \xdef\Check{##1}% + \ifx\Check\ALGO\gdef\Boldhead{true}\else% + \ifx\Check\CORO\gdef\Boldhead{true}\else% + \ifx\Check\FACT\gdef\Boldhead{true}\else% + \ifx\Check\PROPRT\gdef\Boldhead{true}\else% + \ifx\Check\RESULT\gdef\Boldhead{true}\else% + \ifx\Check\LEMMA\gdef\Boldhead{true}\else% + \ifx\Check\THRM\gdef\Boldhead{true}\else% + \gdef\Boldhead{false}\fi\fi\fi\fi\fi\fi\fi% + \item[\hskip\parindent \theorem@headerfont %labelsep + \ifx\Boldhead\TRUE{\reset@font\normalfont~~\sc##1\ ##2}\ {\rm (##3)}{\reset@font\sc:}\enspace\else% + \ifx\thname\PROOF{\reset@font\sc##1\ {\rm(##3)}:}\enspace\else% + ##1\ ##2\ {\rm (##3):\enspace}\fi\fi] + \ifx\Boldhead\TRUE\itshape\fi}} +%% +\let\bm\bmath +%% +\ifSFB@referee + \usepackage[nolists]{endfloat} + \AtBeginDocument{\usepackage{endrotfloat}} +\fi +% end of Biom.cls + + + diff --git a/inst/rmarkdown/templates/biometrics_article/skeleton/endrotfloat.sty b/inst/rmarkdown/templates/biometrics_article/skeleton/endrotfloat.sty new file mode 100644 index 000000000..5bc489f16 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/skeleton/endrotfloat.sty @@ -0,0 +1,92 @@ +\def\filename{endrotfloat} +\def\fileversion{v1.0} +\def\filedate{2007/01/23} + +\NeedsTeXFormat{LaTeX2e}[1994/06/01] +\ProvidesPackage{endrotfloat}[\filedate\space\fileversion\space + LaTeX2e package puts sideways figures and tables at end] + +\let\@bbfig\sidewaysfigure % bj +\let\@bbtab\sidewaystable % bj + +\def\sidewaysfigure{% + \efloat@condopen{fff} + \efloat@iwrite{fff}{\string\begin{sidewaysfigure*}}% + \if@domarkers% + \addtocounter{postfig}{1}% % bj + \figureplace% % bj + \fi% + \def\@currenvir{efloat@float}% + \begingroup% + \let\do\ef@makeinnocent \dospecials% + \ef@makeinnocent\^^L% and whatever other special cases + \endlinechar`\^^M \catcode`\^^M=12 \ef@xfigure}% +{\catcode`\^^M=12 \endlinechar=-1 % +\gdef\ef@xfigure#1^^M{\def\test{#1}% + \ifx\test\ef@endfiguretest + \efloat@foundend{fff}{figure*} + \else\ifx\test\ef@enddblfiguretest + \efloat@foundend{fff}{figure*} + \else\ifx\test\ef@endrotfiguretest + \efloat@foundend{fff}{sidewaysfigure*} + \else\ifx\test\ef@enddblrotfiguretest + \efloat@foundend{fff}{sidewaysfigure*} + \else% + \efloat@iwrite{fff}{#1}% + \let\next\ef@xfigure% + \fi \fi \fi \fi \next}% +}% +{\escapechar=-1% + \xdef\ef@endfiguretest{\string\\end\string\{figure\string\}}% + \xdef\ef@enddblfiguretest{\string\\end\string\{figure*\string\}}% + \xdef\ef@endrotfiguretest{\string\\end\string\{sidewaysfigure\string\}}% + \xdef\ef@enddblrotfiguretest{\string\\end\string\{sidewaysfigure*\string\}}% +}% +% +\def\sidewaystable{\efloat@condopen{ttt}% + \efloat@iwrite{ttt}{\string\begin{sidewaystable*}}% + \if@domarkers + \addtocounter{posttbl}{1} % bj + \tableplace % bj + \fi + \def\@currenvir{efloat@float}% + \begingroup + \let\do\ef@makeinnocent \dospecials + \ef@makeinnocent\^^L% and whatever other special cases + \endlinechar`\^^M \catcode`\^^M=12 \ef@xtable} +{\catcode`\^^M=12 \endlinechar=-1 % + \gdef\ef@xtable#1^^M{\def\test{#1} + \ifx\test\ef@enddbltabletest + \efloat@foundend{ttt}{table*} + \else\ifx\test\ef@endtabletest + \efloat@foundend{ttt}{table*} + \else\ifx\test\ef@endrottabletest + \efloat@foundend{ttt}{sidewaystable*} + \else\ifx\test\ef@enddblrottabletest + \efloat@foundend{ttt}{sidewaystable*} + \else + \efloat@iwrite{ttt}{#1}% + \let\next\ef@xtable + \fi \fi \fi \fi \next} +} +{\escapechar=-1 +\xdef\ef@enddblrottabletest{\string\\end\string\{sidewaystable*\string\}} +\xdef\ef@endrottabletest{\string\\end\string\{sidewaystable\string\}} +\xdef\ef@enddbltabletest{\string\\end\string\{table*\string\}} +\xdef\ef@endtabletest{\string\\end\string\{table\string\}} +} + +\@namedef{sidewaystable*}{\sidewaystable} + +\renewcommand{\processdelayedfloats}{{% + \def\baselinestretch{1}\normalsize + \let\figure\@bfig + \let\table\@btab + \let\sidewaysfigure\@bbfig + \let\sidewaystable\@bbtab + \processdelayedfloats@hook + \if@tablesfirst \processtables\processfigures + \else \processfigures\processtables \fi + \processotherdelayedfloats}} + +\endinput \ No newline at end of file diff --git a/inst/rmarkdown/templates/biometrics_article/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/biometrics_article/skeleton/skeleton.Rmd new file mode 100644 index 000000000..95152d5b7 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/skeleton/skeleton.Rmd @@ -0,0 +1,90 @@ +--- +title: Title here + +author: +- name: Author 1 + affiliation: Department of YYY, University of XXX + email: abc@def + +- name: Author 2 + affiliation: Department of ZZZ, University of WWW + email: djf@wef + +keywords: +- key +- dictionary +- word + +abstract: | + The text of your summary. Should not exceed 225 words. + +bibliography: bibliography.bib +output: rticles::biometrics_article +month: "`r format(Sys.Date(), '%b')`" +year: "`r format(Sys.Date(), '%Y')`" +referee: true # Papers submitted to Biometrics should ALWAYS be prepared + # using the referee option!!!! Turn off only to preview + # two column-format +--- + +# Introduction {#intro} + +Your text comes here. Separate text sections with + +# Section title {#sec:1} + +Text with citations by @heagerty2000time, [@pepe2003statistical]. + +## Subsection title {#sec:2} + +as required [@hoerl1970ridge; @zou2005regularization]. Don't forget to give each section +and subsection a unique label (see Sect. \ref{sec:1}). + +#### Paragraph headings + +Use paragraph headings as needed. + +## Equations + +Here is an equation: + +$$ f_{X}(x) = \left(\frac{\alpha}{\beta}\right)\left(\frac{x}{\beta}\right)^{\alpha-1}e^{-\left(\frac{x}{\beta}\right)^{\alpha}}; \alpha,\beta,x > 0 $$ + +Here is another: +\begin{align} +a^2+b^2=c^2 +\end{align} + +Inline equations: $\sum_{i = 2}^\infty\{\alpha_i^\beta\}$ + +# Figures and tables + + +## Figures coming from R + +#### Normal figure embedded in text + +```{r fig2, fig.width = 4, fig.height = 4, fig.cap = "Output from `pdf()`", echo = FALSE, dev = "pdf"} +plot(runif(25) ~ runif(25)) +``` + +\clearpage + +## Tables coming from R + + +```{r tab1, results = 'asis'} +print(xtable::xtable(head(mtcars)[,1:4], +caption = "Caption centered under table", label = "tab1"), +comment = FALSE, timestamp = FALSE, caption.placement = "top") +``` + +Table \ref{tab1} shows these numbers. Some of those numbers are plotted in Figure \ref{fig:fig1}. + + +```{r tab2} +head(mtcars[,1:4]) +``` + + +# References diff --git a/inst/rmarkdown/templates/biometrics_article/template.yaml b/inst/rmarkdown/templates/biometrics_article/template.yaml new file mode 100644 index 000000000..07fb4b905 --- /dev/null +++ b/inst/rmarkdown/templates/biometrics_article/template.yaml @@ -0,0 +1,4 @@ +name: Biometrics Journal Article +description: > + Template for creating an article for submission to Biometrics journal +create_dir: true diff --git a/man/biometrics_article.Rd b/man/biometrics_article.Rd new file mode 100644 index 000000000..665a361ad --- /dev/null +++ b/man/biometrics_article.Rd @@ -0,0 +1,28 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/biometrics_article.R +\name{biometrics_article} +\alias{biometrics_article} +\title{Biometrics Journal format.} +\usage{ +biometrics_article(..., keep_tex = TRUE, citation_package = "natbib") +} +\arguments{ +\item{...}{Arguments to \code{rmarkdown::pdf_document}} + +\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF} + +\item{citation_package}{The LaTeX package to process citations, \code{natbib} +or \code{biblatex}. Use \code{none} if neither package is to be used.} +} +\value{ +R Markdown output format to pass to \code{\link[rmarkdown:render]{render}} +} +\description{ +This format was adapted from the Biometrics Macro package. +} +\examples{ +\dontrun{ +rmarkdown::draft("MyArticle.Rmd", template = "biometrics_article", package = "rticles") +} + +} diff --git a/tests/testit/test-formats.R b/tests/testit/test-formats.R index e33fbac19..38a291d9d 100644 --- a/tests/testit/test-formats.R +++ b/tests/testit/test-formats.R @@ -30,6 +30,7 @@ test_format("acs_article") test_format("aea_article") test_format("ams_article") test_format("asa_article") +test_format("biometrics_article") test_format("elsevier_article") test_format("jss_article") test_format("rss_article")