适配为文章模版

.gitignore

@@ -1 +1,3 @@
 /.quarto/
+site_libs/
+*.html.md

AC/index.qmd

@@ -1,8 +1,9 @@
 ---
-subtitle: "主要成果"
+subtitle: "文章成果"
+lang: "zh"
 ---
 
-# 论文
+# 项目
 
 # 专利
 

MS/CL.qmd

@@ -0,0 +1,33 @@
+---
+format:
+  html: 
+    css: _extensions/inst/css/style.css
+  pdf:
+    latex_engine: xelatex
+    keep-tex: false
+    keep-md: false
+    template: _extensions/inst/tex/cv.tex
+date: today
+author: "Min Yang"
+affliction: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
+from_email: "yangmin@rcees.ac.cn"
+from_phone: "+86 (10) 62843038"
+from_institution_logo: "_extensions/inst/img/rceeslonglogo.png"
+from_sign: "_extensions/inst/img/signmy.png"
+from_position: "Vice Director, Professor"
+from_professional_title: "Ph.D."
+from_institution: "Chinese Academy of Sciences"
+from_department: "Research Center for Eco-Environmental Sciences"
+from_address: "P.O. Box 2871, Beijing"
+to_professional_title: ""
+to_name: "Editor-in-Chief"
+to_journal: "Water Research"
+opening_greeting: "Dear Editor,"
+closing_greeting: "Yours Sincerely,"
+---
+
+Thank you for your consideration our manuscript (`{{< meta submitid >}}`) in publishing in {{< meta submitjournal >}}, and we also thank the reviewers for their kind and valuable comments.
+
+We have carefully revised the manuscripte according to each comment from the reviewers. As requested, revision note with point to point responses and actions, change tracking manuscript and revised manuscript have been prepared and included in the revision submission. 
+
+We believe that the paper has been greatly improved. Looking forward to your further instruction regarding its publication.

MS/GA.qmd

@@ -0,0 +1,22 @@
+---
+format:
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-html:
+    filters:
+      - author-info-blocks
+    css: _extensions/inst/css/style.css
+  elsevier-pdf:
+    header-includes:
+      - \setmainfont{Calibri}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+---
+
+# Graphical Abstract {-}
+
+
+<!-- ![](./figures/GA3.pdf) -->
+

MS/HL.qmd

@@ -0,0 +1,24 @@
+---
+format:
+  elsevier-html:
+    filters:
+      - author-info-blocks
+    css: _extensions/inst/css/style.css
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-pdf:
+    header-includes:
+      - \setmainfont{Calibri}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+---
+
+# Highlights {-}
+
+- A comprehensive model was contructed to evaluate the risk of odor occurrences
+- Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
+- Increasing flowrate leading high turbidity that can control *Planktothrix* and MIB
+- Odor control based on flow regulation in source water is "green" and fundamental
+

MS/MS.pdf.md

@@ -0,0 +1,101 @@
+---
+msname: MS
+smname: SM
+abstract: ABSTRACT
+keywords: 
+  - KEYWORD1
+  - KEYWORD2
+  - KEYWORD3
+# date: last-modified
+bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+# csl: https://www.zotero.org/styles/elsevier-harvard
+csl: _extensions/inst/tex/elsevier-harvard.csl
+format:
+  elsevier-html:
+    css: _extensions/inst/css/style.css
+    keep-md: true
+    filters:
+      - author-info-blocks
+  epub: default
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-pdf:
+    keep-tex: true
+    keep-md: true
+    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    latex-clean: false
+    header-includes:
+      # - \usepackage{threeparttable}
+      # - \usepackage{fontspec}
+      # - \usepackage{endfloat}
+      - \setmainfont{Calibri}
+      # - \usepackage[UTF8, scheme=plain]{ctex}
+      # - \usepackage{float}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+      - \usepackage{lineno}
+      - \linenumbers
+    journal:
+      formatting: preprint # preprint | review | doublebind
+      model: 1p
+      cite-style: authoryear
+      # graphical-abstract: "![](./figures/GA3.pdf)"
+      # highlights:
+      #   - A comprehensive model was contructed to evaluate the risk of odor occurrences
+      #   - Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
+      #   - Increasing flowrate increases turbidity that can control *Planktothrix* and MIB
+      #   - Odor control based on flow regulation in source water is "green" and fundamental
+filters:
+   - latex-environment
+commands: [clab]
+---
+
+
+
+
+
+
+::: {.content-visible when-format="html"}
+# Color tip {.unnumbered}
+
+-   [Something should be deleted]{.del}
+-   [Something bad]{.bad}
+-   [Something good]{.good}
+-   [Something todo]{.todo}
+-   [Something should be added]{.add}
+-   [I am a comment]{.com}
+:::
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Introduction
+
+Blabla. [Bla blaBla blaBla blaBla blaBla bla     Bla bla.]{.clab options=r1q0101}
+
+# Materials and methods
+
+# Results
+
+# Discussion
+
+# Conclusions
+
+# Acknowledgements {.unnumbered}
+
+This work was financially supported by the National Natural Science Foundation of China (52030002, 51878649), and Youth Innovation Promotion Association CAS.
+
+# References {.unnumbered}
+

MS/MS.qmd

@@ -0,0 +1,104 @@
+---
+msname: MS
+smname: SM
+abstract: ABSTRACT
+keywords: 
+  - KEYWORD1
+  - KEYWORD2
+  - KEYWORD3
+# date: last-modified
+bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+# csl: https://www.zotero.org/styles/elsevier-harvard
+csl: _extensions/inst/tex/elsevier-harvard.csl
+format:
+  elsevier-html:
+    css: _extensions/inst/css/style.css
+    keep-md: true
+    filters:
+      - author-info-blocks
+  epub: default
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-pdf:
+    keep-tex: true
+    keep-md: true
+    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    latex-clean: false
+    header-includes:
+      # - \usepackage{threeparttable}
+      # - \usepackage{fontspec}
+      # - \usepackage{endfloat}
+      - \setmainfont{Calibri}
+      # - \usepackage[UTF8, scheme=plain]{ctex}
+      # - \usepackage{float}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+      - \usepackage{lineno}
+      - \linenumbers
+    journal:
+      formatting: preprint # preprint | review | doublebind
+      model: 1p
+      cite-style: authoryear
+      # graphical-abstract: "![](./figures/GA3.pdf)"
+      # highlights:
+      #   - A comprehensive model was contructed to evaluate the risk of odor occurrences
+      #   - Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
+      #   - Increasing flowrate increases turbidity that can control *Planktothrix* and MIB
+      #   - Odor control based on flow regulation in source water is "green" and fundamental
+filters:
+   - latex-environment
+commands: [clab]
+---
+
+::: {.content-visible when-format="html"}
+# Color tip {.unnumbered}
+
+-   [Something should be deleted]{.del}
+-   [Something bad]{.bad}
+-   [Something good]{.good}
+-   [Something todo]{.todo}
+-   [Something should be added]{.add}
+-   [I am a comment]{.com}
+:::
+
+
+```{r}
+#| label: setup
+#| include: false
+#| cache: false
+lang <- "en"
+RM <- "F"   # global rendermode, L: load pdata; F: fast load pdf # nolint
+isRendering <- isTRUE(getOption("knitr.in.progress"))
+require(tidyverse)
+require(drwateR)
+require(rmdify)
+rmdify::rmd_init()
+require(dateR)
+require(uniteR)
+require(langeR)
+require(patchwork)
+require(lubridate)
+```
+
+
+
+# Introduction
+
+Blabla. [Bla blaBla blaBla blaBla blaBla bla     Bla bla.]{.clab options=r1q0101}
+
+# Materials and methods
+
+# Results
+
+# Discussion
+
+# Conclusions
+
+# Acknowledgements {.unnumbered}
+
+This work was financially supported by the National Natural Science Foundation of China (52030002, 51878649), and Youth Innovation Promotion Association CAS.
+
+# References {.unnumbered}
+

MS/MS.tex

@@ -0,0 +1,284 @@
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
+%
+\documentclass[
+  authoryear,
+  preprint,
+  1p]{elsarticle}
+
+\usepackage{amsmath,amssymb}
+\usepackage{iftex}
+\ifPDFTeX
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+  \usepackage{unicode-math}
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
+\fi
+\usepackage{lmodern}
+\ifPDFTeX\else  
+    % xetex/luatex font selection
+\fi
+% Use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\IfFileExists{microtype.sty}{% use microtype if available
+  \usepackage[]{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+  \IfFileExists{parskip.sty}{%
+    \usepackage{parskip}
+  }{% else
+    \setlength{\parindent}{0pt}
+    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+  \KOMAoptions{parskip=half}}
+\makeatother
+\usepackage{xcolor}
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\setcounter{secnumdepth}{5}
+% Make \paragraph and \subparagraph free-standing
+\ifx\paragraph\undefined\else
+  \let\oldparagraph\paragraph
+  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+  \let\oldsubparagraph\subparagraph
+  \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+
+
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}\usepackage{longtable,booktabs,array}
+\usepackage{calc} % for calculating minipage widths
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+\usepackage{graphicx}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+
+\usepackage{adjustbox}
+% \usepackage{xcolor}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+% setup hyperlink for page and line number
+\def\msname{MS}
+\def\smname{SM}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+\newcommand{\clab}[2][]{
+		\protected@write\@auxout{\let\clab\@secondoftwo}{
+				\string\newlabel{r:#1}{{#2}{}}}%
+		\hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+
+\setmainfont{Calibri}
+\usepackage[normalem]{ulem}
+\usepackage[doublespacing]{setspace}
+\usepackage{lineno}
+\linenumbers
+\makeatletter
+\@ifpackageloaded{caption}{}{\usepackage{caption}}
+\AtBeginDocument{%
+\ifdefined\contentsname
+  \renewcommand*\contentsname{Table of contents}
+\else
+  \newcommand\contentsname{Table of contents}
+\fi
+\ifdefined\listfigurename
+  \renewcommand*\listfigurename{List of Figures}
+\else
+  \newcommand\listfigurename{List of Figures}
+\fi
+\ifdefined\listtablename
+  \renewcommand*\listtablename{List of Tables}
+\else
+  \newcommand\listtablename{List of Tables}
+\fi
+\ifdefined\figurename
+  \renewcommand*\figurename{Fig.}
+\else
+  \newcommand\figurename{Fig.}
+\fi
+\ifdefined\tablename
+  \renewcommand*\tablename{Table}
+\else
+  \newcommand\tablename{Table}
+\fi
+}
+\@ifpackageloaded{float}{}{\usepackage{float}}
+\floatstyle{ruled}
+\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
+\floatname{codelisting}{Listing}
+\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
+\makeatother
+\makeatletter
+\makeatother
+\makeatletter
+\@ifpackageloaded{caption}{}{\usepackage{caption}}
+\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
+\makeatother
+\ifLuaTeX
+\usepackage[bidi=basic]{babel}
+\else
+\usepackage[bidi=default]{babel}
+\fi
+\babelprovide[main,import]{english}
+% get rid of language-specific shorthands (see #6817):
+\let\LanguageShortHands\languageshorthands
+\def\languageshorthands#1{}
+\ifLuaTeX
+  \usepackage{selnolig}  % disable illegal ligatures
+\fi
+\usepackage[]{natbib}
+\bibliographystyle{elsarticle-harv}
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\urlstyle{same} % disable monospaced font for URLs
+\hypersetup{
+  pdftitle={MANUSCRIPT TITLE},
+  pdfauthor={Ming Su; Min Yang},
+  pdflang={en},
+  pdfkeywords={KEYWORD1, KEYWORD2, KEYWORD3},
+  colorlinks=true,
+  linkcolor={blue},
+  filecolor={Maroon},
+  citecolor={Blue},
+  urlcolor={Blue},
+  pdfcreator={LaTeX via pandoc}}
+
+\setlength{\parindent}{6pt}
+\begin{document}
+\begin{frontmatter}
+\title{MANUSCRIPT TITLE  }
+
+\author[1,2]{Ming Su%
+%
+}
+ \ead{mingsu@rcees.ac.cn} 
+\author[1,2]{Min Yang%
+\corref{cor1}%
+}
+ \ead{yangmin@rcees.ac.cn} 
+
+\affiliation[1]{organization={State Key Laboratory of Environmental
+Aquatic Chemistry, Research Center for Eco-Environmental Sciences,
+Chinese Academy of Sciences},addressline={P.O. Box
+2871},city={Beijing},postcode={100085}}
+\affiliation[2]{organization={University of Chinese Academy of
+Sciences},city={Beijing},postcode={100049}}
+
+\cortext[cor1]{Corresponding author}
+
+
+        
+\begin{abstract}
+ABSTRACT
+\end{abstract}
+
+
+
+
+
+\begin{keyword}
+    KEYWORD1 \sep KEYWORD2 \sep 
+    KEYWORD3
+\end{keyword}
+\end{frontmatter}
+\section{Introduction}\label{introduction}
+
+Blabla. \clab[r1q0101]{Bla blaBla blaBla blaBla blaBla bla Bla bla.}
+
+\section{Materials and methods}\label{materials-and-methods}
+
+\section{Results}\label{results}
+
+\section{Discussion}\label{discussion}
+
+\section{Conclusions}\label{conclusions}
+
+\section*{Acknowledgements}\label{acknowledgements}
+\addcontentsline{toc}{section}{Acknowledgements}
+
+This work was financially supported by the National Natural Science
+Foundation of China (52030002, 51878649), and Youth Innovation Promotion
+Association CAS.
+
+
+\renewcommand\refname{References}
+  \bibliography{../BB/Ref.bib,../BB/localRef.bib}
+
+
+\end{document}

MS/RN.qmd

@@ -0,0 +1,80 @@
+---
+subtitle: "Revision Note"
+msname: MS
+smname: SM
+# date: last-modified
+bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+csl: _extensions/inst/tex/elsevier-harvard.csl
+format:
+  elsevier-html:
+    filters:
+      - author-info-blocks
+    css: _extensions/inst/css/style.css
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-pdf:
+    number-sections: true
+    classoption: [nopreprintline]
+    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    latex-clean: true
+    header-includes:
+      # - \usepackage{threeparttable}
+      # - \usepackage{fontspec}
+      # - \usepackage{endfloat}
+      - \setmainfont{Calibri}
+      - \usepackage[UTF8, scheme=plain]{ctex}
+      # - \usepackage{float}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+      - \renewcommand{\thetable}{R\arabic{table}}
+      - \renewcommand{\thefigure}{R\arabic{figure}}
+      - \renewcommand{\theequation}{R\arabic{equation}}
+      - \renewcommand{\figurename}{Figure}
+      - \renewcommand{\tablename}{Table}
+    journal:
+      name: {{< meta submitjournal >}}
+      formatting: preprint # preprint | review | doublebind
+      model: 1p
+      cite-style: authoryear
+---
+
+```{r}
+#| include: false
+#| cache: false
+lang <- "en"
+RM <- "F"   # global rendermode, L: load pdata; F: fast load pdf
+isrendering = isTRUE(getOption('knitr.in.progress'))
+require(lubridate)
+require(tidyverse)
+require(patchwork)
+require(drwateR)
+require(dwfun)
+require(rmdify)
+rmdify::rmd_init()
+require(langeR)
+require(dateR)
+require(uniteR)
+require(readxl)
+Palette <- c("#515ee8", "#62e856", "#e86056", "#e8de51", "#0072B2", "#D551C0", "#CC79A7","#56E9AC")
+```
+
+# Response to Editor
+
+> 0. I very much regret to have to tell you that publication in our journal is not recommended. An explanation for this decision is given in the attached review reports (and on https://www.editorialmanager.com/wr/). I hope that the comments contained therein will be of use to you.
+
+**Response/Action:**
+
+Thank you. 
+
+# Reviewer #1:
+
+> 0. COMMENT 1
+
+**Response/Action:**
+
+Thank you very much for your revision. We made changes as shown below.
+
+`r cref("r1q0101")`
+

MS/SM.qmd

@@ -0,0 +1,69 @@
+---
+msname: MS
+smname: SM
+bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+csl: _extensions/inst/tex/elsevier-harvard.csl
+format:
+  elsevier-html:
+    filters:
+      - author-info-blocks
+    css: _extensions/inst/css/style.css
+  docx:
+    reference-doc: _extensions/inst/word/MS.docx
+    filters:
+      - author-info-blocks
+  elsevier-pdf:
+    classoption: [nopreprintline]
+    revision: true
+    keep-tex: true
+    latex-clean: false
+    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    header-includes:
+      # - \usepackage{threeparttable}
+      # - \usepackage{fontspec}
+      # - \usepackage[nomarkers]{endfloat}
+      - \usepackage[normalem]{ulem}
+      - \renewcommand{\thetable}{S\arabic{table}}
+      - \renewcommand{\thefigure}{S\arabic{figure}}
+      - \renewcommand{\theequation}{S\arabic{equation}}
+      - \setmainfont{Calibri}
+      # - \usepackage[UTF8, scheme=plain]{ctex}
+      # - \usepackage{float}
+      - \usepackage[normalem]{ulem}
+      - \usepackage[doublespacing]{setspace}
+      - \usepackage{lineno}
+      - \linenumbers
+filters:
+   - latex-environment
+commands: [clab]
+---
+
+
+```{r}
+#| label: setup
+#| include: false
+#| cache: false
+options(tinytex.clean = FALSE)
+lang <- "en"
+RM <- "F"   # global rendermode, L: load pdata; F: fast load pdf
+isRendering <- isTRUE(getOption('knitr.in.progress'))
+require(lubridate)
+require(tidyverse)
+require(patchwork)
+require(drwateR)
+require(dwfun)
+require(rmdify)
+rmdify::rmd_init()
+require(langeR)
+require(dateR)
+require(uniteR)
+```
+
+# Supplementary Material {-}
+
+Figures and/or tables are provided below as the supplementary evidences to the main text.
+
+
+\pagebreak
+
+

MS/SM.tex

@@ -0,0 +1,266 @@
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
+%
+\documentclass[
+  nopreprintline,
+  number]{elsarticle}
+
+\usepackage{amsmath,amssymb}
+\usepackage{iftex}
+\ifPDFTeX
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+  \usepackage{unicode-math}
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
+\fi
+\usepackage{lmodern}
+\ifPDFTeX\else  
+    % xetex/luatex font selection
+\fi
+% Use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\IfFileExists{microtype.sty}{% use microtype if available
+  \usepackage[]{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+  \IfFileExists{parskip.sty}{%
+    \usepackage{parskip}
+  }{% else
+    \setlength{\parindent}{0pt}
+    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+  \KOMAoptions{parskip=half}}
+\makeatother
+\usepackage{xcolor}
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\setcounter{secnumdepth}{5}
+% Make \paragraph and \subparagraph free-standing
+\ifx\paragraph\undefined\else
+  \let\oldparagraph\paragraph
+  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+  \let\oldsubparagraph\subparagraph
+  \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+
+
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}\usepackage{longtable,booktabs,array}
+\usepackage{calc} % for calculating minipage widths
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+\usepackage{graphicx}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+
+\usepackage{adjustbox}
+% \usepackage{xcolor}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+% setup hyperlink for page and line number
+\def\msname{MS}
+\def\smname{SM}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+\newcommand{\clab}[2][]{
+		\protected@write\@auxout{\let\clab\@secondoftwo}{
+				\string\newlabel{r:#1}{{#2}{}}}%
+		\hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+
+\usepackage[normalem]{ulem}
+\renewcommand{\thetable}{S\arabic{table}}
+\renewcommand{\thefigure}{S\arabic{figure}}
+\renewcommand{\theequation}{S\arabic{equation}}
+\setmainfont{Calibri}
+\usepackage[doublespacing]{setspace}
+\usepackage{lineno}
+\linenumbers
+\makeatletter
+\@ifpackageloaded{caption}{}{\usepackage{caption}}
+\AtBeginDocument{%
+\ifdefined\contentsname
+  \renewcommand*\contentsname{Table of contents}
+\else
+  \newcommand\contentsname{Table of contents}
+\fi
+\ifdefined\listfigurename
+  \renewcommand*\listfigurename{List of Figures}
+\else
+  \newcommand\listfigurename{List of Figures}
+\fi
+\ifdefined\listtablename
+  \renewcommand*\listtablename{List of Tables}
+\else
+  \newcommand\listtablename{List of Tables}
+\fi
+\ifdefined\figurename
+  \renewcommand*\figurename{Fig.}
+\else
+  \newcommand\figurename{Fig.}
+\fi
+\ifdefined\tablename
+  \renewcommand*\tablename{Table}
+\else
+  \newcommand\tablename{Table}
+\fi
+}
+\@ifpackageloaded{float}{}{\usepackage{float}}
+\floatstyle{ruled}
+\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
+\floatname{codelisting}{Listing}
+\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
+\makeatother
+\makeatletter
+\makeatother
+\makeatletter
+\@ifpackageloaded{caption}{}{\usepackage{caption}}
+\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
+\makeatother
+\ifLuaTeX
+\usepackage[bidi=basic]{babel}
+\else
+\usepackage[bidi=default]{babel}
+\fi
+\babelprovide[main,import]{english}
+% get rid of language-specific shorthands (see #6817):
+\let\LanguageShortHands\languageshorthands
+\def\languageshorthands#1{}
+\ifLuaTeX
+  \usepackage{selnolig}  % disable illegal ligatures
+\fi
+\usepackage[]{natbib}
+\bibliographystyle{elsarticle-num}
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\urlstyle{same} % disable monospaced font for URLs
+\hypersetup{
+  pdftitle={MANUSCRIPT TITLE},
+  pdfauthor={Ming Su; Min Yang},
+  pdflang={en},
+  colorlinks=true,
+  linkcolor={blue},
+  filecolor={Maroon},
+  citecolor={Blue},
+  urlcolor={Blue},
+  pdfcreator={LaTeX via pandoc}}
+
+\setlength{\parindent}{6pt}
+\begin{document}
+\begin{frontmatter}
+\title{MANUSCRIPT TITLE  }
+
+\author[1,2]{Ming Su%
+%
+}
+ \ead{mingsu@rcees.ac.cn} 
+\author[1,2]{Min Yang%
+\corref{cor1}%
+}
+ \ead{yangmin@rcees.ac.cn} 
+
+\affiliation[1]{organization={State Key Laboratory of Environmental
+Aquatic Chemistry, Research Center for Eco-Environmental Sciences,
+Chinese Academy of Sciences},addressline={P.O. Box
+2871},city={Beijing},postcode={100085}}
+\affiliation[2]{organization={University of Chinese Academy of
+Sciences},city={Beijing},postcode={100049}}
+
+\cortext[cor1]{Corresponding author}
+
+
+        
+
+
+
+
+
+\end{frontmatter}
+\section*{Supplementary Material}\label{supplementary-material}
+\addcontentsline{toc}{section}{Supplementary Material}
+
+Figures and/or tables are provided below as the supplementary evidences
+to the main text.
+
+\pagebreak
+
+
+  \bibliography{../BB/Ref.bib,../BB/localRef.bib}
+
+
+\end{document}

MS/_extensions

@@ -0,0 +1 @@
+../_extensions

MS/index.qmd

@@ -0,0 +1,25 @@
+---
+subtitle: Graphical abstract
+format: html
+---
+
+```{r}
+#| label: fig-GA3
+#| fig-cap: "Graphical abstract"
+#| out-width: "100%"
+#| echo: false
+#| message: false
+# dwfun::ggsavep("./figures/GA3.pdf", loadit = TRUE)
+```
+
+
+# README
+
+Below are the typical links.
+
+- [Cover Letter](CL.html)
+- [Highlights](HL.html)
+- [Manuscript](MS.html)
+- [Supplementary Material](SM.html)
+- [Revision Note](RN.html)
+- [Author Credits](AC.html)

PP/1-申请书/index.html.md

@@ -1,77 +0,0 @@
----
-subtitle: "申请书"
-author: "中国科学院生态环境研究中心"
-lang: zh
-date: today
-csl: _extensions/inst/china-national-standard-gb-t-7714-2015-numeric.csl
-format:
-  html:
-    theme: cosmo
-    keep-md: true
-    css: _extensions/inst/style.css
-    code-link: true
-  epub: default
-  pdf:
-    pdf-engine: xelatex
-    keep-tex: false
-    toc-title: 目录
-    classoption:
-      - 12pt
-      - lang=cn
-      - chinesefont=founder # founder|ctexfont|nofont
-      - scheme=chinese
-      - color=blue # blue|green|
-      - titlestyle=hang
-      # - twoside
-    header-includes:
-      - \usepackage{ctex}
-      - \linespread{1.5}
-  docx:
-    toc: false
-    highlight-style: github
-    reference-doc: _extensions/inst/repcn.docx
----
-
-
-
-
-
-
-::: {.content-visible when-format="html"}
-# Color tip {.unnumbered}
-
--   [Something should be deleted]{.del}
--   [Something bad]{.bad}
--   [Something good]{.good}
--   [Something todo]{.todo}
--   [Something should be added]{.add}
--   [I am a comment]{.com}
-:::
-
-
-
-
-
-
-
-
-
-
-
-
-# 摘要
-
-# 项目背景与国内外现状介绍
-
-# 研究内容与目标
-
-# 研究方案
-
-# 预期目标
-
-# 年度计划
-
-# 经费预算
-
-
-# 参考文献{-}

PP/1-申请书/index.qmd

@@ -1,82 +0,0 @@
----
-subtitle: "申请书"
-author: "中国科学院生态环境研究中心"
-lang: zh
-date: today
-csl: _extensions/inst/china-national-standard-gb-t-7714-2015-numeric.csl
-format:
-  html:
-    theme: cosmo
-    keep-md: true
-    css: _extensions/inst/style.css
-    code-link: true
-  epub: default
-  pdf:
-    pdf-engine: xelatex
-    keep-tex: false
-    toc-title: 目录
-    classoption:
-      - 12pt
-      - lang=cn
-      - chinesefont=founder # founder|ctexfont|nofont
-      - scheme=chinese
-      - color=blue # blue|green|
-      - titlestyle=hang
-      # - twoside
-    header-includes:
-      - \usepackage{ctex}
-      - \linespread{1.5}
-  docx:
-    toc: false
-    highlight-style: github
-    reference-doc: _extensions/inst/repcn.docx
----
-
-::: {.content-visible when-format="html"}
-# Color tip {.unnumbered}
-
--   [Something should be deleted]{.del}
--   [Something bad]{.bad}
--   [Something good]{.good}
--   [Something todo]{.todo}
--   [Something should be added]{.add}
--   [I am a comment]{.com}
-:::
-
-
-```{r}
-#| label: setup
-#| include: false
-#| cache: false
-lang <- "cn"
-RM <- "F"   # global rendermode, L: load pdata; F: fast load pdf
-isRendering <- !isTRUE(getOption('knitr.in.progress'))
-require(lubridate)
-require(tidyverse)
-require(patchwork)
-require(drwateR)
-require(rmdify)
-rmdify::rmd_init()
-require(langeR)
-require(dateR)
-require(uniteR)
-require(limvis)
-require(sf)
-```
-
-# 摘要
-
-# 项目背景与国内外现状介绍
-
-# 研究内容与目标
-
-# 研究方案
-
-# 预期目标
-
-# 年度计划
-
-# 经费预算
-
-
-# 参考文献{-}

PP/index.qmd

@@ -1,20 +0,0 @@
----
-subtitle: "申请书"
----
-
-```{r}
-#| include: false
-
-require(drwateR)
-require(rmdify)
-rmdify::rmd_init()
-```
-
-```{r}
-#| output: asis
-dir(".", pattern = "[_-]") |>
-purrr::map(~paste0("## [", .x, "](", .x, "/index.qmd)\n\n")) |>
-  unlist() |>
-  cat()
-
-```

RP/20231231_XX项目报告/index.qmd

@@ -2,12 +2,12 @@
 author: "中国科学院生态环境研究中心"
 lang: zh
 date: today
-csl: _extensions/inst/china-national-standard-gb-t-7714-2015-numeric.csl
+csl: _extensions/inst/tex/china-national-standard-gb-t-7714-2015-numeric.csl
 format:
   html:
     theme: cosmo
     keep-md: true
-    css: _extensions/inst/style.css
+    css: _extensions/inst/css/style.css
     code-link: true
   epub: default
   pdf:
@@ -28,7 +28,7 @@ format:
   docx:
     toc: false
     highlight-style: github
-    reference-doc: _extensions/inst/repcn.docx
+    reference-doc: _extensions/inst/word/repcn.docx
 ---
 
 ::: {.content-visible when-format="html"}

RP/20231231_项目中期汇报/_extensions

@@ -1 +0,0 @@
-../../_extensions

RP/20231231_项目中期汇报/index.html.md

@@ -1,72 +0,0 @@
----
-author: "中国科学院生态环境研究中心"
-lang: zh
-date: today
-csl: _extensions/inst/china-national-standard-gb-t-7714-2015-numeric.csl
-format:
-  html:
-    theme: cosmo
-    keep-md: true
-    css: _extensions/inst/style.css
-    code-link: true
-  epub: default
-  pdf:
-    pdf-engine: xelatex
-    keep-tex: false
-    toc-title: 目录
-    classoption:
-      - 12pt
-      - lang=cn
-      - chinesefont=founder # founder|ctexfont|nofont
-      - scheme=chinese
-      - color=blue # blue|green|
-      - titlestyle=hang
-      # - twoside
-    header-includes:
-      - \usepackage{ctex}
-      - \linespread{1.5}
-  docx:
-    toc: false
-    highlight-style: github
-    reference-doc: _extensions/inst/repcn.docx
----
-
-
-
-
-
-
-::: {.content-visible when-format="html"}
-# Color tip {.unnumbered}
-
--   [Something should be deleted]{.del}
--   [Something bad]{.bad}
--   [Something good]{.good}
--   [Something todo]{.todo}
--   [Something should be added]{.add}
--   [I am a comment]{.com}
-:::
-
-
-
-
-
-
-
-
-
-
-
-
-# 摘要
-
-# 项目背景与国内外现状介绍
-
-# 主要进展1
-
-# 主要进展2
-
-# 结论与下一步计划
-
-
-# 参考文献{-}

RP/index.qmd

@@ -1,5 +1,6 @@
 ---
 subtitle: "研究报告"
+lang: "zh"
 ---
 
 ```{r}
@@ -12,9 +13,19 @@ rmdify::rmd_init()
 
 ```{r}
 #| output: asis
-dir(".", pattern = "[_-]") |>
+
-purrr::map(~paste0("## [", .x, "](", .x, "/index.qmd)\n\n")) |>
+data.frame(fd = dir(".", pattern = "[-_]")) |>
-  unlist() |>
+  dplyr::mutate(fn = purrr::map_chr(fd, ~ file.path(.x, dir(.x,
+    pattern = "index.qmd|index.doc|index.pdf|index.ppt")))) |>
+  dplyr::transmute(htmlstr = purrr::map_chr(fn, ~ paste0("## [", .x, "](", .x, ")\n\n",
+    ifelse(!grepl("qmd$", .x), "",
+    paste0("<iframe title='",
+    gsub("^.*[_-]([^\\/]*)\\/.*$", "\\1", .x),
+      "' width=800 height=600 src = '",
+      gsub("qmd$", "html", .x),
+    "'></iframe>\n\n"))))) |>
+  dplyr::pull(htmlstr) |>
+  paste(collapse = "") |>
   cat()
 
 ```

SD/20230101_文章讨论/index.qmd

@@ -0,0 +1,5 @@
+---
+title: "文章讨论"
+format: revealjs
+---
+

SD/20230101_项目启动/index.qmd

@@ -1,12 +0,0 @@
----
-title: "项目启动汇报"
-format: revealjs
----
-
-# 项目背景
-
-# 科学问题
-
-# 主要进展
-
-# 小结与计划

SD/index.qmd

@@ -2,6 +2,28 @@
 subtitle: "演示材料"
 ---
 
-## [项目启动汇报](./20230101_项目启动/index.qmd)
-
 <iframe title="项目启动汇报" width=800 height=600 src = "./20230101_项目启动/index.html"></iframe>
+
+```{r}
+#| include: false
+require(drwateR)
+require(rmdify)
+rmdify::rmd_init()
+```
+
+```{r}
+#| output: asis
+data.frame(fd = dir(".", pattern = "[-_]")) |>
+  dplyr::mutate(fn = purrr::map_chr(fd, ~ file.path(.x, dir(.x,
+    pattern = "index.qmd|index.doc|index.pdf|index.ppt")))) |>
+  dplyr::transmute(htmlstr = purrr::map_chr(fn, ~ paste0("## [", .x, "](", .x, ")\n\n",
+    ifelse(!grepl("qmd$", .x), "",
+    paste0("<iframe title='",
+    gsub("^.*[_-]([^\\/]*)\\/.*$", "\\1", .x),
+      "' width=800 height=600 src = '",
+      gsub("qmd$", "html", .x),
+    "'></iframe>\n\n"))))) |>
+  dplyr::pull(htmlstr) |>
+  paste(collapse = "") |>
+  cat()
+```

TC/index.qmd

@@ -0,0 +1,29 @@
+---
+subtitle: "演示材料"
+---
+
+<iframe title="项目启动汇报" width=800 height=600 src = "./20230101_项目启动/index.html"></iframe>
+
+```{r}
+#| include: false
+require(drwateR)
+require(rmdify)
+rmdify::rmd_init()
+```
+
+```{r}
+#| output: asis
+data.frame(fd = dir(".", pattern = "[-_]")) |>
+  dplyr::mutate(fn = purrr::map_chr(fd, ~ file.path(.x, dir(.x,
+    pattern = "index.qmd|index.doc|index.pdf|index.ppt")))) |>
+  dplyr::transmute(htmlstr = purrr::map_chr(fn, ~ paste0("## [", .x, "](", .x, ")\n\n",
+    ifelse(!grepl("qmd$", .x), "",
+    paste0("<iframe title='",
+    gsub("^.*[_-]([^\\/]*)\\/.*$", "\\1", .x),
+      "' width=800 height=600 src = '",
+      gsub("qmd$", "html", .x),
+    "'></iframe>\n\n"))))) |>
+  dplyr::pull(htmlstr) |>
+  paste(collapse = "") |>
+  cat()
+```

_extensions/inst/tex/american-chemical-society.csl

@@ -0,0 +1,280 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" page-range-format="expanded" default-locale="en-US">
+  <info>
+    <title>American Chemical Society</title>
+    <title-short>ACS</title-short>
+    <id>http://www.zotero.org/styles/american-chemical-society</id>
+    <link href="http://www.zotero.org/styles/american-chemical-society" rel="self"/>
+    <link href="https://pubs.acs.org/doi/full/10.1021/acsguide.40303" rel="documentation"/>
+    <link href="https://pubs.acs.org/doi/book/10.1021/acsguide" rel="documentation"/>
+    <author>
+      <name>Julian Onions</name>
+      <email>julian.onions@gmail.com</email>
+    </author>
+    <contributor>
+      <name>Ivan Bushmarinov</name>
+      <email>ib@ineos.ac.ru</email>
+    </contributor>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="chemistry"/>
+    <summary>The American Chemical Society style</summary>
+    <updated>2021-06-04T03:27:50+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <locale xml:lang="en">
+    <terms>
+      <term name="editortranslator" form="short">
+        <single>ed. and translator</single>
+        <multiple>eds. and translators</multiple>
+      </term>
+      <term name="translator" form="short">
+        <single>translator</single>
+        <multiple>translators</multiple>
+      </term>
+      <term name="collection-editor" form="short">
+        <single>series ed.</single>
+        <multiple>series eds.</multiple>
+      </term>
+    </terms>
+  </locale>
+  <macro name="editor">
+    <group delimiter="; ">
+      <names variable="editor translator" delimiter="; ">
+        <name sort-separator=", " initialize-with=". " name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+        <label form="short" prefix=", " text-case="title"/>
+      </names>
+      <names variable="collection-editor">
+        <name sort-separator=", " initialize-with=". " name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+        <label form="short" prefix=", " text-case="title"/>
+      </names>
+    </group>
+  </macro>
+  <macro name="author">
+    <names variable="author" suffix=".">
+      <name sort-separator=", " initialize-with=". " name-as-sort-order="all" delimiter="; " delimiter-precedes-last="always"/>
+      <label form="short" prefix=", " text-case="capitalize-first"/>
+    </names>
+  </macro>
+  <macro name="publisher">
+    <choose>
+      <if type="thesis" match="any">
+        <group delimiter=", ">
+          <text variable="publisher"/>
+          <text variable="publisher-place"/>
+        </group>
+      </if>
+      <else>
+        <group delimiter=": ">
+          <text variable="publisher"/>
+          <text variable="publisher-place"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <text variable="title" text-case="title" font-style="italic"/>
+      </if>
+      <else>
+        <text variable="title" text-case="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="volume">
+    <group delimiter=" ">
+      <text term="volume" form="short" text-case="capitalize-first"/>
+      <text variable="volume"/>
+    </group>
+  </macro>
+  <macro name="series">
+    <text variable="collection-title"/>
+  </macro>
+  <macro name="pages">
+    <label variable="page" form="short" suffix=" " strip-periods="true"/>
+    <text variable="page"/>
+  </macro>
+  <macro name="book-container">
+    <group delimiter=". ">
+      <text macro="title"/>
+      <choose>
+        <if type="entry-dictionary entry-encyclopedia" match="none">
+          <group delimiter=" ">
+            <text term="in" text-case="capitalize-first"/>
+            <text variable="container-title" font-style="italic"/>
+          </group>
+        </if>
+        <else>
+          <text variable="container-title" font-style="italic"/>
+        </else>
+      </choose>
+    </group>
+  </macro>
+  <macro name="issued">
+    <date variable="issued" delimiter=" ">
+      <date-part name="year"/>
+    </date>
+  </macro>
+  <macro name="full-issued">
+    <date variable="issued" delimiter=" ">
+      <date-part name="month" form="long" suffix=" "/>
+      <date-part name="day" suffix=", "/>
+      <date-part name="year"/>
+    </date>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout delimiter="," vertical-align="sup">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography second-field-align="flush" entry-spacing="0">
+    <layout suffix=".">
+      <text variable="citation-number" prefix="(" suffix=") "/>
+      <text macro="author" suffix=" "/>
+      <choose>
+        <if type="article-journal review" match="any">
+          <group delimiter=" ">
+            <text macro="title" suffix="."/>
+            <text variable="container-title" font-style="italic" form="short"/>
+            <group delimiter=", ">
+              <text macro="issued" font-weight="bold"/>
+              <choose>
+                <if variable="volume">
+                  <group delimiter=" ">
+                    <text variable="volume" font-style="italic"/>
+                    <text variable="issue" prefix="(" suffix=")"/>
+                  </group>
+                </if>
+                <else>
+                  <group delimiter=" ">
+                    <text term="issue" form="short" text-case="capitalize-first"/>
+                    <text variable="issue"/>
+                  </group>
+                </else>
+              </choose>
+              <text variable="page"/>
+            </group>
+          </group>
+        </if>
+        <else-if type="article-magazine article-newspaper article" match="any">
+          <group delimiter=" ">
+            <text macro="title" suffix="."/>
+            <text variable="container-title" font-style="italic" suffix="."/>
+            <text macro="edition"/>
+            <text macro="publisher"/>
+            <group delimiter=", ">
+              <text macro="full-issued"/>
+              <text macro="pages"/>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="thesis">
+          <group delimiter=", ">
+            <group delimiter=". ">
+              <text macro="title"/>
+              <text variable="genre"/>
+            </group>
+            <text macro="publisher"/>
+            <text macro="issued"/>
+            <text macro="volume"/>
+            <text macro="pages"/>
+          </group>
+        </else-if>
+        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+          <group delimiter="; ">
+            <group delimiter=", ">
+              <text macro="title"/>
+              <text macro="edition"/>
+            </group>
+            <text macro="editor" prefix=" "/>
+            <text macro="series"/>
+            <choose>
+              <if type="report">
+                <group delimiter=" ">
+                  <text variable="genre"/>
+                  <text variable="number"/>
+                </group>
+              </if>
+            </choose>
+            <group delimiter=", ">
+              <text macro="publisher"/>
+              <text macro="issued"/>
+            </group>
+            <group delimiter=", ">
+              <text macro="volume"/>
+              <text macro="pages"/>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="patent">
+          <group delimiter=", ">
+            <group delimiter=". ">
+              <text macro="title"/>
+              <text variable="number"/>
+            </group>
+            <date variable="issued" form="text"/>
+          </group>
+        </else-if>
+        <else-if type="chapter paper-conference entry-dictionary entry-encyclopedia" match="any">
+          <group delimiter="; ">
+            <text macro="book-container"/>
+            <text macro="editor"/>
+            <text macro="series"/>
+            <group delimiter=", ">
+              <text macro="publisher"/>
+              <text macro="issued"/>
+            </group>
+            <group delimiter=", ">
+              <text macro="volume"/>
+              <text macro="pages"/>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="webpage">
+          <group delimiter=" ">
+            <text variable="title"/>
+            <text variable="URL"/>
+            <date variable="accessed" prefix="(accessed " suffix=")" delimiter=" ">
+              <date-part name="year"/>
+              <date-part name="month" prefix="-" form="numeric-leading-zeros"/>
+              <date-part name="day" prefix="-" form="numeric-leading-zeros"/>
+            </date>
+          </group>
+        </else-if>
+        <else>
+          <group delimiter=", ">
+            <group delimiter=". ">
+              <text macro="title"/>
+              <text variable="container-title" font-style="italic"/>
+            </group>
+            <group delimiter=", ">
+              <text macro="issued"/>
+              <text variable="volume" font-style="italic"/>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else>
+      </choose>
+      <text variable="DOI" prefix=". https://doi.org/"/>
+    </layout>
+  </bibliography>
+</style>

_extensions/inst/tex/cv.tex

@@ -0,0 +1,240 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Academic Letter LaTeX and RMarkdown Structure                       %
+% Author: Pedro Henrique Pereira Braga                                %
+%                                                                     %
+% License:                                                            %
+% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/) %
+%                                                                     %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Set the font size (11pt, for now) and paper size (e.g. letterpaper, a4paper)
+\documentclass[11pt, letterpaper]{letter} 
+
+%----------------------------------------------------------------------
+%	PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
+%----------------------------------------------------------------------
+
+\usepackage{graphicx} % Required for including pictures
+\usepackage{fancyhdr} % Allows the use of fancy headers and footers
+
+\usepackage{microtype} % For typography improvement
+
+\usepackage{url} % Allows the use of hyperlinks
+\urlstyle{same} % Allows hyperlink fonts to be the same as the mainfont
+\usepackage[hidelinks]{hyperref} % Allows the use of hyperlinks and 
+% removes the blue boxes around the link
+
+\pagestyle{empty} % Removes headers and footers
+
+\usepackage{setspace} % Allows the use of double spacing in the letter body
+
+\setlength\parindent{1cm} % Paragraph indentation
+
+% Create a new command for the horizontal rule in the document which allows 
+% thickness specification
+\makeatletter
+  \def\@texttop{} % force the address to start above
+\renewcommand*{\opening}[1]{\ifx\@empty\fromaddress
+  \thispagestyle{firstpage}%
+    {\raggedleft\@date\par}%
+  \else  % home address
+    \thispagestyle{empty}%
+    {\raggedleft\begin{tabular}{l@{}}\ignorespaces
+      \fromaddress \\*[2\parskip]%
+      \@date \end{tabular}\par}%
+  \fi
+  %\vspace{2\parskip}%                        <-- Removed
+  %{\raggedright \toname \\ \toaddress \par}% <-- Removed
+  %\vspace{2\parskip}%                        <-- Removed
+  #1\par\nobreak}
+\let\ps@empty\ps@plain
+\let\ps@firstpage\ps@plain
+\makeatother
+
+%--------------------------------------------------------------------------
+%	FONTS
+%--------------------------------------------------------------------------
+
+\usepackage[T1]{fontenc} % Output font encoding for international characters
+% \usepackage[utf8]{inputenc} % Required for inputting international characters
+\usepackage[quiet]{fontspec} % Allows the use of fontspec
+\setmainfont{Calibri}
+% \usepackage{txfonts} % Allows the use of Lato fonts
+
+
+%----------------------------------------------------------------------------
+%	DOCUMENT MARGINS
+%----------------------------------------------------------------------------
+
+\usepackage{geometry} % Required for adjusting page dimensions
+
+\geometry{
+    headheight = 0.7in, % Header height
+	top=1.5in, % Top margin
+	bottom=1.5cm, % Bottom margin
+	left=3cm, % Left margin
+	right=3cm, % Right margin
+	% showframe, % Uncomment to show how the type block is set on the page
+}
+
+%-----------------------------------------------------------------------------
+%	AUTHOR AND RECIPIENTS NEW COMMANDS AND DETAILS STRUCTURE
+%-----------------------------------------------------------------------------
+
+\newcommand{\authordetails}[1]{\renewcommand{\authordetails}{#1}}
+\newcommand{\recipientdetails}[1]{\renewcommand{\recipientdetails}{#1}}
+
+%-----------------------------------------------------------------------------
+%	HEADER STRUCTURE
+%-----------------------------------------------------------------------------
+
+\address{
+ % Include the author's details on the right side of the page under the line
+	\raggedleft{
+		\footnotesize{ % Use a smaller font size
+		$author$\\ % Author name
+		\authordetails\\
+       \hspace{1mm}
+       }
+	}
+	\vspace{-0.05\textheight} % Move the date and letter content up
+}
+
+%------------------------------------------------------------------------------
+%	COMPOSE THE ENTIRE HEADER
+%------------------------------------------------------------------------------
+
+\renewcommand{\opening}[1]{
+	{\fromaddress
+    \vspace{0.05\textheight}\\ % Print the sender's address here and add some whitespace to allow the printing of the date
+    \raggedleft{$date$} % Include the date, aligned to the right
+    \par % par
+    }
+	{\raggedright 
+    \toname\\ 
+    \toaddress 
+    \par} % Print the recipient's name and adress
+	\vspace{0.25cm} % White vertical space after recipient's address
+	\noindent #1 % Following this, insert the opening info
+}
+
+%------------------------------------------------------------------------------
+%	SIGNATURE STRUCTURE
+%------------------------------------------------------------------------------
+% The signature is a combination of the author's name, title and institution
+\signature{$author$, on behalf of all authors\\
+           Email: $from_email$} 
+
+% I will later combine the option of inserting a signature within it
+           
+\renewcommand{\closing}[1]{
+	\vspace{2.5mm} % Some whitespace after the letter content and before the signature
+	\noindent % Stop paragraph indentation
+	% \hspace*{\longindentation} % Move the signature right to the value of \longindentation
+	\parbox{\indentedwidth}{
+		\raggedright
+		#1 % Print the signature text
+		% \vskip 1.65cm % Whitespace between the closing text and author's name for a physical signature
+                \\\includegraphics[height=0.6in, keepaspectratio=true]{$from_sign$}\\
+		\fromsig % Prints the value of \signature{}, i.e. author name and title
+	}
+}
+
+%-------------------------------------------------------------------------------
+%	AUTHOR'S INFORMATION
+%-------------------------------------------------------------------------------
+
+\authordetails{
+    $from_position$\\
+	$from_department$\\ % Sender's department/institution
+    $from_institution$\\
+    $from_address$ % Sender's address
+	% $from_city$, $from_state_province$\\ % Sender's city, state or province,
+    % $from_postalcode$\\ % postal code
+    % $from_country$
+}
+
+%------------------------------------------------------------------------------
+%	RECIPIENT'S INFORMATION
+%------------------------------------------------------------------------------
+
+\recipientdetails{
+$to_professional_title$ $to_name$\\
+    $if(to_journal)$
+\textit{$to_journal$}
+$endif$
+}
+
+%------------------------------------------------------------------------------
+%	HEADER CONTENTS
+%------------------------------------------------------------------------------
+
+\fancypagestyle{firstpage}{
+    \fancyhf{}
+        \fancyhead[L]{
+            \includegraphics[height=0.6in, keepaspectratio=true]{$from_institution_logo$}
+            }
+        \fancyhead[R]{$author$\\
+            \footnotesize{
+              $from_email$\\ % Sender's email address
+              % $from_personal_website$ \\ % Sender's URL
+              $from_phone$ % Sender's phone number
+              }
+            }
+        }
+
+\fancypagestyle{plain}{
+    \fancyhf{}
+        \fancyhead[L]{
+            \includegraphics[height=0.6in, keepaspectratio=true]{$from_institution_logo$}
+            }
+        \fancyhead[R]{$author$\\
+            \footnotesize{
+              $from_email$\\ % Sender's email address
+              % $from_personal_website$ \\ % Sender's URL
+              $from_phone$ % Sender's phone number
+              }
+            }
+        }
+
+\fancypagestyle{empty}{
+    \fancyhf{}
+        \fancyhead[L]{
+            \includegraphics[height=0.6in, keepaspectratio=true]{$from_institution_logo$}
+            }
+        \fancyhead[R]{$author$\\
+            \footnotesize{
+              $from_email$\\ % Sender's email address
+              % $from_personal_website$ \\ % Sender's URL
+              $from_phone$ % Sender's phone number
+              }
+            }
+        }
+
+%------------------------------------------------------------------------------
+\pagestyle{plain}
+
+\begin{document}
+
+%------------------------------------------------------------------------------
+%	TO ADDRESS
+%------------------------------------------------------------------------------
+
+\begin{letter}{\recipientdetails}
+
+%------------------------------------------------------------------------------
+%	LETTER CONTENT
+%------------------------------------------------------------------------------
+
+\opening{$opening_greeting$}
+% \begin{doublespacing}
+
+$body$
+
+% \end{doublespacing}
+\closing{$closing_greeting$}
+
+%------------------------------------------------------------------------------
+
+\end{letter}
+\end{document}

_extensions/inst/tex/els.tex

@@ -0,0 +1,426 @@
+$-- Keeping in template layout for backward compatibility
+\documentclass[$if(layout)$$layout$$else$$for(classoption)$$classoption$$sep$,$endfor$$endif$]{elsarticle} %review=doublespace preprint=single 5p=2 column
+%%% Begin My package additions %%%%%%%%%%%%%%%%%%%
+\usepackage[hyphens]{url}
+$if(journal)$
+\journal{$journal$} % Sets Journal name
+$endif$
+\usepackage{lineno} % add
+$if(linenumbers)$
+\linenumbers % turns line numbering on
+$endif$
+\usepackage{graphicx}
+\usepackage{xstring}
+\usepackage[table]{xcolor}
+%%%%%%%%%%%%%%%% end my additions to header
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+    \usepackage[utf8]{inputenc}
+    $if(euro)$
+    \usepackage{eurosym}
+    $endif$
+\else % if luatex or xelatex
+    \usepackage{fontspec}
+    \ifxetex
+    \usepackage{xltxtra,xunicode}
+    \fi
+    \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
+    \newcommand{\euro}{€}
+    $if(mainfont)$
+    \setmainfont{$mainfont$}
+    $endif$
+    $if(sansfont)$
+    \setsansfont{$sansfont$}
+    $endif$
+    $if(monofont)$
+    \setmonofont{$monofont$}
+    $endif$
+    $if(mathfont)$
+    \setmathfont{$mathfont$}
+    $endif$
+\fi
+% use microtype if available
+\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
+$if(geometry)$
+\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$if(natbib)$
+\usepackage{natbib}
+\setcitestyle{$natbiboptions$}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(listings)$
+\usepackage{listings}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+$if(graphics)$
+\usepackage{graphicx}
+$endif$
+\ifxetex
+    \usepackage[setpagesize=false, % page size defined by xetex
+                unicode=false, % unicode breaks when used with xetex
+                xetex]{hyperref}
+\else
+    \usepackage[unicode=true]{hyperref}
+\fi
+\hypersetup{breaklinks=true,
+            bookmarks=true,
+            pdfauthor={$author-meta$},
+            pdftitle={$title-meta$},
+            colorlinks=$if(colorlinks)$true$else$false$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
+            pdfborder={0 0 0}}
+\urlstyle{same}  % don't use monospace font for urls
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+$if(numbersections)$
+\setcounter{secnumdepth}{5}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(lang)$
+\ifxetex
+    \usepackage{polyglossia}
+    \setmainlanguage{$mainlang$}
+\else
+    \usepackage[$lang$]{babel}
+\fi
+$endif$
+% Pandoc toggle for numbering sections (defaults to be off)
+$if(numbersections)$
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(highlighting-macros)$
+% Pandoc syntax highlighting
+$highlighting-macros$
+$endif$
+% tightlist command for lists without linebreak
+\providecommand{\tightlist}{%
+    \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(tables)$
+% From pandoc table feature
+\usepackage{longtable,booktabs,array}
+$if(multirow)$
+\usepackage{multirow}
+$endif$
+\usepackage{calc} % for calculating minipage widths
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+$endif$
+$if(csl-refs)$
+% Pandoc citation processing
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacingunit} % times entry-spacing
+\setlength{\cslentryspacingunit}{\parskip}
+% for Pandoc 2.8 to 2.10.1
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+% For Pandoc 2.11+
+\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
+{% don't indent paragraphs
+    \setlength{\parindent}{0pt}
+    % turn on hanging indent if param 1 is 1
+    \ifodd #1
+    \let\oldpar\par
+    \def\par{\hangindent=\cslhangindent\oldpar}
+    \fi
+    % set entry spacing
+    \setlength{\parskip}{#2\cslentryspacingunit}
+    }%
+{}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+\usepackage{xifthen}
+% set special color for EST
+\ifthenelse{\equal{$journal$}{Environmental Science \& Technology}}
+{\definecolor{seccol}{RGB}{56, 95, 66}}
+{\definecolor{seccol}{RGB}{0, 0, 0}}
+
+$if(uppersections)$
+\usepackage{titlesec}
+\titleformat{\section}
+{\color{seccol}\large\bfseries\MakeUppercase}{\thesection}{1em}{}
+$endif$
+$if(sectiononnewpage)$
+\AddToHook{cmd/section/before}{\clearpage}
+$endif$
+
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\setmainfont{Helvetica}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+% force to use \zref
+$if(msname)$
+\def\msname{$msname$}
+\zexternaldocument*{\msname}
+\renewcommand{\ref}{\zref}
+$endif$
+$if(smname)$
+\def\smname{$smname$}
+\zexternaldocument*{\smname}
+$endif$
+
+\zxrsetup{toltxlabel=true}
+{\catcode`\#=12 \gdef\hashchar{#1}}
+\makeatletter
+\newcommand\hzref[1]{\edef\next{%
+    \noexpand\href{%
+      \zref@extractdefault{#1}{url}{}%
+      \zref@ifrefcontainsprop{#1}{anchor}{%
+      \hashchar\zref@extract{#1}{anchor}}{}}%
+      {\noexpand\zref{#1}}}\next}
+\makeatother
+
+
+
+$if(revision)$
+% \usepackage{xcolor}
+\usepackage{adjustbox}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+% setup hyperlink for page and line number
+\def\msname{$if(msname)$$msname$$else$MS$endif$}
+\def\smname{$if(smname)$$smname$$else$SM$endif$}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+    \newcommand{\clab}[2]{%
+        \protected@write\@auxout{\let\clab\@secondoftwo}{
+        \string\newlabel{r:#1}{{#2}{}}}%
+        \hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+$endif$
+
+% def default corresponding authors and equal contributing authors variables
+\def\hascorr{0}
+\def\haseqc{0}
+% check if corresponding author(s) and equal contributing authors are available
+$for(author)$$if(author.correspondence)$\def\hascorr{1}$endif$$if(author.equalcontribution)$\def\haseqc{1}$endif$ $endfor$
+
+\newcommand{\getcorrauthinfo}{
+    \subsection{Corresponding Author(s)}
+    \def\a{} \def\b{} \def\c{}
+    \hspace{-2.2em}
+    $for(author)$
+    $if(author.correspondence)$
+    \textbf{$author.name$:}
+    \vspace{-1em}
+    \begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
+    $for(author.institute)$ \def\a{$author.institute$}
+    $for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
+        \ifx \a\b \item \c; \fi
+    $endfor$ 
+    $endfor$ 
+        $if(author.email)$\item email: $author.email$;$endif$
+        $if(author.orcid)$\item orcid: $author.orcid$;$endif$
+        $if(author.tel)$\item Tel: $author.tel$;$endif$
+        $if(author.fax)$\item Fax: $author.fax$$endif$
+    \end{enumerate}
+    $endif$
+    $endfor$
+}
+
+\newcommand{\getotherauthinfo}{
+    \subsection{Author(s)}
+    \def\a{} \def\b{} \def\c{}
+    \hspace{-2.2em}
+    $for(author)$
+    $if(author.correspondence)$
+    $else$
+    \textbf{$author.name$:}
+    \vspace{-1em}
+    \begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
+    $for(author.institute)$ \def\a{$author.institute$} $for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
+        \ifx \a\b \item \c; \fi
+    $endfor$ 
+    $endfor$ 
+        $if(author.email)$\item email: $author.email$;$endif$
+        $if(author.orcid)$\item orcid: $author.orcid$;$endif$
+        $if(author.tel)$\item Tel: $author.tel$;$endif$
+        $if(author.fax)$\item Fax: $author.fax$$endif$
+    \end{enumerate}
+    $endif$
+    $endfor$
+}
+
+$preamble$
+
+% remove the two line around Abstract
+$if(abstract)$
+$else$
+\makeatletter
+\renewcommand{\MaketitleBox}{%
+    \resetTitleCounters
+    \def\baselinestretch{1}%
+    \begin{center}
+        \def\baselinestretch{1}%
+        \large \@title \par
+        \vskip 18pt
+        \normalsize\elsauthors \par
+        \vskip 30pt
+        \footnotesize \itshape \elsaddress \par
+    \end{center}
+    \vskip 12pt
+}
+\makeatother
+$endif$
+
+\begin{document}
+$for(include-before)$
+$include-before$
+$endfor$
+\begin{frontmatter}
+
+   \title{$title$$if(subtitle)$\\\Large{$subtitle$}$endif$}
+   $for(author)$\author$if(authorwithinstitute)$[$for(author.institute)$$author.institute$$sep$,$endfor$]$endif${$author.name$$if(author.correspondence)$\corref{corrauth}$endif$$if(author.equalcontribution)$\corref{eqcon}$endif$ $if(author.footnote)$\fnref{$author.footnote$}$endif$}$if(author.email)$\ead{$author.email$}$endif$$endfor$
+   $if(authorwithinstitute)$ $for(institute)$ \address[$institute.id$]{$institute.name$} $endfor$ $endif$
+    % generate corresponding authors.
+    % \StrBehind is from xstring package
+    \ifnum \hascorr=1
+        \def\corrauths{
+            $for(author)$$if(author.correspondence)$and $author.name$ ($author.email$) $endif$$endfor$}
+        \cortext[corrauth]{Corresponding to \StrBehind*{\corrauths}{and }.}
+    \fi
+
+    % generate equal contributing authors.
+    \ifnum \haseqc=1
+        \def\eqa{$for(author)$$if(author.equalcontribution)$and $author.name$ $endif$$endfor$}
+        \cortext[eqcon]{\StrBehind*{\eqa}{and } are equally contributed to this work.}
+    \fi
+
+    $for(footnote)$
+    \fntext[$footnote.id$]{$footnote.text$}
+    $endfor$
+
+    $if(abstract)$
+    \begin{abstract}
+        $abstract$
+    \end{abstract}
+    $if(keywords)$
+    \begin{keyword}
+        $for(keywords/allbutlast)$$keywords$ \sep $endfor$
+        $for(keywords/last)$$keywords$$endfor$
+    \end{keyword}
+    $endif$
+    $endif$
+\end{frontmatter}
+
+$body$
+
+$if(authorwithinstitute)$
+$else$
+\section{Author Information}
+
+\getcorrauthinfo{}
+
+\getotherauthinfo{}
+
+$endif$
+
+
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(book-class)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+\bibliography{$bibliography$}
+$endif$
+$endif$
+
+$for(include-after)$
+$include-after$
+$endfor$
+\end{document}

_extensions/inst/tex/elsevier-harvard.csl

@@ -0,0 +1,239 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
+  <info>
+    <title>Elsevier - Harvard (with titles)</title>
+    <id>http://www.zotero.org/styles/elsevier-harvard</id>
+    <link href="http://www.zotero.org/styles/elsevier-harvard" rel="self"/>
+    <link href="http://www.zotero.org/styles/ecology-letters" rel="template"/>
+    <link href="http://www.elsevier.com/journals/biological-conservation/0006-3207/guide-for-authors#68000" rel="documentation"/>
+    <author>
+      <name>David Kaplan</name>
+      <email>david.kaplan@ird.fr</email>
+    </author>
+    <contributor>
+      <name>Simon Kornblith</name>
+      <email>simon@simonster.com</email>
+    </contributor>
+    <contributor>
+      <name>Bruce D'Arcus</name>
+    </contributor>
+    <contributor>
+      <name>Curtis M. Humphrey</name>
+    </contributor>
+    <contributor>
+      <name>Richard Karnesky</name>
+      <email>karnesky+zotero@gmail.com</email>
+      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
+    </contributor>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <category field="generic-base"/>
+    <updated>2014-03-04T00:09:00+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="container">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <text term="in" prefix=", " suffix=": "/>
+        <names variable="editor translator" delimiter=", " suffix=", ">
+          <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+          <label form="short" text-case="capitalize-first" prefix=" (" suffix=")"/>
+        </names>
+        <group delimiter=", ">
+          <text variable="container-title" text-case="title"/>
+          <text variable="collection-title" text-case="title"/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <group prefix=", " delimiter=", ">
+          <text variable="container-title"/>
+          <text variable="collection-title"/>
+        </group>
+      </else-if>
+      <else>
+        <group prefix=". " delimiter=", ">
+          <text variable="container-title" form="short"/>
+          <text variable="collection-title"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+      <label form="short" prefix=" (" suffix=")" text-case="capitalize-first"/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text macro="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-short">
+    <names variable="author">
+      <name form="short" and="text" delimiter=", " initialize-with=". "/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <choose>
+          <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+            <text variable="title" form="short" font-style="italic"/>
+          </if>
+          <else>
+            <text variable="title" form="short" quotes="true"/>
+          </else>
+        </choose>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="DOI">
+        <text variable="DOI" prefix="https://doi.org/"/>
+      </if>
+      <else-if type="webpage post-weblog" match="any">
+        <group delimiter=" ">
+          <text value="URL"/>
+          <text variable="URL"/>
+          <group prefix="(" suffix=").">
+            <text term="accessed" suffix=" "/>
+            <date variable="accessed">
+              <date-part name="month" form="numeric" suffix="."/>
+              <date-part name="day" suffix="."/>
+              <date-part name="year" form="short"/>
+            </date>
+          </group>
+        </group>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="report thesis" match="any">
+        <text variable="title"/>
+        <group prefix=" (" suffix=")" delimiter=" ">
+          <text variable="genre"/>
+          <text variable="number" prefix="No. "/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song speech" match="any">
+        <text variable="title"/>
+        <text macro="edition" prefix=", "/>
+      </else-if>
+      <else-if type="webpage">
+        <text variable="title"/>
+        <text value="WWW Document" prefix=" [" suffix="]"/>
+      </else-if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=", ">
+      <text variable="publisher"/>
+      <text variable="publisher-place"/>
+    </group>
+  </macro>
+  <macro name="event">
+    <choose>
+      <if variable="event">
+        <text term="presented at" text-case="capitalize-first" suffix=" "/>
+        <text variable="event"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issued">
+    <choose>
+      <if variable="issued">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else>
+        <text term="no date" form="short"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <group delimiter=" ">
+      <choose>
+        <if is-numeric="edition">
+          <number variable="edition" form="ordinal"/>
+        </if>
+        <else>
+          <text variable="edition" suffix="."/>
+        </else>
+      </choose>
+      <text value="ed"/>
+    </group>
+  </macro>
+  <macro name="locators">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper" match="any">
+        <group prefix=" " delimiter=", ">
+          <group>
+            <text variable="volume"/>
+          </group>
+          <text variable="page"/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
+        <group delimiter=", " prefix=". ">
+          <text macro="event"/>
+          <text macro="publisher"/>
+        </group>
+      </else-if>
+      <else-if type="chapter paper-conference" match="any">
+        <group delimiter=", " prefix=". ">
+          <text macro="event"/>
+          <text macro="publisher"/>
+          <group>
+            <label variable="page" form="short" suffix=" "/>
+            <text variable="page"/>
+          </group>
+        </group>
+      </else-if>
+      <else-if type="patent">
+        <text variable="number" prefix=". "/>
+      </else-if>
+    </choose>
+  </macro>
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-givenname="true" disambiguate-add-year-suffix="true" collapse="year" cite-group-delimiter=", ">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued" sort="descending"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=", ">
+        <text macro="author-short"/>
+        <text macro="issued"/>
+        <group delimiter=" ">
+          <label variable="locator" form="short"/>
+          <text variable="locator"/>
+        </group>
+      </group>
+    </layout>
+  </citation>
+  <bibliography hanging-indent="true" entry-spacing="0" line-spacing="1">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued" sort="descending"/>
+    </sort>
+    <layout>
+      <group suffix=".">
+        <text macro="author" suffix=","/>
+        <text macro="issued" prefix=" "/>
+        <group prefix=". ">
+          <text macro="title"/>
+          <text macro="container"/>
+          <text macro="locators"/>
+        </group>
+      </group>
+      <text macro="access" prefix=". "/>
+    </layout>
+  </bibliography>
+</style>

_extensions/inst/tex/supp.tex

@@ -0,0 +1,432 @@
+$-- Keeping in template layout for backward compatibility
+\documentclass[$if(layout)$$layout$$else$$for(classoption)$$classoption$$sep$,$endfor$$endif$]{_extensions/inst/tex/supp} %review=doublespace preprint=single 5p=2 column
+%%% Begin My package additions %%%%%%%%%%%%%%%%%%%
+\usepackage[hyphens]{url}
+$if(journal)$
+\journal{$journal$} % Sets Journal name
+$endif$
+\usepackage{lineno} % add
+$if(linenumbers)$
+\linenumbers % turns line numbering on
+$endif$
+\usepackage{graphicx}
+\usepackage{xstring}
+\usepackage{xcolor}
+%%%%%%%%%%%%%%%% end my additions to header
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+    \usepackage[utf8]{inputenc}
+    $if(euro)$
+    \usepackage{eurosym}
+    $endif$
+\else % if luatex or xelatex
+    \usepackage{fontspec}
+    \ifxetex
+    \usepackage{xltxtra,xunicode}
+    \fi
+    \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
+    \newcommand{\euro}{€}
+    $if(mainfont)$
+    \setmainfont{$mainfont$}
+    $endif$
+    $if(sansfont)$
+    \setsansfont{$sansfont$}
+    $endif$
+    $if(monofont)$
+    \setmonofont{$monofont$}
+    $endif$
+    $if(mathfont)$
+    \setmathfont{$mathfont$}
+    $endif$
+\fi
+% use microtype if available
+\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
+$if(geometry)$
+\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$if(natbib)$
+\usepackage{natbib}
+\setcitestyle{$natbiboptions$}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(listings)$
+\usepackage{listings}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+$if(graphics)$
+\usepackage{graphicx}
+$endif$
+\ifxetex
+    \usepackage[setpagesize=false, % page size defined by xetex
+                unicode=false, % unicode breaks when used with xetex
+                xetex]{hyperref}
+\else
+    \usepackage[unicode=true]{hyperref}
+\fi
+\hypersetup{breaklinks=true,
+            bookmarks=true,
+            pdfauthor={$author-meta$},
+            pdftitle={$title-meta$},
+            colorlinks=$if(colorlinks)$true$else$false$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
+            pdfborder={0 0 0}}
+\urlstyle{same}  % don't use monospace font for urls
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+$if(numbersections)$
+\setcounter{secnumdepth}{5}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(lang)$
+\ifxetex
+    \usepackage{polyglossia}
+    \setmainlanguage{$mainlang$}
+\else
+    \usepackage[$lang$]{babel}
+\fi
+$endif$
+% Pandoc toggle for numbering sections (defaults to be off)
+$if(numbersections)$
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(highlighting-macros)$
+% Pandoc syntax highlighting
+$highlighting-macros$
+$endif$
+% tightlist command for lists without linebreak
+\providecommand{\tightlist}{%
+    \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(tables)$
+% From pandoc table feature
+\usepackage{longtable,booktabs,array}
+$if(multirow)$
+\usepackage{multirow}
+$endif$
+\usepackage{calc} % for calculating minipage widths
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+$endif$
+$if(csl-refs)$
+% Pandoc citation processing
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacingunit} % times entry-spacing
+\setlength{\cslentryspacingunit}{\parskip}
+% for Pandoc 2.8 to 2.10.1
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+% For Pandoc 2.11+
+\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
+{% don't indent paragraphs
+    \setlength{\parindent}{0pt}
+    % turn on hanging indent if param 1 is 1
+    \ifodd #1
+    \let\oldpar\par
+    \def\par{\hangindent=\cslhangindent\oldpar}
+    \fi
+    % set entry spacing
+    \setlength{\parskip}{#2\cslentryspacingunit}
+    }%
+{}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+
+\usepackage{xifthen}
+% set special color for EST
+\ifthenelse{\equal{$journal$}{Environmental Science \& Technology}}
+{\definecolor{seccol}{RGB}{56, 95, 66}}
+{\definecolor{seccol}{RGB}{0, 0, 0}}
+
+$if(uppersections)$
+\usepackage{titlesec}
+\titleformat{\section}
+{\color{seccol}\large\bfseries\MakeUppercase}{\thesection}{1em}{}
+$endif$
+$if(sectiononnewpage)$
+\AddToHook{cmd/section/before}{\clearpage}
+$endif$
+
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\setmainfont{Helvetica}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+% force to use \zref
+$if(msname)$
+\def\msname{$msname$}
+\zexternaldocument*{\msname}
+\renewcommand{\ref}{\zref}
+$endif$
+$if(smname)$
+\def\smname{$smname$}
+\zexternaldocument*{\smname}
+$endif$
+
+\zxrsetup{toltxlabel=true}
+{\catcode`\#=12 \gdef\hashchar{#1}}
+\makeatletter
+\newcommand\hzref[1]{\edef\next{%
+    \noexpand\href{%
+      \zref@extractdefault{#1}{url}{}%
+      \zref@ifrefcontainsprop{#1}{anchor}{%
+      \hashchar\zref@extract{#1}{anchor}}{}}%
+      {\noexpand\zref{#1}}}\next}
+\makeatother
+
+
+
+$if(revision)$
+% \usepackage{xcolor}
+\usepackage{adjustbox}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+% setup hyperlink for page and line number
+\def\msname{$if(msname)$$msname$$else$MS$endif$}
+\def\smname{$if(smname)$$smname$$else$SM$endif$}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+    \newcommand{\clab}[2]{%
+        \protected@write\@auxout{\let\clab\@secondoftwo}{
+        \string\newlabel{r:#1}{{#2}{}}}%
+        \hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+$endif$
+
+
+% def default corresponding authors and equal contributing authors variables
+\def\hascorr{0}
+\def\haseqc{0}
+% check if corresponding author(s) and equal contributing authors are available
+$for(author)$$if(author.correspondence)$\def\hascorr{1}$endif$$if(author.equalcontribution)$\def\haseqc{1}$endif$ $endfor$
+
+\newcommand{\getcorrauthinfo}{
+    \subsection{Corresponding Author(s)}
+    \def\a{} \def\b{} \def\c{}
+    \hspace{-2.2em}
+    $for(author)$
+    $if(author.correspondence)$
+    \textbf{$author.name$:}
+    \vspace{-1em}
+    \begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
+    $for(author.institute)$ \def\a{$author.institute$}
+    $for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
+        \ifx \a\b \item \c; \fi
+    $endfor$ 
+    $endfor$ 
+        $if(author.email)$\item email: $author.email$;$endif$
+        $if(author.orcid)$\item orcid: $author.orcid$;$endif$
+        $if(author.tel)$\item Tel: $author.tel$;$endif$
+        $if(author.fax)$\item Fax: $author.fax$$endif$
+    \end{enumerate}
+    $endif$
+    $endfor$
+}
+
+\newcommand{\getotherauthinfo}{
+    \subsection{Author(s)}
+    \def\a{} \def\b{} \def\c{}
+    \hspace{-2.2em}
+    $for(author)$
+    $if(author.correspondence)$
+    $else$
+    \textbf{$author.name$:}
+    \vspace{-1em}
+    \begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
+    $for(author.institute)$ \def\a{$author.institute$} $for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
+        \ifx \a\b \item \c; \fi
+    $endfor$ 
+    $endfor$ 
+        $if(author.email)$\item email: $author.email$;$endif$
+        $if(author.orcid)$\item orcid: $author.orcid$;$endif$
+        $if(author.tel)$\item Tel: $author.tel$;$endif$
+        $if(author.fax)$\item Fax: $author.fax$$endif$
+    \end{enumerate}
+    $endif$
+    $endfor$
+}
+
+$preamble$
+
+% remove the two line around Abstract
+$if(abstract)$
+$else$
+\makeatletter
+\renewcommand{\MaketitleBox}{%
+    \resetTitleCounters
+    \def\baselinestretch{1}%
+    \begin{center}
+        \def\baselinestretch{1}%
+        \large \@title \par
+        \vskip 18pt
+        \normalsize\elsauthors \par
+        \vskip 30pt
+        \footnotesize \itshape \elsaddress \par
+    \end{center}
+    \vskip 12pt
+}
+\makeatother
+$endif$
+
+\begin{document}
+$for(include-before)$
+$include-before$
+$endfor$
+\begin{frontmatter}
+
+   \title{$title$$if(subtitle)$\\\Large{$subtitle$}$endif$}
+   $for(author)$\author$if(authorwithinstitute)$[$for(author.institute)$$author.institute$$sep$,$endfor$]$endif${$author.name$$if(author.correspondence)$\corref{corrauth}$endif$$if(author.equalcontribution)$\corref{eqcon}$endif$ $if(author.footnote)$\fnref{$author.footnote$}$endif$}$if(author.email)$\ead{$author.email$}$endif$$endfor$
+   $if(authorwithinstitute)$ $for(institute)$ \address[$institute.id$]{$institute.name$} $endfor$ $endif$
+    % generate corresponding authors.
+    % \StrBehind is from xstring package
+    \ifnum \hascorr=1
+        \def\corrauths{
+            $for(author)$$if(author.correspondence)$and $author.name$ ($author.email$) $endif$$endfor$}
+        \cortext[corrauth]{Corresponding to \StrBehind*{\corrauths}{and }.}
+    \fi
+
+    % generate equal contributing authors.
+    \ifnum \haseqc=1
+        \def\eqa{$for(author)$$if(author.equalcontribution)$and $author.name$ $endif$$endfor$}
+        \cortext[eqcon]{\StrBehind*{\eqa}{and } are equally contributed to this work.}
+    \fi
+
+    $for(footnote)$
+    \fntext[$footnote.id$]{$footnote.text$}
+    $endfor$
+
+    $if(abstract)$
+    \begin{abstract}
+        $abstract$
+    \end{abstract}
+    $if(keywords)$
+    \begin{keyword}
+        $for(keywords/allbutlast)$$keywords$ \sep $endfor$
+        $for(keywords/last)$$keywords$$endfor$
+    \end{keyword}
+    $endif$
+    $endif$
+\end{frontmatter}
+
+$body$
+
+$if(authorwithinstitute)$
+$else$
+\section{Author Information}
+
+\getcorrauthinfo{}
+
+\getotherauthinfo{}
+
+\section{Notes}
+
+The authors declare no competing financial interest.
+
+$endif$
+
+
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(book-class)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+\bibliography{$bibliography$}
+$endif$
+$endif$
+
+$for(include-after)$
+$include-after$
+$endfor$
+\end{document}

_extensions/inst/tex/the-isme-j.csl

@@ -0,0 +1,181 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
+  <info>
+    <title>The ISME Journal</title>
+    <id>http://www.zotero.org/styles/the-isme-journal</id>
+    <link href="http://www.zotero.org/styles/the-isme-journal" rel="self"/>
+    <link href="http://www.zotero.org/styles/journal-of-frailty-and-aging" rel="template"/>
+    <link href="http://www.nature.com/ismej/ismej_new_gta.pdf" rel="documentation"/>
+    <author>
+      <name>Patrick O'Brien</name>
+      <email>obrienpat86@gmail.com</email>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="biology"/>
+    <issn>1751-7362</issn>
+    <eissn>1751-7370</eissn>
+    <summary>The ISME Journal style, which is not the same as for Nature</summary>
+    <updated>2018-03-19T15:30:26+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="short" strip-periods="true" prefix=" (" suffix=")"/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="editor">
+    <text term="in" text-case="capitalize-first" suffix=": "/>
+    <names variable="editor">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="short" strip-periods="true" prefix=" (" suffix=")."/>
+    </names>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short" strip-periods="true"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="book">
+        <group delimiter=", " suffix=". ">
+          <text variable="title"/>
+          <text macro="edition"/>
+        </group>
+      </if>
+      <else>
+        <text variable="title" suffix=". "/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=", ">
+      <text variable="publisher"/>
+      <text variable="publisher-place"/>
+    </group>
+  </macro>
+  <macro name="year-date">
+    <date variable="issued">
+      <date-part name="year"/>
+    </date>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout prefix="[" suffix="]" delimiter=", ">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="7" et-al-use-first="6" second-field-align="flush" line-spacing="2" entry-spacing="0">
+    <layout>
+      <text variable="citation-number" suffix=". "/>
+      <group delimiter=". ">
+        <text macro="author"/>
+        <text macro="title"/>
+      </group>
+      <choose>
+        <if type="chapter">
+          <text macro="editor"/>
+          <group delimiter=". " suffix=". ">
+            <group prefix=" " delimiter=", ">
+              <text variable="container-title" font-style="italic"/>
+              <text macro="edition"/>
+            </group>
+            <text macro="year-date"/>
+            <group delimiter=", ">
+              <text macro="publisher"/>
+              <group delimiter=" ">
+                <label variable="page" form="short" strip-periods="true"/>
+                <text variable="page"/>
+              </group>
+            </group>
+          </group>
+        </if>
+        <else-if type="paper-conference">
+          <text macro="editor"/>
+          <group delimiter=". " suffix=". ">
+            <group prefix=" " delimiter=", ">
+              <text variable="container-title" form="short" font-style="italic"/>
+              <text macro="edition"/>
+            </group>
+            <text macro="year-date"/>
+            <group delimiter=", ">
+              <text macro="publisher"/>
+              <group delimiter=" ">
+                <label variable="page" form="short" strip-periods="true"/>
+                <text variable="page"/>
+              </group>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="article-journal">
+          <group delimiter="; " suffix=". ">
+            <group delimiter=" ">
+              <text variable="container-title" suffix=" " form="short" strip-periods="true" font-style="italic"/>
+              <text macro="year-date"/>
+            </group>
+            <group delimiter=": ">
+              <text variable="volume" font-weight="bold"/>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+          <group delimiter=". " suffix=". ">
+            <text variable="container-title" suffix=" " font-style="italic"/>
+            <text macro="year-date"/>
+            <text macro="publisher"/>
+          </group>
+        </else-if>
+        <else-if type="webpage">
+          <group suffix=". ">
+            <text variable="container-title" suffix=". " font-style="italic"/>
+            <text variable="URL" suffix=". "/>
+            <date variable="accessed">
+              <date-part prefix="Accessed " name="day" suffix=" "/>
+              <date-part name="month" form="short" suffix=" " strip-periods="true"/>
+              <date-part name="year"/>
+            </date>
+          </group>
+        </else-if>
+        <else-if type="thesis">
+          <group delimiter=". " suffix=". ">
+            <text variable="container-title" suffix=" " font-style="italic"/>
+            <text macro="year-date"/>
+            <group delimiter=", ">
+              <text variable="genre"/>
+              <text variable="publisher"/>
+            </group>
+          </group>
+        </else-if>
+        <else>
+          <group>
+            <group delimiter=". " suffix=". ">
+              <text variable="container-title" form="short" suffix=" " strip-periods="true" font-style="italic"/>
+              <text macro="year-date"/>
+              <text macro="publisher"/>
+            </group>
+            <group prefix=", " delimiter=": ">
+              <text variable="volume" font-weight="bold"/>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else>
+      </choose>
+    </layout>
+  </bibliography>
+</style>

_extensions/pandoc-ext/abstract-section/_extension.yaml

@@ -0,0 +1,6 @@
+name: abstract-section
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - abstract-section.lua

_extensions/pandoc-ext/abstract-section/abstract-section.lua

@@ -0,0 +1,59 @@
+--[[
+abstract-to-meta – move an "abstract" section into document metadata
+
+Copyright: © 2017–2021 Albert Krewinkel
+License:   MIT – see LICENSE file for details
+]]
+local abstract = {}
+
+--- Extract abstract from a list of blocks.
+function abstract_from_blocklist (blocks)
+  local body_blocks = {}
+  local looking_at_abstract = false
+
+  for _, block in ipairs(blocks) do
+    if block.t == 'Header' and block.level == 1 then
+      if block.identifier == 'abstract' then
+        looking_at_abstract = true
+      else
+        looking_at_abstract = false
+        body_blocks[#body_blocks + 1] = block
+      end
+    elseif looking_at_abstract then
+      if block.t == 'HorizontalRule' then
+        looking_at_abstract = false
+      else
+        abstract[#abstract + 1] = block
+      end
+    else
+      body_blocks[#body_blocks + 1] = block
+    end
+  end
+
+  return body_blocks
+end
+
+if PANDOC_VERSION >= {2,9,2} then
+  -- Check all block lists with pandoc 2.9.2 or later
+  return {{
+      Blocks = abstract_from_blocklist,
+      Meta = function (meta)
+        if not meta.abstract and #abstract > 0 then
+          meta.abstract = pandoc.MetaBlocks(abstract)
+        end
+        return meta
+      end
+  }}
+else
+  -- otherwise, just check the top-level block-list
+  return {{
+      Pandoc = function (doc)
+        local meta = doc.meta
+        local other_blocks = abstract_from_blocklist(doc.blocks)
+        if not meta.abstract and #abstract > 0 then
+          meta.abstract = pandoc.MetaBlocks(abstract)
+        end
+        return pandoc.Pandoc(other_blocks, meta)
+      end,
+  }}
+end

_extensions/pandoc-ext/author-info-blocks/_extension.yaml

@@ -0,0 +1,6 @@
+name: author-info-blocks
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - author-info-blocks.lua

_extensions/pandoc-ext/author-info-blocks/author-info-blocks.lua

@@ -0,0 +1,179 @@
+local List = require("pandoc.List")
+local utils = require("pandoc.utils")
+local stringify = utils.stringify
+local byAuthor
+local byAffiliation
+local Authors = {}
+local Affiliations = {}
+
+local authorHoriz
+
+local Corresponding = nil
+local function make_correspondance(name, email)
+	correspondance = List:new({
+		pandoc.Str("* Corresponding Author: "),
+		pandoc.Str(name),
+		pandoc.Str(" ("),
+		pandoc.Link(email, "mailto:" .. email),
+		pandoc.Str(")"),
+	})
+	Corresponding = List:new({ pandoc.Para(correspondance) })
+end
+
+local equalCont
+local function make_equal_contributor()
+	eq_statement = pandoc.Str("† These authors contributed equally to this work.")
+	equalCont = List:new({ pandoc.Para(eq_statement) })
+end
+
+local function create_author_list(byAuthor)
+	local authors = {}
+	for i, author in ipairs(byAuthor) do
+		local sups = {}
+
+		for j, aff in ipairs(author.affiliations) do
+			table.insert(sups, aff.number)
+		end
+		sups_str = table.concat(sups, ",")
+
+		local name = stringify(author.name.literal)
+
+		if author.attributes ~= nil then
+			if author.attributes["equal-contributor"] ~= nil and author.attributes["equal-contributor"] then
+				sups_str = sups_str .. ",†"
+				make_equal_contributor()
+			end
+			if author.attributes.corresponding ~= nil and author.attributes.corresponding then
+				local email = stringify(author.email)
+				sups_str = sups_str .. ",*"
+				make_correspondance(name, email)
+			end
+		end
+
+		local authorEntry = List:new({
+			pandoc.Str(name),
+			pandoc.Superscript(pandoc.Str(sups_str)),
+		})
+
+		if authorHoriz and i < #byAuthor then
+			authorEntry:extend({ pandoc.Str(", ") })
+		end
+
+		table.insert(authors, pandoc.Span(authorEntry))
+	end
+
+	if authorHoriz then
+		Authors = { pandoc.Para(authors) }
+	else
+		Authors = authors
+	end
+end
+
+local function create_affiliation_list(byAffiliation)
+	for i, aff in ipairs(byAffiliation) do
+		local full_aff = pandoc.List({})
+		if aff.name then
+			full_aff:insert(stringify(aff.name))
+		end
+
+		if aff.address then
+			full_aff:insert(stringify(aff.address))
+		end
+
+		if aff.city then
+			full_aff:insert(stringify(aff.city))
+		end
+
+		if aff["postal-code"] then
+			full_aff:insert(stringify(aff["postal-code"]))
+		end
+
+		if aff.region then
+			full_aff:insert(stringify(aff.region))
+		end
+
+		if aff.country then
+			full_aff:insert(stringify(aff.country))
+		end
+
+		local entry = table.concat(full_aff, ", ")
+		entry = aff.number .. ". " .. entry .. "."
+		table.insert(Affiliations, pandoc.Para(pandoc.Str(entry)))
+	end
+end
+
+local Abstract = nil
+local function create_abstract(ab)
+	Abstract = {}
+	table.insert(Abstract, pandoc.Header(1, "Abstract"))
+	table.insert(Abstract, pandoc.Para(ab))
+end
+
+local Keywords = nil
+local function create_keyword_list(kw)
+	Keywords = {}
+	-- quarto.log.output(kw)
+	local kws = pandoc.List({})
+	for i, keyword in ipairs(kw) do
+		kws:insert(stringify(keyword))
+	end
+	local kwentry = table.concat(kws, "; ")
+	kwentry = "Keywords: " .. kwentry .. "."
+	table.insert(Keywords, pandoc.Para(pandoc.Str(kwentry)))
+end
+
+local function remove_author_meta(meta)
+	meta.author = nil
+	meta.authors = nil
+	meta.affiliations = nil
+	meta["by-author"] = nil
+	meta["by-affiliation"] = nil
+	meta["abstract"] = nil
+	return meta
+end
+
+return {
+	{
+		Meta = function(meta)
+			byAuthor = meta["by-author"]
+			byAffiliation = meta["by-affiliation"]
+			if meta["author-horizontal"] ~= nil then
+				authorHoriz = meta["author-horizontal"]
+			else
+				authorHoriz = true
+			end
+			create_author_list(byAuthor)
+			create_affiliation_list(byAffiliation)
+			if meta["abstract"] ~= nil then
+				create_abstract(meta["abstract"])
+			end
+			if meta["keywords"] ~= nil then
+				create_keyword_list(meta["keywords"])
+			end
+			return meta
+		end,
+	},
+	{
+		Pandoc = function(doc)
+			local meta = doc.meta
+			local body = List:new({})
+			body:extend(Authors)
+			body:extend(Affiliations)
+			if equalCont ~= nil then
+				body:extend(equalCont)
+			end
+			if Corresponding ~= nil then
+				body:extend(Corresponding)
+			end
+			if Abstract then
+				body:extend(Abstract)
+			end
+			if Keywords then
+				body:extend(Keywords)
+			end
+			body:extend(doc.blocks)
+			meta = remove_author_meta(meta)
+			return pandoc.Pandoc(body, meta)
+		end,
+	},
+}

_extensions/pandoc-ext/scholarly-metadata/_extension.yaml

@@ -0,0 +1,6 @@
+name: scholarly-metadata
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - scholarly-metadata.lua

_extensions/pandoc-ext/scholarly-metadata/scholarly-metadata.lua

@@ -0,0 +1,197 @@
+--[[
+ScholarlyMeta – normalize author/affiliation meta variables
+
+Copyright (c) 2017-2021 Albert Krewinkel, Robert Winkler
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+local List = require("pandoc.List")
+
+--- Returns the type of a metadata value.
+--
+-- @param v a metadata value
+-- @treturn string one of `Blocks`, `Inlines`, `List`, `Map`, `string`, `boolean`
+local function metatype(v)
+	if PANDOC_VERSION <= "2.16.2" then
+		local metatag = type(v) == "table" and v.t and v.t:gsub("^Meta", "")
+		return metatag and metatag ~= "Map" and metatag or type(v)
+	end
+	return pandoc.utils.type(v)
+end
+
+local type = pandoc.utils.type or metatype
+
+-- Split a string at commas.
+local function comma_separated_values(str)
+	local acc = List:new({})
+	for substr in str:gmatch("([^,]*)") do
+		acc[#acc + 1] = substr:gsub("^%s*", ""):gsub("%s*$", "") -- trim
+	end
+	return acc
+end
+
+--- Ensure the return value is a list.
+local function ensure_list(val)
+	if type(val) == "List" then
+		return val
+	elseif type(val) == "Inlines" then
+		-- check if this is really a comma-separated list
+		local csv = comma_separated_values(pandoc.utils.stringify(val))
+		if #csv >= 2 then
+			return csv
+		end
+		return List:new({ val })
+	elseif type(val) == "table" and #val > 0 then
+		return List:new(val)
+	else
+		-- Anything else, use as a singleton (or empty list if val == nil).
+		return List:new({ val })
+	end
+end
+
+--- Returns a function which checks whether an object has the given ID.
+local function has_id(id)
+	return function(x)
+		return x.id == id
+	end
+end
+
+--- Copy all key-value pairs of the first table into the second iff there is no
+-- such key yet in the second table.
+-- @returns the second argument
+function add_missing_entries(a, b)
+	for k, v in pairs(a) do
+		b[k] = b[k] or v
+	end
+	return b
+end
+
+--- Create an object with a name. The name is either taken directly from the
+-- `name` field, or from the *only* field name (i.e., key) if the object is a
+-- dictionary with just one entry. If neither exists, the name is left unset
+-- (`nil`).
+function to_named_object(obj)
+	local named = {}
+	if type(obj) == "Inlines" then
+		-- Treat inlines as the name
+		named.name = obj
+		named.id = pandoc.utils.stringify(obj)
+	elseif type(obj) ~= "table" then
+		-- if the object isn't a table, just use its value as a name.
+		named.name = pandoc.MetaInlines({ pandoc.Str(tostring(obj)) })
+		named.id = tostring(obj)
+	elseif obj.name ~= nil then
+		-- object has name attribute → just create a copy of the object
+		add_missing_entries(obj, named)
+		named.id = pandoc.utils.stringify(named.id or named.name)
+	elseif next(obj) and next(obj, next(obj)) == nil then
+		-- Single-entry table. The entry's key is taken as the name, the value
+		-- contains the attributes.
+		key, attribs = next(obj)
+		if type(attribs) == "string" or type(attribs) == "Inlines" then
+			named.name = attribs
+		else
+			add_missing_entries(attribs, named)
+			named.name = named.name or pandoc.MetaInlines({ pandoc.Str(tostring(key)) })
+		end
+		named.id = named.id and pandoc.utils.stringify(named.id) or key
+	else
+		-- this is not a named object adhering to the usual conventions.
+		error("not a named object: " .. tostring(obj))
+	end
+	return named
+end
+
+--- Resolve affiliations placeholders to full named objects
+local function resolve_affiliations(affiliations, known_affiliations)
+	local unresolved_affiliations
+	if affiliations == nil then
+		unresolved_affiliations = {}
+	elseif type(affiliations) == "string" or type(affiliations) == "number" then
+		unresolved_affiliations = { affiliations }
+	else
+		unresolved_affiliations = affiliations
+	end
+
+	local result = List:new({})
+	for i, inst in ipairs(unresolved_affiliations) do
+		result[i] = known_affiliations[tonumber(inst)]
+			or known_affiliations:find_if(has_id(pandoc.utils.stringify(inst)))
+			or to_named_object(inst)
+	end
+	return result
+end
+
+--- Insert a named object into a list; if an object of the same name exists
+-- already, add all properties only present in the new object to the existing
+-- item.
+function merge_on_id(list, namedObj)
+	local elem, idx = list:find_if(has_id(namedObj.id))
+	local res = elem and add_missing_entries(namedObj, elem) or namedObj
+	local obj_idx = idx or (#list + 1)
+	-- return res, obj_idx
+	list[obj_idx] = res
+	return res, #list
+end
+
+--- Flatten a list of lists.
+local function flatten(lists)
+	local result = List:new({})
+	for _, lst in ipairs(lists) do
+		result:extend(lst)
+	end
+	return result
+end
+
+--- Canonicalize authors and affiliations
+local function canonicalize(raw_author, raw_affiliations)
+	local affiliations = ensure_list(raw_affiliations):map(to_named_object)
+	local authors = ensure_list(raw_author):map(to_named_object)
+
+	for _, author in ipairs(authors) do
+		author.affiliations = resolve_affiliations(ensure_list(author.affiliations), affiliations)
+	end
+
+	-- Merge affiliations defined in author objects with those defined in the
+	-- top-level list.
+	local author_insts = flatten(authors:map(function(x)
+		return x.affiliations
+	end))
+	for _, inst in ipairs(author_insts) do
+		merge_on_id(affiliations, inst)
+	end
+
+	-- Add list indices to affiliations for numbering and reference purposes
+	for idx, inst in ipairs(affiliations) do
+		inst.index = pandoc.MetaInlines({ pandoc.Str(tostring(idx)) })
+	end
+
+	-- replace affiliations with their indices
+	local to_index = function(inst)
+		return tostring(select(2, affiliations:find_if(has_id(inst.id))))
+	end
+	for _, author in ipairs(authors) do
+		author.affiliations = pandoc.MetaList(author.affiliations:map(to_index))
+	end
+
+	return authors, affiliations
+end
+
+return {
+	{
+		Meta = function(meta)
+			meta.author, meta.affiliations = canonicalize(meta.author, meta.affiliations)
+			return meta
+		end,
+	},
+}

_extensions/quarto-ext/latex-environment/_extension.yml

@@ -0,0 +1,9 @@
+title: LaTeX Environment
+author: RStudio, PBC
+version: 1.1.0
+quarto-required: ">=1.2.198"
+contributes:
+  filters:
+    - latex-environment.lua
+  format:
+    pdf: default

_extensions/quarto-ext/latex-environment/latex-environment.lua

@@ -0,0 +1,133 @@
+-- environment.lua
+-- Copyright (C) 2020 by RStudio, PBC
+
+local classEnvironments = pandoc.MetaMap({})
+local classCommands = pandoc.MetaMap({})
+
+-- helper that identifies arrays
+local function tisarray(t)
+  local i = 0
+  for _ in pairs(t) do
+    i = i + 1
+    if t[i] == nil then return false end
+  end
+  return true
+end
+
+-- reads the environments
+local function readEnvironments(meta)
+  local env = meta['environments']
+  if env ~= nil then
+    if tisarray(env) then
+      -- read an array of strings
+      for i, v in ipairs(env) do
+        local value = pandoc.utils.stringify(v)
+        classEnvironments[value] = value
+      end
+    else
+      -- read key value pairs
+      for k, v in pairs(env) do
+        local key = pandoc.utils.stringify(k)
+        local value = pandoc.utils.stringify(v)
+        classEnvironments[key] = value
+      end
+    end
+  end
+end
+
+local function readCommands(meta)
+  local env = meta['commands']
+  if env ~= nil then
+    if tisarray(env) then
+      -- read an array of strings
+      for i, v in ipairs(env) do
+        local value = pandoc.utils.stringify(v)
+        classCommands[value] = value
+      end
+    else
+      -- read key value pairs
+      for k, v in pairs(env) do
+        local key = pandoc.utils.stringify(k)
+        local value = pandoc.utils.stringify(v)
+        classCommands[key] = value
+      end
+    end
+  end
+end
+
+local function readEnvsAndCommands(meta)
+  readEnvironments(meta)
+  readCommands(meta)
+end
+
+-- use the environments from metadata to
+-- emit a custom environment for latex
+local function writeEnvironments(divEl)
+  if quarto.doc.is_format("latex") then
+    for k, v in pairs(classEnvironments) do
+      if divEl.attr.classes:includes(k) then
+        -- process this into a latex environment
+        local beginEnv = '\\begin' .. '{' .. v .. '}'
+        local endEnv = '\n\\end{' .. v .. '}'
+        
+        -- check if custom options or arguments are present
+        -- and add them to the environment accordingly
+        local opts = divEl.attr.attributes['options']
+        if opts then
+          beginEnv = beginEnv .. '[' .. opts .. ']'
+        end
+
+        local args = divEl.attr.attributes['arguments']
+        if args then
+          beginEnv = beginEnv .. '{' .. args .. '}'
+        end
+        
+        -- if the first and last div blocks are paragraphs then we can
+        -- bring the environment begin/end closer to the content
+        if divEl.content[1].t == "Para" and divEl.content[#divEl.content].t == "Para" then
+          table.insert(divEl.content[1].content, 1, pandoc.RawInline('tex', beginEnv .. "\n"))
+          table.insert(divEl.content[#divEl.content].content, pandoc.RawInline('tex', "\n" .. endEnv))
+        else
+          table.insert(divEl.content, 1, pandoc.RawBlock('tex', beginEnv))
+          table.insert(divEl.content, pandoc.RawBlock('tex', endEnv))
+        end
+        return divEl
+      end
+    end
+  end
+end
+
+-- use the environments from metadata to
+-- emit a custom environment for latex
+local function writeCommands(spanEl)
+  if quarto.doc.is_format("latex") then
+    for k, v in pairs(classCommands) do
+      if spanEl.attr.classes:includes(k) then
+
+        -- resolve the begin command
+        local beginCommand = pandoc.RawInline('latex', '\\' .. pandoc.utils.stringify(v) .. '{')
+        local opts = spanEl.attr.attributes['options']
+        if opts then
+          beginCommand = pandoc.RawInline('latex', '\\' .. pandoc.utils.stringify(v) .. '[' .. opts .. ']{')
+        end
+
+        -- the end command
+        local endCommand = pandoc.RawInline('latex', '}')
+
+        -- attach the raw inlines to the span contents
+        local result = spanEl.content
+        table.insert(result, 1, beginCommand)
+        table.insert(result, endCommand)
+
+        return result
+      end
+    end
+  end
+end
+
+-- Run in two passes so we process metadata
+-- and then process the divs
+return {
+  { Meta = readEnvsAndCommands },
+  { Div = writeEnvironments, Span = writeCommands }
+}

_extensions/quarto-journals/elsevier/_extension.yml

@@ -0,0 +1,19 @@
+title: Elsevier Journal Format
+author: Charles Teague
+version: 0.2.0
+quarto-required: ">=1.2.198"
+contributes:
+  formats:
+    common:
+      date-format: full
+      filters:
+        - elsevier.lua
+    pdf:
+      documentclass: elsarticle
+      template-partials: ["partials/before-body.tex", "partials/title.tex"]
+      format-resources:
+        - elsarticle.cls
+      cite-method: natbib
+      number-sections: true
+    html:
+      theme: styles/elsevier.scss

_extensions/quarto-journals/elsevier/bib/elsevier-harvard.csl

@@ -0,0 +1,239 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
+  <info>
+    <title>Elsevier - Harvard (with titles)</title>
+    <id>http://www.zotero.org/styles/elsevier-harvard</id>
+    <link href="http://www.zotero.org/styles/elsevier-harvard" rel="self"/>
+    <link href="http://www.zotero.org/styles/ecology-letters" rel="template"/>
+    <link href="http://www.elsevier.com/journals/biological-conservation/0006-3207/guide-for-authors#68000" rel="documentation"/>
+    <author>
+      <name>David Kaplan</name>
+      <email>david.kaplan@ird.fr</email>
+    </author>
+    <contributor>
+      <name>Simon Kornblith</name>
+      <email>simon@simonster.com</email>
+    </contributor>
+    <contributor>
+      <name>Bruce D'Arcus</name>
+    </contributor>
+    <contributor>
+      <name>Curtis M. Humphrey</name>
+    </contributor>
+    <contributor>
+      <name>Richard Karnesky</name>
+      <email>karnesky+zotero@gmail.com</email>
+      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
+    </contributor>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <category field="generic-base"/>
+    <updated>2019-01-22T15:57:12+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="container">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <text term="in" prefix=", " suffix=": "/>
+        <names variable="editor translator" delimiter=", " suffix=", ">
+          <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+          <label form="short" text-case="capitalize-first" prefix=" (" suffix=")"/>
+        </names>
+        <group delimiter=", ">
+          <text variable="container-title" text-case="title"/>
+          <text variable="collection-title" text-case="title"/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <group prefix=", " delimiter=", ">
+          <text variable="container-title"/>
+          <text variable="collection-title"/>
+        </group>
+      </else-if>
+      <else>
+        <group prefix=". " delimiter=", ">
+          <text variable="container-title" form="short"/>
+          <text variable="collection-title"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+      <label form="short" prefix=" (" suffix=")" text-case="capitalize-first"/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text macro="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-short">
+    <names variable="author">
+      <name form="short" and="text" delimiter=", " initialize-with=". "/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <choose>
+          <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+            <text variable="title" form="short" font-style="italic"/>
+          </if>
+          <else>
+            <text variable="title" form="short" quotes="true"/>
+          </else>
+        </choose>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="DOI">
+        <text variable="DOI" prefix="https://doi.org/"/>
+      </if>
+      <else-if type="webpage post-weblog" match="any">
+        <group delimiter=" ">
+          <text value="URL"/>
+          <text variable="URL"/>
+          <group prefix="(" suffix=").">
+            <text term="accessed" suffix=" "/>
+            <date variable="accessed">
+              <date-part name="month" form="numeric" suffix="."/>
+              <date-part name="day" suffix="."/>
+              <date-part name="year" form="short"/>
+            </date>
+          </group>
+        </group>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="title">
+    <choose>
+      <if type="report thesis" match="any">
+        <text variable="title"/>
+        <group prefix=" (" suffix=")" delimiter=" ">
+          <text variable="genre"/>
+          <text variable="number" prefix="No. "/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song speech" match="any">
+        <text variable="title"/>
+        <text macro="edition" prefix=", "/>
+      </else-if>
+      <else-if type="webpage">
+        <text variable="title"/>
+        <text value="WWW Document" prefix=" [" suffix="]"/>
+      </else-if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=", ">
+      <text variable="publisher"/>
+      <text variable="publisher-place"/>
+    </group>
+  </macro>
+  <macro name="event">
+    <choose>
+      <if variable="event">
+        <text term="presented at" text-case="capitalize-first" suffix=" "/>
+        <text variable="event"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issued">
+    <choose>
+      <if variable="issued">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else>
+        <text term="no date" form="short"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <group delimiter=" ">
+      <choose>
+        <if is-numeric="edition">
+          <number variable="edition" form="ordinal"/>
+        </if>
+        <else>
+          <text variable="edition" suffix="."/>
+        </else>
+      </choose>
+      <text value="ed"/>
+    </group>
+  </macro>
+  <macro name="locators">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper" match="any">
+        <group prefix=" " delimiter=", ">
+          <group>
+            <text variable="volume"/>
+          </group>
+          <text variable="page"/>
+        </group>
+      </if>
+      <else-if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
+        <group delimiter=", " prefix=". ">
+          <text macro="event"/>
+          <text macro="publisher"/>
+        </group>
+      </else-if>
+      <else-if type="chapter paper-conference" match="any">
+        <group delimiter=", " prefix=". ">
+          <text macro="event"/>
+          <text macro="publisher"/>
+          <group>
+            <label variable="page" form="short" suffix=" "/>
+            <text variable="page"/>
+          </group>
+        </group>
+      </else-if>
+      <else-if type="patent">
+        <text variable="number" prefix=". "/>
+      </else-if>
+    </choose>
+  </macro>
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-givenname="true" disambiguate-add-year-suffix="true" collapse="year" cite-group-delimiter=", ">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued" sort="descending"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=", ">
+        <text macro="author-short"/>
+        <text macro="issued"/>
+        <group delimiter=" ">
+          <label variable="locator" form="short"/>
+          <text variable="locator"/>
+        </group>
+      </group>
+    </layout>
+  </citation>
+  <bibliography hanging-indent="true" entry-spacing="0" line-spacing="1">
+    <sort>
+      <key macro="author"/>
+      <key macro="issued" sort="descending"/>
+    </sort>
+    <layout>
+      <group suffix=".">
+        <text macro="author" suffix=","/>
+        <text macro="issued" prefix=" "/>
+        <group prefix=". ">
+          <text macro="title"/>
+          <text macro="container"/>
+          <text macro="locators"/>
+        </group>
+      </group>
+      <text macro="access" prefix=". "/>
+    </layout>
+  </bibliography>
+</style>

_extensions/quarto-journals/elsevier/elsevier.lua

@@ -0,0 +1,166 @@
+-- cite style constants
+local kBibStyleDefault = 'number'
+local kBibStyles = { 'number', 'numbername', 'authoryear' }
+local kBibStyleAuthYr = 'elsarticle-harv'
+local kBibStyleNumber = 'elsarticle-num'
+local kBibStyleNumberName = 'elsarticle-num-names'
+local kBibStyleUnknown = kBibStyleNumberName
+
+-- layout and style
+local kFormatting = pandoc.List({ 'preprint', 'review', 'doubleblind' })
+local kModels = pandoc.List({ '1p', '3p', '5p' })
+local kLayouts = pandoc.List({ 'onecolumn', 'twocolumn' })
+
+
+local function setBibStyle(meta, style)
+  meta['biblio-style'] = style
+  quarto.doc.add_format_resource('bib/' .. style .. '.bst')
+end
+
+local function hasClassOption(meta, option)
+  if meta['classoption'] == nil then
+    return false
+  end
+
+  for i, v in ipairs(meta['classoption']) do
+    if v[1].text == option then
+      return true
+    end
+  end
+  return false
+end
+
+local function addClassOption(meta, option)
+  if meta['classoption'] == nil then
+    meta['classoption'] = pandoc.List({})
+  end
+
+  if not hasClassOption(meta, option) then
+    meta['classoption']:insert({ pandoc.Str(option) })
+  end
+end
+
+local function printList(list)
+  local result = ''
+  local sep = ''
+  for i, v in ipairs(list) do
+    result = result .. sep .. v
+    sep = ', '
+  end
+  return result
+end
+
+local bibstyle = kBibStyleDefault
+
+return {
+  {
+    Meta = function(meta)
+      -- If citeproc is being used, switch to the proper
+      -- CSL file
+      if quarto.doc.cite_method() == 'citeproc' and meta['csl'] == nil then
+        meta['csl'] = quarto.utils.resolve_path('bib/elsevier-harvard.csl')
+      end
+
+      if quarto.doc.is_format("pdf") then
+
+        -- read the journal settings
+        local journal = meta['journal']
+        local citestyle = nil
+        local formatting = nil
+        local model = nil
+        local layout = nil
+        local name = nil
+
+        if journal ~= nil then
+          citestyle = journal['cite-style']
+          formatting = journal['formatting']
+          model = journal['model']
+          layout = journal['layout']
+          name = journal['name']
+        end
+
+        -- process the site style
+        if citestyle ~= nil then
+          citestyle = pandoc.utils.stringify(citestyle)
+        else
+          citestyle = kBibStyleDefault
+        end
+
+        -- capture the bibstyle
+        bibstyle = citestyle
+        if citestyle == 'numbername' then
+          setBibStyle(meta, kBibStyleNumberName)
+          addClassOption(meta, 'number')
+        elseif citestyle == 'authoryear' then
+          setBibStyle(meta, kBibStyleAuthYr)
+          addClassOption(meta, 'authoryear')
+        elseif citestyle == 'number' then
+          setBibStyle(meta, kBibStyleNumber)
+          addClassOption(meta, 'number')
+        else
+          error("Unknown journal cite-style " .. citestyle .. "\nPlease use one of " .. printList(kBibStyles))
+          setBibStyle(meta, kBibStyleUnknown)
+        end
+
+        -- process the layout
+        if formatting ~= nil then
+          formatting = pandoc.utils.stringify(formatting)
+          if kFormatting:includes(formatting) then
+            addClassOption(meta, formatting)
+          else
+            error("Unknown journal formatting " .. formatting .. "\nPlease use one of " .. printList(kFormatting))
+          end
+        end
+
+        -- process the type
+        if model ~= nil then
+          model = pandoc.utils.stringify(model)
+          if kModels:includes(model) then
+            addClassOption(meta, model)
+          else
+            error("Unknown journal model " .. model .. "\nPlease use one of " .. printList(kModels))
+          end
+        end
+
+        -- 5p models should be two column always
+        if model == '5p' and layout == nil then
+          layout = 'twocolumn'
+        end
+
+        -- process the type
+        if layout ~= nil then
+          layout = pandoc.utils.stringify(layout)
+          if kLayouts:includes(layout) then
+            addClassOption(meta, layout)
+            if layout == 'twocolumn' then
+              quarto.doc.include_file('in-header', 'partials/_two-column-longtable.tex')
+            end
+          else
+            error("Unknown journal layout " .. layout .. "\nPlease use one of " .. printList(kLayouts))
+          end
+        end
+
+        -- process the name
+        if name ~= nil then
+          name = pandoc.utils.stringify(name)
+          quarto.doc.include_text('in-header', '\\journal{' .. name .. '}')
+        end
+      end
+
+      return meta
+    end
+  },
+  {
+    Cite = function(cite)
+      if bibstyle == 'number' then
+        -- If we are numbered, force citations into normal mode
+        -- as the author styles don't make sense
+        for i, v in ipairs(cite.citations) do
+          v.mode = 'NormalCitation'
+        end
+        return cite
+      end
+    end,
+
+  }
+}

_extensions/quarto-journals/elsevier/partials/_two-column-longtable.tex

@@ -0,0 +1,20 @@
+\usepackage{float}
+\makeatletter
+\let\oldlt\longtable
+\let\endoldlt\endlongtable
+\def\longtable{\@ifnextchar[\longtable@i \longtable@ii}
+\def\longtable@i[#1]{\begin{figure}[H]
+\onecolumn
+\begin{minipage}{0.5\textwidth}
+\oldlt[#1]
+}
+\def\longtable@ii{\begin{figure}[H]
+\onecolumn
+\begin{minipage}{0.5\textwidth}
+\oldlt
+}
+\def\endlongtable{\endoldlt
+\end{minipage}
+\twocolumn
+\end{figure}}
+\makeatother

_extensions/quarto-journals/elsevier/partials/before-body.tex

@@ -0,0 +1,41 @@
+\begin{frontmatter}
+\title{$title$ $if(subtitle)$ \\\large{$subtitle$} $endif$ }
+
+$for(by-author)$\author[$for(by-author.affiliations)$$it.number$$sep$,$endfor$]{$by-author.name.literal$%
+$if(by-author.attributes.corresponding)$\corref{cor1}$endif$%
+$if(by-author.note.text)$\fnref{fn$by-author.note.number$}$endif$}
+$if(by-author.email)$ \ead{$by-author.email$} $endif$
+$endfor$
+$for(by-affiliation)$
+\affiliation[$it.number$]{organization={$it.name$},$if(it.address)$addressline={$it.address$}$endif$$if(it.city)$$if(it.address)$,$endif$city={$it.city$}$endif$$if(it.country)$$if(it.city)$,$elseif(it.address)$,$endif$country={$it.country$}$endif$$if(it.postal-code)$$if(it.country)$,$elseif(it.city)$,$elseif(it.address)$,$endif$postcode={$it.postal-code$}$endif$}
+$endfor$
+
+\cortext[cor1]{Corresponding author}
+$for(by-author)$
+$if(by-author.note.text)$\fntext[fn$by-author.note.number$]{$by-author.note.text$}$endif$
+$endfor$
+        
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+
+$if(journal.graphical-abstract)$\begin{graphicalabstract}
+$journal.graphical-abstract$
+\end{graphicalabstract}
+$endif$
+
+$if(journal.highlights)$\begin{highlights}
+$for(journal.highlights)$\item $it$$endfor$
+\end{highlights}
+$endif$
+
+$if(keywords)$
+\begin{keyword}
+    $for(keywords/allbutlast)$$keywords$ \sep $endfor$
+    $for(keywords/last)$$keywords$$endfor$
+\end{keyword}
+$endif$
+\end{frontmatter}
+

_extensions/quarto-journals/elsevier/partials/revision.tex

@@ -0,0 +1,66 @@
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+
+\usepackage{adjustbox}
+% \usepackage{xcolor}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+% setup hyperlink for page and line number
+\def\msname{MS}
+\def\smname{SM}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+\newcommand{\clab}[2][]{
+		\protected@write\@auxout{\let\clab\@secondoftwo}{
+				\string\newlabel{r:#1}{{#2}{}}}%
+		\hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+

_extensions/quarto-journals/elsevier/partials/title.tex

@@ -0,0 +1 @@
+\setlength{\parindent}{6pt}

_extensions/quarto-journals/elsevier/styles/elsevier.scss

@@ -0,0 +1 @@
+/*--  scss:defaults --*/

_quarto.yml

@@ -1,17 +1,62 @@
-project:
+title: "MANUSCRIPT TITLE"
-  type: website
+submitjournal: "Water Research"
-  output-dir: ../www/project/protected/su2023temp/@main
+submitid: WR73679
-
+lang: en
-title: "项目名称"
-lang: zh
 date: today
 bibliography: [BB/Ref.bib, BB/localRef.bib]
+author:
+  - name: Ming Su
+    email: mingsu@rcees.ac.cn
+    orcid: 0000-0001-9821-1268
+    url: https://drwater.rcees.ac.cn
+    affiliations:
+      - ref: skleac
+      - ref: ucas
+  - name: Min Yang
+    email: yangmin@rcees.ac.cn
+    affiliations:
+      - ref: skleac
+      - ref: ucas
+    attributes:
+      corresponding: true
+affiliations:
+  - id: skleac
+    name: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
+    address: P.O. Box 2871
+    city: Beijing
+    postal-code: 100085
+    url: https://www.skleac.ac.cn
+  - id: ucas
+    name: University of Chinese Academy of Sciences
+    city: Beijing
+    postal-code: 100049
+    url: https://www.ucas.ac.cn
+crossref:
+  fig-title: Fig. # (default is "Figure")
+  tbl-title: Table # (default is "Table")
+  eq-title: Eq. # (default is "Equation")
+  title-delim: "" # (default is ":")
+  fig-prefix: Fig. # (default is "Figure")
+  tbl-prefix: Table # (default is "Table")
+  eq-prefix: Eq.
+  ref-hyperlink: true # (default is true)
 
+project:
+  type: website
+  output-dir: ../www/manuscript/protected/su2023temp/@main
+  # render:
+  #   - index.qmd
+  #   - MS/SM.qmd
+  #   - MS/MS.qmd
+  #   - MS/CL.qmd
+  #   - MS/HL.qmd
+  #   - MS/RN.qmd
+  #   - MS/AC.qmd
 website:
   title: "Version: main"
   reader-mode: true
-  site-url: https://drwater.rcees.ac.cn/project/protected/su2023temp/@main
+  site-url: https://drwater.rcees.ac.cn/manuscript/protected/su2023temp/@main
-  repo-url: https://drwater.rcees.ac.cn/git/project/su2023temp/src/branch/main
+  repo-url: https://drwater.rcees.ac.cn/git/manuscript/su2023temp/src/branch/main
   repo-actions: [edit, source, issue]
   page-navigation: true
   page-footer: "Copyright 2023, [Ming Su](https://drwater.rcees.ac.cn)"
@@ -22,22 +67,35 @@ website:
       - icon: house
         text: "Home"
         file: index.qmd
-      - text: "Proposal"
+        menu:
-        file: PP/index.qmd
+        - text: "Highlights"
-      - text: "Report"
+          file: MS/HL.qmd
-        file: RP/index.qmd
+        - text: "Cover Letter"
+          file: MS/CL.qmd
+        - text: "Author Credits"
+          file: MS/AC.qmd
+        - text: "Trackchanges"
+          file: TC/index.qmd
+      - text: "Manuscript"
+        file: MS/MS.qmd
+      - text: "Supplementary Materials"
+        file: MS/SM.qmd
+      - text: "Revision Notes"
+        file: MS/RN.qmd
       - text: "Slides"
         file: SD/index.qmd
-      - href: AC/index.qmd
+      - text: "Other"
-        text: Achievement
+        menu:
-      - text: "About"
+        - text: "Report"
-        file: about.qmd
+          file: RP/index.qmd
+        - text: "Acomplishment"
+          file: AC/index.qmd
       - icon: git
         menu:
           - text: Edit
-            url: https://drwater.rcees.ac.cn/git/project/su2023temp/_edit/
+            url: https://drwater.rcees.ac.cn/git/manuscript/su2023temp/_edit/
           - text: Issue
-            url: https://drwater.rcees.ac.cn/git/project/su2023temp/issues
+            url: https://drwater.rcees.ac.cn/git/manuscript/su2023temp/issues
   comments: 
     hypothesis:
       theme: clean
@@ -46,8 +104,5 @@ website:
 format:
   html:
     theme: cosmo
-    css: styles.css
+    css: _extensions/inst/css/style.css
     toc: true
-
-
-