update

MS/MS.qmd

@@ -1,33 +1,23 @@
 ---
 msname: MS
 smname: SM
-abstract: ABSTRACT
+# abstract: ""
-keywords: 
+# keywords:
-  - KEYWORD1
+#   - KEYWORD1;
-  - KEYWORD2
+# date: last-modified
-  - KEYWORD3
+highlights: ""
-date: last-modified
+date: ""
 bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
 # csl: https://www.zotero.org/styles/elsevier-harvard
-csl: _extensions/inst/tex/elsevier-harvard.csl
+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
+  epub: default
-  # nature-pdf:
-  #   # journal.cite-style is included in the tex file but ignored by pandoc if 
-  #   # cite-method is not `natbib`.
-  #   journal:
-  #     cite-style: sn-nature
-  #   # `citeproc` is the pandoc default. Set `cite-method: natbib` if required
-  #   # to use the bst styles from the upstream template.
-  #   cite-method: natbib
-  #   keep-tex: true
-  #   equal-margins: false
-  # acs-pdf:
-  #   keep-tex: true 
   docx:
     reference-doc: _extensions/inst/word/MS.docx
   pdf:
@@ -35,11 +25,12 @@ format:
     latex-clean: false # to keep aux
     citecolor: blue
     colorlinks: true
-    number-sections: true
+    number-sections: false
     sansfont: "Gill Sans"
     papersize: a4paper
     sansfontoptions: 
-      - Color=39729E
+      # - 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"
@@ -48,78 +39,86 @@ format:
     keep-md: false
     include-in-header: "./_extensions/inst/tex/header.tex"
     header-includes:
+      # - \usepackage{threeparttable}
       # - \usepackage{fontspec}
-      - \usepackage{endfloat}
+      # - \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]
-editor: 
-  markdown: 
-    wrap: sentence
 ---
 
 
-::: {.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}
 #| 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(lubridate)
-require(patchwork)
 require(drwateR)
+require(patchwork)
 rmdify::rmd_init()
-biburl <- "https://drc.drwater.net/datapool/public/BB/Ref.bib"
+dwfun::init()
-if (!isRendering) {
-  download.file(biburl, destfile = "Ref.bib")
-}
 ```
 
-# Introduction
 
-Blabla. [Bla blaBla blaBla blaBla blaBla bla     Bla bla.]{.clab options=r1q0101}
+{{< pagebreak >}}
 
-# Materials and methods
+# Abstract {-}
-
-To cite a figure in `SM.qmd`, use this syntax: `r zref("sfg-demofigure")`.
-
-# Results
-
-# Discussion
-
-# Conclusions
 
 
-<!-- {{< include _acs.qmd >}} -->
+{{< pagebreak >}}
 
-# Acknowledgements {.unnumbered}
+{{< include MS_main.qmd >}}
+{{< include MS_methods.qmd >}}
+{{< include MS_results.qmd >}}
+<!-- {{< include MS_discussion.qmd >}} -->
 
-This work was financially supported by the National Natural Science Foundation of China (52030002, 51878649), and Youth Innovation Promotion Association CAS.
+{{< pagebreak >}}
 
-# References {.unnumbered}
+<!-- {{< include _est.qmd >}} -->
 
-```{r}
+# References {-}
 
-```
+::: {#refs}
+:::
 
+{{< pagebreak >}}
+
+<!-- {{< include _nature.qmd >}} -->

MS/MS_main.qmd

@@ -0,0 +1,2 @@
+# Main
+

MS/MS_methods.qmd

@@ -0,0 +1,2 @@
+# Methods
+

MS/MS_results.qmd

@@ -0,0 +1,2 @@
+# Results
+

MS/SM.qmd

@@ -1,9 +1,12 @@
 ---
 msname: MS
 smname: SM
-subtitle: Supplementary Material
 bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
-csl: _extensions/inst/tex/elsevier-harvard.csl
+# csl: _extensions/inst/tex/elsevier-harvard.csl
+# csl: ./_extensions/inst/tex/american-chemical-society.csl
+csl: ./_extensions/inst/tex/nature.csl
+subtitle: "Supplementary Information"
+date: ""
 format:
   elsevier-html:
     css: _extensions/inst/css/style.css
@@ -12,23 +15,30 @@ format:
   pdf:
     # documentclass: article
     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=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
+    fontsize: 11pt
     keep-md: false
+    keep-tex: true
     include-in-header: "./_extensions/inst/tex/header.tex"
     header-includes:
       - \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}
@@ -37,8 +47,8 @@ format:
       - \usepackage{float}
       - \usepackage[normalem]{ulem}
       - \usepackage[doublespacing]{setspace}
-      - \usepackage{lineno}
+      # - \usepackage{lineno}
-      - \linenumbers
+      # - \linenumbers
 filters:
    - latex-environment
    - authors-block
@@ -46,54 +56,58 @@ lightbox: auto
 commands: [clab]
 ---
 
+\thispagestyle{empty}
 
 ```{r}
-#| label: setup
 #| include: false
 #| cache: false
+options(tinytex.clean = FALSE)
 lang <- "en"
-RM <- "F"   # global rendermode, L: load pdata; F: fast load pdf # nolint
+RM <- "F" # global rendermode, L: load pdata; F: fast load pdf
-isRendering <- isTRUE(getOption("knitr.in.progress"))
+isRendering <- isTRUE(getOption('knitr.in.progress'))
 require(tidyverse)
-require(lubridate)
 require(patchwork)
 require(drwateR)
 rmdify::rmd_init()
-biburl <- "https://drc.drwater.net/datapool/public/BB/Ref.bib"
-if (!isRendering) { download.file(biburl, destfile = "Ref.bib") }
 ```
 
-# Supplementary Material {-}
-
 Figures and/or tables are provided below as the supplementary evidences to the main text.
 
+{{< pagebreak >}}
 
-\pagebreak
 
-::: {#sfg-demofigure}
-
-```{r}
-#| out-width: 60%
-#| lightbox:
-#|   group: all
-
-if (!isRendering) {
-
-  mtcars |>
-  ggplot(aes(x = wt, y = mpg)) +
-    geom_point() +
-    labs(x = "Weight", y = "Miles per Gallon") +
-    dwfun::theme_sci(3, 3)
-
-  ggsavep("../figures/demofigure.pdf", loadit = FALSE)
-
-} # End of isrendering
-
-ggsavep("../figures/demofigure.pdf", loadit = TRUE)
 
+```{=latex}
+\clearpage
+{
+\hypersetup{linkcolor=black}
+\setcounter{tocdepth}{3}
+\tableofcontents
+}
 ```
 
-This is demo figure in supplementary material
+
+{{< pagebreak >}}
+
+
+::: {#sfg-demo}
+
+```{r}
+#| out-width: "40%"
+
+if (!isRendering) {
+  data.frame(x = 1:10, y = 1:10) |>
+    ggplot(aes(x, y)) +
+    geom_point() +
+    theme_sci(3, 2.0)
+
+  ggsavep("../figures/demo.pdf", loadit = FALSE)
+}
+
+ggsavep("../figures/demo", loadit = TRUE)
+```
+
+Caption of demo figure
 
 :::
 

MS/_nature.qmd

@@ -0,0 +1,23 @@
+# Data availability
+
+The data that support the findings of this study are available upon request.
+
+# Code availability  
+
+Analysis scripts are available via GitHub at https://git.drwater.net/.
+
+# Acknowledgements
+
+This research was financially supported by the National Natural Science Foundation of China (52030002, W2412156, 51878649) and the National Key R&D Program of China (2022YFC3203603).
+
+# Author contributions
+
+J.F. led data curation, methodology development, formal analysis, contributed to manuscript writing. editing, while supporting visualisation. M.S. (Corresponding Author) led conceptualization, formal analysis, and visualization while supporting methodology and co-leading manuscript writing and editing. Y.G., Y.A., and T.C. supported methodology and formal analysis. S.H. provided methodological and analytical support. M.Y. (Corresponding Author) co-led conceptualization and project administration, providing supervision and validation.
+
+# Competing interests
+
+The authors declare no competing interests.
+
+# Additional information
+
+Correspondence and requests for materials should be addressed to Ming Su or Min Yang.

Makefile

@@ -150,7 +150,8 @@ pull:
 			else \
 			echo "尝试将远程main分枝合并至本地$$current_branch 分枝."; \
 			git pull --rebase origin main; \
-		fi
+		fi; \
+	git pull
 
 # Pull changes from the main branch
 pullmain:
@@ -161,6 +162,7 @@ pullmain:
 
 push:
 	@echo "推送到远程..."; \
+		git pull; \
 		git push
 
 filehash:

TC/index.qmd

@@ -13,13 +13,27 @@ rmdify::rmd_init()
 #| output: asis
 data.frame(fn = dir("./", pattern = ".*-.*.docx")) |>
   # dplyr::mutate(oldfn = gsub("^MS([0-9]*)-([0-9]*)_([a-z0-9]*)-([a-z0-9]*).docx$", "MS\\1_\\3.docx", fn)) |>
-  dplyr::mutate(newfn = gsub("^MS([0-9]*)-([0-9]*)_([a-z0-9]*)-([a-z0-9]*).docx$", "MS\\2_\\4.docx", fn)) |>
+  dplyr::mutate(
+    newfn = gsub(
+      "^MS([0-9]*)-([0-9]*)_([a-z0-9]*)-([a-z0-9]*).docx$",
+      "MS\\2_\\4.docx",
+      fn
+    )
+  ) |>
   # dplyr::mutate(time1 = lubridate::ymd_hm(gsub("MS([0-9]*)_([a-z0-9]*).docx$", "\\1", oldfn))) |>
-  dplyr::mutate(time2 = lubridate::ymd_hm(gsub("MS([0-9]*)_([a-z0-9]*).docx$", "\\1", newfn))) |>
+  dplyr::mutate(
+    time2 = lubridate::ymd_hm(gsub(
+      "MS([0-9]*)_([a-z0-9]*).docx$",
+      "\\1",
+      newfn
+    ))
+  ) |>
   # dplyr::arrange(dplyr::desc(time2), newfn, dplyr::desc(time1)) |>
   # dplyr::mutate(htmlstr = paste0("- [**", oldfn, "**](MS/", oldfn, ") ← [**",
   #   newfn, "**](MS/", newfn, ") ⇨ [**", fn, "**](", fn, ")\n\n")) |>
-  dplyr::mutate(htmlstr = paste0("[- ", time2, ": **", fn, "**](", fn, ")\n\n")) |>
+  dplyr::mutate(
+    htmlstr = paste0("[- ", time2, ": **", fn, "**](", fn, ")\n\n")
+  ) |>
   dplyr::pull(htmlstr) |>
   paste(collapse = "") |>
   cat()

_extensions/christopherkenny/nature/_extension.yml

@@ -1,27 +0,0 @@
-title: Nature Journal Template
-author: Christopher Kenny, Cameron Smith
-version: 1.0.1
-quarto-required: ">=1.4.0"
-contributes:
-  formats:
-    common:
-      toc: false
-      biblio-config: false
-    pdf:
-      include-in-header: header.tex
-      format-resources:
-        - sn-jnl.cls
-        - sn-apacite.bst
-        - sn-aps.bst
-        - sn-basic.bst
-        - sn-chicago.bst
-        - sn-mathphys-ay.bst
-        - sn-mathphys-num.bst
-        - sn-nature.bst
-        - sn-vancouver.bst
-      template-partials:
-        - "partials/doc-class.tex"
-        - "partials/title.tex"
-        - "partials/_author.tex"
-        - "partials/_affiliation.tex"
-        - "partials/before-body.tex"

_extensions/christopherkenny/nature/csl/nature-no-superscript.csl

@@ -1,127 +0,0 @@
-<?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>Nature (no superscript)</title>
-    <id>http://www.zotero.org/styles/nature-no-superscript</id>
-    <link href="http://www.zotero.org/styles/nature-no-superscript" rel="self"/>
-    <link href="http://www.nature.com/clpt/clptguidetoauthors.pdf" rel="documentation"/>
-    <author>
-      <name>Michael Berkowitz</name>
-      <email>mberkowi@gmu.edu</email>
-    </author>
-    <category citation-format="numeric"/>
-    <category field="science"/>
-    <category field="generic-base"/>
-    <updated>2022-07-02T13:18:26+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="title">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <text variable="title" font-style="italic"/>
-      </if>
-      <else-if type="chapter" match="any"/>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="author">
-    <names variable="author">
-      <name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
-      <label form="short" prefix=", "/>
-      <et-al font-style="italic"/>
-    </names>
-  </macro>
-  <macro name="access">
-    <choose>
-      <if variable="volume" type="article" match="any"/>
-      <else-if variable="DOI">
-        <text variable="DOI" prefix="doi:"/>
-      </else-if>
-      <else-if variable="URL">
-        <text term="at"/>
-        <text variable="URL" prefix=" &lt;" suffix="&gt;"/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="issuance">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song chapter paper-conference" match="any">
-        <group delimiter=", " prefix="(" suffix=").">
-          <text variable="publisher" form="long"/>
-          <date variable="issued">
-            <date-part name="year"/>
-          </date>
-        </group>
-      </if>
-      <else-if type="article">
-        <group delimiter=" ">
-          <choose>
-            <if variable="genre" match="any">
-              <text variable="genre" text-case="capitalize-first"/>
-            </if>
-            <else>
-              <text term="article" text-case="capitalize-first"/>
-            </else>
-          </choose>
-          <text term="at"/>
-          <choose>
-            <if variable="DOI" match="any">
-              <text variable="DOI" prefix="https://doi.org/"/>
-            </if>
-            <else>
-              <text variable="URL"/>
-            </else>
-          </choose>
-          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
-        </group>
-      </else-if>
-      <else>
-        <date prefix="(" suffix=")." variable="issued">
-          <date-part name="year"/>
-        </date>
-      </else>
-    </choose>
-  </macro>
-  <macro name="editor">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <names variable="editor" prefix="(" suffix=")">
-          <label form="short" suffix=" "/>
-          <name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
-        </names>
-      </if>
-    </choose>
-  </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="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
-    <layout>
-      <text variable="citation-number" suffix="."/>
-      <group delimiter=" ">
-        <text macro="author" suffix="."/>
-        <text macro="title" suffix="."/>
-        <choose>
-          <if type="chapter paper-conference" match="any">
-            <text term="in" form="long" plural="false"/>
-          </if>
-        </choose>
-        <text variable="container-title" font-style="italic" form="short"/>
-        <text macro="editor"/>
-        <group font-weight="bold">
-          <text variable="volume" suffix=","/>
-        </group>
-        <text variable="page"/>
-        <text macro="issuance"/>
-        <text macro="access"/>
-      </group>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-basic-author-date.csl

@@ -1,239 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" default-locale="en-US" version="1.0" demote-non-dropping-particle="never">
-  <info>
-    <title>Springer - Basic (author-date)</title>
-    <id>http://www.zotero.org/styles/springer-basic-author-date</id>
-    <link href="http://www.zotero.org/styles/springer-basic-author-date" rel="self"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/instruct-authors-e.pdf" rel="documentation"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
-    <!-- This style corresponds to 'Springer Basic' in the pdf document 'Key Style Points' at this url -->
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <author>
-      <name>Jens Allmer</name>
-      <email>jens@allmer.de</email>
-      <uri>http://jens.allmer.de</uri>
-    </author>
-    <contributor>
-      <name>Sebastian Karcher</name>
-    </contributor>
-    <category citation-format="author-date"/>
-    <category field="generic-base"/>
-    <summary>Springer Author Date Style for the disciplines Medicine, Biomedicine, Life Sciences, Chemistry, Geosciences, Computer Science, Engineering, Economics. This style is based on Harvard style and recommendations of the Council of Biology Editors.</summary>
-    <updated>2020-02-18T04:57:50+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>
-    <terms>
-      <term name="and others">et al</term>
-      <term name="et-al">et al.</term>
-      <term name="edition" form="short">edn.</term>
-    </terms>
-  </locale>
-  <macro name="author-short">
-    <names variable="author">
-      <name form="short" and="text"/>
-      <et-al/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </names>
-  </macro>
-  <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=")"/>
-      <et-al term="and others"/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </names>
-  </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"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="year">
-    <date variable="issued">
-      <date-part name="year"/>
-    </date>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if type="book">
-        <group delimiter=". ">
-          <group delimiter=", ">
-            <text variable="title"/>
-            <text macro="edition"/>
-          </group>
-          <choose>
-            <!-- Replace with type="software" as that becomes available -->
-            <if type="book" match="any" variable="version">
-              <text variable="version" prefix="Version "/>
-            </if>
-          </choose>
-        </group>
-      </if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="year-parenth">
-    <date prefix="(" suffix=")" variable="issued">
-      <date-part name="year"/>
-    </date>
-  </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year-suffix" cite-group-delimiter=", ">
-    <sort>
-      <key variable="issued"/>
-      <key macro="author"/>
-    </sort>
-    <layout prefix="(" suffix=")" delimiter="; ">
-      <group delimiter=", ">
-        <group delimiter=" ">
-          <text macro="author-short"/>
-          <text macro="year"/>
-        </group>
-        <group delimiter=" ">
-          <label variable="locator" form="short"/>
-          <text variable="locator"/>
-        </group>
-      </group>
-    </layout>
-  </citation>
-  <bibliography et-al-min="5" et-al-use-first="3" hanging-indent="true">
-    <sort>
-      <key macro="author"/>
-      <key variable="author" sort="ascending"/>
-    </sort>
-    <layout>
-      <group delimiter=" ">
-        <text macro="author"/>
-        <text macro="year-parenth"/>
-        <text macro="title"/>
-      </group>
-      <choose>
-        <!--    Book chapter
-             Brown B, Aaron M (2001) The politics of nature.
-             In: Smith J (ed) The rise of modern genomics, 3rd edn.
-             Wiley, New York, pp 230-257 -->
-        <if type="chapter paper-conference" match="any">
-          <group delimiter=" " prefix=". ">
-            <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>
-            <group delimiter=", ">
-              <text variable="container-title"/>
-              <text macro="edition"/>
-            </group>
-          </group>
-          <group prefix=". " delimiter=", ">
-            <text variable="publisher"/>
-            <text variable="publisher-place"/>
-            <group delimiter=" ">
-              <label variable="page" form="short" strip-periods="true"/>
-              <text variable="page"/>
-            </group>
-          </group>
-        </if>
-        <else-if type="article-journal">
-          <choose>
-            <if variable="page volume" match="any">
-              <!--    Journal article
-                   Gamelin FX, Baquet G, Berthoin S, Thevenet D, Nourry C, Nottin S, Bosquet L (2009)
-                   Effect of high intensity intermittent training on heart rate variability in prepubescent children.
-                   Eur J Appl Physiol 105:731-738. doi: 10.1007/s00421-008-0955-8
-                   Ideally, the names of all authors should be provided, but the usage of "et al"
-                   in long author lists will also be accepted:
-                   Smith J, Jones M Jr, Houghton L et al (1999)
-                   Future of health insurance. N Engl J Med 965:325-329   -->
-              <group prefix=". " delimiter=". ">
-                <group delimiter=" ">
-                  <text variable="container-title" form="short" strip-periods="true"/>
-                  <group delimiter=":">
-                    <text variable="volume" suffix=":"/>
-                    <text variable="page"/>
-                  </group>
-                </group>
-                <text prefix="https://doi.org/" variable="DOI"/>
-              </group>
-            </if>
-            <else>
-              <!--    Article by DOI
-       Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production.
-       J Mol Med. doi:10.1007/s001090000086     -->
-              <group prefix=". " delimiter=". ">
-                <text variable="container-title" form="short" strip-periods="true"/>
-                <text prefix="https://doi.org/" variable="DOI"/>
-              </group>
-            </else>
-          </choose>
-        </else-if>
-        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <!--    Book
-               South J, Blass B (2001) The future of modern genomics. Blackwell, London    -->
-          <group delimiter=". ">
-            <group prefix=". " delimiter=", ">
-              <text variable="publisher"/>
-              <text variable="publisher-place"/>
-            </group>
-            <group>
-              <choose>
-                <if match="any" variable="version">
-                  <text variable="URL" prefix="URL "/>
-                </if>
-              </choose>
-            </group>
-          </group>
-        </else-if>
-        <else-if type="webpage post-weblog post" match="any">
-          <!--    Online document
-               Doe J (1999) Title of subordinate document. In: The dictionary of substances and their effects.
-               Royal Society of Chemistry. Available via DIALOG.
-               http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999
-               Unfortunately, "Royal Society of Chemistry. Available via DIALOG." cannot seem to be mapped here -->
-          <group prefix=". " delimiter=". ">
-            <text prefix="In: " variable="container-title" form="short"/>
-            <text variable="URL"/>
-            <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">
-          <!--    Dissertation
-               Trent JW (1975) Experimental acute renal failure. Dissertation, University of California       -->
-          <group prefix=". " delimiter=", ">
-            <text variable="genre" text-case="capitalize-first"/>
-            <text variable="publisher"/>
-          </group>
-        </else-if>
-        <else>
-          <!--    None of the provided formats need to add manually (some data provided) -->
-          <group prefix=". " delimiter=" ">
-            <text variable="container-title" form="short"/>
-            <group delimiter=":">
-              <text variable="volume"/>
-              <text variable="page"/>
-            </group>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-basic-brackets-no-et-al.csl

@@ -1,184 +0,0 @@
-<?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-US">
-  <info>
-    <title>Springer - Basic (numeric, brackets, no "et al.")</title>
-    <id>http://www.zotero.org/styles/springer-basic-brackets-no-et-al</id>
-    <link href="http://www.zotero.org/styles/springer-basic-brackets-no-et-al" rel="self"/>
-    <link href="http://www.zotero.org/styles/springer-basic-author-date" rel="template"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/instruct-authors-e.pdf" rel="documentation"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
-    <!-- This style corresponds to 'Springer Basic' in the pdf document 'Key Style Points' at this url -->
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <author>
-      <name>Charles Parnot</name>
-      <email>charles.parnot@gmail.com</email>
-      <uri>http://twitter.com/cparnot</uri>
-    </author>
-    <category citation-format="numeric"/>
-    <category field="generic-base"/>
-    <summary>Springer Numbered Style for the disciplines Medicine, Biomedicine, Life Sciences, Chemistry, Geosciences, Computer Science, Engineering, Economics. This style is based on Harvard style and recommendations of the Council of Biology Editors.</summary>
-    <updated>2022-02-24T13:06:32+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"/>
-      <!--<et-al strip-periods="true"/> -->
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </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=", ">
-          <text variable="title"/>
-          <text macro="edition"/>
-        </group>
-      </if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="year-parenth">
-    <date prefix="(" suffix=")" 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 second-field-align="flush">
-    <layout>
-      <text variable="citation-number" suffix=". "/>
-      <group delimiter=" ">
-        <text macro="author"/>
-        <text macro="year-parenth"/>
-        <text macro="title"/>
-      </group>
-      <choose>
-        <!--    Book chapter
-             Brown B, Aaron M (2001) The politics of nature.
-             In: Smith J (ed) The rise of modern genomics, 3rd edn.
-             Wiley, New York, pp 230-257 -->
-        <if type="chapter paper-conference" match="any">
-          <group delimiter=" " prefix=". ">
-            <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>
-            <group delimiter=", ">
-              <text variable="container-title"/>
-              <text macro="edition"/>
-            </group>
-          </group>
-          <group prefix=". " delimiter=", ">
-            <text variable="publisher"/>
-            <text variable="publisher-place"/>
-            <group delimiter=" ">
-              <label variable="page" form="short" strip-periods="true"/>
-              <text variable="page"/>
-            </group>
-          </group>
-        </if>
-        <else-if type="article-journal">
-          <choose>
-            <if variable="page volume" match="any">
-              <!--    Journal article
-                   Gamelin FX, Baquet G, Berthoin S, Thevenet D, Nourry C, Nottin S, Bosquet L (2009)
-                   Effect of high intensity intermittent training on heart rate variability in prepubescent children.
-                   Eur J Appl Physiol 105:731-738. doi: 10.1007/s00421-008-0955-8
-                   Ideally, the names of all authors should be provided, but the usage of "et al"
-                   in long author lists will also be accepted:
-                   Smith J, Jones M Jr, Houghton L et al (1999)
-                   Future of health insurance. N Engl J Med 965:325-329   -->
-              <group prefix=". ">
-                <group delimiter=" ">
-                  <text variable="container-title" form="short" strip-periods="true"/>
-                  <group delimiter=":">
-                    <text variable="volume" suffix=":"/>
-                    <text variable="page"/>
-                  </group>
-                </group>
-                <text prefix=". https://doi.org/" variable="DOI"/>
-              </group>
-            </if>
-            <else>
-              <!--    Article by DOI
-       Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production.
-       J Mol Med. doi:10.1007/s001090000086     -->
-              <group prefix=". " delimiter=". ">
-                <text variable="container-title" form="short" strip-periods="true"/>
-                <text prefix="https://doi.org/" variable="DOI"/>
-              </group>
-            </else>
-          </choose>
-        </else-if>
-        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <!--    Book
-               South J, Blass B (2001) The future of modern genomics. Blackwell, London    -->
-          <group prefix=". " delimiter=", ">
-            <text variable="publisher"/>
-            <text variable="publisher-place"/>
-          </group>
-        </else-if>
-        <else-if type="webpage post-weblog" match="any">
-          <!--    Online document
-               Doe J (1999) Title of subordinate document. In: The dictionary of substances and their effects.
-               Royal Society of Chemistry. Available via DIALOG.
-               http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999
-               Unfortunately, "Royal Society of Chemistry. Available via DIALOG." cannot seem to be mapped here -->
-          <group prefix=". " delimiter=". ">
-            <text prefix="In: " variable="container-title" form="short"/>
-            <text variable="URL"/>
-            <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">
-          <!--    Dissertation
-               Trent JW (1975) Experimental acute renal failure. Dissertation, University of California       -->
-          <group prefix=". " delimiter=", ">
-            <text variable="genre" text-case="capitalize-first"/>
-            <text variable="publisher"/>
-          </group>
-        </else-if>
-        <else>
-          <!--    None of the provided formats need to add manually (some data provided) -->
-          <group prefix=". " delimiter=" ">
-            <text variable="container-title" form="short"/>
-            <group delimiter=":">
-              <text variable="volume"/>
-              <text variable="page"/>
-            </group>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-humanities-author-date.csl

@@ -1,473 +0,0 @@
-<?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-US">
-  <info>
-    <title>Springer - Humanities (author-date)</title>
-    <id>http://www.zotero.org/styles/springer-humanities-author-date</id>
-    <link href="http://www.zotero.org/styles/springer-humanities-author-date" rel="self"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <author>
-      <name>Sebastian Karcher</name>
-    </author>
-    <contributor>
-      <name>Julian Onions</name>
-      <email>julian.onions@gmail.com</email>
-    </contributor>
-    <contributor>
-      <name>Richard Karnesky</name>
-      <email>karnesky+zotero@gmail.com</email>
-      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
-    </contributor>
-    <contributor>
-      <name>Charles Parnot</name>
-      <email>charles.parnot@gmail.com</email>
-      <uri>http://twitter.com/cparnot</uri>
-    </contributor>
-    <category citation-format="author-date"/>
-    <category field="generic-base"/>
-    <category field="humanities"/>
-    <summary>Style for Springer's humanities journals - the journals do look slightly different from each other, but this should work quite closely</summary>
-    <updated>2019-10-01T00:21:45+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>
-    <terms>
-      <term name="container-author" form="verb">by</term>
-    </terms>
-  </locale>
-  <macro name="secondary-contributors">
-    <choose>
-      <if type="chapter paper-conference" match="none">
-        <group delimiter=". ">
-          <choose>
-            <if variable="author">
-              <names variable="editor">
-                <label form="verb" text-case="capitalize-first" suffix=" " plural="never"/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-          <choose>
-            <if variable="author editor" match="any">
-              <names variable="translator">
-                <label form="verb" text-case="capitalize-first" suffix=" " plural="never"/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="container-contributors">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <group prefix=", " delimiter=", ">
-          <choose>
-            <if variable="author">
-              <names variable="container-author editor" delimiter=", ">
-                <label form="short" suffix=" " plural="never"/>
-                <name and="text" delimiter=", " initialize="false" initialize-with=". "/>
-              </names>
-            </if>
-          </choose>
-          <choose>
-            <if variable="author editor" match="any">
-              <names variable="translator">
-                <label form="short" plural="never" suffix=" "/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="recipient">
-    <choose>
-      <if type="personal_communication">
-        <choose>
-          <if variable="genre">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-          <else>
-            <text term="letter" text-case="capitalize-first"/>
-          </else>
-        </choose>
-      </if>
-    </choose>
-    <names variable="recipient" delimiter=", ">
-      <label form="verb" prefix=" " suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="contributors">
-    <names variable="author">
-      <name and="text" name-as-sort-order="first" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" plural="never" prefix=", "/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-        <text macro="title"/>
-      </substitute>
-    </names>
-    <text macro="recipient"/>
-  </macro>
-  <macro name="contributors-short">
-    <names variable="author">
-      <name form="short" and="text" delimiter=", " initialize-with=". "/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-        <text macro="title"/>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="interviewer">
-    <names variable="interviewer" delimiter=", ">
-      <label form="verb" prefix=" " text-case="capitalize-first" suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="archive">
-    <group delimiter=". ">
-      <text variable="archive_location" text-case="capitalize-first"/>
-      <text variable="archive"/>
-      <text variable="archive-place"/>
-    </group>
-  </macro>
-  <macro name="access">
-    <group delimiter=". ">
-      <choose>
-        <if type="graphic report" match="any">
-          <text macro="archive"/>
-        </if>
-        <else-if type="article-magazine article-newspaper bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="none">
-          <text macro="archive"/>
-        </else-if>
-      </choose>
-      <text variable="DOI" prefix="https://doi.org/"/>
-      <choose>
-        <if variable="DOI issued" match="none">
-          <choose>
-            <if variable="URL accessed" match="all">
-              <choose>
-                <if type="legal_case" match="none">
-                  <text variable="URL"/>
-                </if>
-              </choose>
-              <group delimiter=" ">
-                <text term="accessed" text-case="capitalize-first"/>
-                <date variable="accessed" delimiter=" ">
-                  <date-part name="month"/>
-                  <date-part name="day"/>
-                </date>
-              </group>
-            </if>
-          </choose>
-        </if>
-        <else-if type="webpage">
-          <date variable="issued" delimiter=" ">
-            <date-part name="month"/>
-            <date-part name="day"/>
-          </date>
-        </else-if>
-      </choose>
-    </group>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if variable="title" match="none">
-        <choose>
-          <if type="personal_communication" match="none">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-        </choose>
-      </if>
-      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <text variable="title" font-style="italic"/>
-      </else-if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="edition">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=". ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" prefix=". "/>
-          </else>
-        </choose>
-      </if>
-      <else-if type="chapter  paper-conference" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=", ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" prefix=", "/>
-          </else>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators">
-    <choose>
-      <if type="article-journal">
-        <text variable="volume" prefix=" "/>
-      </if>
-      <else-if type="legal_case">
-        <text variable="volume" prefix=", "/>
-        <text variable="container-title" prefix=" "/>
-        <text variable="page" prefix=" "/>
-      </else-if>
-      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <group prefix=". " delimiter=". ">
-          <group>
-            <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-            <number variable="volume" form="numeric"/>
-          </group>
-          <group>
-            <number variable="number-of-volumes" form="numeric"/>
-            <text term="volume" form="short" prefix=" " plural="true"/>
-          </group>
-        </group>
-      </else-if>
-      <else-if type="chapter paper-conference" match="any">
-        <choose>
-          <if variable="page" match="none">
-            <group prefix=". ">
-              <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-              <number variable="volume" form="numeric"/>
-            </group>
-          </if>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators-chapter">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <choose>
-          <if variable="page">
-            <group prefix=", ">
-              <text variable="volume" suffix=":"/>
-              <text variable="page"/>
-            </group>
-          </if>
-        </choose>
-      </if>
-    </choose>
-  </macro>
-  <macro name="locators-article">
-    <choose>
-      <if type="article-newspaper">
-        <group prefix=", " delimiter=", ">
-          <group delimiter=" ">
-            <text variable="edition"/>
-            <text term="edition"/>
-          </group>
-          <group>
-            <text term="section" form="short" suffix=" "/>
-            <text variable="section"/>
-          </group>
-        </group>
-      </if>
-      <else-if type="article-journal">
-        <text variable="page" prefix=": "/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="point-locators">
-    <choose>
-      <if variable="locator">
-        <choose>
-          <if locator="page" match="none">
-            <choose>
-              <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-                <choose>
-                  <if variable="volume">
-                    <group>
-                      <text term="volume" form="short" suffix=" "/>
-                      <number variable="volume" form="numeric"/>
-                      <label variable="locator" form="short" prefix=", " suffix=" "/>
-                    </group>
-                  </if>
-                  <else>
-                    <label variable="locator" form="short" suffix=" "/>
-                  </else>
-                </choose>
-              </if>
-              <else>
-                <label variable="locator" form="short" suffix=" "/>
-              </else>
-            </choose>
-          </if>
-          <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-            <number variable="volume" form="numeric" suffix=":"/>
-          </else-if>
-        </choose>
-        <text variable="locator"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="container-prefix">
-    <text term="in" text-case="capitalize-first"/>
-  </macro>
-  <macro name="container-title">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <text macro="container-prefix" suffix=" "/>
-      </if>
-    </choose>
-    <choose>
-      <if type="legal_case" match="none">
-        <text variable="container-title" font-style="italic"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <group delimiter=": ">
-      <text variable="publisher-place"/>
-      <text variable="publisher"/>
-    </group>
-  </macro>
-  <macro name="date">
-    <choose>
-      <if variable="issued">
-        <date variable="issued">
-          <date-part name="year"/>
-        </date>
-      </if>
-      <else-if variable="accessed">
-        <date variable="accessed">
-          <date-part name="year"/>
-        </date>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="day-month">
-    <date variable="issued">
-      <date-part name="month"/>
-      <date-part name="day" prefix=" "/>
-    </date>
-  </macro>
-  <macro name="collection-title">
-    <text variable="collection-title" text-case="title"/>
-    <text variable="collection-number" prefix=" "/>
-  </macro>
-  <macro name="event">
-    <group>
-      <text term="presented at" suffix=" "/>
-      <text variable="event"/>
-    </group>
-  </macro>
-  <macro name="description">
-    <choose>
-      <if type="interview">
-        <group delimiter=". ">
-          <text macro="interviewer"/>
-          <text variable="medium" text-case="capitalize-first"/>
-        </group>
-      </if>
-      <else>
-        <text variable="medium" text-case="capitalize-first" prefix=". "/>
-      </else>
-    </choose>
-    <choose>
-      <if variable="title" match="none"/>
-      <else-if type="thesis"/>
-      <else>
-        <group delimiter=" " prefix=". ">
-          <text variable="genre" text-case="capitalize-first"/>
-          <choose>
-            <if type="report">
-              <text variable="number"/>
-            </if>
-          </choose>
-        </group>
-      </else>
-    </choose>
-    <!--This is for computer programs only. Localization new to 1.0.1, so may be missing in many locales-->
-    <group delimiter=" " prefix=" (" suffix=")">
-      <text term="version"/>
-      <text variable="version"/>
-    </group>
-  </macro>
-  <macro name="issue">
-    <choose>
-      <if type="legal_case">
-        <text variable="authority" prefix=". "/>
-      </if>
-      <else-if type="speech">
-        <group prefix=" " delimiter=", ">
-          <text macro="event"/>
-          <text macro="day-month"/>
-          <text variable="event-place"/>
-        </group>
-      </else-if>
-      <else-if type="article-newspaper article-magazine" match="any">
-        <text macro="day-month" prefix=", "/>
-      </else-if>
-      <else>
-        <group prefix=". " delimiter=", ">
-          <choose>
-            <if type="thesis">
-              <text variable="genre" text-case="capitalize-first"/>
-            </if>
-          </choose>
-          <text macro="publisher"/>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" givenname-disambiguation-rule="primary-name">
-    <sort>
-      <key macro="date"/>
-      <key macro="contributors-short"/>
-    </sort>
-    <layout prefix="(" suffix=")" delimiter="; ">
-      <group delimiter=", ">
-        <group delimiter=" ">
-          <text macro="contributors-short"/>
-          <text macro="date"/>
-        </group>
-        <text macro="point-locators"/>
-      </group>
-    </layout>
-  </citation>
-  <bibliography hanging-indent="true" et-al-min="11" et-al-use-first="7" entry-spacing="0">
-    <sort>
-      <key macro="contributors"/>
-      <key variable="issued"/>
-    </sort>
-    <layout suffix=".">
-      <group delimiter=". ">
-        <text macro="contributors"/>
-        <text macro="date"/>
-        <text macro="title"/>
-      </group>
-      <text macro="description"/>
-      <text macro="secondary-contributors" prefix=". "/>
-      <text macro="container-title" prefix=". "/>
-      <text macro="container-contributors"/>
-      <text macro="edition"/>
-      <text macro="locators-chapter"/>
-      <text macro="locators"/>
-      <text macro="collection-title" prefix=". "/>
-      <text macro="issue"/>
-      <text macro="locators-article"/>
-      <text macro="access" prefix=". "/>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-humanities-brackets.csl

@@ -1,421 +0,0 @@
-<?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-US">
-  <info>
-    <title>Springer - Humanities (numeric, brackets)</title>
-    <id>http://www.zotero.org/styles/springer-humanities-brackets</id>
-    <link href="http://www.zotero.org/styles/springer-humanities-brackets" rel="self"/>
-    <link href="http://www.zotero.org/styles/springer-humanities-author-date" rel="template"/>
-    <link href="www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_Aug2012.pdf" rel="documentation"/>
-    <author>
-      <name>Sebastian Karcher</name>
-    </author>
-    <contributor>
-      <name>Julian Onions</name>
-      <email>julian.onions@gmail.com</email>
-    </contributor>
-    <contributor>
-      <name>Richard Karnesky</name>
-      <email>karnesky+zotero@gmail.com</email>
-      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
-    </contributor>
-    <contributor>
-      <name>Charles Parnot</name>
-      <email>charles.parnot@gmail.com</email>
-      <uri>http://twitter.com/cparnot</uri>
-    </contributor>
-    <category citation-format="numeric"/>
-    <category field="generic-base"/>
-    <category field="humanities"/>
-    <summary>Style for Springer's humanities journals - the journals do look slightly different from each other, but this should work quite closely</summary>
-    <updated>2019-10-01T00:21:45+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>
-    <terms>
-      <term name="container-author" form="verb">by</term>
-    </terms>
-  </locale>
-  <macro name="secondary-contributors">
-    <choose>
-      <if type="chapter paper-conference" match="none">
-        <group delimiter=". ">
-          <choose>
-            <if variable="author">
-              <names variable="editor">
-                <label form="verb" text-case="capitalize-first" suffix=" " plural="never"/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-          <choose>
-            <if variable="author editor" match="any">
-              <names variable="translator">
-                <label form="verb" text-case="capitalize-first" suffix=" " plural="never"/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="container-contributors">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <group prefix=", " delimiter=", ">
-          <choose>
-            <if variable="author">
-              <names variable="container-author editor" delimiter=", ">
-                <label form="short" suffix=" " plural="never"/>
-                <name and="text" delimiter=", " initialize="false" initialize-with=". "/>
-              </names>
-            </if>
-          </choose>
-          <choose>
-            <if variable="author editor" match="any">
-              <names variable="translator">
-                <label form="short" plural="never" suffix=" "/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </if>
-          </choose>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="recipient">
-    <choose>
-      <if type="personal_communication">
-        <choose>
-          <if variable="genre">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-          <else>
-            <text term="letter" text-case="capitalize-first"/>
-          </else>
-        </choose>
-      </if>
-    </choose>
-    <names variable="recipient" delimiter=", ">
-      <label form="verb" prefix=" " suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="contributors">
-    <names variable="author">
-      <name and="text" name-as-sort-order="first" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" plural="never" prefix=", "/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-        <text macro="title"/>
-      </substitute>
-    </names>
-    <text macro="recipient"/>
-  </macro>
-  <macro name="interviewer">
-    <names variable="interviewer" delimiter=", ">
-      <label form="verb" prefix=" " text-case="capitalize-first" suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="archive">
-    <group delimiter=". ">
-      <text variable="archive_location" text-case="capitalize-first"/>
-      <text variable="archive"/>
-      <text variable="archive-place"/>
-    </group>
-  </macro>
-  <macro name="access">
-    <group delimiter=". ">
-      <choose>
-        <if type="graphic report" match="any">
-          <text macro="archive"/>
-        </if>
-        <else-if type="article-magazine article-newspaper bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="none">
-          <text macro="archive"/>
-        </else-if>
-      </choose>
-      <text variable="DOI" prefix="https://doi.org/"/>
-      <choose>
-        <if variable="DOI issued" match="none">
-          <choose>
-            <if variable="URL accessed" match="all">
-              <choose>
-                <if type="legal_case" match="none">
-                  <text variable="URL"/>
-                </if>
-              </choose>
-              <group delimiter=" ">
-                <text term="accessed" text-case="capitalize-first"/>
-                <date variable="accessed" delimiter=" ">
-                  <date-part name="month"/>
-                  <date-part name="day"/>
-                </date>
-              </group>
-            </if>
-          </choose>
-        </if>
-        <else-if type="webpage">
-          <date variable="issued" delimiter=" ">
-            <date-part name="month"/>
-            <date-part name="day"/>
-          </date>
-        </else-if>
-      </choose>
-    </group>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if variable="title" match="none">
-        <choose>
-          <if type="personal_communication" match="none">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-        </choose>
-      </if>
-      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <text variable="title" font-style="italic"/>
-      </else-if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="edition">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=". ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" prefix=". "/>
-          </else>
-        </choose>
-      </if>
-      <else-if type="chapter  paper-conference" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=", ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" prefix=", "/>
-          </else>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators">
-    <choose>
-      <if type="article-journal">
-        <text variable="volume" prefix=" "/>
-      </if>
-      <else-if type="legal_case">
-        <text variable="volume" prefix=", "/>
-        <text variable="container-title" prefix=" "/>
-        <text variable="page" prefix=" "/>
-      </else-if>
-      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <group prefix=". " delimiter=". ">
-          <group>
-            <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-            <number variable="volume" form="numeric"/>
-          </group>
-          <group>
-            <number variable="number-of-volumes" form="numeric"/>
-            <text term="volume" form="short" prefix=" " plural="true"/>
-          </group>
-        </group>
-      </else-if>
-      <else-if type="chapter paper-conference" match="any">
-        <choose>
-          <if variable="page" match="none">
-            <group prefix=". ">
-              <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-              <number variable="volume" form="numeric"/>
-            </group>
-          </if>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators-chapter">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <choose>
-          <if variable="page">
-            <group prefix=", ">
-              <text variable="volume" suffix=":"/>
-              <text variable="page"/>
-            </group>
-          </if>
-        </choose>
-      </if>
-    </choose>
-  </macro>
-  <macro name="locators-article">
-    <choose>
-      <if type="article-newspaper">
-        <group prefix=", " delimiter=", ">
-          <group delimiter=" ">
-            <text variable="edition"/>
-            <text term="edition"/>
-          </group>
-          <group>
-            <text term="section" form="short" suffix=" "/>
-            <text variable="section"/>
-          </group>
-        </group>
-      </if>
-      <else-if type="article-journal">
-        <text variable="page" prefix=": "/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="container-prefix">
-    <text term="in" text-case="capitalize-first"/>
-  </macro>
-  <macro name="container-title">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <text macro="container-prefix" suffix=" "/>
-      </if>
-    </choose>
-    <choose>
-      <if type="legal_case" match="none">
-        <text variable="container-title" font-style="italic"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <group delimiter=": ">
-      <text variable="publisher-place"/>
-      <text variable="publisher"/>
-    </group>
-  </macro>
-  <macro name="date">
-    <choose>
-      <if variable="issued">
-        <date variable="issued">
-          <date-part name="year"/>
-        </date>
-      </if>
-      <else-if variable="accessed">
-        <date variable="accessed">
-          <date-part name="year"/>
-        </date>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="day-month">
-    <date variable="issued">
-      <date-part name="month"/>
-      <date-part name="day" prefix=" "/>
-    </date>
-  </macro>
-  <macro name="collection-title">
-    <text variable="collection-title" text-case="title"/>
-    <text variable="collection-number" prefix=" "/>
-  </macro>
-  <macro name="event">
-    <group>
-      <text term="presented at" suffix=" "/>
-      <text variable="event"/>
-    </group>
-  </macro>
-  <macro name="description">
-    <choose>
-      <if type="interview">
-        <group delimiter=". ">
-          <text macro="interviewer"/>
-          <text variable="medium" text-case="capitalize-first"/>
-        </group>
-      </if>
-      <else>
-        <text variable="medium" text-case="capitalize-first" prefix=". "/>
-      </else>
-    </choose>
-    <choose>
-      <if variable="title" match="none"/>
-      <else-if type="thesis"/>
-      <else>
-        <group delimiter=" " prefix=". ">
-          <text variable="genre" text-case="capitalize-first"/>
-          <choose>
-            <if type="report">
-              <text variable="number"/>
-            </if>
-          </choose>
-        </group>
-      </else>
-    </choose>
-    <!--This is for computer programs only. Localization new to 1.0.1, so may be missing in many locales-->
-    <group delimiter=" " prefix=" (" suffix=")">
-      <text term="version"/>
-      <text variable="version"/>
-    </group>
-  </macro>
-  <macro name="issue">
-    <choose>
-      <if type="legal_case">
-        <text variable="authority" prefix=". "/>
-      </if>
-      <else-if type="speech">
-        <group prefix=" " delimiter=", ">
-          <text macro="event"/>
-          <text macro="day-month"/>
-          <text variable="event-place"/>
-        </group>
-      </else-if>
-      <else-if type="article-newspaper article-magazine" match="any">
-        <text macro="day-month" prefix=", "/>
-      </else-if>
-      <else>
-        <group prefix=". " delimiter=", ">
-          <choose>
-            <if type="thesis">
-              <text variable="genre" text-case="capitalize-first"/>
-            </if>
-          </choose>
-          <text macro="publisher"/>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <citation collapse="citation-number">
-    <sort>
-      <key variable="citation-number"/>
-    </sort>
-    <layout prefix="[" suffix="]" delimiter=", ">
-      <text variable="citation-number"/>
-    </layout>
-  </citation>
-  <bibliography second-field-align="flush" et-al-min="11" et-al-use-first="7" entry-spacing="0">
-    <layout suffix=".">
-      <text variable="citation-number" suffix=". "/>
-      <group delimiter=". ">
-        <text macro="contributors"/>
-        <text macro="date"/>
-        <text macro="title"/>
-      </group>
-      <text macro="description"/>
-      <text macro="secondary-contributors" prefix=". "/>
-      <text macro="container-title" prefix=". "/>
-      <text macro="container-contributors"/>
-      <text macro="edition"/>
-      <text macro="locators-chapter"/>
-      <text macro="locators"/>
-      <text macro="collection-title" prefix=". "/>
-      <text macro="issue"/>
-      <text macro="locators-article"/>
-      <text macro="access" prefix=". "/>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-mathphys-author-date.csl

@@ -1,198 +0,0 @@
-<?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">
-  <info>
-    <title>Springer - MathPhys (author-date)</title>
-    <id>http://www.zotero.org/styles/springer-mathphys-author-date</id>
-    <link href="http://www.zotero.org/styles/springer-mathphys-author-date" rel="self"/>
-    <link href="http://www.zotero.org/styles/springer-lecture-notes-in-computer-science" rel="template"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <author>
-      <name>Charles Parnot</name>
-      <email>charles.parnot@gmail.com</email>
-      <uri>http://twitter.com/cparnot</uri>
-    </author>
-    <category citation-format="author-date"/>
-    <category field="generic-base"/>
-    <category field="science"/>
-    <summary>This style is used by a number of Springer publications.</summary>
-    <updated>2019-10-01T00:21:45+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-short-in-citation">
-    <names variable="author">
-      <name form="short" and="text"/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="author-in-citation">
-    <names variable="author">
-      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="year-in-citation">
-    <date variable="issued">
-      <date-part name="year"/>
-    </date>
-  </macro>
-  <macro name="issued-sort">
-    <choose>
-      <if type="article-journal bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="none">
-        <date variable="issued">
-          <date-part name="year"/>
-          <date-part name="month"/>
-          <date-part name="day"/>
-        </date>
-      </if>
-      <else>
-        <date variable="issued">
-          <date-part name="year"/>
-        </date>
-      </else>
-    </choose>
-  </macro>
-  <macro name="author">
-    <group>
-      <names variable="author">
-        <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
-        <label form="short" prefix=" " text-case="lowercase" strip-periods="true"/>
-        <substitute>
-          <names variable="editor"/>
-        </substitute>
-      </names>
-    </group>
-  </macro>
-  <macro name="editor">
-    <names variable="editor">
-      <name initialize-with="." delimiter=", " and="text" name-as-sort-order="all" sort-separator=", "/>
-      <label form="short" prefix=" (" text-case="lowercase" suffix=")"/>
-    </names>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <text variable="title"/>
-      </if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <text variable="publisher"/>
-    <text variable="publisher-place" prefix=", "/>
-  </macro>
-  <macro name="page">
-    <group>
-      <label variable="page" form="short" suffix=" "/>
-      <text variable="page"/>
-    </group>
-  </macro>
-  <macro name="access">
-    <text variable="DOI" prefix="https://doi.org/"/>
-  </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true">
-    <sort>
-      <key macro="author-in-citation"/>
-      <key variable="issued" sort="descending"/>
-    </sort>
-    <layout prefix="(" suffix=")" delimiter="; ">
-      <group delimiter=" ">
-        <text macro="author-short-in-citation"/>
-        <text macro="year-in-citation"/>
-      </group>
-    </layout>
-  </citation>
-  <bibliography entry-spacing="0">
-    <sort>
-      <key macro="author-in-citation"/>
-      <key macro="issued-sort" sort="ascending"/>
-    </sort>
-    <layout>
-      <text macro="author" prefix=" " suffix=": "/>
-      <choose>
-        <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text macro="publisher"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </if>
-        <else-if type="article-journal">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text variable="container-title" form="short" suffix="."/>
-            <text variable="volume" suffix=","/>
-            <text variable="page"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-          <text macro="access" prefix=". "/>
-        </else-if>
-        <else-if type="chapter paper-conference" match="any">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <choose>
-              <if variable="container-title">
-                <text term="in" text-case="capitalize-first" suffix=": "/>
-                <text macro="editor" suffix=" "/>
-                <group delimiter=". ">
-                  <text variable="container-title"/>
-                  <text macro="page"/>
-                  <text macro="publisher"/>
-                </group>
-              </if>
-              <else>
-                <text term="presented at" text-case="capitalize-first" suffix=" "/>
-                <text variable="event"/>
-                <text variable="event-place" prefix=", "/>
-                <date variable="issued" prefix=" ">
-                  <date-part name="month" suffix=" "/>
-                  <date-part name="day" suffix=" "/>
-                </date>
-              </else>
-            </choose>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else-if>
-        <else-if type="webpage">
-          <group delimiter=", ">
-            <text macro="title"/>
-            <text variable="URL"/>
-          </group>
-        </else-if>
-        <else-if type="speech">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text variable="event" suffix="."/>
-            <text variable="event-place" prefix=", "/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else-if>
-        <else>
-          <group delimiter=", ">
-            <text macro="title"/>
-            <text variable="URL"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-mathphys-brackets.csl

@@ -1,152 +0,0 @@
-<?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">
-  <info>
-    <title>Springer - MathPhys (numeric, brackets)</title>
-    <id>http://www.zotero.org/styles/springer-mathphys-brackets</id>
-    <link href="http://www.zotero.org/styles/springer-mathphys-brackets" rel="self"/>
-    <link href="http://www.zotero.org/styles/springer-lecture-notes-in-computer-science" rel="template"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
-    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
-    <author>
-      <name>Charles Parnot</name>
-      <email>charles.parnot@gmail.com</email>
-      <uri>http://twitter.com/cparnot</uri>
-    </author>
-    <category citation-format="numeric"/>
-    <category field="generic-base"/>
-    <category field="science"/>
-    <summary>This style is used by a number of Springer publications.</summary>
-    <updated>2019-10-01T00:21:45+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">
-    <group>
-      <names variable="author">
-        <name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
-        <label form="short" prefix=" " text-case="lowercase" strip-periods="true"/>
-        <substitute>
-          <names variable="editor"/>
-        </substitute>
-      </names>
-    </group>
-  </macro>
-  <macro name="editor">
-    <names variable="editor">
-      <name initialize-with="." delimiter=", " and="text" name-as-sort-order="all" sort-separator=", "/>
-      <label form="short" prefix=" (" text-case="lowercase" suffix=")"/>
-    </names>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <text variable="title"/>
-      </if>
-      <else>
-        <text variable="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <text variable="publisher"/>
-    <text variable="publisher-place" prefix=", "/>
-  </macro>
-  <macro name="page">
-    <group>
-      <label variable="page" form="short" suffix=" "/>
-      <text variable="page"/>
-    </group>
-  </macro>
-  <macro name="access">
-    <text variable="DOI" prefix="https://doi.org/"/>
-  </macro>
-  <citation collapse="citation-number">
-    <sort>
-      <key variable="citation-number"/>
-    </sort>
-    <layout prefix="[" suffix="]" delimiter=", ">
-      <text variable="citation-number"/>
-    </layout>
-  </citation>
-  <bibliography entry-spacing="0" second-field-align="flush">
-    <layout>
-      <text variable="citation-number" suffix=". "/>
-      <text macro="author" suffix=": "/>
-      <choose>
-        <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text macro="publisher"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </if>
-        <else-if type="article-journal">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text variable="container-title" form="short" suffix="."/>
-            <text variable="volume" suffix=","/>
-            <text variable="page"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-          <text macro="access" prefix=". "/>
-        </else-if>
-        <else-if type="chapter paper-conference" match="any">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <choose>
-              <if variable="container-title">
-                <text term="in" text-case="capitalize-first" suffix=": "/>
-                <text macro="editor" suffix=" "/>
-                <group delimiter=". ">
-                  <text variable="container-title"/>
-                  <text macro="page"/>
-                  <text macro="publisher"/>
-                </group>
-              </if>
-              <else>
-                <text term="presented at" text-case="capitalize-first" suffix=" "/>
-                <text variable="event"/>
-                <text variable="event-place" prefix=", "/>
-                <date variable="issued" prefix=" ">
-                  <date-part name="month" suffix=" "/>
-                  <date-part name="day" suffix=" "/>
-                </date>
-              </else>
-            </choose>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else-if>
-        <else-if type="webpage">
-          <group delimiter=", ">
-            <text macro="title"/>
-            <text variable="URL"/>
-          </group>
-        </else-if>
-        <else-if type="speech">
-          <group delimiter=" ">
-            <text macro="title" suffix="."/>
-            <text variable="event" suffix="."/>
-            <text variable="event-place" prefix=", "/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else-if>
-        <else>
-          <group delimiter=", ">
-            <text macro="title"/>
-            <text variable="URL"/>
-            <date variable="issued">
-              <date-part name="year" prefix="(" suffix=")"/>
-            </date>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/csl/springer-vancouver.csl

@@ -1,179 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" default-locale="en-US" version="1.0" demote-non-dropping-particle="sort-only">
-  <info>
-    <title>Springer - Vancouver</title>
-    <id>http://www.zotero.org/styles/springer-vancouver</id>
-    <link href="http://www.zotero.org/styles/springer-vancouver" rel="self"/>
-    <link href="http://www.springer.com/medicine/psychiatry/journal/127" rel="documentation"/>
-    <author>
-      <name>Sebastian Karcher</name>
-    </author>
-    <contributor>
-      <name>Jens Allmer</name>
-      <email>jens@allmer.de</email>
-      <uri>http://jens.allmer.de</uri>
-    </contributor>
-    <category citation-format="numeric"/>
-    <category field="generic-base"/>
-    <summary>Springer Vancouver style - like the author-date style, but numeric</summary>
-    <updated>2019-10-01T00:21:45+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="et-al">et al</term>
-    </terms>
-  </locale>
-  <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="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="year-parenth">
-    <date prefix="(" suffix=")" 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="11" et-al-use-first="3" second-field-align="flush">
-    <layout>
-      <text variable="citation-number" suffix=". "/>
-      <group delimiter=" ">
-        <text macro="author"/>
-        <text macro="year-parenth"/>
-        <text macro="title"/>
-      </group>
-      <choose>
-        <if variable="page">
-          <choose>
-            <!--    Book chapter
-		 Brown B, Aaron M (2001) The politics of nature.
-		 In: Smith J (ed) The rise of modern genomics, 3rd edn.
-		 Wiley, New York, pp 230-257 -->
-            <if type="chapter paper-conference" match="any">
-              <group delimiter=" " suffix=". ">
-                <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>
-                <group delimiter=", ">
-                  <text variable="container-title" form="short"/>
-                  <text macro="edition"/>
-                </group>
-              </group>
-              <text variable="publisher" suffix=", "/>
-              <text variable="publisher-place" suffix=", "/>
-              <group delimiter=" ">
-                <label variable="page" form="short" strip-periods="true"/>
-                <text variable="page"/>
-              </group>
-            </if>
-            <else>
-              <!--    Journal article
-		   Gamelin FX, Baquet G, Berthoin S, Thevenet D, Nourry C, Nottin S, Bosquet L (2009)
-		   Effect of high intensity intermittent training on heart rate variability in prepubescent children.
-		   Eur J Appl Physiol 105:731-738. doi: 10.1007/s00421-008-0955-8
-		   Ideally, the names of all authors should be provided, but the usage of "et al"
-		   in long author lists will also be accepted:
-		   Smith J, Jones M Jr, Houghton L et al (1999)
-		   Future of health insurance. N Engl J Med 965:325-329   -->
-              <group>
-                <text variable="container-title" suffix=" " form="short" strip-periods="true"/>
-                <text variable="volume" suffix=":"/>
-                <text variable="page"/>
-              </group>
-            </else>
-          </choose>
-        </if>
-        <else-if variable="DOI">
-          <!--    Article by DOI
-	       Slifka MK, Whitton JL (2000) Clinical implications of dysregulated cytokine production.
-	       J Mol Med. doi:10.1007/s001090000086     -->
-          <group delimiter=". ">
-            <text variable="container-title" form="short" strip-periods="true"/>
-            <text prefix="https://doi.org/" variable="DOI"/>
-          </group>
-        </else-if>
-        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <!--    Book
-	       South J, Blass B (2001) The future of modern genomics. Blackwell, London    -->
-          <group delimiter=", ">
-            <text variable="publisher"/>
-            <text variable="publisher-place"/>
-          </group>
-        </else-if>
-        <else-if type="webpage">
-          <!--    Online document
-	       Doe J (1999) Title of subordinate document. In: The dictionary of substances and their effects.
-	       Royal Society of Chemistry. Available via DIALOG.
-	       http://www.rsc.org/dose/title of subordinate document. Accessed 15 Jan 1999
-	       Unfortunately, "Royal Society of Chemistry. Available via DIALOG." cannot seem to be mapped here -->
-          <group>
-            <text prefix="In: " variable="container-title" suffix=". " form="short"/>
-            <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">
-          <!--    Dissertation
-	       Trent JW (1975) Experimental acute renal failure. Dissertation, University of California       -->
-          <group delimiter=", ">
-            <text variable="genre"/>
-            <text variable="publisher"/>
-          </group>
-        </else-if>
-        <else>
-          <!--    None of the provided formats need to add manually (some data provided) -->
-          <group>
-            <text variable="container-title" form="short" suffix=" "/>
-            <text variable="volume" suffix=":"/>
-            <text variable="page" suffix="."/>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

_extensions/christopherkenny/nature/header.tex

@@ -1,20 +0,0 @@
-%%%% Standard Packages
-
-\usepackage{graphicx}%
-\usepackage{multirow}%
-\usepackage{amsmath,amssymb,amsfonts}%
-\usepackage{amsthm}%
-\usepackage{mathrsfs}%
-\usepackage[title]{appendix}%
-\usepackage{xcolor}%
-\usepackage{textcomp}%
-\usepackage{manyfoot}%
-\usepackage{booktabs}%
-\usepackage{algorithm}%
-\usepackage{algorithmicx}%
-\usepackage{algpseudocode}%
-\usepackage{listings}%
-
-%%%%
-
-\raggedbottom

_extensions/christopherkenny/nature/partials/_affiliation.tex

@@ -1 +0,0 @@
-$if(it.department)$\orgdiv{$it.department$}$endif$$if(it.name)$, \orgname{$it.name$}$endif$$if(it.address)$, \orgaddress{\street{$it.address$}$if(it.city)$, \city{$it.city$}$endif$$if(it.state)$, \state{$it.state$}$endif$$if(it.postal-code)$, \postcode{$it.postal-code$}$endif$$if(it.country)$, \country{$it.country$}$endif$}$endif$

_extensions/christopherkenny/nature/partials/_author.tex

@@ -1 +0,0 @@
-$if(it.name.given)$\fnm{$it.name.given$}$endif$ $if(it.name.family)$\sur{$it.name.family$}$endif$

_extensions/christopherkenny/nature/partials/before-body.tex

@@ -1,3 +0,0 @@
-$if(title)$
-\maketitle
-$endif$

_extensions/christopherkenny/nature/partials/doc-class.tex

@@ -1,17 +0,0 @@
-\documentclass[
-$if(journal.cite-style)$
-  $journal.cite-style$,
-$else$
-  default,
-$endif$
-$if(fontsize)$
-  $fontsize$,
-$endif$
-$for(classoption)$
-  $classoption$$sep$,
-$endfor$
-]{sn-jnl}
-
-$if(equal-margins)$
-\setlength\evensidemargin{\oddsidemargin}
-$endif$

_extensions/christopherkenny/nature/partials/title.tex

@@ -1,25 +0,0 @@
-$if(title)$
-\title[$title$]{$title$}
-$endif$
-
-% author setup
-$for(by-author)$
-\author$if(by-author.attributes.corresponding)$*$endif$[$if(by-author.affiliations)$$for(by-author.affiliations)$$it.id$$sep$,$endfor$$endif$]{$_author.tex()$}$if(by-author.email)$
-\email{$by-author.email$}$endif$$if(by-author.attributes.equal-contributor)$
-\equalcont{These authors contributed equally to this work.}$endif$$endfor$
-
-% affil setup
-$for(by-affiliation)$
-\affil[$it.id$]{$_affiliation.tex()$}
-$endfor$
-
-% abstract 
-
-$if(abstract)$
-\abstract{$abstract$}
-$endif$
-
-% keywords
-$if(keywords)$
-\keywords{$for(keywords)$$keywords$$sep$,  $endfor$}
-$endif$

_extensions/kazuyanagimoto/academic/_extension.yml

@@ -1,12 +0,0 @@
-title: Quarto Academic Typst
-author: Kazuharu Yanagimoto
-version: 0.1.0
-quarto-required: ">=1.4.0"
-contributes:
-  formats:
-    typst:
-      shortcodes:
-        - shortcodes.lua
-      template-partials:
-        - typst-template.typ
-        - typst-show.typ

_extensions/kazuyanagimoto/academic/shortcodes.lua

@@ -1,3 +0,0 @@
-function appendix()
-    return pandoc.RawBlock('typst', '#show: appendix')
-end

_extensions/kazuyanagimoto/academic/typst-show.typ

@@ -1,88 +0,0 @@
-#show: doc => article(
-$if(title)$
-  title: [$title$],
-$endif$
-$if(subtitle)$
-  subtitle: [$subtitle$],
-$endif$
-$if(header)$
-  header: [$header$],
-$endif$
-$if(code-repo)$
-  code-repo: [$code-repo$],
-$endif$
-$if(by-author)$
-  authors: (
-$for(by-author)$
-$if(it.name.literal)$
-    ( name: [$it.name.literal$],
-      affiliation: [$for(it.affiliations)$$it.name$$sep$, $endfor$],
-      email: [$it.email$],
-      orcid: [$it.orcid$]
-    ),
-$endif$
-$endfor$
-    ),
-$endif$
-$if(date)$
-  date: [$date$],
-$endif$
-$if(lang)$
-  lang: "$lang$",
-$endif$
-$if(region)$
-  region: "$region$",
-$endif$
-$if(abstract)$
-  abstract: [$abstract$],
-$endif$
-$if(keywords)$
-  keywords: [$for(keywords)$$keywords$$sep$, $endfor$],
-$endif$
-$if(custom-keywords)$
-  custom-keywords: (
-    $for(custom-keywords)$
-      ( name: [$it.name$],
-        values: [$for(it.values)$$it$$sep$, $endfor$]
-      ),
-    $endfor$
-  ),
-$endif$
-$if(thanks)$
-  thanks: [$thanks$],
-$endif$
-$if(margin)$
-  margin: ($for(margin/pairs)$$margin.key$: $margin.value$,$endfor$),
-$endif$
-$if(papersize)$
-  paper: "$papersize$",
-$endif$
-$if(mainfont)$
-  font: ("$mainfont$",),
-$endif$
-$if(mainfontoptions)$
-  $if(mainfontoptions.number-type)$
-    number-type: "$mainfontoptions.number-type$",
-  $endif$
-  $if(mainfontoptions.number-width)$
-    number-width: "$mainfontoptions.number-width$",
-  $endif$
-$endif$
-$if(sansfont)$
-  sansfont: ("$sansfont$",),
-$endif$
-$if(mathfont)$
-  mathfont: ("$mathfont$",),
-$endif$
-$if(fontsize)$
-  fontsize: $fontsize$,
-$endif$
-$if(section-numbering)$
-  sectionnumbering: "$section-numbering$",
-$endif$
-$if(toc)$
-  toc: $toc$,
-$endif$
-  cols: $if(columns)$$columns$$else$1$endif$,
-  doc,
-)

_extensions/kazuyanagimoto/academic/typst-template.typ

@@ -1,197 +0,0 @@
-#import "@preview/fontawesome:0.3.0": *
-
-#let color-link = rgb("#483d8b")
-
-#let article(
-  title: none,
-  subtitle: none,
-  header: none,
-  code-repo: none,
-  authors: none,
-  date: none,
-  abstract: none,
-  keywords: none,
-  custom-keywords: none,
-  thanks: none,
-  cols: 1,
-  margin: (x: 1.25in, y: 1.25in),
-  paper: "us-letter",
-  lang: "en",
-  region: "US",
-  font: (),
-  sansfont: (),
-  mathfont: (),
-  number-type: auto,
-  number-width: auto,
-  fontsize: 11pt,
-  sectionnumbering: none,
-  toc: false,
-  doc,
-) = {
-  set page(
-    paper: paper,
-    margin: margin,
-    numbering: "1",
-  )
-  set par(justify: true)
-  set text(lang: lang,
-           region: region,
-           font: font,
-           size: fontsize,
-           number-type: number-type,
-           number-width: number-width,)
-  show math.equation: set text(font: mathfont)
-  set heading(numbering: sectionnumbering)
-
-  show heading: set text(font: sansfont, weight: "semibold")
-
-  show figure.caption: it => [
-    #set text(font: sansfont, size: 0.9em)
-    #if it.supplement == [Figure] {
-      set align(left)
-      text(weight: "semibold")[#it.supplement #it.counter.display(it.numbering): ]
-      it.body
-    } else {
-      text(weight: "semibold")[#it.supplement #it.counter.display(it.numbering): ]
-      it.body
-    }
-    
-  ]
-  
-  show ref: it => {
-    let eq = math.equation
-    let el = it.element
-    if el == none {
-      it
-    } else if el.func() == eq {
-      link(el.location())[
-        #numbering(el.numbering,
-        ..counter(eq).at(el.location())
-        )
-      ]
-      
-    } else if el.func() == figure {
-      el.supplement.text
-      link(el.location())[
-        #set text(fill: color-link)
-        #numbering(el.numbering,..el.counter.at(el.location()))
-      ]
-    } else {
-      it
-    }
-  }
-
-  show link: set text(fill: color-link)
-  set bibliography(title: "References")
-
-  if date != none {
-    align(left)[#block()[
-      #text(weight: "semibold", font: sansfont, size: 0.8em)[
-        #date
-        #if header != none {
-          h(3em)
-          text(weight: "regular")[#header]
-        }
-      ]
-    ]]
-  }
-
-  if code-repo != none {
-    align(left)[#block()[
-      #text(weight: "regular", font: sansfont, size: 0.8em)[
-        #code-repo
-      ]
-    ]]
-  }
-  
-  if title != none {
-    align(left)[#block(spacing: 4em)[
-      #text(weight: "semibold", size: 1.5em, font: sansfont)[
-        #title
-        #if thanks != none {
-          footnote(numbering: "*", thanks)
-        }\
-        #if subtitle != none {
-          text(weight: "regular", style: "italic", size: 0.8em)[#subtitle]
-        }
-      ]
-    ]]
-  }
-
-  if authors != none {
-    let count = authors.len()
-    let ncols = calc.min(count, 3)
-    grid(
-      columns: (1fr,) * ncols,
-      row-gutter: 1.5em,
-      ..authors.map(author =>
-          align(left)[
-            #text(size: 1.2em, font: sansfont)[#author.name]
-            #if author.orcid != [] {
-                link("https://orcid.org/" + author.orcid.text)[
-                  #set text(size: 0.85em, fill: rgb("a6ce39"))
-                  #fa-orcid()
-                ]
-            } \
-            #text(size: 0.85em, font: sansfont)[#author.affiliation] \
-            #text(size: 0.7em, font: sansfont, fill: color-link)[
-              #link("mailto:" + author.email.children.map(email => email.text).join())[#author.email]
-            ]
-          ]
-      )
-    )
-  }  
-
-  if abstract != none {
-    block(inset: 2em)[
-      #text(weight: "semibold", font: sansfont, size: 0.9em)[ABSTRACT] #h(0.5em)
-      #text(font: sansfont)[#abstract]
-      #if keywords != none {
-         text(weight: "semibold", font: sansfont, size: 0.9em)[\ Keywords:]
-         h(0.5em)
-         text(font: sansfont)[#keywords]
-      }
-      #if custom-keywords != none {
-        for it in custom-keywords {
-          text(weight: "semibold", font: sansfont, size: 0.9em)[\ #it.name:]
-          h(0.5em)
-          text(font: sansfont)[#it.values]
-        }
-      }
-    ]
-  }  
-
-  if toc {
-    block(above: 0em, below: 2em)[
-    #outline(
-      title: auto,
-      depth: none
-    );
-    ]
-  }
-
-  if cols == 1 {
-    doc
-  } else {
-    columns(cols, doc)
-  }
-
-}
-
-#let appendix(content) = {
-  // Reset Numbering
-  set heading(numbering: "A.1.1")
-  counter(heading).update(0)
-  counter(figure.where(kind: "quarto-float-fig")).update(0)
-  counter(figure.where(kind: "quarto-float-tbl")).update(0)
-
-  // Figure & Table Numbering
-  set figure(numbering: it => {
-    [A.#it]
-  })
-
-  // Appendix Start
-  pagebreak(weak: true)
-  text(size: 2em)[Appendix]
-  content
-}

_extensions/quarto-journals/acs/_affiliation.tex

@@ -1 +0,0 @@
-$if(it.department)$$it.department$,$endif$ $if(it.name)$$it.name$,$endif$ $if(it.city)$$it.city$,$endif$ $if(it.country)$$it.country$$endif$

_extensions/quarto-journals/acs/_extension.yml

@@ -1,30 +0,0 @@
-title: ACS Journal Format
-author: Charles Teague
-version: 0.9.2
-contributes:
-  formats:
-    common:
-      csl: american-chemical-society.csl
-      shortcodes:
-        - fancy-text
-      filters:
-        - latex-environment
-      environments:
-        - scheme
-        - chart
-        - graph
-        - tocentry
-        - acknowledgement
-        - suppinfo
-      commands:
-        - ce
-    html: default
-    pdf:
-      cite-method: natbib
-      biblio-config: false
-      format-resources:
-        - achemso.bst
-      template-partials:
-        - "doc-class.tex"
-        - "title.tex"
-        - "_affiliation.tex"

_extensions/quarto-journals/acs/_extensions/quarto-ext/fancy-text/_extension.yml

@@ -1,7 +0,0 @@
-title: Fancy Text
-author: Posit Software, PBC
-version: 1.1.1
-quarto-required: ">=1.2.198"
-contributes:
-  shortcodes:
-    - fancy-text.lua

_extensions/quarto-journals/acs/_extensions/quarto-ext/fancy-text/fancy-text.lua

@@ -1,78 +0,0 @@
--- shortcode that provides a nicely formatted 'LaTeX' string
-function latex()
-  if quarto.doc.is_format("pdf") then
-    return pandoc.RawBlock('tex', '{\\LaTeX}')
-  elseif quarto.doc.is_format("html") then
-    return pandoc.Math('InlineMath', "\\LaTeX")
-  else 
-    return pandoc.Span('LaTeX')
-  end
-end
-
-function tex() 
-  if quarto.doc.is_format("pdf") then
-    return pandoc.RawBlock('tex', '{\\TeX}')
-  elseif quarto.doc.is_format("html") then
-    return pandoc.Math('InlineMath', "\\TeX")
-  else 
-    return pandoc.Span('TeX')
-  end
-end
-  
--- shortcode that provides a nicely formatted 'bibtex' string
-function bibtex()
-  if quarto.doc.is_format("pdf") then
-    return pandoc.RawBlock('tex', '\\textsc{Bib}{\\TeX}')
-  elseif quarto.doc.is_format("html") then
-    return pandoc.RawBlock('html', '<span style="font-variant: small-caps;">Bib</span><span style="letter-spacing:-2px;">T</span><sub style="font-size: inherit; letter-spacing:-1px;">E</sub>X')
-  else
-    return pandoc.Span('BibTeX')
-  end
-end
-
-function ldots()
-  if quarto.doc.is_format("pdf") then
-    return pandoc.RawBlock('tex', '\\ldots')
-  elseif quarto.doc.is_format("html") then
-    return pandoc.RawBlock('html', '&#8230;')
-  else
-    return "..."
-  end
-end
-
-function vdots()
-  if quarto.doc.is_format("pdf") then
-    return pandoc.Math('InlineMath', "\\vdots")
-  elseif quarto.doc.is_format("html") then
-    return pandoc.RawBlock('html', '&#8942;')
-  else
-    return "..."
-  end
-end
-
-function ddots() 
-  if quarto.doc.is_format("pdf") then
-    return pandoc.Math('InlineMath', "\\ddots")
-  elseif quarto.doc.is_format("html") then
-    return pandoc.RawBlock('html', '&#8945;')
-  else
-    return "..."
-  end
-end
-
-function pct()
-  local pct
-  if quarto.doc.is_format("pdf") then
-    return pandoc.Math('InlineMath', '\\%')
-  else 
-    return pandoc.Str("%")
-  end
-end
- 
-function R2() 
-  if quarto.doc.is_format("pdf") then
-    return pandoc.Math('InlineMath', "R^2")
-  else
-    return {pandoc.Str("R"), pandoc.Superscript("2")} 
-  end
-end

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

@@ -1,9 +0,0 @@
-title: LaTeX Environment
-author: Posit Software, PBC
-version: 1.2.1
-quarto-required: ">=1.3"
-contributes:
-  filters:
-    - latex-environment.lua
-  format:
-    pdf: default

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

@@ -1,150 +0,0 @@
--- 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 > 0 and 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
-
-local function buildCommandArgs(opts, format)
-  local function wrap(o) 
-    return string.format(format, o)
-  end 
-  local t = pandoc.List()
-  for str in string.gmatch(opts, "([^"..",".."]+)") do
-    t:insert(str)
-  end
-  return table.concat(t:map(wrap), "")
-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.utils.stringify(v)
-        local opts = spanEl.attr.attributes['options']
-        local args = spanEl.attr.attributes['arguments']
-        if opts then
-          beginCommand = beginCommand .. buildCommandArgs(opts, "[%s]")
-        end
-        if args then
-          beginCommand = beginCommand .. buildCommandArgs(args, "{%s}")
-        end
-
-        local beginCommandRaw = pandoc.RawInline('latex', beginCommand .. '{')
-
-        -- the end command
-        local endCommandRaw = pandoc.RawInline('latex', '}')
-
-        -- attach the raw inlines to the span contents
-        local result = spanEl.content
-        table.insert(result, 1, beginCommandRaw)
-        table.insert(result, endCommandRaw)
-
-        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/acs/american-chemical-society.csl

@@ -1,252 +0,0 @@
-<?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="http://pubs.acs.org/doi/pdf/10.1021/bk-2006-STYG.ch014" 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>
-    <category citation-format="numeric"/>
-    <category field="chemistry"/>
-    <summary>The American Chemical Society style.</summary>
-    <updated>2015-09-18T15:13:17+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">
-    <group delimiter=": ">
-      <text variable="publisher"/>
-      <text variable="publisher-place"/>
-    </group>
-  </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=" ">
-      <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 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-if variable="issue">
-                  <group delimiter=" ">
-                    <text term="issue" form="short" text-case="capitalize-first"/>
-                    <text variable="issue"/>
-                  </group>
-                </else-if>
-              </choose>
-              <text variable="page"/>
-            </group>
-          </group>
-        </if>
-        <else-if type="article-magazine article-newspaper article" match="any">
-          <group delimiter=" ">
-            <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 variable="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 variable="title" font-style="italic"/>
-              <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 variable="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="month" form="short" strip-periods="true"/>
-              <date-part name="day" suffix=", "/>
-              <date-part name="year"/>
-            </date>
-          </group>
-        </else-if>
-        <else>
-          <group delimiter=", ">
-            <group delimiter=". ">
-              <text variable="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>
-    </layout>
-  </bibliography>
-</style>

_extensions/quarto-journals/acs/doc-class.tex

@@ -1,5 +0,0 @@
-\documentclass[journal=$journal.id$,manuscript=$journal.type$$if(journal.layout)$,layout=$journal.layout$$endif$$if(journal.hide-email)$,email=false$endif$]{achemso}
-\usepackage[version=3]{mhchem}
-\newcommand*\mycommand[1]{\texttt{\emph{#1}}}
-
-

_extensions/quarto-journals/acs/title.tex

@@ -1,40 +0,0 @@
-$for(by-author)$
-\author{$by-author.name.literal$}
-$if(by-author.affiliations)$
-$if(by-author.affiliations/first)$
-$for(by-author.affiliations/first)$
-\affiliation{$_affiliation.tex()$}
-$endfor$
-$if(by-author.affiliations/rest/first)$
-$for(by-author.affiliations/rest/first)$
-\affiliation{$_affiliation.tex()$}
-$endfor$
-$endif$
-$endif$
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-\abbreviations{$journal.abbreviations$}
-$endif$
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-$if(keywords)$
-\keywords{$keywords$}
-$endif$
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-\title[$title-short$]{$title$}
-\makeatletter

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index.qmd

@@ -4,13 +4,10 @@ author: ""
 engine: knitr
 ---
 
-
 ```{r}
 #| echo: false
 #| out-width: 100%
-#| eval: false
+dwfun::ggsavep("./figures/GA20240729.pdf", loadit = TRUE)
-#| include: false
-# dwfun::ggsavep("./figures/GA.pdf", loadit = TRUE)
 ```