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准备第7次课

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Ming Su
2024-03-21 22:30:54 +08:00
parent 67a4f22e5f
commit efb50900ef
468 changed files with 80663 additions and 5 deletions
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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/_extension.yml Executable file
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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

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/bib/elsarticle-harv.bst Executable file
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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/bib/elsarticle-num-names.bst Executable file
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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/bib/elsarticle-num.bst Executable file
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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/bib/elsevier-harvard.csl Executable file
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<?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>

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/elsarticle.cls Executable file
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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/elsevier.lua Executable file
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-- 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,
}
}

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/partials/_two-column-longtable.tex Executable file
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\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

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/partials/before-body.tex Executable file
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\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}

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/partials/revision.tex Executable file
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\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}}

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/partials/title.tex Executable file
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\setlength{\parindent}{6pt}

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SD/20240326_4_datatidy/_extensions/quarto-journals/elsevier/styles/elsevier.scss Executable file
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/*-- scss:defaults --*/