update template to adapt new drwater extensions

This commit is contained in:
2025-07-28 21:09:10 +08:00
parent e3a53e3177
commit c419bb7fda
64 changed files with 714 additions and 44873 deletions
+5 -20
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@@ -1,26 +1,11 @@
---
format:
elsevier-html:
css: _extensions/inst/css/style.css
docx:
reference-doc: _extensions/inst/word/MS.docx
elsevier-pdf:
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}
journal:
formatting: preprint
model: 1p
cite-style: authoryear
dwms-html: default
dwms-docx: default
dwms-pdf: default
filters:
- authors-block
- latex-environment
- authoraffil
---
# CRediT authorship contribution statement {-}
+6 -9
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@@ -1,19 +1,15 @@
---
format:
html:
css: _extensions/inst/css/style.css
pdf:
latex_engine: xelatex
keep-tex: false
keep-md: false
template: _extensions/inst/tex/cv.tex
dwcl-html: default
dwcl-docx: default
dwcl-pdf: default
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_institution_logo: "_extensions/drwater/dwcl/inst/rceeslonglogo.pdf"
from_sign: "_extensions/drwater/dwcl/inst/signmy.pdf"
from_position: "Vice Director, Professor"
from_professional_title: "Ph.D."
from_institution: "Chinese Academy of Sciences"
@@ -31,3 +27,4 @@ Thank you for your consideration our manuscript (`{{< meta submitid >}}`) in pub
We have carefully revised the manuscript 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.
+8 -15
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@@ -1,22 +1,15 @@
---
subtitle: "Graphical Abstract"
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}
dwms-html: default
dwms-docx: default
dwms-pdf: default
filters:
- latex-environment
- authoraffil
---
# Graphical Abstract {-}
#
<!-- ![](./figures/GA3.pdf) -->
+9 -14
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@@ -1,21 +1,16 @@
---
subtitle: "Highlights"
date: ""
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}
dwms-html: default
dwms-docx: default
dwms-pdf: default
filters:
- latex-environment
- authoraffil
---
# Highlights {-}
#
- A comprehensive model was contructed to evaluate the risk of odor occurrences
- Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
-21
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@@ -1,21 +0,0 @@
\relax
\providecommand\zref@newlabel[2]{}
\providecommand*\new@tpo@label[2]{}
\providecommand \babel@aux [2]{\global \let \babel@toc \@gobbletwo }
\@nameuse{bbl@beforestart}
\providecommand\hyper@newdestlabel[2]{}
\providecommand*\HyPL@Entry[1]{}
\HyPL@Entry{0<</S/D>>}
\babel@aux{english}{}
\newlabel{abstract}{{}{2}{Abstract}{section*.1}{}}
\@writefile{toc}{\contentsline {section}{Abstract}{2}{section*.1}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\nonumberline Main}{3}{section*.3}\protected@file@percent }
\newlabel{main}{{}{3}{Main}{section*.3}{}}
\@writefile{toc}{\contentsline {section}{\nonumberline Methods}{3}{section*.5}\protected@file@percent }
\newlabel{methods}{{}{3}{Methods}{section*.5}{}}
\@writefile{toc}{\contentsline {section}{\nonumberline Results}{3}{section*.7}\protected@file@percent }
\newlabel{results}{{}{3}{Results}{section*.7}{}}
\newlabel{references}{{}{4}{References}{section*.8}{}}
\@writefile{toc}{\contentsline {section}{References}{4}{section*.8}\protected@file@percent }
\newlabel{refs}{{}{4}{References}{section*.9}{}}
\gdef \@abspage@last{4}
-119
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@@ -1,119 +0,0 @@
---
msname: MS
smname: SM
# abstract: ""
# keywords:
# - KEYWORD1;
# date: last-modified
highlights: ""
date: ""
bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
# csl: https://www.zotero.org/styles/elsevier-harvard
csl: ./_extensions/inst/tex/american-chemical-society.csl
# csl: ./_extensions/inst/tex/nature.csl
# titlegraphical: "../figures/GA.pdf"
format:
elsevier-html:
toc: true
css: _extensions/inst/css/style.css
keep-md: true
epub: default
docx:
reference-doc: _extensions/inst/word/MS.docx
pdf:
# documentclass: article
latex-clean: false # to keep aux
citecolor: blue
colorlinks: true
number-sections: false
sansfont: "Gill Sans"
papersize: a4paper
sansfontoptions:
# - Color=39729E
- Color=2A303B
mainfont: "Source Sans 3" #| Verdana (fontsize: 11pt) # Source Sans 3 | Times New Roman| Helvetica | PT Sans
monofont: "JetBrains Mono"
mathfont: "Cambria Math"
CJKmainfont: SimHei
fontsize: 12pt
keep-md: false
include-in-header: "./_extensions/inst/tex/header.tex"
header-includes:
# - \usepackage{threeparttable}
# - \usepackage{fontspec}
# - \usepackage{endfloat}
# - \usepackage[UTF8, scheme=plain]{ctex}
- \usepackage{float}
- \usepackage[normalem]{ulem}
- \usepackage[doublespacing]{setspace}
- \usepackage{lineno}
- \linenumbers
- \usepackage{caption}
- \captionsetup{singlelinecheck=off}
# elsevier-pdf:
# keep-tex: true
# keep-md: false
# 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:
# # - 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
# formatting: preprint # preprint | review | doublebind
# model: 1p
# cite-style: authoryear
# # graphical-abstract: "![](../figures/GA.pdf)"
# # highlights:
filters:
- latex-environment
- authors-block
lightbox: auto
commands: [clab]
---
{{< pagebreak >}}
# Abstract {-}
{{< pagebreak >}}
# Main
# Methods
# Results
<!-- {{< include MS_discussion.qmd >}} -->
{{< pagebreak >}}
<!-- {{< include _est.qmd >}} -->
# References {-}
::: {#refs}
:::
{{< pagebreak >}}
<!-- {{< include _nature.qmd >}} -->
+8 -65
View File
@@ -8,79 +8,22 @@ smname: SM
highlights: ""
date: ""
bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
# csl: https://www.zotero.org/styles/elsevier-harvard
csl: ./_extensions/inst/tex/american-chemical-society.csl
# csl: ./_extensions/inst/tex/nature.csl
csl: _extensions/drwater/dwinst/nature.csl
# titlegraphical: "../figures/GA.pdf"
format:
elsevier-html:
toc: true
css: _extensions/inst/css/style.css
keep-md: true
epub: default
docx:
reference-doc: _extensions/inst/word/MS.docx
pdf:
# documentclass: article
latex-clean: false # to keep aux
citecolor: blue
colorlinks: true
number-sections: false
sansfont: "Gill Sans"
papersize: a4paper
sansfontoptions:
# - Color=39729E
- Color=2A303B
mainfont: "Source Sans 3" #| Verdana (fontsize: 11pt) # Source Sans 3 | Times New Roman| Helvetica | PT Sans
monofont: "JetBrains Mono"
mathfont: "Cambria Math"
CJKmainfont: SimHei
dwms-html: default
dwms-docx: default
dwms-pdf:
fontsize: 12pt
keep-md: false
include-in-header: "./_extensions/inst/tex/header.tex"
keep-tex: true
header-includes:
# - \usepackage{threeparttable}
# - \usepackage{fontspec}
# - \usepackage{endfloat}
# - \usepackage[UTF8, scheme=plain]{ctex}
- \usepackage{float}
- \usepackage[normalem]{ulem}
- \usepackage[doublespacing]{setspace}
- \usepackage{lineno}
- \usepackage{endfloat}
- \doublespacing
- \linenumbers
- \usepackage{caption}
- \captionsetup{singlelinecheck=off}
# elsevier-pdf:
# keep-tex: true
# keep-md: false
# 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:
# # - 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
# formatting: preprint # preprint | review | doublebind
# model: 1p
# cite-style: authoryear
# # graphical-abstract: "![](../figures/GA.pdf)"
# # highlights:
filters:
- latex-environment
- authors-block
lightbox: auto
commands: [clab]
- authoraffil
---
+418
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@@ -0,0 +1,418 @@
% Options for packages loaded elsewhere
% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
\PassOptionsToPackage{hyphens}{url}
\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
\PassOptionsToPackage{space}{xeCJK}
%
\documentclass[
english,
12pt,
letterpaper,
]{article}
\usepackage{xcolor}
\usepackage[margin=1in]{geometry}
\usepackage{amsmath,amssymb}
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\usepackage{iftex}
\ifPDFTeX
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
\usepackage{unicode-math} % this also loads fontspec
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
\usepackage{lmodern}
\ifPDFTeX\else
% xetex/luatex font selection
\setmainfont[]{Source Sans 3}
\setsansfont[Color=39729E]{Gill Sans}
\setmonofont[]{JetBrains Mono}
\setmathfont[]{Cambria Math}
\ifXeTeX
\usepackage{xeCJK}
\setCJKmainfont[]{SimHei}
\fi
\ifLuaTeX
\usepackage[]{luatexja-fontspec}
\setmainjfont[]{SimHei}
\fi
\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{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
\newsavebox\pandoc@box
\newcommand*\pandocbounded[1]{% scales image to fit in text height/width
\sbox\pandoc@box{#1}%
\Gscale@div\@tempa{\textheight}{\dimexpr\ht\pandoc@box+\dp\pandoc@box\relax}%
\Gscale@div\@tempb{\linewidth}{\wd\pandoc@box}%
\ifdim\@tempb\p@<\@tempa\p@\let\@tempa\@tempb\fi% select the smaller of both
\ifdim\@tempa\p@<\p@\scalebox{\@tempa}{\usebox\pandoc@box}%
\else\usebox{\pandoc@box}%
\fi%
}
% Set default figure placement to htbp
\def\fps@figure{htbp}
\makeatother
\ifLuaTeX
\usepackage[bidi=basic]{babel}
\else
\usepackage[bidi=default]{babel}
\fi
\ifPDFTeX
\else
\babelfont{rm}[]{Source Sans 3}
\fi
% get rid of language-specific shorthands (see #6817):
\let\LanguageShortHands\languageshorthands
\def\languageshorthands#1{}
\ifLuaTeX
\usepackage[english]{selnolig} % disable illegal ligatures
\fi
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
% -----------------------
% CUSTOM PREAMBLE STUFF
% -----------------------
\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[normalem]{ulem}
\usepackage{setspace}
\usepackage{lineno}
\usepackage{caption}
\captionsetup{singlelinecheck=off}
\usepackage[UTF8, scheme=plain]{ctex}
\usepackage{orcidlink}
% \setkomafont{author}{\normalsize}
% for revision
\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}}
% -----------------
% Title block stuff
% -----------------
% Title
\makeatletter
\renewcommand{\title}[1]{\gdef\@title{\large\textbf{#1}}} % Adjust \Huge or other font commands
\makeatother
% ------------------
% Section headings
% ------------------
\usepackage{titlesec}
\titleformat*{\section}{\Large\sffamily\bfseries\raggedright}
\titleformat*{\subsection}{\large\sffamily\bfseries\raggedright}
\titleformat*{\subsubsection}{\normalsize\sffamily\bfseries\raggedright}
\titleformat*{\paragraph}{\small\sffamily\bfseries\raggedright}
%\titlespacing{<command>}{<left>}{<before-sep>}{<after-sep>}
% Starred version removes indentation in following paragraph
\titlespacing*{\section}{0em}{2em}{0.1em}
\titlespacing*{\subsection}{0em}{1.25em}{0.1em}
\titlespacing*{\subsubsection}{0em}{0.75em}{0em}
% ------------------
% Headers/Footers
% ------------------
% \usepackage{fancyhdr}
% \pagestyle{fancy}
% \fancyhf{}
% \fancyhead[L,C,R]{}
% \fancyfoot[L,C]{}
% \fancyfoot[R]{\thepage}
% \renewcommand{\headrulewidth}{1pt}
% \fancypagestyle{plain}{%
% \renewcommand{\headrulewidth}{0pt}%
% \fancyhf{}%
% \fancyfoot[R]{\thepage}%
% }
% \renewcommand\footnoterule{\rule{\linewidth}{0.1pt}\vspace{5pt}}
% ------------------
% Captions
% ------------------
\usepackage[labelfont=bf,labelsep=period]{caption}
\captionsetup[figure]{font=footnotesize,justification=raggedright,singlelinecheck=false,format=hang}
% ---------------------------
% END CUSTOM PREAMBLE STUFF
% ---------------------------
\usepackage{endfloat}
\doublespacing
\linenumbers
\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{sfg}{h}{lost}}{\newfloat{sfg}{h}{lost}[chapter]}
\floatname{sfg}{Supplementary Fig.}
\newcommand*\listofsfgs{\listof{sfg}{List of Supplementary Figures}}
\makeatother
\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{stb}{h}{lost}}{\newfloat{stb}{h}{lost}[chapter]}
\floatname{stb}{Supplementary Table}
\newcommand*\listofstbs{\listof{stb}{List of Supplementary Tables}}
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\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{seq}{h}{lost}}{\newfloat{seq}{h}{lost}[chapter]}
\floatname{seq}{Supplementary Eq.}
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\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{rfg}{h}{lost}}{\newfloat{rfg}{h}{lost}[chapter]}
\floatname{rfg}{Fig. R}
\newcommand*\quartorfgref[1]{Fig. \hyperref[#1]{R\ref{#1}}}
\@ifpackageloaded{caption}{}{\usepackage{caption}}
\DeclareCaptionLabelFormat{quartorfgreflabelformat}{#1#2}
\captionsetup[rfg]{labelformat=quartorfgreflabelformat}
\newcommand*\listofrfgs{\listof{rfg}{List of Revision Figures}}
\makeatother
\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{rtb}{h}{lost}}{\newfloat{rtb}{h}{lost}[chapter]}
\floatname{rtb}{Table R}
\newcommand*\quartortbref[1]{Table \hyperref[#1]{R\ref{#1}}}
\@ifpackageloaded{caption}{}{\usepackage{caption}}
\DeclareCaptionLabelFormat{quartortbreflabelformat}{#1#2}
\captionsetup[rtb]{labelformat=quartortbreflabelformat}
\newcommand*\listofrtbs{\listof{rtb}{List of Revision Tables}}
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\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
\@ifundefined{c@chapter}{\newfloat{req}{h}{lost}}{\newfloat{req}{h}{lost}[chapter]}
\floatname{req}{Eq R}
\newcommand*\quartoreqref[1]{Eq \hyperref[#1]{R\ref{#1}}}
\@ifpackageloaded{caption}{}{\usepackage{caption}}
\DeclareCaptionLabelFormat{quartoreqreflabelformat}{#1#2}
\captionsetup[req]{labelformat=quartoreqreflabelformat}
\newcommand*\listofreqs{\listof{req}{List of Revision Equations}}
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\makeatletter
\@ifpackageloaded{caption}{}{\usepackage{caption}}
\AtBeginDocument{%
\ifdefined\contentsname
\renewcommand*\contentsname{Table of contents}
\else
\newcommand\contentsname{Table of contents}
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\ifdefined\listfigurename
\renewcommand*\listfigurename{List of Figures}
\else
\newcommand\listfigurename{List of Figures}
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\ifdefined\listtablename
\renewcommand*\listtablename{List of Tables}
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\newcommand\listtablename{List of Tables}
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\ifdefined\tablename
\renewcommand*\tablename{Table}
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}
\@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}}
\captionsetup{labelsep=colon}
\makeatother
\makeatletter
\makeatother
\makeatletter
\@ifpackageloaded{caption}{}{\usepackage{caption}}
\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
\makeatother
\usepackage{bookmark}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\urlstyle{same}
\hypersetup{
pdftitle={MANUSCRIPT TITLE},
pdfauthor={, , and },
pdflang={en},
colorlinks=true,
linkcolor={blue},
filecolor={Maroon},
citecolor={Blue},
urlcolor={blue},
pdfcreator={LaTeX via pandoc}}
\title{MANUSCRIPT TITLE}
\author{\footnotesize Xxxxx
Yyyy\textsuperscript{a,\#} \and \footnotesize Ming
Su\textsuperscript{\orcidlink{0000000198211268},a,b,\#,*} \and \footnotesize Min
Yang\textsuperscript{a,b,*}}
\date{}
\begin{document}
% for some reason this does not work in header
\renewcommand{\abstractname}{Abstract.}
% add the short title to the fancy header
\maketitle
%\noindent \rule{\linewidth}{.5pt}
%\noindent \rule{\linewidth}{.5pt}
\textsuperscript{\#} These authors contributed equally to this work.
\textsuperscript{a} State Key Laboratory of Environmental Aquatic
Chemistry, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China.\\
\textsuperscript{b} University of Chinese Academy of Sciences, Beijing
100049, China.
\textsuperscript{*} Corresponding to:
\href{mailto:mingsu@rcees.ac.cn}{Ming Su (mingsu@rcees.ac.cn)},
\href{mailto:yangmin@rcees.ac.cn}{Min Yang (yangmin@rcees.ac.cn)}
\newpage{}
\section*{Abstract}\label{abstract}
\addcontentsline{toc}{section}{Abstract}
\newpage{}
\section{Main}\label{main}
\section{Methods}\label{methods}
\section{Results}\label{results}
\newpage{}
\section*{References}\label{references}
\addcontentsline{toc}{section}{References}
\phantomsection\label{refs}
\newpage{}
\end{document}
+9 -35
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@@ -4,60 +4,34 @@ msname: MS
smname: SM
# date: last-modified
bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
csl: _extensions/inst/tex/elsevier-harvard.csl
csl: _extensions/drwater/dwinst/nature.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:
dwms-html: default
dwms-docx: default
dwms-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
filters:
- latex-environment
- authoraffil
---
```{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)
RM <- "F" # global rendermode, L: load pdata; F: fast load pdf
isrendering <- isTRUE(getOption('knitr.in.progress'))
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
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@@ -1,6 +1,5 @@
\relax
\providecommand\zref@newlabel[2]{}
\providecommand*\new@tpo@label[2]{}
\providecommand \babel@aux [2]{\global \let \babel@toc \@gobbletwo }
\@nameuse{bbl@beforestart}
\providecommand\hyper@newdestlabel[2]{}
@@ -8,7 +7,5 @@
\HyPL@Entry{0<</S/D>>}
\babel@aux{english}{}
\@writefile{lost}{\contentsline {sfg}{\numberline {1}{\ignorespaces Caption of demo figure}}{3}{sfg.1}\protected@file@percent }
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
\newlabel{sfg-demo}{{1}{3}{Caption of demo figure}{sfg.1}{}}
\@writefile{toc}{\providecommand\tocbasic@end@toc@file{}\tocbasic@end@toc@file}
\gdef \@abspage@last{3}
+8 -40
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@@ -2,58 +2,26 @@
msname: MS
smname: SM
bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
# csl: _extensions/inst/tex/elsevier-harvard.csl
# csl: ./_extensions/inst/tex/american-chemical-society.csl
csl: ./_extensions/inst/tex/nature.csl
csl: _extensions/drwater/dwinst/nature.csl
subtitle: "Supplementary Information"
date: ""
format:
elsevier-html:
css: _extensions/inst/css/style.css
docx:
reference-doc: _extensions/inst/word/MS.docx
pdf:
# documentclass: article
dwms-html: default
dwms-docx: default
dwms-pdf:
latex-clean: false # to keep aux
# toc: true
# toc-location: body
citecolor: blue
colorlinks: true
number-sections: false
sansfont: "Gill Sans"
papersize: a4paper
sansfontoptions:
# - Color=39729E
- Color=2A303B
mainfont: "Source Sans 3" #| Verdana (fontsize: 11pt) # Source Sans 3 | Times New Roman| Helvetica | PT Sans
monofont: "JetBrains Mono"
mathfont: "Cambria Math"
CJKmainfont: SimHei
fontsize: 11pt
keep-md: false
keep-tex: true
include-in-header: "./_extensions/inst/tex/header.tex"
header-includes:
- \doublespacing
- \linenumbers
- \let\oldsection\section
- \renewcommand{\section}{\clearpage\oldsection}
- \let\oldsubsection\subsection
- \renewcommand{\subsection}{\clearpage\oldsubsection}
# - \renewcommand{\thepage}{S\arabic{page}}
# - \usepackage{threeparttable}
# - \usepackage{fontspec}
# - \usepackage{endfloat}
# - \setmainfont{Calibri}
# - \usepackage[UTF8, scheme=plain]{ctex}
- \usepackage{float}
- \usepackage[normalem]{ulem}
- \usepackage[doublespacing]{setspace}
# - \usepackage{lineno}
# - \linenumbers
filters:
- latex-environment
- authors-block
lightbox: auto
commands: [clab]
- latex-environment
- authoraffil
---
\thispagestyle{empty}
+98 -53
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@@ -7,11 +7,11 @@
%
\documentclass[
english,
11pt,
a4paperpaper,
DIV=11,
numbers=noendperiod]{scrartcl}
12pt,
letterpaper,
]{article}
\usepackage{xcolor}
\usepackage[margin=1in]{geometry}
\usepackage{amsmath,amssymb}
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\usepackage{iftex}
@@ -28,7 +28,7 @@
\ifPDFTeX\else
% xetex/luatex font selection
\setmainfont[]{Source Sans 3}
\setsansfont[Color=2A303B]{Gill Sans}
\setsansfont[Color=39729E]{Gill Sans}
\setmonofont[]{JetBrains Mono}
\setmathfont[]{Cambria Math}
\ifXeTeX
@@ -56,29 +56,6 @@
}{% if KOMA class
\KOMAoptions{parskip=half}}
\makeatother
% Make \paragraph and \subparagraph free-standing
\makeatletter
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}{
\@ifstar
\xxxParagraphStar
\xxxParagraphNoStar
}
\newcommand{\xxxParagraphStar}[1]{\oldparagraph*{#1}\mbox{}}
\newcommand{\xxxParagraphNoStar}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}{
\@ifstar
\xxxSubParagraphStar
\xxxSubParagraphNoStar
}
\newcommand{\xxxSubParagraphStar}[1]{\oldsubparagraph*{#1}\mbox{}}
\newcommand{\xxxSubParagraphNoStar}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
\makeatother
\usepackage{longtable,booktabs,array}
@@ -136,6 +113,9 @@
% -----------------------
% CUSTOM PREAMBLE STUFF
% -----------------------
\usepackage{enumitem}
\usepackage{fontspec}
\usepackage{float}
@@ -144,16 +124,17 @@
\usepackage{nameref} %needed by zref-xr
\usepackage{zref-xr,zref-hyperref,zref-user}
\usepackage{xr-hyper}
\usepackage[normalem]{ulem}
\usepackage{setspace}
\usepackage{lineno}
\usepackage{caption}
\captionsetup{singlelinecheck=off}
\usepackage[UTF8, scheme=plain]{ctex}
\usepackage{orcidlink}
% \setkomafont{author}{\normalsize}
\setkomafont{author}{\normalsize}
\makeatletter
\renewcommand{\title}[1]{\gdef\@title{\large\textbf{#1}}} % Adjust \Huge or other font commands
% \renewcommand{\author}[1]{\gdef\@author{\normalsize\textrm{#1}}} % Adjust \Huge or other font commands
% \renewcommand{\author}[1]{\normalsize\textit{#1}} % Use \normalsize and \textit for customization
\makeatother
% for revision
\usepackage{adjustbox}
% \usepackage{xcolor}
\usepackage{mdframed}
@@ -210,14 +191,67 @@
\renewenvironment{quote}{\begin{question}}{\end{question}}
% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
\KOMAoption{captions}{tableheading}
% -----------------
% Title block stuff
% -----------------
% Title
\makeatletter
\renewcommand{\title}[1]{\gdef\@title{\large\textbf{#1}}} % Adjust \Huge or other font commands
\makeatother
% ------------------
% Section headings
% ------------------
\usepackage{titlesec}
\titleformat*{\section}{\Large\sffamily\bfseries\raggedright}
\titleformat*{\subsection}{\large\sffamily\bfseries\raggedright}
\titleformat*{\subsubsection}{\normalsize\sffamily\bfseries\raggedright}
\titleformat*{\paragraph}{\small\sffamily\bfseries\raggedright}
%\titlespacing{<command>}{<left>}{<before-sep>}{<after-sep>}
% Starred version removes indentation in following paragraph
\titlespacing*{\section}{0em}{2em}{0.1em}
\titlespacing*{\subsection}{0em}{1.25em}{0.1em}
\titlespacing*{\subsubsection}{0em}{0.75em}{0em}
% ------------------
% Headers/Footers
% ------------------
% \usepackage{fancyhdr}
% \pagestyle{fancy}
% \fancyhf{}
% \fancyhead[L,C,R]{}
% \fancyfoot[L,C]{}
% \fancyfoot[R]{\thepage}
% \renewcommand{\headrulewidth}{1pt}
% \fancypagestyle{plain}{%
% \renewcommand{\headrulewidth}{0pt}%
% \fancyhf{}%
% \fancyfoot[R]{\thepage}%
% }
% \renewcommand\footnoterule{\rule{\linewidth}{0.1pt}\vspace{5pt}}
% ------------------
% Captions
% ------------------
\usepackage[labelfont=bf,labelsep=period]{caption}
\captionsetup[figure]{font=footnotesize,justification=raggedright,singlelinecheck=false,format=hang}
% ---------------------------
% END CUSTOM PREAMBLE STUFF
% ---------------------------
\doublespacing
\linenumbers
\let\oldsection\section
\renewcommand{\section}{\clearpage\oldsection}
\let\oldsubsection\subsection
\renewcommand{\subsection}{\clearpage\oldsubsection}
\usepackage{float}
\usepackage[normalem]{ulem}
\usepackage[doublespacing]{setspace}
\makeatletter
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{plain}
@@ -324,8 +358,8 @@
colorlinks=true,
linkcolor={blue},
filecolor={Maroon},
citecolor={blue},
urlcolor={Blue},
citecolor={Blue},
urlcolor={blue},
pdfcreator={LaTeX via pandoc}}
@@ -333,27 +367,38 @@
\usepackage{etoolbox}
\makeatletter
\providecommand{\subtitle}[1]{% add subtitle to \maketitle
\apptocmd{\@title}{\par {\large #1 \par}}{}{}
\apptocmd{\@title}{\par {\large\sffamily\bfseries #1 \par}}{}{}
}
\makeatother
\subtitle{Supplementary Information}
\author{Xxxxx Yyyy\textsuperscript{1} \and Ming
Su\textsuperscript{1,2,*} \and Min Yang\textsuperscript{1,2,*}}
\author{\footnotesize Xxxxx
Yyyy\textsuperscript{a,\#} \and \footnotesize Ming
Su\textsuperscript{\orcidlink{0000000198211268},a,b,\#,*} \and \footnotesize Min
Yang\textsuperscript{a,b,*}}
\date{}
\begin{document}
% for some reason this does not work in header
\renewcommand{\abstractname}{Abstract.}
% add the short title to the fancy header
\maketitle
%\noindent \rule{\linewidth}{.5pt}
%\noindent \rule{\linewidth}{.5pt}
\textsuperscript{1} State Key Laboratory of Environmental Aquatic
\textsuperscript{\#} These authors contributed equally to this work.
\textsuperscript{a} State Key Laboratory of Environmental Aquatic
Chemistry, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences\\
\textsuperscript{2} University of Chinese Academy of Sciences
Academy of Sciences, Beijing 100085, China.\\
\textsuperscript{b} University of Chinese Academy of Sciences, Beijing
100049, China.
\textsuperscript{*} Correspondence:
\href{mailto:mingsu@rcees.ac.cn}{Ming Su
\textless{}mingsu@rcees.ac.cn\textgreater{}},
\href{mailto:yangmin@rcees.ac.cn}{Min Yang
\textless{}yangmin@rcees.ac.cn\textgreater{}}
\textsuperscript{*} Corresponding to:
\href{mailto:mingsu@rcees.ac.cn}{Ming Su (mingsu@rcees.ac.cn)},
\href{mailto:yangmin@rcees.ac.cn}{Min Yang (yangmin@rcees.ac.cn)}
\thispagestyle{empty}
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@@ -1,2 +1 @@
\babel@toc {english}{}\relax
\providecommand \tocbasic@end@toc@file {}\tocbasic@end@toc@file
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@@ -1,6 +1,6 @@
---
subtitle: Graphical abstract
format: html
format: dwhm-html
---
```{r}