add extensions

_extensions/authors-block/_extension.yml

@@ -0,0 +1,13 @@
+title: Authors-block
+authors:
+  - name: Lorenz A. Kapsner
+    orcid: 0000-0003-1866-860X
+  - name: Albert Krewinkel
+    orcid: 0000-0002-9455-0796
+  - name: Robert Winkler
+version: 0.2.1
+quarto-required: ">=1.3.0"
+contributes:
+  filters:
+    - authors-block.lua
+

_extensions/authors-block/authors-block.lua

@@ -0,0 +1,64 @@
+--[[
+authors-block – affiliations block extension for quarto
+
+Copyright (c) 2023 Lorenz A. Kapsner
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+
+-- [import]
+local from_utils = require "utils"
+local normalize_affiliations = from_utils.normalize_affiliations
+local normalize_authors = from_utils.normalize_authors
+local normalize_latex_authors = from_utils.normalize_latex_authors
+
+local from_authors = require "from_author_info_blocks"
+local default_marks = from_authors.default_marks
+local create_equal_contributors_block = from_authors.create_equal_contributors_block
+local create_affiliations_blocks = from_authors.create_affiliations_blocks
+local create_correspondence_blocks = from_authors.create_correspondence_blocks
+local is_corresponding_author = from_authors.is_corresponding_author
+local author_inline_generator = from_authors.author_inline_generator
+local create_authors_inlines = from_authors.create_authors_inlines
+-- [/import]
+
+-- This is the main-part
+function Pandoc(doc)
+  local meta = doc.meta
+  local body = List:new{}
+  
+  local mark = function (mark_name) return default_marks[mark_name] end
+
+  body:extend(create_equal_contributors_block(meta.authors, mark) or {})
+  body:extend(create_affiliations_blocks(meta.affiliations) or {})
+  body:extend(create_correspondence_blocks(meta.authors, mark) or {})
+  body:extend(doc.blocks)
+  
+  for _i, author in ipairs(meta.authors) do
+    author.test = is_corresponding_author(author)
+  end
+  
+  meta.affiliations = normalize_affiliations(meta.affiliations)
+  meta.author = meta.authors:map(normalize_authors(meta.affiliations))
+  
+  -- Overwrite authors with formatted values. We use a single, formatted
+  -- string for most formats. LaTeX output, however, looks nicer if we
+  -- provide a authors as a list.
+  meta.author = pandoc.MetaInlines(create_authors_inlines(meta.author, mark))
+  -- Institute info is now baked into the affiliations block.
+  meta.affiliations = nil
+  
+  return pandoc.Pandoc(body, meta)
+end

_extensions/authors-block/from_author_info_blocks.lua

@@ -0,0 +1,197 @@
+-- https://github.com/pandoc/lua-filters/commit/ca72210b453cc0d045360e0ae36448d019d7dfbf
+--[[
+affiliation-blocks – generate title components
+
+Copyright © 2017–2021 Albert Krewinkel
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+-- from @kapsner
+-- [import]
+local from_utils = require "utils"
+local has_key = from_utils.has_key
+-- [/import]
+local M = {}
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local default_marks
+local default_marks = {
+  corresponding_author = FORMAT == 'latexAA'
+    and {pandoc.RawInline('latex', '*')}
+    or {pandoc.Str '✉'},
+  equal_contributor = FORMAT == 'latexAA'
+    and {pandoc.RawInline('latex', '$\\dagger{}$')}
+    or {pandoc.Str '*'},
+}
+M.default_marks = default_marks
+
+-- modified by @kapsner
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local function is_equal_contributor(author)
+  if has_key(author, "attributes") then
+    return author.attributes["equalcontributor"]
+  end
+  return nil
+end
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Create equal contributors note.
+local function create_equal_contributors_block(authors, mark)
+  local has_equal_contribs = List:new(authors):find_if(is_equal_contributor)
+  if not has_equal_contribs then
+    return nil
+  end
+  local contributors = {
+    pandoc.Superscript(mark'equal_contributor'),
+    pandoc.Space(),
+    pandoc.Str 'These authors contributed equally to this work.'
+  }
+  return List:new{pandoc.Para(contributors)}
+end
+M.create_equal_contributors_block = create_equal_contributors_block
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local function intercalate(lists, elem)
+  local result = List:new{}
+  for i = 1, (#lists - 1) do
+    result:extend(lists[i])
+    result:extend(elem)
+  end
+  if #lists > 0 then
+    result:extend(lists[#lists])
+  end
+  return result
+end
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Check whether the given author is a corresponding author
+local function is_corresponding_author(author)
+  if has_key(author, "attributes") then
+    if author.attributes["corresponding"] then
+      return author.email
+    end
+  end
+  return nil
+end
+M.is_corresponding_author = is_corresponding_author
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a block element containing the correspondence information
+local function create_correspondence_blocks(authors, mark)
+  local corresponding_authors = List:new{}
+  for _, author in ipairs(authors) do
+    if is_corresponding_author(author) then
+      local mailto = 'mailto:' .. utils.stringify(author.email)
+      local author_with_mail = List:new(
+        -- modified by @kapsner
+        author.name.literal .. List:new{pandoc.Space(),  pandoc.Str '<'} ..
+        author.email .. List:new{pandoc.Str '>'}
+      )
+      local link = pandoc.Link(author_with_mail, mailto)
+      table.insert(corresponding_authors, {link})
+    end
+  end
+  if #corresponding_authors == 0 then
+    return nil
+  end
+  local correspondence = List:new{
+    pandoc.Superscript(mark'corresponding_author'),
+    pandoc.Space(),
+    pandoc.Str'Correspondence:',
+    pandoc.Space()
+  }
+  local sep = List:new{pandoc.Str',',  pandoc.Space()}
+  return {
+    pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
+  }
+end
+M.create_correspondence_blocks = create_correspondence_blocks
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Create inlines for a single author (includes all author notes)
+local function author_inline_generator (get_mark)
+  return function (author)
+    local author_marks = List:new{}
+    -- modified by @kapsner
+    if has_key(author, "attributes") then
+      if author.attributes["equalcontributor"] then
+        author_marks[#author_marks + 1] = get_mark 'equal_contributor'
+      end
+    end
+    local idx_str
+    for _, idx in ipairs(author.affiliations) do
+      if type(idx) ~= 'table' then
+        idx_str = tostring(idx)
+      else
+        idx_str = stringify(idx)
+      end
+      author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
+    end
+    if is_corresponding_author(author) then
+      author_marks[#author_marks + 1] = get_mark 'corresponding_author'
+    end
+    -- modified by @kapsner
+    if FORMAT:match 'latexAA' then
+      author.name.literal[#author.name.literal + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+      return author
+    else
+      local res = List.clone(author.name.literal)
+      res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+      return res
+    end
+  end
+end
+M.author_inline_generator = author_inline_generator
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a list of inlines containing all authors.
+local function create_authors_inlines(authors, mark)
+  local inlines_generator = author_inline_generator(mark)
+  local inlines = List:new(authors):map(inlines_generator)
+  local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
+
+  local last_author = inlines[#inlines]
+  inlines[#inlines] = nil
+  local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
+  if #authors > 1 then
+    result:extend(List:new{pandoc.Str ","} .. and_str)
+  end
+  result:extend(last_author)
+  return result
+end
+M.create_authors_inlines = create_authors_inlines
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a block list all affiliations, marked with arabic numbers.
+local function create_affiliations_blocks(affiliations)
+  local affil_lines = List:new(affiliations):map(
+    function (affil, i)
+      local num_inlines = List:new{
+        pandoc.Superscript{pandoc.Str(affil.number)},
+        pandoc.Space()
+      }
+      return num_inlines .. affil.name
+    end
+  )
+  return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
+end
+M.create_affiliations_blocks = create_affiliations_blocks
+
+return M

_extensions/authors-block/from_scholarly_metadata.lua

@@ -0,0 +1,59 @@
+--[[
+ScholarlyMeta – normalize author/affiliation meta variables
+
+Copyright (c) 2017-2021 Albert Krewinkel, Robert Winkler
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+local M = {}
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua
+--- Returns a function which checks whether an object has the given ID.
+local function has_id(id)
+  return function(x) return x.id == id end
+end
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua
+--- Resolve institute placeholders to full named objects
+local function resolve_institutes(institute, known_institutes)
+  local unresolved_institutes
+  if institute == nil then
+    unresolved_institutes = {}
+  elseif type(institute) == "string" or type(institute) == "number" then
+    unresolved_institutes = {institute}
+  else
+    unresolved_institutes = institute
+  end
+
+  local result = List:new{}
+  for i, inst in ipairs(unresolved_institutes) do
+    -- this has been modified by @kapsner
+    --result[i] =
+    --  known_institutes[tonumber(inst)] or
+    --  known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or
+    --  to_named_object(inst)
+    intermed_val = known_institutes:find_if(has_id(stringify(inst)))
+    result[i] = pandoc.MetaString(stringify(intermed_val.index))
+  end
+  return result
+end
+M.resolve_institutes = resolve_institutes
+
+return M

_extensions/authors-block/utils.lua

@@ -0,0 +1,62 @@
+--[[
+authors-block – affiliations block extension for quarto
+
+Copyright (c) 2023 Lorenz A. Kapsner
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+-- [import]
+local from_scholarly = require "from_scholarly_metadata"
+local resolve_institutes = from_scholarly.resolve_institutes
+-- [/import]
+
+local M = {}
+
+-- from @kapsner
+local function normalize_affiliations(affiliations)
+  local affiliations_norm = List:new(affiliations):map(
+    function(affil, i)
+      affil.index = pandoc.MetaInlines(pandoc.Str(tostring(i)))
+      affil.id = pandoc.MetaString(stringify(affil.id))
+      return affil
+    end
+  )
+  return affiliations_norm
+end
+M.normalize_affiliations = normalize_affiliations
+
+-- from https://stackoverflow.com/a/2282547
+local function has_key(set, key)
+  return set[key] ~= nil
+end
+M.has_key = has_key
+
+-- from @kapsner
+local function normalize_authors(affiliations)
+  return function(auth)
+    auth.id = pandoc.MetaString(stringify(auth.name))
+    auth.affiliations = resolve_institutes(
+      auth.affiliations,
+      affiliations
+    )
+    return auth
+  end
+end
+M.normalize_authors = normalize_authors
+
+return M

_extensions/bootstrap/googlefonts.css

@@ -0,0 +1,225 @@
+/* cyrillic-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmhdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F,
+    U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwkxdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmxdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlBdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0370-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmBdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1,
+    U+01AF-01B0, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmRdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB,
+    U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdu3cOWxw.woff2)
+    format("woff2");
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA,
+    U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215,
+    U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qNa7lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F,
+    U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qPK7lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qNK7lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qO67lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+0370-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qN67lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1,
+    U+01AF-01B0, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qNq7lujVj9_mf.woff2)
+    format("woff2");
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB,
+    U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(./googlefonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7lujVj9w.woff2)
+    format("woff2");
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA,
+    U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215,
+    U+FEFF, U+FFFD;
+}
+/* cyrillic-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmhdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0460-052F, U+1C80-1C88, U+20B4, U+2DE0-2DFF, U+A640-A69F,
+    U+FE2E-FE2F;
+}
+/* cyrillic */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwkxdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
+}
+/* greek-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmxdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+1F00-1FFF;
+}
+/* greek */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlBdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0370-03FF;
+}
+/* vietnamese */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmBdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1,
+    U+01AF-01B0, U+1EA0-1EF9, U+20AB;
+}
+/* latin-ext */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmRdu3cOWxy40.woff2)
+    format("woff2");
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB,
+    U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: "Source Sans Pro";
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(./googlefonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdu3cOWxw.woff2)
+    format("woff2");
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA,
+    U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215,
+    U+FEFF, U+FFFD;
+}

_extensions/d2/_extension.yml

@@ -0,0 +1,8 @@
+title: D2
+author: Data Intuitive
+version: 1.1.0
+quarto-required: ">=1.3"
+contributes:
+  filters:
+    - d2.lua
+

_extensions/d2/d2.lua

@@ -0,0 +1,272 @@
+-- Enum for D2Theme
+local D2Theme = {
+  NeutralDefault = 0,
+  NeutralGrey = 1,
+  FlagshipTerrastruct = 3,
+  CoolClassics = 4,
+  MixedBerryBlue = 5,
+  GrapeSoda = 6,
+  Aubergine = 7,
+  ColorblindClear = 8,
+  VanillaNitroCola = 100,
+  OrangeCreamsicle = 101,
+  ShirelyTemple = 102,
+  EarthTones = 103,
+  EvergladeGreen = 104,
+  ButteredToast = 105,
+  DarkMauve = 200,
+  Terminal = 300,
+  TerminalGrayscale = 301,
+  Origami = 302
+}
+
+-- Enum for D2Layout
+local D2Layout = {
+  dagre = 'dagre',
+  elk = 'elk'
+}
+
+-- Enum for D2Format
+local D2Format = {
+  svg = 'svg',
+  png = 'png',
+  pdf = 'pdf'
+}
+-- Enum for Embed mode
+local EmbedMode = {
+  inline = "inline",
+  link = "link",
+  raw = "raw"
+}
+
+-- Helper function to copy a table
+function copyTable(obj, seen)
+  -- Handle non-tables and previously-seen tables.
+  if type(obj) ~= 'table' then return obj end
+  if seen and seen[obj] then return seen[obj] end
+
+  -- New table; mark it as seen and copy recursively.
+  local s = seen or {}
+  local res = {}
+  s[obj] = res
+  for k, v in pairs(obj) do res[copyTable(k, s)] = copyTable(v, s) end
+  return setmetatable(res, getmetatable(obj))
+end
+
+-- Helper function for debugging
+function dump(o)
+  if type(o) == 'table' then
+     local s = '{ '
+     for k,v in pairs(o) do
+        if type(k) ~= 'number' then k = '"'..k..'"' end
+        s = s .. '['..k..'] = ' .. dump(v) .. ','
+     end
+     return s .. '} '
+  else
+     return tostring(o)
+  end
+end
+
+
+-- Counter for the diagram files
+local counter = 0
+
+local function render_graph(globalOptions)
+  local filter = {
+    CodeBlock = function(cb)
+      -- Check if the CodeBlock has the 'd2' class
+      if not cb.classes:includes('d2') or cb.text == nil then
+        return nil
+      end
+
+      counter = counter + 1
+
+      -- Initialise options table
+      local options = copyTable(globalOptions)
+
+      -- Process codeblock attributes
+      for k, v in pairs(cb.attributes) do
+        options[k] = v
+      end
+
+      -- Transform options
+      if options.theme ~= nil and type(options.theme) == "string" then
+        assert(D2Theme[options.theme] ~= nil, "Invalid theme: " .. options.theme .. ". Options are: " .. dump(D2Theme))
+        options.theme = D2Theme[options.theme]
+      end
+      if options.layout ~= nil and type(options.layout) == "string" then
+        assert(D2Layout[options.layout] ~= nil, "Invalid layout: " .. options.layout .. ". Options are: " .. dump(D2Layout))
+        options.layout = D2Layout[options.layout]
+      end
+      if options.format ~= nil and type(options.format) == "string" then
+        assert(D2Format[options.format] ~= nil, "Invalid format: " .. options.format .. ". Options are: " .. dump(D2Format))
+        options.format = D2Format[options.format]
+      end
+      if options.embed_mode ~= nil and type(options.embed_mode) == "string" then
+        assert(EmbedMode[options.embed_mode] ~= nil, "Invalid embed_mode: " .. options.embed_mode .. ". Options are: " .. dump(EmbedMode))
+        options.embed_mode = EmbedMode[options.embed_mode]
+      end
+      if options.sketch ~= nil and type(options.sketch) == "string" then
+        assert(options.sketch == "true" or options.sketch == "false", "Invalid sketch: " .. options.sketch .. ". Options are: true, false")
+        options.sketch = options.sketch == "true"
+      end
+      if options.pad ~= nil and type(options.pad) == "string" then
+        assert(tonumber(options.pad) ~= nil, "Invalid pad: " .. options.pad .. ". Must be a number")
+        options.pad = tonumber(options.pad)
+      end
+      if options.echo ~= nil and type(options.echo) == "string" then
+        assert(options.echo == "true" or options.echo == "false", "Invalid echo: " .. options.echo .. ". Options are: true, false")
+        options.echo = options.echo == "true"
+      end
+
+      -- Set default filename
+      if options.filename == nil then
+        options.filename = "diagram-" .. counter
+      end
+
+      -- Set the default format to pdf since svg is not supported in PDF output
+      if options.format == D2Format.svg and quarto.doc.is_format("latex") then
+        options.format = D2Format.pdf
+      end
+      -- Set the default embed_mode to link if the quarto format is not html or the figure format is pdf
+      if not quarto.doc.is_format("html") or options.format == D2Format.pdf then
+        options.embed_mode = EmbedMode.link
+      end
+
+      -- Set the default folder to ./images when embed_mode is link
+      if options.folder == nil and options.embed_mode == EmbedMode.link then
+        options.folder = "./images"
+      end
+
+      -- Generate diagram using `d2` CLI utility
+      local result = pandoc.system.with_temporary_directory('svg-convert', function (tmpdir)
+        -- determine path name of input file
+        local inputPath = pandoc.path.join({tmpdir, "temp_" .. counter .. ".txt"})
+
+        -- determine path name of output file
+        local outputPath
+        if options.folder ~= nil then
+          os.execute("mkdir -p " .. options.folder)
+          outputPath = options.folder .. "/" .. options.filename .. "." .. options.format
+        else
+          outputPath = pandoc.path.join({tmpdir, options.filename .. "." .. options.format})
+        end
+
+        -- write graph text to file
+        local tmpFile = io.open(inputPath, "w")
+        if tmpFile == nil then
+          print("Error: Could not open file for writing")
+          return nil
+        end
+        tmpFile:write(cb.text)
+        tmpFile:close()
+        
+        -- run d2
+        os.execute(
+          "d2" ..
+          " --theme=" .. options.theme ..
+          " --layout=" .. options.layout ..
+          " --sketch=" .. tostring(options.sketch) .. 
+          " --pad=" .. options.pad ..
+          " " .. inputPath .. 
+          " " .. outputPath
+        )
+
+        if options.embed_mode == EmbedMode.link then
+          return outputPath
+        else
+          local file = io.open(outputPath, "rb")
+          local data
+          if file then
+            data = file:read('*all')
+            file:close()
+          end
+          os.remove(outputPath)
+
+          if options.embed_mode == EmbedMode.raw then
+            return data
+          elseif options.embed_mode == EmbedMode.inline then
+            dump(options)
+            
+            if options.format == "svg" then
+              return "data:image/svg+xml;base64," .. quarto.base64.encode(data)
+            elseif options.format == "png" then
+              return "data:image/png;base64," .. quarto.base64.encode(data)
+            else
+              print("Error: Unsupported format")
+              return nil
+            end
+          end
+        end
+      end)
+
+      -- Read the generated output into a Pandoc Image element
+      local output
+      if options.embed_mode == EmbedMode.raw then
+        output = pandoc.Div({pandoc.RawInline("html", result)})
+        
+        if options.width ~= nil then
+          output.attributes.style = "width: " .. options.width .. ";"
+        end
+        if options.height ~= nil then
+          output.attributes.style = output.attributes.style .. "height: " .. options.height .. ";"
+        end
+        
+      else
+        local image = pandoc.Image({}, result)
+
+        -- Set the width and height attributes, if they exist
+        if options.width ~= nil then
+          image.attributes.width = options.width
+        end
+
+        if options.height ~= nil then
+          image.attributes.height = options.height
+        end
+
+        if options.caption ~= '' then
+          image.caption = pandoc.Str(options.caption)
+        end
+
+        output = pandoc.Para({image})
+      end
+
+      -- Wrap the Image element in a Para element and return it
+      if options.echo then
+        local codeBlock = pandoc.CodeBlock(cb.text, cb.attr)
+        output = pandoc.Div({codeBlock, output})
+      end
+      return output
+    end
+  }
+  return filter
+end
+
+
+function Pandoc(doc)
+
+  local options = {
+    theme = D2Theme.NeutralDefault,
+    layout = D2Layout.dagre,
+    format = D2Format.svg,
+    sketch = false,
+    pad = 100,
+    folder = nil,
+    filename = nil,
+    caption = '',
+    width = nil,
+    height = nil,
+    echo = false,
+    embed_mode = "inline"
+  }
+
+  -- Process global attributes
+  local globalOptions = doc.meta["d2"]
+  if type(globalOptions) == "table" then
+    for k, v in pairs(globalOptions) do
+      options[k] = pandoc.utils.stringify(v)
+    end
+  end
+
+  return doc:walk(render_graph(options))
+end

_extensions/inst/css/revealjs.css

@@ -0,0 +1,328 @@
+:root {
+  --r-background-color: #fff;
+  --r-main-font: Source Sans Pro, simhei, microsoft yahei;
+  --r-main-font-size: 32px;
+  --r-main-color: #222;
+  --r-block-margin: 12px;
+  --r-heading-margin: 0 0 12px 0;
+  --r-heading-font: Source Sans Pro, microsoft yahei, simhei;
+  --r-heading-color: #0c4c8a;
+  --r-heading-line-height: 1.2em;
+  --r-heading-letter-spacing: normal;
+  --r-heading-text-transform: none;
+  --r-heading-text-shadow: none;
+  --r-heading-font-weight: 900;
+  --r-heading1-text-shadow: none;
+  --r-heading1-size: 2.5em;
+  --r-heading2-size: 1.6em;
+  --r-heading3-size: 1.3em;
+  --r-heading4-size: 1em;
+  --r-code-font: SFMono-Regular, Menlo, Monaco, Consolas, Liberation Mono,
+    Courier New, monospace;
+  --r-link-color: #ef562d;
+  --r-link-color-dark: #ef562d;
+  --r-link-color-hover: #d13076;
+  --r-selection-background-color: #98bdef;
+  --r-selection-color: #fff;
+  --quarto-hl-fu-color: #c53800;
+}
+
+.reveal .title-slide h1 {
+  text-align: center;
+  line-height: var(--r-heading-line-height);
+}
+
+section#title-slide p.author,
+section#title-slide p.institute,
+section#title-slide p.date {
+  font-size: var(--r-heading2-size);
+  color: gray;
+}
+
+section#title-slide h1.title:after {
+  content: " ";
+  display: block;
+  border: 3px solid;
+  border-image: linear-gradient(to right, white, var(--r-heading-color), white)
+    1;
+  border-radius: 1px;
+}
+
+section#title-slide p.subtitle {
+  font-size: var(--r-heading3-size);
+  text-decoration: underline;
+  color: gray;
+}
+
+section#title-slide a {
+  color: gray;
+}
+
+.reveal .slide-number a {
+  color: #bbbbbb;
+  font-size: 10pt;
+}
+
+section#title-slide a:hover {
+  color: var(--r-link-color-hover);
+}
+
+.reveal[data-navigation-mode="linear"] .title-slide h1 {
+  font-size: var(--r-heading2-size);
+}
+
+section#TOC {
+  vertical-align: middle;
+  text-align: center;
+}
+
+section#TOC h2 {
+  font-size: var(--r-heading2-size);
+  font-weight: bold;
+  text-align: center;
+}
+
+section#TOC h2:after {
+  content: " ";
+  display: block;
+  border: 3px solid;
+  border-image: linear-gradient(to right, white, var(--r-heading-color), white)
+    1;
+  border-radius: 1px;
+}
+
+section#TOC ul {
+  text-align: left;
+  vertical-align: middle;
+  margin-top: 3em;
+  line-height: 1.6em;
+}
+
+section#TOC ol li {
+  font-size: var(--r-heading3-size);
+  font-weight: bold;
+  color: gray;
+  list-style-type: number;
+  line-height: 1.6em;
+}
+
+section#TOC strong,
+section#TOC b {
+  color: black;
+}
+
+section#TOC ul li {
+  font-size: var(--r-heading3-size);
+  font-weight: bold;
+  color: gray;
+  list-style-type: circle;
+  line-height: 1.6em;
+}
+
+section#TOC a {
+  color: black;
+}
+
+section#TOC a:hover {
+  color: var(--r-link-color-hover);
+}
+
+.reveal h2 {
+  text-align: left;
+  margin-top: 0px;
+  line-height: var(--r-heading-line-height);
+}
+
+.reveal .title-slide h1:after {
+  content: " ";
+  display: block;
+  border: 3px solid;
+  border-image: linear-gradient(to right, white, var(--r-heading-color), white)
+    1;
+  border-radius: 1px;
+}
+
+.reveal h2:after {
+  content: " ";
+  display: block;
+  border: 3px solid;
+  border-image: linear-gradient(to right, var(--r-heading-color), white) 1;
+  border-radius: 1px;
+}
+
+.reveal ul {
+  list-style-type: circle;
+}
+
+.reveal ul li {
+  line-height: 1.2em;
+}
+
+.reveal .thank h2 {
+  font-size: var(--r-heading1-size);
+  line-height: var(--r-heading-line-height);
+}
+
+.reveal .thank {
+  text-align: center;
+}
+
+.reveal .thank h2:after {
+  content: " ";
+  display: block;
+  border: 3px solid;
+  border-image: linear-gradient(to right, white, var(--r-heading-color), white)
+    1;
+  border-radius: 1px;
+}
+
+.panel-tabset [role="tab"] {
+  border-bottom: 1px solid red;
+}
+
+.panel-tabset [role="tab"][aria-selected="true"] {
+  background-color: #ffdddd;
+  border-bottom: 1px solid red;
+}
+
+.white {
+  color: #ffffff;
+}
+.orange {
+  color: #e09a25;
+}
+.green {
+  color: #006e51;
+}
+.pink {
+  color: #d13076;
+}
+
+.dusty {
+  color: #ad5d5d;
+}
+
+.flame {
+  color: #ef562d;
+}
+.kale {
+  color: #5c7148;
+}
+.blue {
+  color: #0c4c8a;
+}
+.red {
+  color: #b93a32;
+}
+.clay {
+  color: #9e4624;
+}
+.bodacious {
+  color: #b76ba3;
+}
+.serenity {
+  color: #91a8d0;
+}
+
+.cognac {
+  color: #60413c;
+}
+.sangria {
+  color: #760030;
+}
+
+.alumium {
+  color: #75796a;
+}
+
+.marsala {
+  color: #964f4c;
+}
+.purple {
+  color: #702fa8;
+}
+
+.blank {
+  background-color: "Yellow";
+  width: 100%;
+  color: red;
+}
+
+.reveal .slide aside {
+  position: absolute;
+  margin: 0 auto;
+  left: 2%;
+  font-size: 0.7em;
+  text-align: end;
+  max-width: 90%;
+  width: fit-content;
+  color: gray;
+  bottom: -6%;
+}
+
+.ref {
+  position: absolute;
+  margin: 0 auto;
+  right: 2%;
+  font-size: 1em;
+  text-align: end;
+  max-width: 90%;
+  width: fit-content;
+  color: gray;
+  bottom: -6%;
+}
+
+.con {
+  position: absolute;
+  margin: 0 auto;
+  font-size: 1.4em;
+  text-align: center;
+  font-family: inherit;
+  max-width: 100%;
+  width: fit-content;
+  color: #023047;
+  bottom: -2%;
+}
+
+.center {
+  text-align: center;
+}
+
+.tiny {
+  font-size: 60%;
+}
+
+figure > figcaption {
+  margin-top: -0.5em;
+}
+
+.reveal .slide figure > figcaption,
+.reveal .slide img.stretch + p.caption,
+.reveal .slide img.r-stretch + p.caption {
+  font-size: 0.9em;
+  text-align: center;
+}
+
+.reveal strong, .reveal b {
+    font-weight: bold;
+    color: crimson;
+}
+
+.reveal pre code {
+    background-color: #554433;
+    line-height: 1.2em;
+    color: #fff;
+    font-size: x-large;
+}
+
+section#title-slide p.subtitle {
+    font-size: var(--r-heading3-size);
+    text-decoration: none;
+    color: gray;
+}
+
+.reveal div.sourceCode pre code {
+    background-color: #002233;
+    min-height: 100%;
+    font-size: x-large;
+}

_extensions/inst/css/style.css

@@ -0,0 +1,126 @@
+.udot {
+  text-decoration-line: underline;
+  text-decoration-color: rgb(50, 50, 50);
+  text-decoration-style: dashed;
+  text-decoration-thickness: 1px;
+}
+
+.good {
+    background-color: forestgreen;
+    color: lightyellow;
+}
+
+.bad {
+    background-color: orangered;
+    color: lightyellow;
+}
+
+.del {
+    /* text-decoration-color: rgb(222 13 13); */
+    text-decoration: line-through;
+    background-color: rgba(255, 0, 0, 0.2); 
+    text-decoration-style: initial;
+    text-decoration-thickness: 1.5px;
+}
+
+
+.todo {
+    background-color: darkorange;
+    color: lightyellow;
+}
+
+.com {
+    background-color: #0025ff;
+    font-weight: bold;
+    color: lightyellow;
+}
+
+.add .ins {
+    text-decoration: underline;
+    background-color: rgba(0, 128, 0, 0.2);
+    /* text-decoration-color: rgb(222 13 13); */
+    background-color: violet;
+    text-decoration-style: initial;
+    text-decoration-thickness: 2px;
+}
+
+
+del {
+    text-decoration-line: line-through;
+    text-decoration-color: rgb(222 13 13);
+    text-decoration-style: initial;
+    text-decoration-thickness: 1.0px;
+}
+
+
+ins {
+    text-decoration: underline;
+    background-color: rgba(0, 128, 0, 0.2); 
+    text-decoration-style: initial;
+    text-decoration-thickness: 2px;
+}
+
+.clab {
+    background-color: rgb(255, 245, 240);
+}
+
+.rem {
+    background-color: darkorange;
+    color: lightyellow;
+    text-decoration-thickness: 2px;
+}
+
+
+#criticnav {
+    position: fixed;
+    z-index: 1100;
+    top: 0;
+    right: 0;
+    width: 120px;
+    border-bottom: solid 1px #ffffff;
+    margin: 0;
+    padding: 10;
+    background-color: rgb(143 38 38 / 95%);
+    color: #ffffff;
+    font-size: 12px;
+    font-family: "Helvetica Neue", helvetica, arial, sans-serif !important
+}
+
+#criticnav ul {
+    list-style-type: none;
+    width: 90%;
+    margin: 0 auto;
+    padding: 0
+}
+
+#criticnav ul li {
+    display: block;
+    width: 100px;
+    min-width: 80px;
+    text-align: center;
+    padding: 5px 0 3px !important;
+    margin: 5px 2px !important;
+    line-height: 1em;
+    float: center;
+    text-transform: uppercase;
+    cursor: pointer;
+    border-radius: 20px;
+    border: 3px solid rgba(255,255,255,0);
+    color: #fff !important
+}
+
+.markup del {
+    background-color: rgba(255, 0, 0, 0.2);
+    text-decoration-line: line-through;
+    /* text-decoration-color: rgb(222 13 13); */
+    text-decoration-style: initial;
+    text-decoration-thickness: 1.5px;
+}
+
+.markup ins {
+    text-decoration: underline;
+    background-color: rgba(0, 128, 0, 0.2); 
+    /* text-decoration-color: rgb(222 93 93); */
+    text-decoration-style: initial;
+    text-decoration-thickness: 2px;
+}

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

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

_extensions/inst/tex/china-national-standard-gb-t-7714-2015-numeric.csl

@@ -0,0 +1,435 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" class="in-text" names-delimiter=". " name-as-sort-order="all" sort-separator=" " demote-non-dropping-particle="never" initialize-with=" " initialize-with-hyphen="false" page-range-format="expanded" default-locale="zh-CN">
+  <info>
+    <title>China National Standard GB/T 7714-2015 (numeric, 中文)</title>
+    <id>http://www.zotero.org/styles/china-national-standard-gb-t-7714-2015-numeric</id>
+    <link href="http://www.zotero.org/styles/china-national-standard-gb-t-7714-2015-numeric" rel="self"/>
+    <link href="http://std.samr.gov.cn/gb/search/gbDetailed?id=71F772D8055ED3A7E05397BE0A0AB82A" rel="documentation"/>
+    <author>
+      <name>牛耕田</name>
+      <email>buffalo_d@163.com</email>
+    </author>
+    <contributor>
+      <name>Zeping Lee</name>
+      <email>zepinglee@gmail.com</email>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="generic-base"/>
+    <summary>The Chinese GB/T 7714-2015 numeric style</summary>
+    <updated>2022-02-23T10:44:01+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="zh-CN">
+    <date form="text">
+      <date-part name="year" suffix="年" range-delimiter="&#8212;"/>
+      <date-part name="month" form="numeric" suffix="月" range-delimiter="&#8212;"/>
+      <date-part name="day" suffix="日" range-delimiter="&#8212;"/>
+    </date>
+    <terms>
+      <term name="edition" form="short">版</term>
+      <term name="open-quote">“</term>
+      <term name="close-quote">”</term>
+      <term name="open-inner-quote">‘</term>
+      <term name="close-inner-quote">’</term>
+    </terms>
+  </locale>
+  <locale>
+    <date form="numeric">
+      <date-part name="year" range-delimiter="/"/>
+      <date-part name="month" form="numeric-leading-zeros" prefix="-" range-delimiter="/"/>
+      <date-part name="day" form="numeric-leading-zeros" prefix="-" range-delimiter="/"/>
+    </date>
+    <terms>
+      <term name="page-range-delimiter">-</term>
+    </terms>
+  </locale>
+  <!-- 引用日期 -->
+  <macro name="accessed-date">
+    <date variable="accessed" form="numeric" prefix="[" suffix="]"/>
+  </macro>
+  <!-- 主要责任者 -->
+  <macro name="author">
+    <names variable="author">
+      <name>
+        <name-part name="family" text-case="uppercase"/>
+        <name-part name="given"/>
+      </name>
+      <substitute>
+        <names variable="composer"/>
+        <names variable="illustrator"/>
+        <names variable="director"/>
+        <choose>
+          <if variable="container-title" match="none">
+            <names variable="editor"/>
+          </if>
+        </choose>
+      </substitute>
+    </names>
+  </macro>
+  <!-- 书籍的卷号（“第 x 卷”或“第 x 册”） -->
+  <macro name="book-volume">
+    <choose>
+      <if type="article article-journal article-magazine article-newspaper periodical" match="none">
+        <choose>
+          <if is-numeric="volume">
+            <group delimiter=" ">
+              <label variable="volume" form="short" text-case="capitalize-first"/>
+              <text variable="volume"/>
+            </group>
+          </if>
+          <else>
+            <text variable="volume"/>
+          </else>
+        </choose>
+      </if>
+    </choose>
+  </macro>
+  <!-- 专著主要责任者 -->
+  <macro name="container-author">
+    <names variable="editor">
+      <name>
+        <name-part name="family" text-case="uppercase"/>
+        <name-part name="given"/>
+      </name>
+      <substitute>
+        <names variable="editorial-director"/>
+        <names variable="collection-editor"/>
+        <names variable="container-author"/>
+      </substitute>
+    </names>
+  </macro>
+  <!-- 专著题名 -->
+  <macro name="container-title">
+    <group delimiter=", ">
+      <group delimiter=": ">
+        <choose>
+          <if variable="container-title">
+            <text variable="container-title"/>
+          </if>
+          <else>
+            <text variable="event"/>
+          </else>
+        </choose>
+        <text macro="book-volume"/>
+      </group>
+      <choose>
+        <if variable="event-date">
+          <date variable="event-date" form="text"/>
+          <text variable="event-place"/>
+        </if>
+      </choose>
+    </group>
+  </macro>
+  <!-- 版本项 -->
+  <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>
+  <!-- 电子资源的更新或修改日期 -->
+  <macro name="issued-date">
+    <date variable="issued" form="numeric"/>
+  </macro>
+  <!-- 出版年 -->
+  <macro name="issued-year">
+    <choose>
+      <if is-uncertain-date="issued">
+        <date variable="issued" prefix="[" suffix="]">
+          <date-part name="year" range-delimiter="-"/>
+        </date>
+      </if>
+      <else>
+        <date variable="issued">
+          <date-part name="year" range-delimiter="-"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <!-- 专著的出版项 -->
+  <macro name="publishing">
+    <group delimiter=": ">
+      <group delimiter=", ">
+        <group delimiter=": ">
+          <text variable="publisher-place"/>
+          <text variable="publisher"/>
+        </group>
+        <!-- 非电子资源显示“出版年” -->
+        <choose>
+          <if variable="publisher page" type="book chapter paper-conference thesis" match="any">
+            <text macro="issued-year"/>
+          </if>
+          <else-if variable="URL DOI" match="none">
+            <text macro="issued-year"/>
+          </else-if>
+        </choose>
+      </group>
+      <text variable="page"/>
+    </group>
+    <choose>
+      <!-- 纯电子资源显示“更新或修改日期” -->
+      <if variable="publisher page" type="book chapter paper-conference thesis" match="none">
+        <choose>
+          <if variable="URL DOI" match="any">
+            <text macro="issued-date" prefix="(" suffix=")"/>
+          </if>
+        </choose>
+      </if>
+    </choose>
+    <text macro="accessed-date"/>
+  </macro>
+  <!-- 其他责任者 -->
+  <macro name="secondary-contributor">
+    <names variable="translator">
+      <name>
+        <name-part name="family" text-case="uppercase"/>
+        <name-part name="given"/>
+      </name>
+      <label form="short" prefix=", "/>
+    </names>
+  </macro>
+  <!-- 连续出版物中的析出文献的出处项（年、卷、期等信息） -->
+  <macro name="periodical-publishing">
+    <group>
+      <group delimiter=": ">
+        <group>
+          <group delimiter=", ">
+            <text macro="container-title" text-case="title"/>
+            <choose>
+              <if type="article-newspaper">
+                <text macro="issued-date"/>
+              </if>
+              <else>
+                <text macro="issued-year"/>
+              </else>
+            </choose>
+            <text variable="volume"/>
+          </group>
+          <text variable="issue" prefix="(" suffix=")"/>
+        </group>
+        <text variable="page"/>
+      </group>
+      <text macro="accessed-date"/>
+    </group>
+  </macro>
+  <!-- 题名 -->
+  <macro name="title">
+    <group delimiter=", ">
+      <group delimiter=": ">
+        <text variable="title"/>
+        <group delimiter="&#8195;">
+          <choose>
+            <if variable="container-title" type="paper-conference" match="none">
+              <text macro="book-volume"/>
+            </if>
+          </choose>
+          <choose>
+            <if type="bill legal_case legislation patent regulation report standard" match="any">
+              <text variable="number"/>
+            </if>
+          </choose>
+        </group>
+      </group>
+      <choose>
+        <if variable="container-title" type="paper-conference" match="none">
+          <choose>
+            <if variable="event-date">
+              <text variable="event-place"/>
+              <date variable="event-date" form="text"/>
+            </if>
+          </choose>
+        </if>
+      </choose>
+    </group>
+    <text macro="type-code" prefix="[" suffix="]"/>
+  </macro>
+  <!-- 文献类型标识 -->
+  <macro name="type-code">
+    <group delimiter="/">
+      <choose>
+        <if type="article">
+          <choose>
+            <if variable="archive">
+              <text value="A"/>
+            </if>
+            <else>
+              <text value="M"/>
+            </else>
+          </choose>
+        </if>
+        <else-if type="article-journal article-magazine periodical" match="any">
+          <text value="J"/>
+        </else-if>
+        <else-if type="article-newspaper">
+          <text value="N"/>
+        </else-if>
+        <else-if type="bill collection legal_case legislation regulation" match="any">
+          <text value="A"/>
+        </else-if>
+        <else-if type="book chapter" match="any">
+          <text value="M"/>
+        </else-if>
+        <else-if type="dataset">
+          <text value="DS"/>
+        </else-if>
+        <else-if type="map">
+          <text value="CM"/>
+        </else-if>
+        <else-if type="paper-conference">
+          <text value="C"/>
+        </else-if>
+        <else-if type="patent">
+          <text value="P"/>
+        </else-if>
+        <else-if type="post post-weblog webpage" match="any">
+          <text value="EB"/>
+        </else-if>
+        <else-if type="report">
+          <text value="R"/>
+        </else-if>
+        <else-if type="software">
+          <text value="CP"/>
+        </else-if>
+        <else-if type="standard">
+          <text value="S"/>
+        </else-if>
+        <else-if type="thesis">
+          <text value="D"/>
+        </else-if>
+        <else>
+          <text value="Z"/>
+        </else>
+      </choose>
+      <choose>
+        <if variable="URL DOI" match="any">
+          <text value="OL"/>
+        </if>
+      </choose>
+    </group>
+  </macro>
+  <!-- 获取和访问路径以及 DOI -->
+  <macro name="url-doi">
+    <group delimiter=". ">
+      <text variable="URL"/>
+      <text variable="DOI" prefix="DOI:"/>
+    </group>
+  </macro>
+  <!-- 连续出版物的年卷期 -->
+  <macro name="year-volume-issue">
+    <group>
+      <group delimiter=", ">
+        <text macro="issued-year"/>
+        <text variable="volume"/>
+      </group>
+      <text variable="issue" prefix="(" suffix=")"/>
+    </group>
+  </macro>
+  <!-- 专著和电子资源 -->
+  <macro name="monograph-layout">
+    <group delimiter=". " suffix=".">
+      <text macro="author"/>
+      <text macro="title"/>
+      <text macro="secondary-contributor"/>
+      <text macro="edition"/>
+      <text macro="publishing"/>
+      <text macro="url-doi"/>
+    </group>
+  </macro>
+  <!-- 专著中的析出文献 -->
+  <macro name="chapter-in-book-layout">
+    <group delimiter=". " suffix=".">
+      <text macro="author"/>
+      <group delimiter="//">
+        <group delimiter=". ">
+          <text macro="title"/>
+          <text macro="secondary-contributor"/>
+        </group>
+        <group delimiter=". ">
+          <text macro="container-author"/>
+          <text macro="container-title"/>
+        </group>
+      </group>
+      <text macro="edition"/>
+      <text macro="publishing"/>
+      <text macro="url-doi"/>
+    </group>
+  </macro>
+  <!-- 连续出版物 -->
+  <macro name="serial-layout">
+    <group delimiter=". " suffix=".">
+      <text macro="author"/>
+      <text macro="title"/>
+      <text macro="year-volume-issue"/>
+      <text macro="publishing"/>
+      <text variable="URL"/>
+      <text variable="DOI" prefix="DOI:"/>
+    </group>
+  </macro>
+  <!-- 连续出版物中的析出文献 -->
+  <macro name="article-in-periodical-layout">
+    <group delimiter=". " suffix=".">
+      <text macro="author"/>
+      <text macro="title"/>
+      <text macro="periodical-publishing"/>
+      <text macro="url-doi"/>
+    </group>
+  </macro>
+  <!-- 专利文献 -->
+  <macro name="patent-layout">
+    <group delimiter=". " suffix=".">
+      <text macro="author"/>
+      <text macro="title"/>
+      <group>
+        <text macro="issued-date"/>
+        <text macro="accessed-date"/>
+      </group>
+      <text macro="url-doi"/>
+    </group>
+  </macro>
+  <!-- 正文中引用的文献标注格式 -->
+  <macro name="citation-layout">
+    <group>
+      <text variable="citation-number"/>
+    </group>
+  </macro>
+  <!-- 参考文献表格式 -->
+  <macro name="entry-layout">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper" match="any">
+        <text macro="article-in-periodical-layout"/>
+      </if>
+      <else-if type="periodical">
+        <text macro="serial-layout"/>
+      </else-if>
+      <else-if type="patent">
+        <text macro="patent-layout"/>
+      </else-if>
+      <else-if type="paper-conference" variable="container-title" match="any">
+        <text macro="chapter-in-book-layout"/>
+      </else-if>
+      <else>
+        <text macro="monograph-layout"/>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number" after-collapse-delimiter=",">
+    <layout vertical-align="sup" delimiter="," prefix="[" suffix="]">
+      <text macro="citation-layout"/>
+    </layout>
+  </citation>
+  <bibliography entry-spacing="0" et-al-min="4" et-al-use-first="3" second-field-align="flush">
+    <!-- 取消这部分注释可以使用 CSL-M 的功能支持双语 -->
+    <!-- <layout locale="en"><text variable="citation-number" prefix="[" suffix="]"/><text macro="entry-layout"/></layout> -->
+    <layout>
+      <text variable="citation-number" prefix="[" suffix="]"/>
+      <text macro="entry-layout"/>
+    </layout>
+  </bibliography>
+</style>

_extensions/inst/tex/cv.tex

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

_extensions/inst/tex/els.tex

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

_extensions/inst/tex/elsevier-harvard.csl

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

_extensions/inst/tex/nature-biotechnology.csl

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
+  <!-- Generated with https://github.com/citation-style-language/utilities/tree/master/generate_dependent_styles/data/npg -->
+  <info>
+    <title>Nature Biotechnology</title>
+    <id>http://www.zotero.org/styles/nature-biotechnology</id>
+    <link href="http://www.zotero.org/styles/nature-biotechnology" rel="self"/>
+    <link href="http://www.zotero.org/styles/nature" rel="independent-parent"/>
+    <link href="http://www.nature.com/nbt/pdf/gta.pdf" rel="documentation"/>
+    <category citation-format="numeric"/>
+    <category field="biology"/>
+    <issn>1087-0156</issn>
+    <eissn>1546-1696</eissn>
+    <updated>2014-06-17T02:29:16+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>
+</style>

_extensions/inst/tex/nature.csl

@@ -0,0 +1,154 @@
+<?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</title>
+    <id>http://www.zotero.org/styles/nature</id>
+    <link href="http://www.zotero.org/styles/nature" rel="self"/>
+    <link href="http://www.nature.com/nature/authors/gta/index.html#a5.4" rel="documentation"/>
+    <link href="http://www.nature.com/srep/publish/guidelines#references" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>mberkowi@gmu.edu</email>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="generic-base"/>
+    <issn>0028-0836</issn>
+    <eissn>1476-4687</eissn>
+    <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>
+        <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>
+    </choose>
+  </macro>
+  <macro name="issuance">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture song thesis chapter paper-conference" match="any">
+        <group delimiter="; " suffix=".">
+          <group delimiter=", " prefix="(" suffix=")">
+            <text variable="publisher" form="long"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+        </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-if type="report webpage post post-weblog" match="any">
+        <group delimiter=" ">
+          <text variable="URL"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else>
+        <date variable="issued" prefix="(" suffix=")">
+          <date-part name="year"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal">
+        <text variable="container-title" font-style="italic" form="short"/>
+      </if>
+      <else>
+        <text variable="container-title" font-style="italic"/>
+      </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>
+  <macro name="volume">
+    <choose>
+      <if type="article-journal" match="any">
+        <text variable="volume" font-weight="bold" suffix=","/>
+      </if>
+      <else>
+        <group delimiter=" ">
+          <label variable="volume" form="short"/>
+          <text variable="volume"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout vertical-align="sup" 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 suffix=".">
+      <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"/>
+          </if>
+        </choose>
+        <text macro="container-title"/>
+        <text macro="editor"/>
+        <text macro="volume"/>
+        <text variable="page"/>
+        <text macro="issuance"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>

_extensions/inst/tex/supp.tex

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

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

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

_extensions/martinomagnifico/simplemenu/_extension.yml

@@ -0,0 +1,21 @@
+title: Simplemenu
+author:  Martijn De Jongh (Martino)
+version: 2.0.0
+quarto-required: ">=1.2.198"
+contributes:
+  revealjs-plugins:
+    -
+      name: Simplemenu
+      script: simplemenu.js
+      stylesheet: simplemenu.css
+      config:
+        simplemenu:
+          menubarclass: "menubar"
+          menuclass: "menu"
+          activeclass: "active"
+          activeelement: "li"
+          flat: false
+          barhtml:
+              header: ""
+              footer: ""
+          scale: 0.67

_extensions/martinomagnifico/simplemenu/simplemenu.css

@@ -0,0 +1,190 @@
+.menubar {
+  display: -webkit-box;
+  display: -ms-flexbox;
+  display: flex;
+  -webkit-transition: -webkit-transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  transition: -webkit-transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  -o-transition: transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  transition: transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  transition: transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985), -webkit-transform 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  -webkit-transform: translateY(-100%);
+      -ms-transform: translateY(-100%);
+          transform: translateY(-100%);
+  color: inherit;
+  z-index: 2;
+  position: absolute;
+  -webkit-box-sizing: border-box;
+          box-sizing: border-box;
+  -webkit-box-pack: justify;
+      -ms-flex-pack: justify;
+          justify-content: space-between;
+  width: 100%;
+  font-size: clamp(16px, var(--r-main-font-size) * var(--simplemenu-scale, 0.75), 80px);
+  line-height: 1;
+}
+.menubar * {
+  -webkit-box-sizing: border-box;
+          box-sizing: border-box;
+}
+html:not(.print-pdf) body:not(.hide-menubar) .reveal.ready:not(.hide-menubar) .menubar {
+  -webkit-transform: translateY(0);
+      -ms-transform: translateY(0);
+          transform: translateY(0);
+}
+body.hide-menubar .reveal.ready .menubar a {
+  -webkit-transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  -o-transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+}
+.menubar.bottom {
+  -webkit-transform: translateY(100%);
+      -ms-transform: translateY(100%);
+          transform: translateY(100%);
+}
+.menubar:before, .menubar:after {
+  content: "";
+  position: absolute;
+  left: 0;
+  right: 0;
+  border-bottom: 1px solid currentColor;
+  opacity: 0.3;
+}
+.menubar:before {
+  top: 0;
+}
+.menubar:after {
+  bottom: 0;
+}
+.menubar:before {
+  opacity: 0;
+}
+.menubar.bottom:after {
+  opacity: 0;
+}
+.menubar.bottom:before {
+  opacity: 0.3;
+}
+.print-pdf .pdf-page:not(.hide-menubar) .menubar {
+  -webkit-transform: translateY(0);
+      -ms-transform: translateY(0);
+          transform: translateY(0);
+}
+.menubar a {
+  -webkit-transition: opacity 0.2s ease-in-out;
+  -o-transition: opacity 0.2s ease-in-out;
+  transition: opacity 0.2s ease-in-out;
+  display: -webkit-box;
+  display: -ms-flexbox;
+  display: flex;
+  -webkit-font-smoothing: subpixel-antialiased;
+  -moz-osx-font-smoothing: grayscale;
+  padding: 0.4em 0;
+}
+.menubar > ul {
+  -webkit-transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  -o-transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  transition: opacity 0.8s cubic-bezier(0.26, 0.86, 0.44, 0.985);
+  display: -webkit-box;
+  display: -ms-flexbox;
+  display: flex;
+  -ms-flex-wrap: wrap;
+      flex-wrap: wrap;
+  -webkit-box-orient: horizontal;
+  -webkit-box-direction: normal;
+      -ms-flex-direction: row;
+          flex-direction: row;
+  -webkit-box-pack: center;
+      -ms-flex-pack: center;
+          justify-content: center;
+  -webkit-box-align: center;
+      -ms-flex-align: center;
+          align-items: center;
+  list-style-type: none;
+  padding: 0;
+  margin: 0 auto;
+  gap: 1.5em;
+}
+.menubar > ul li {
+  -webkit-box-sizing: border-box;
+          box-sizing: border-box;
+  -webkit-box-flex: 1;
+      -ms-flex: 1;
+          flex: 1;
+  display: -webkit-box;
+  display: -ms-flexbox;
+  display: flex;
+}
+.menubar > ul li:before {
+  display: none;
+}
+.menubar > ul li + li {
+  margin: 0;
+}
+.menubar > ul a {
+  -webkit-box-flex: 0;
+      -ms-flex: 0;
+          flex: 0;
+  white-space: nowrap;
+  -webkit-box-align: center;
+      -ms-flex-align: center;
+          align-items: center;
+  opacity: 0.33;
+  padding: 0.5em;
+  color: currentColor;
+}
+.menubar > ul a:hover {
+  color: currentColor;
+  opacity: 0.75;
+}
+.menubar > ul li a.active, .menubar > ul li.active a {
+  opacity: 1;
+}
+
+.hide-menu .menu, .hide-menu .menu, [data-state=hide-menu] .menu {
+  opacity: 0;
+}
+
+.reveal .slide-number, .menubar .slide-number {
+  background: none;
+  font-family: inherit;
+  color: inherit;
+}
+.reveal .slide-number a, .menubar .slide-number a {
+  padding: 0;
+  opacity: 0.33;
+  color: currentColor;
+}
+.reveal .slide-number a:hover, .menubar .slide-number a:hover {
+  color: currentColor;
+  opacity: 0.75;
+}
+
+.menubar .slide-number {
+  display: -webkit-box !important;
+  display: -ms-flexbox !important;
+  display: flex !important;
+  -webkit-box-orient: horizontal;
+  -webkit-box-direction: normal;
+      -ms-flex-direction: row;
+          flex-direction: row;
+  -webkit-box-align: center;
+      -ms-flex-align: center;
+          align-items: center;
+  justify-items: center;
+  font-size: 0.75em;
+  height: 100%;
+  right: 0;
+  bottom: auto;
+  z-index: 0;
+  padding: 0;
+  padding-right: 1em;
+}
+
+.slides ~ .menubar, .menubar.bottom {
+  top: auto;
+  bottom: 0;
+}
+
+.slides ~ .menubar ~ .controls {
+  margin-bottom: clamp(16px, 2.5 * var(--r-main-font-size) * var(--simplemenu-scale, 0.75), 100px);
+}

_extensions/martinomagnifico/simplemenu/simplemenu.js

@@ -0,0 +1,644 @@
+
+/*****************************************************************
+ * @author: Martijn De Jongh (Martino), martijn.de.jongh@gmail.com
+ * https://github.com/Martinomagnifico
+ *
+ * Simplemenu.js for Reveal.js 
+ * Version 2.0.1
+ * 
+ * @license 
+ * MIT licensed
+ *
+ * Thanks to:
+ *  - Hakim El Hattab, Reveal.js 
+ ******************************************************************/
+
+
+
+(function (global, factory) {
+	typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
+	typeof define === 'function' && define.amd ? define(factory) :
+	(global = typeof globalThis !== 'undefined' ? globalThis : global || self, global.Simplemenu = factory());
+})(this, (function () { 'use strict';
+
+	const Plugin = () => {
+	  let options = {};
+	  const vars = {};
+	  const sections = {};
+	  const mainArray = [];
+	  let autoListItems = [];
+	  let manualListItems = [];
+
+	  const debugLog = text => {
+	    if (options.debug) console.log(text);
+	  };
+
+	  const isObject = item => {
+	    return item && typeof item === 'object' && !Array.isArray(item);
+	  };
+
+	  const mergeDeep = function (target) {
+	    for (var _len = arguments.length, sources = new Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) {
+	      sources[_key - 1] = arguments[_key];
+	    }
+
+	    if (!sources.length) return target;
+	    const source = sources.shift();
+
+	    if (isObject(target) && isObject(source)) {
+	      for (const key in source) {
+	        if (isObject(source[key])) {
+	          if (!target[key]) Object.assign(target, {
+	            [key]: {}
+	          });
+	          mergeDeep(target[key], source[key]);
+	        } else {
+	          Object.assign(target, {
+	            [key]: source[key]
+	          });
+	        }
+	      }
+	    }
+
+	    return mergeDeep(target, ...sources);
+	  };
+
+	  const selectionArray = (container, selectors) => {
+	    let selections = container.querySelectorAll(selectors);
+	    let selectionarray = Array.prototype.slice.call(selections);
+	    return selectionarray;
+	  };
+
+	  const pluginPath = filename => {
+	    let path;
+	    let pluginScript = document.querySelector(`script[src$="${filename}"]`);
+
+	    if (pluginScript) {
+	      path = pluginScript.getAttribute("src").slice(0, -1 * filename.length);
+	    } else {
+	      path = (typeof document === 'undefined' && typeof location === 'undefined' ? new (require('u' + 'rl').URL)('file:' + __filename).href : typeof document === 'undefined' ? location.href : (document.currentScript && document.currentScript.src || new URL('simplemenu.js', document.baseURI).href)).slice(0, (typeof document === 'undefined' && typeof location === 'undefined' ? new (require('u' + 'rl').URL)('file:' + __filename).href : typeof document === 'undefined' ? location.href : (document.currentScript && document.currentScript.src || new URL('simplemenu.js', document.baseURI).href)).lastIndexOf('/') + 1);
+	    }
+
+	    return path;
+	  };
+
+	  const isBefore = (a, b) => {
+	    var all = document.getElementsByTagName('*');
+
+	    for (var i = 0; i < all.length; ++i) {
+	      if (all[i] === a) return true;else if (all[i] === b) return false;
+	    }
+	  };
+
+	  const isStack = section => {
+	    let isStack = false;
+
+	    for (let i = 0; i < section.childNodes.length; i++) {
+	      if (section.childNodes[i].tagName == "SECTION") {
+	        isStack = true;
+	        break;
+	      }
+	    }
+
+	    return isStack;
+	  };
+
+	  const createNode = thehtml => {
+	    const fragment = document.createRange().createContextualFragment(thehtml);
+	    return fragment.firstElementChild;
+	  };
+
+	  const loadStyle = (url, type, callback) => {
+	    let head = document.querySelector('head');
+	    let style = document.createElement('link');
+	    style.rel = 'stylesheet';
+	    style.href = url;
+
+	    let finish = () => {
+	      if (typeof callback === 'function') {
+	        callback.call();
+	        callback = null;
+	      }
+	    };
+
+	    style.onload = finish;
+
+	    style.onreadystatechange = function () {
+	      if (this.readyState === 'loaded') {
+	        finish();
+	      }
+	    };
+
+	    head.appendChild(style);
+	  };
+
+	  const checkOccurrence = (array, element) => {
+	    let counter = 0;
+
+	    for (let i = 0; i <= array.length; i++) {
+	      if (array[i] == element) {
+	        counter++;
+	      }
+	    }
+
+	    return counter;
+	  };
+
+	  const menuArray = () => {
+	    const matchString = vars.matchString;
+	    let menulist = selectionArray(vars.viewport, `.${options.menuclass}`) ? selectionArray(vars.viewport, `.${options.menuclass}`) : [];
+	    let automenus = [];
+	    let manualmenus = [];
+
+	    if (menulist.length) {
+	      menulist.forEach(menu => {
+	        if (menu.getElementsByTagName('li').length < 1) {
+	          menu.setAttribute('data-simplemenu-auto', '');
+	          automenus.push(menu);
+	        } else {
+	          if (options.selectby == "data-name" || options.selectby == "name") {
+	            let existingListItems = selectionArray(menu, `.${options.menuclass} ${options.activeelement}`);
+	            existingListItems.forEach(listItem => {
+	              if (!listItem.dataset[matchString]) {
+	                let content = listItem.textContent || listItem.querySelector('a').textContent;
+	                listItem.setAttribute(`data-${matchString}`, content);
+	              }
+	            });
+	          }
+
+	          manualmenus.push(menu);
+	        }
+	      });
+	      return {
+	        automenus: automenus,
+	        manualmenus: manualmenus
+	      };
+	    } else {
+	      return false;
+	    }
+	  };
+
+	  const setScale = revealScale => {
+	    let totalScale = revealScale * vars.userScale;
+	    vars.viewport.style.setProperty('--simplemenu-scale', totalScale.toFixed(3));
+	  };
+
+	  const moveRevealUI = (curUiEl, newUiEl) => {
+	    let newUiElClassList = newUiEl.classList;
+	    newUiEl.parentNode.replaceChild(curUiEl, newUiEl);
+	    curUiEl.classList = newUiElClassList;
+	  };
+
+	  const getRevealUI = () => {
+	    let revealUIs = ['controls', 'slide-number'];
+	    revealUIs.forEach(uielement => {
+	      let curUiEl = vars.deck.getRevealElement().querySelector(`.reveal > .${uielement}`);
+	      let newUiEl = vars.deck.getRevealElement().querySelector(`.reveal > * .${uielement}`);
+
+	      if (curUiEl && newUiEl) {
+	        moveRevealUI(curUiEl, newUiEl);
+	      }
+	    });
+	  };
+
+	  function copyDataAttributes(source, target) {
+	    [...source.attributes].filter(attr => attr.nodeName.indexOf('data') > -1).forEach(attr => {
+	      target.setAttribute(attr.nodeName, attr.nodeValue);
+	    });
+	  }
+
+	  const prepareSlides = () => {
+	    debugLog("Preparing slides");
+	    sections.all = selectionArray(vars.viewport, "section");
+	    sections.all.forEach(section => {
+	      // In Markdown environments, setting a data-name of a stack is not directly possible. 
+	      // Satting a data-stack-name on the first child solves this.
+	      if (!section.parentNode.dataset.name && section.dataset && section.dataset.stackName) {
+	        section.parentNode.dataset.name = section.dataset.stackName;
+	      } // If a section has a data-sm='none', it will also remove the data-name.
+
+
+	      if (section.dataset && section.dataset[vars.matchString] && section.dataset[vars.matchString] == "false" && section.dataset.name) {
+	        delete section.dataset.name;
+	      }
+	    }); // Get all of the kinds of sections
+
+	    sections.top = sections.all.filter(section => section.parentNode.classList.contains('slides') && !(section.dataset[vars.matchString] && section.dataset[vars.matchString] == "false"));
+	    sections.named = sections.top.filter(section => section.dataset.name || section.getAttribute('name'));
+	    sections.namedvisible = sections.named.filter(section => section.dataset.visibility != "hidden"); // Go through all the named sections
+
+	    let namedsectionMatches = [];
+	    sections.named.forEach(namedsection => {
+	      // The 'name' attribute is also allowed. 
+	      let matchName = namedsection.dataset.name || namedsection.getAttribute('name'); // Named sections can have the same name, but should then be differentiated.
+
+	      namedsectionMatches.push(matchName);
+	      let dupsBefore = matchName && checkOccurrence(namedsectionMatches, matchName) > 1 ? `-${checkOccurrence(namedsectionMatches, matchName)}` : null;
+	      let match = dupsBefore ? matchName + dupsBefore : matchName; // We set the name of the match as a data-attribute
+
+	      namedsection.setAttribute(`data-${vars.matchString}`, match); // If the (named) section is not a stack and does not have an ID, we need to give it one.
+
+	      if (!isStack(namedsection) && !namedsection.id) {
+	        // Note: Quarto will already have assigned an ID, but it may also have been done manually.
+	        namedsection.id = match.toLowerCase().replace(/\W/g, '');
+	      } else if (isStack(namedsection)) {
+	        // Find the first (visible) section inside a stack.
+	        let allsects = selectionArray(namedsection, `section`);
+	        let allVisibleSects = allsects.filter(section => section.dataset.visibility != "hidden");
+	        let firstChildSection = allVisibleSects[0];
+
+	        if (firstChildSection && !firstChildSection.id) {
+	          firstChildSection.id = match.toLowerCase().replace(/\W/g, '');
+
+	          if (namedsection.id == firstChildSection.id) {
+	            namedsection.removeAttribute('id');
+	          }
+	        }
+	      }
+	    });
+	    let currentMatch = null;
+	    let currentid = null; // Get all the sections that are actually slides
+
+	    sections.regular = sections.all.filter(section => !isStack(section) && section.dataset.visibility != "hidden"); // Go through all the sections
+
+	    sections.regular.forEach((section, i) => {
+	      // Filling an array with the needed comparison information
+	      let isChildSection = isStack(section.parentNode) && section.parentNode.tagName == "SECTION";
+	      let theSection = isChildSection ? section.parentNode : section;
+	      let dataname = theSection.dataset.name;
+	      let name = theSection.getAttribute(`name`);
+	      let dataintl = theSection.getAttribute(vars.langattribute) ? theSection.getAttribute(vars.langattribute) : null;
+	      let parentid = section.parentNode.id ? section.parentNode.id : null;
+	      let id = section.id ? section.id : isChildSection ? parentid : null;
+	      let match = theSection.dataset[vars.matchString];
+
+	      if (match) {
+	        currentMatch = match;
+	      }
+
+	      if (id || match == "false") {
+	        currentid = i;
+	      }
+
+	      if (options.flat) {
+	        if (match != "false") {
+	          match = currentMatch;
+	        }
+	      }
+
+	      if (match == "false") {
+	        match = null;
+	      }
+
+	      if (dataname == "false") {
+	        dataname = null;
+	      }
+
+	      let sectionObject = {
+	        index: i,
+	        ...(section && {
+	          section
+	        }),
+	        ...(dataname && {
+	          dataname
+	        }),
+	        ...(name && {
+	          name
+	        }),
+	        ...(id && {
+	          id
+	        }),
+	        ...(match && {
+	          match
+	        }),
+	        ...(currentid && {
+	          currentid
+	        }),
+	        ...(dataintl && {
+	          dataintl
+	        })
+	      };
+	      mainArray.push(sectionObject);
+	    });
+	  };
+
+	  const prepareMenubars = () => {
+	    debugLog("Preparing menubars");
+	    let menubars = selectionArray(vars.viewport, `.${options.menubarclass}`) ? selectionArray(vars.viewport, `.${options.menubarclass}`) : [];
+
+	    if (options.barhtml.header) {
+	      // Generate header menubar
+	      let bar = createNode(options.barhtml.header);
+	      menubars.push(bar);
+	      vars.slides.before(bar);
+	    }
+
+	    if (options.barhtml.footer) {
+	      // Generate footer menubar
+	      let bar = createNode(options.barhtml.footer);
+	      menubars.push(bar);
+	      vars.slides.after(bar);
+	    }
+
+	    if (menubars.length) {
+	      // If menubar (pre-existing or just added):
+	      setScale(vars.deck.getScale());
+	      menubars.forEach((menubar, i) => {
+	        let barLocation = isBefore(menubar, vars.slides) ? "top" : "bottom";
+	        menubar.classList.add(barLocation);
+
+	        if (!menubar.id) {
+	          menubar.id = `${options.menubarclass}${barLocation}`;
+	        }
+
+	        menubar.classList.add("ready");
+	      });
+	      vars.menubars = menubars;
+	    } else {
+	      console.log("There are no menubars. You can still use Simplemenu to populate empty menus like in an Agenda or Table Of Contents.");
+	    }
+	  };
+
+	  const prepareMenus = () => {
+	    debugLog("Preparing menus");
+	    let menus = menuArray();
+
+	    if (!menus || menus && !menus.automenus) {
+	      console.log("There are no menus. Please add one or more menus manually or through the 'barhtml' option.");
+	      return;
+	    }
+
+	    if (menus.automenus.length >= 1 && sections.namedvisible.length >= 1) {
+	      // There are empty menus. Autofill them.
+	      let idArray = [];
+	      const autoMenuLinks = sections.namedvisible.map(section => {
+	        let match = section.dataset[vars.matchString];
+	        let name = section.dataset.name || section.getAttribute(`name`) || section.id;
+	        let id = section.id || name.toLowerCase().replace(/\W/g, '');
+	        idArray.push(id);
+
+	        if (vars.quarto) {
+	          id = mainArray.find(item => item.match === match).id;
+	        }
+
+	        let duplicatesBefore = checkOccurrence(idArray, id) > 1 ? `-${checkOccurrence(idArray, id)}` : '';
+	        let href = vars.quarto ? id : id + duplicatesBefore;
+	        let smmatchString = ` data-${vars.matchString}="${match}"`;
+	        let nameString = section.getAttribute(`name`) ? ` name="${section.getAttribute(`name`)}"` : '';
+	        let intlString = section.getAttribute(vars.langattribute) ? ` ${vars.langattribute}="${section.getAttribute(vars.langattribute)}"` : '';
+	        return `<li><a href="#/${href}"${intlString}${nameString}${smmatchString}>${name}</a></li>`;
+	      }).reduce((combinedHTML, itemHTML) => {
+	        let orderedHTML = vars.rtl ? itemHTML + combinedHTML : combinedHTML + itemHTML;
+	        return orderedHTML;
+	      });
+	      menus.automenus.forEach(automenu => {
+	        automenu.innerHTML = autoMenuLinks;
+	      });
+	      autoListItems = menus.automenus.map(menu => Array.from(menu.querySelectorAll(options.activeelement))).flat();
+	    }
+
+	    if (menus.manualmenus.length >= 1) {
+	      // There are pre-existing menus. Fix link to ID if needed.
+	      // Only get the listitems
+	      manualListItems = menus.manualmenus.map(menu => Array.from(menu.querySelectorAll(options.activeelement))).flat();
+	      manualListItems.forEach(listItem => {
+	        // Get the anchorlinks
+	        let linker = listItem.tagName == "a" ? listItem : listItem.querySelector('a');
+	        let linkhref = linker.getAttribute('href');
+
+	        if (linkhref === "#") {
+	          let newLink = listItem.dataset[vars.matchString].toLowerCase().replace(/\W/g, '');
+	          linker.href = `#/${newLink}`;
+	        }
+	      });
+	    }
+	  };
+
+	  const preparePrint = () => {
+	    const urlParams = new URLSearchParams(window.location.search);
+	    const hasPrintParam = urlParams.has('print-pdf');
+
+	    if (hasPrintParam) {
+	      mainArray.forEach(item => {
+	        let printSection = item.section;
+	        let datainfo = document.createElement("div");
+	        datainfo.classList.add("datainfo");
+	        copyDataAttributes(printSection, datainfo);
+	        let moreData = ['match', 'name', 'dataname', 'currentid', 'id', 'dataintl'];
+	        moreData.forEach(moreDataItem => {
+	          if (item[moreDataItem]) {
+	            datainfo.dataset[moreDataItem] = item[moreDataItem];
+	          }
+	        });
+	        printSection.appendChild(datainfo);
+	      });
+	    }
+	  };
+
+	  const prepare = resolve => {
+	    prepareSlides();
+	    prepareMenubars();
+	    prepareMenus();
+	    preparePrint();
+	    return setTimeout(resolve, 0);
+	  };
+
+	  const compare = (listItem, section) => {
+	    let menukind = listItem.parentNode.hasAttribute('data-simplemenu-auto') ? "auto" : "manual";
+	    let sectionmatch = section.match ? section.match : null;
+
+	    if (menukind == "manual") {
+	      if (options.selectby == "id") {
+	        sectionmatch = section.id ? section.id : section.currentid ? mainArray[section.currentid].id : null;
+	      } else if (options.selectby == "name") {
+	        sectionmatch = section.name;
+	      } else {
+	        sectionmatch = section.dataname;
+	      }
+	    }
+
+	    if (sectionmatch) {
+	      let menumatch = listItem.dataset[vars.matchString] || listItem.querySelector('a').dataset[vars.matchString];
+
+	      if (options.selectby == "id" && menukind == "manual") {
+	        let href = listItem.href || listItem.querySelector('a').href;
+	        let lastHref = href ? href.substring(href.lastIndexOf("/") + 1) : '';
+	        menumatch = lastHref;
+	      }
+
+	      if (options.selectby == "data-name" && menukind == "manual") {
+	        sectionmatch = section.dataname ? section.dataname : null;
+	      }
+
+	      if (menumatch && menumatch == sectionmatch) {
+	        listItem.classList.add(options.activeclass);
+	      } else {
+	        listItem.classList.remove(options.activeclass);
+	      }
+	    } else {
+	      listItem.classList.remove(options.activeclass);
+	    }
+	  };
+
+	  const checkSlidesNormal = event => {
+	    const index = sections.regular.indexOf(event.currentSlide);
+	    let section = mainArray[index];
+	    autoListItems.filter(listItem => {
+	      compare(listItem, section);
+	    });
+	    manualListItems.filter(listItem => {
+	      compare(listItem, section);
+	    });
+	  };
+
+	  const checkSlidesPDF = event => {
+	    let pdfPages = selectionArray(vars.viewport, '.slides .pdf-page'); // Check if any menubar has a slide number
+
+	    let anyMenubarHasSlidenumber = false;
+
+	    if (vars.menubars) {
+	      vars.menubars.forEach(menubar => {
+	        anyMenubarHasSlidenumber = !!menubar.getElementsByClassName("slide-number");
+	      });
+	    }
+
+	    pdfPages.forEach(pdfPage => {
+	      // The original section has gone, so we rebuild it with the saved data-attributes
+	      let datainfo = pdfPage.getElementsByClassName("datainfo")[0];
+	      let section = {};
+	      section.name = datainfo.dataset.name;
+	      section.dataname = datainfo.dataset.dataname;
+	      section.currentid = datainfo.dataset.currentid;
+	      section.match = datainfo.dataset.match;
+	      section.id = datainfo.dataset.id;
+
+	      if (datainfo.dataset.state) {
+	        let newClasses = datainfo.dataset.state.split(" ");
+	        newClasses.forEach(newClass => {
+	          pdfPage.classList.add(newClass);
+	          let vp = vars.deck.getRevealElement().closest(".reveal-viewport");
+	          vp.classList.remove(newClass);
+	        });
+	      } // If any menubar has a slide number, turn the original one on this slide off
+
+
+	      if (anyMenubarHasSlidenumber && pdfPage.getElementsByClassName("slide-number").length > 0) {
+	        pdfPage.getElementsByClassName("slide-number")[0].style.display = "none";
+	      }
+
+	      if (vars.menubars) {
+	        vars.menubars.forEach(menubar => {
+	          let bar = menubar.cloneNode(true);
+	          pdfPage.appendChild(bar);
+	          let listItems = selectionArray(bar, `.${options.menuclass} ${options.activeelement}`);
+	          listItems.forEach(listItem => {
+	            compare(listItem, section);
+	          }); // If there is a slidenumber in the menu,
+
+	          let newSN = pdfPage.querySelector(`.${options.menubarclass} .slide-number`);
+	          let oldSN = pdfPage.querySelector(`:scope > .slide-number`);
+
+	          if (newSN && oldSN) {
+	            // ...then fill it with the current (total) slidenumber.
+	            newSN.textContent = oldSN.textContent;
+	          }
+	        });
+	      }
+	    });
+
+	    if (vars.menubars) {
+	      vars.menubars.forEach(menubar => {
+	        menubar.parentNode.removeChild(menubar);
+	      });
+	    }
+	  };
+
+	  const chapterize = event => {
+	    if (event && event.type == "ready") {
+	      debugLog(mainArray);
+	      getRevealUI();
+	    }
+
+	    if (event && (event.type == "ready" || event.type == "slidechanged")) {
+	      checkSlidesNormal(event);
+	    }
+
+	    if (event && event.type == "pdf-ready") {
+	      checkSlidesPDF();
+	    }
+	  };
+
+	  const simpleMenu = (deck, options, es5Filename) => {
+	    deck.configure({
+	      hash: true
+	    });
+	    vars.deck = deck;
+	    vars.viewport = deck.getRevealElement().tagName == "BODY" ? document : deck.getRevealElement();
+	    vars.slides = deck.getSlidesElement();
+	    vars.langattribute = deck.getConfig().internation ? deck.getConfig().internation.langattribute ? deck.getConfig().internation.langattribute : "data-i18n" : false;
+	    vars.rtl = deck.getConfig().rtl;
+	    vars.quarto = document.querySelector('[name=generator]') && document.querySelector('[name=generator]').content.includes("quarto") ? true : false;
+	    vars.matchString = "sm";
+	    vars.userScale = options.scale;
+	    deck.addEventListener('ready', chapterize, false);
+	    deck.addEventListener('slidechanged', chapterize, false);
+	    deck.addEventListener('pdf-ready', chapterize, false);
+	    deck.addEventListener('resize', _ref => {
+	      let {
+	        scale
+	      } = _ref;
+	      return setScale(scale);
+	    }, false);
+	    const SimplemenuStylePath = options.csspath ? options.csspath : `${pluginPath(es5Filename)}simplemenu.css` || 'plugin/simplemenu/simplemenu.css';
+	    return new Promise(resolve => {
+	      if (options.csspath === false) {
+	        return prepare(resolve);
+	      } else {
+	        loadStyle(SimplemenuStylePath, 'stylesheet', async () => prepare(resolve));
+	      }
+	    });
+	  };
+
+	  const init = deck => {
+	    let defaultOptions = {
+	      menubarclass: 'menubar',
+	      menuclass: 'menu',
+	      activeclass: 'active',
+	      activeelement: 'li',
+	      selectby: 'id',
+	      barhtml: {
+	        header: '',
+	        footer: ''
+	      },
+	      flat: false,
+	      scale: 0.67,
+	      csspath: ''
+	    };
+	    options = deck.getConfig().simplemenu || {};
+	    options = mergeDeep(defaultOptions, options);
+	    let wronginputs = false;
+	    let warning = '';
+
+	    if (options.selectby !== "id" && options.selectby !== "data-name" && options.selectby !== "name") {
+	      wronginputs = true;
+	      warning = 'The selectby option can be only "id",  "data-name" or "name".';
+	    }
+
+	    if (wronginputs) {
+	      console.log('Simplemenu did not load:');
+	      console.log(warning);
+	      return false;
+	    }
+
+	    return simpleMenu(deck, options, "simplemenu.js");
+	  };
+
+	  return {
+	    id: 'simplemenu',
+	    init: init
+	  };
+	};
+
+	return Plugin;
+
+}));

_extensions/mloubout/critic-markup/_extension.yml

@@ -0,0 +1,8 @@
+title: Critic-markup
+author: mloubout
+version: 1.0.3
+quarto-required: ">=1.2.198"
+contributes:
+  filters:
+    - critic-markup.lua
+

_extensions/mloubout/critic-markup/critic-markup.lua

@@ -0,0 +1,174 @@
+
+local maybesubs = false
+local stk_end = false
+
+add = pandoc.RawInline('html', "<ins>")
+adde = pandoc.RawInline('html', "</ins>")
+
+rm = pandoc.RawInline('html', "<del>")
+rme = pandoc.RawInline('html', "</del>")
+rmeadd = pandoc.RawInline('html', "</del><ins>")
+
+mark = pandoc.RawInline('html', "<mark>")
+marke = pandoc.RawInline('html', "</mark>")
+
+comm = pandoc.RawInline('html', [[<span class="critic comment">]])
+comme = pandoc.RawInline('html', "</span>")
+
+ruless = {['{%+%+']=add, ['{\u{2013}']=rm, ['{==']=mark, ['{>>']=comm, ['{~~']=rm,
+          ['%+%+}']=adde, ['\u{2013}}']=rme, ['==}']=marke, ['<<}']=comme, ['~~}']=rme, ['~>']=rmeadd}
+
+-- Strikeout before/after
+st_b = '{'
+st_e = '}'
+
+local scriptcode = [[
+
+<div id="criticnav">
+<ul>
+<li id="markup-button">Markup</li>
+<li id="original-button">Original</li>
+<li id="edited-button">Edited</li>
+</ul>
+</div>
+
+<script type="text/javascript">
+  function critic() {
+
+      $('.content').addClass('markup');
+      $('#markup-button').addClass('active');
+      $('ins.break').unwrap();
+      $('span.critic.comment').wrap('<span class="popoverc" /></span>');
+      $('span.critic.comment').before('&#8225;');
+  }
+
+  function original() {
+      $('#original-button').addClass('active');
+      $('#edited-button').removeClass('active');
+      $('#markup-button').removeClass('active');
+
+      $('.content').addClass('original');
+      $('.content').removeClass('edited');
+      $('.content').removeClass('markup');
+  }
+
+  function edited() {
+      $('#original-button').removeClass('active');
+      $('#edited-button').addClass('active');
+      $('#markup-button').removeClass('active');
+
+      $('.content').removeClass('original');
+      $('.content').addClass('edited');
+      $('.content').removeClass('markup');
+  } 
+
+  function markup() {
+      $('#original-button').removeClass('active');
+      $('#edited-button').removeClass('active');
+      $('#markup-button').addClass('active');
+
+      $('.content').removeClass('original');
+      $('.content').removeClass('edited');
+      $('.content').addClass('markup');
+  }
+
+  var o = document.getElementById("original-button");
+  var e = document.getElementById("edited-button");
+  var m = document.getElementById("markup-button");
+
+  window.onload = critic();
+  o.onclick = original;
+  e.onclick = edited;
+  m.onclick = markup;
+</script>
+]]
+
+function cirtiblock(blocks, k, v)
+  local newblock = {}
+  for ti,t in pairs(blocks) do
+    if t.text then
+      i, j = t.text:find(k)
+      if i then
+        newblock[#newblock + 1] = pandoc.Str(t.text:sub(1, i-1))
+        newblock[#newblock + 1] = v
+        newblock[#newblock + 1] = pandoc.Str(t.text:sub(j+1, t.text:len()))
+      else
+        newblock[#newblock + 1] = t
+      end
+    else
+      newblock[#newblock + 1] = t
+    end
+  end
+  return newblock
+end
+
+
+if FORMAT:match 'html' then
+
+  function Str (el)
+    local replaced = {el}
+    -- Check for standard substitutions
+    for k,v in pairs(ruless) do
+      replaced = cirtiblock(replaced, k, v)
+    end
+    return replaced
+  end
+
+  function Strikeout (strk)
+    return strk.content
+  end
+
+  -- Check Inlines for Strikeout (~~) and remove brackets before/after for replacement
+  function Inlines (inlines)
+    for i = #inlines-1,2,-1 do
+      if inlines[i] and inlines[i].t == 'Strikeout' and inlines[i+1] then
+        if inlines[i+1].t == 'Str' then
+          if inlines[i+1].text == st_e then
+            inlines[i+1] = adde
+          end
+        end
+      end
+      if inlines[i] and inlines[i].t == 'Strikeout' and inlines[i-1] then
+        if inlines[i-1].t == 'Str' then
+          if inlines[i-1].text == st_b then
+            inlines[i-1] = rm
+          end
+        end
+      end
+    end
+    return inlines
+  end
+end
+
+--- From the lightbox filter
+local function add_header_includes(meta, blocks)
+
+  local header_includes = pandoc.List(blocks)
+
+  -- add any exisiting meta['header-includes']
+  -- it could be a MetaList or a single String
+  if meta['header-includes'] then
+    if type(meta['header-includes']) == 'List' then
+      header_includes:extend(meta['header-includes'])
+    else
+      header_includes:insert(meta['header-includes'])
+    end
+  end
+
+  meta['header-includes'] = pandoc.MetaBlocks(header_includes)
+  return meta
+end
+
+
+function criticheader (meta)
+  quarto.doc.add_html_dependency({
+    name = 'critic',
+    scripts = {'critic.min.js'},
+    stylesheets = {'critic.css'}
+  })
+  -- inject the rendering code
+  quarto.doc.include_text("after-body", scriptcode)
+end
+
+-- All pass with Meta first
+return {{Meta = criticheader}, {Inlines = Inlines}, {Strikeout = Strikeout}, {Str = Str}}

_extensions/mloubout/critic-markup/critic.css

@@ -0,0 +1,131 @@
+.fullcontent {
+    padding-top: 30px !important;
+}
+
+#criticnav {
+    position: fixed;
+    z-index: 1100;
+    top: 0;
+    left: 0;
+    width: 100%;
+    border-bottom: solid 1px #696f75;
+    margin: 0;
+    padding: 0;
+    background-color: rgba(255,255,255,0.95);
+    color: #696f75;
+    font-size: 14px;
+    font-family: "Helvetica Neue", helvetica, arial, sans-serif !important
+}
+
+#criticnav ul {
+    list-style-type: none;
+    width: 90%;
+    margin: 0 auto;
+    padding: 0
+}
+
+#criticnav ul li {
+    display: block;
+    width: 15%;
+    min-width: 100px;
+    text-align: center;
+    padding: 5px 0 3px !important;
+    margin: 5px 2px !important;
+    line-height: 1em;
+    float: left;
+    text-transform: uppercase;
+    cursor: pointer;
+    -webkit-user-select: none;
+    border-radius: 20px;
+    border: 1px solid rgba(255,255,255,0);
+    color: #777 !important
+}
+
+#criticnav ul li:before {
+    content: none !important
+}
+
+#criticnav ul li.active {
+    border: 1px solid #696f75
+}
+
+.original del {
+    
+        text-decoration: none;
+}	
+
+.original ins,
+.original span.popoverc,
+.original ins.break {
+    display: none;
+}
+
+.edited ins {
+    
+        text-decoration: none;
+}	
+
+.edited del,
+.edited span.popoverc,
+.edited ins.break {
+    display: none;
+}
+
+.original mark,
+.edited mark {
+    background-color: transparent;
+}
+
+.markup mark {
+    background-color: #fffd38;
+    text-decoration: none;
+}
+
+.markup del {
+    background-color: rgba(183,47,47,0.4);
+    text-decoration: none;
+}
+
+.markup ins {
+    background-color: rgba(152,200,86,0.4);
+    text-decoration: none;
+}
+
+.markup ins.break {
+    display: block;
+    line-height: 2px;
+    padding: 0 !important;
+    margin: 0 !important;
+}
+
+.markup ins.break span {
+    line-height: 1.5em;
+}
+
+.markup .popoverc {
+    background-color: #e5b000;
+    color: #fff;
+}
+
+.markup .popoverc .critic.comment {
+    display: none;
+}
+
+.markup .popoverc:hover span.critic.comment {
+    display: block;
+    position: absolute;
+    width: 200px;
+    left: 30%;
+    font-size: 0.8em; 
+    color: #ccc;
+    background-color: #333;
+    z-index: 10;
+    padding: 0.5em 1em;
+    border-radius: 0.5em;
+}
+
+@media print {
+    #criticnav {
+        display: none !important
+    }
+}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

_extensions/quarto-ext/pointer/_extension.yml

@@ -0,0 +1,15 @@
+title: Pointer
+author: Posit Software, PBC
+version: 0.1.0
+quarto-required: ">=1.2.198"
+contributes:
+  revealjs-plugins:
+    - name: RevealPointer
+      script: pointer.js
+      stylesheet: pointer.css
+      config:
+        pointer:
+          key: "q"
+          color: "red"
+          pointerSize: 16
+          alwaysVisible: false

_extensions/quarto-ext/pointer/pointer.css

@@ -0,0 +1 @@
+.cursor-dot,.cursor-dot-outline{pointer-events:none;position:absolute;top:0;left:0;border-radius:50%;opacity:0;transform:translate(-50%,-50%);transition:opacity 0.3s ease-in-out,transform 0.3s ease-in-out;}.cursor-dot{width:12px;height:12px;background-color:red;z-index:99;}.no-cursor{cursor:none;}.no-cursor a,.no-cursor div,.no-cursor span{cursor:none;}

_extensions/quarto-ext/pointer/pointer.js

@@ -0,0 +1 @@
+var RevealPointer=function(){"use strict";var e={backspace:8,tab:9,enter:13,shift:16,ctrl:17,alt:18,pausebreak:19,capslock:20,esc:27,space:32,pageup:33,pagedown:34,end:35,home:36,leftarrow:37,uparrow:38,rightarrow:39,downarrow:40,insert:45,delete:46,0:48,1:49,2:50,3:51,4:52,5:53,6:54,7:55,8:56,9:57,a:65,b:66,c:67,d:68,e:69,f:70,g:71,h:72,i:73,j:74,k:75,l:76,m:77,n:78,o:79,p:80,q:81,r:82,s:83,t:84,u:85,v:86,w:87,x:88,y:89,z:90,leftwindowkey:91,rightwindowkey:92,selectkey:93,numpad0:96,numpad1:97,numpad2:98,numpad3:99,numpad4:100,numpad5:101,numpad6:102,numpad7:103,numpad8:104,numpad9:105,multiply:106,add:107,subtract:109,decimalpoint:110,divide:111,f1:112,f2:113,f3:114,f4:115,f5:116,f6:117,f7:118,f8:119,f9:120,f10:121,f11:122,f12:123,numlock:144,scrolllock:145,semicolon:186,equalsign:187,comma:188,dash:189,period:190,forwardslash:191,graveaccent:192,openbracket:219,backslash:220,closebracket:221,singlequote:222};return function(){var t={},o=!1,a=null,n={x:0,y:0,isVisible:!1},i={x:0,y:0,scale:1};function l(o){var a;null==(t=o.pointer||{}).key?t.key="q":t.key=t.key.toLowerCase(),null!=t.pointerSize&&"number"==typeof t.pointerSize||(t.pointerSize=12),null!=t.tailLength&&"number"==typeof t.tailLength||(t.tailLength=10),null!=t.color&&"string"==typeof t.color||(t.color="red"),null!=t.alwaysVisible&&"boolean"==typeof t.alwaysVisible||(t.alwaysVisible=!1),t.keyCode=(a=t.key,e[a])}function s(){a.style.top="".concat((n.y-i.y)/i.scale,"px"),a.style.left="".concat((n.x-i.x)/i.scale,"px"),n.isVisible?a.style.opacity="0.8":a.style.opacity="0",1!==i.scale?(a.style.width="".concat(t.pointerSize/i.scale,"px"),a.style.height="".concat(t.pointerSize/i.scale,"px")):(a.style.width="".concat(t.pointerSize,"px"),a.style.height="".concat(t.pointerSize,"px"))}function c(e){n.x=e.pageX,n.y=e.pageY;var t=document.body.style.transform;""!==t?(i.x=Number.parseInt(/translate\((.*)px,/gm.exec(t)[1]),i.y=Number.parseInt(/px,\s(.*)px\)/gm.exec(t)[1]),i.scale=Number.parseFloat(/scale\((.)\)/gm.exec(t)[1])):(i.x=0,i.y=0,i.scale=1),requestAnimationFrame(s)}function r(){(o=!o)?(document.addEventListener("mousemove",c),document.body.classList.add("no-cursor"),n.isVisible=!0):(document.removeEventListener("mousemove",c),document.body.classList.remove("no-cursor"),n.isVisible=!1,requestAnimationFrame(s))}return{id:"pointer",init:function(e){var o;l(e.getConfig()),t.alwaysVisible?r():e.addKeyBinding({keyCode:t.keyCode,key:t.key},(function(){r()})),(o=document.createElement("div")).className="cursor-dot",o.style.width="".concat(t.pointerSize,"px"),o.style.height="".concat(t.pointerSize,"px"),o.style.backgroundColor=t.color,t.alwaysVisible&&(o.style.opacity="0.8"),document.body.appendChild(o),a=o}}}}();

_extensions/quarto-journals/elsevier/_extension.yml

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

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

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

_extensions/quarto-journals/elsevier/elsevier.lua

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

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

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

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

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

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

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

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

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

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

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

_extensions/shafayetShafee/reveal-header/_extension.yml

@@ -0,0 +1,8 @@
+title: Reveal-header
+author: Shafayet Khan Shafee
+version: 1.2.6
+quarto-required: ">=1.2.0"
+contributes:
+  filters:
+    - reveal-header.lua
+

_extensions/shafayetShafee/reveal-header/resources/css/add_header.css

@@ -0,0 +1,67 @@
+/*@import url('https://fonts.googleapis.com/css2?family=Source+Serif+4:opsz@8..60&display=swap');*/
+
+
+:root {
+  --header-font-size: max(10px, 1.4vw);
+  --header-font-color: #898E8B;
+  --header-margin: 0px 0px 0px 0px;
+  /*--header-font-family: 'Source Serif 4', serif;*/
+}
+
+.reveal .reveal-header {
+  top: 0;
+  margin: 3.2px 0px 2px 0px;
+  width: 100%;
+  position: fixed;
+  z-index: 5;
+  /*font-family: var(--header-font-family);*/
+}
+
+.reveal .reveal-header p {
+  color: var(--header-font-color);
+  text-align: center;
+  margin: var(--header-margin);
+  font-size: var(--header-font-size);
+}
+
+.reveal-header .sc-title p,
+.reveal-header .sb-title p {
+  font-size: max(10px, 1.45vw);
+  filter: brightness(0.85);
+}
+
+.reveal-header .sc-title p { float: left; margin-left: 0.5vw}
+.reveal-header .sb-title p { float: right; margin-right: 0.5vw}
+.reveal-header.no-logo .sc-title p {margin-left: 6vw}
+
+
+.reveal .header-logo img {
+  margin: var(--header-margin);
+  padding-left: 1vw;
+  padding-top: 5px;
+  height: 100%;
+  width: auto;
+  max-width: max(60px, 10vw);
+  max-height: max(60px, 10vh);
+}
+
+
+/* .reveal .slides { margin-top: 3vh !important;} */
+.inverse-header { color: #c5d7ce !important;}
+
+
+div.slides section:not(.title-slide):not(#title-slide):not(.stack) {
+  padding-top: 1em;
+}
+
+/* On screens that are 600px or less*/
+@media screen and (max-width: 600px) {
+  .reveal .header-logo img {
+    padding-top: 0px;
+    margin: 0px 0px 5px 0px;
+  }
+
+  .reveal-header .sc-title p { margin-left: 1vw; }
+  .reveal-header.no-logo .sc-title p {margin-left: 2vw; }
+  div.reveal.has-logo div.slide-number { font-size: 10px; }
+}

_extensions/shafayetShafee/reveal-header/resources/css/grid_htext.css

@@ -0,0 +1,50 @@
+div.header-logo { grid-area: logo;}
+
+.no-logo div.header-logo { grid-area: unset !important; }
+
+div.sc-title { grid-area: sc;}
+div.sb-title { grid-area: sb;}
+div.header-text { grid-area: ht;}
+div.reveal.has-logo div.slide-number {
+  grid-area: sn;
+  top: unset !important;
+  right: unset !important;
+  bottom: unset !important;
+  padding: 5px 5px 5px 5px;
+  justify-self: center;
+  /*font-family: var(--header-font-family);*/
+  font-size: 18px;
+}
+
+div.reveal-header {
+  display: grid;
+  grid-template-columns: 0.4fr 0.4fr 2fr 0.4fr 0.3fr;
+  grid-template-areas: "logo sc ht sb sn";
+  column-gap: 10px;
+  align-items: center;
+}
+
+div.reveal-header.no-logo {
+  grid-template-columns: 0.7fr 2fr 0.7fr 0.05fr;
+  grid-template-areas: "sc ht sb sn";
+  margin-top: 1.5vh;
+}
+
+
+/* On screens that are 600px or less*/
+@media screen and (max-width: 600px) {
+
+  div.reveal-header {
+    grid-template-columns: 0.4fr 0.4fr 1fr 0.4fr 0.3fr;
+    grid-template-areas: "logo sc ht sb sn";
+  }
+
+  div.reveal-header.no-logo {
+    grid-template-columns: 0.7fr 1fr 0.7fr 0.05fr;
+    grid-template-areas: "sc ht sb sn";
+  }
+  
+  .reveal-header .sc-title p { margin-left: 1vw; }
+  .reveal-header.no-logo .sc-title p {margin-left: 2vw; }
+  div.reveal.has-logo div.slide-number { font-size: 10px; }
+}

_extensions/shafayetShafee/reveal-header/resources/css/grid_no_htext.css

@@ -0,0 +1,50 @@
+div.header-logo { grid-area: logo;}
+
+.no-logo div.header-logo { grid-area: unset !important; }
+
+div.sc-title { grid-area: sc;}
+div.header-text { grid-area: ht;}
+div.sb-title { grid-area: sb;}
+div.reveal.has-logo div.slide-number {
+  grid-area: sn;
+  top: unset !important;
+  right: unset !important;
+  bottom: unset !important;
+  padding: 5px 5px 5px 5px;
+  justify-self: center;
+  /*font-family: var(--header-font-family);*/
+  font-size: 18px;
+}
+
+div.reveal-header {
+  display: grid;
+  grid-template-columns: 0.35fr 1.2fr 0.1fr 1.2fr 0.2fr;
+  grid-template-areas: "logo sc ht sb sn";
+  column-gap: 10px;
+  align-items: center;
+}
+
+div.reveal-header.no-logo {
+  grid-template-columns: 1fr 0.1fr 1fr 0.15fr;
+  grid-template-areas: "sc ht sb sn";
+  margin-top: 1.5vh;
+}
+
+
+/* On screens that are 600px or less*/
+@media screen and (max-width: 600px) {
+
+  div.reveal-header {
+    grid-template-columns:  0.2fr 1.2fr 0.1fr 1.2fr 0.4fr;
+    grid-template-areas: "logo sc ht sb sn";
+  }
+
+  div.reveal-header.no-logo {
+    grid-template-columns: 1fr 0.1fr 1fr 0.25fr;
+    grid-template-areas: "sc ht sb sn";
+  }
+  
+  .reveal-header .sc-title p { margin-left: 1vw; }
+  .reveal-header.no-logo .sc-title p {margin-left: 2vw; }
+  div.reveal.has-logo div.slide-number { font-size: 10px; }
+}

_extensions/shafayetShafee/reveal-header/resources/js/add_header.js

@@ -0,0 +1,130 @@
+/**
+ * reveal-header
+ * A filter that adds header text and logo.
+ * 
+ * MIT License
+ * Copyright (c) 2023 Shafayet Khan Shafee.
+ */
+
+function header() {
+  
+  // add the header structure as the firstChild of div.reveal-header
+  function add_header() {
+    let header = document.querySelector("div.reveal-header");
+    let reveal = document.querySelector(".reveal");
+    reveal.insertBefore(header, reveal.firstChild);
+    
+    logo_img = document.querySelector('.header-logo img');
+    if (logo_img.getAttribute('src') == null) {
+      if (logo_img?.getAttribute('data-src') != null) {
+        logo_img.src = logo_img?.getAttribute('data-src') || "";
+        logo_img.removeAttribute('data-src'); 
+      };
+    };
+  };
+    
+  // add the class inverse-header for slide with has-dark-background class
+  // otherwise remove it.
+  function add_class(has_dark, header_paras) {
+    header_paras.forEach(el => {
+      el.classList.remove('inverse-header');
+      if(has_dark) {
+        el.classList.add('inverse-header');
+      };
+    });
+  };
+  
+  
+  // dynamically changing the header
+  function change_header(dheader, cheader, ctext) {
+    // dhead => dynamic header
+    // chead => constant header
+    // ctext => contstant header_text inner html
+    if (dheader !== null) {
+      cheader.innerHTML = dheader.innerHTML;  
+    } else {
+      cheader.innerHTML = ctext;
+    };
+  };
+  
+  function hide_from_title_slide(element) {
+      Reveal.on( 'slidechanged' , event => {
+        if (event.currentSlide.matches('#title-slide')) {
+          element.style.visibility = 'hidden';
+        } else {
+          element.style.visibility = 'visible';
+        }
+      });
+    };
+  
+  
+  if (Reveal.isReady()) {
+    
+    add_header();
+    
+    if (document.querySelector('div.reveal.has-logo') != null) {
+      var slide_number = document.querySelector('div.slide-number');
+      var header = document.querySelector("div.reveal-header");
+      header.appendChild(slide_number);
+    };
+  
+    // Get the default header text element and innner HTML (i.e. literal text)
+    var header_text = document.querySelector("div.header-text p");
+    const header_inner_html = header_text.innerHTML;
+    
+    var header_paras = document.querySelectorAll("div.reveal-header p");
+    var dark = Reveal.getCurrentSlide().classList.contains('has-dark-background');
+    add_class(dark, header_paras);
+    
+    Reveal.on( 'slidechanged', event => {
+      var has_dark = event.currentSlide.classList.contains('has-dark-background');
+      add_class(has_dark, header_paras);
+    });
+    
+    // make the visibility of slide specific header text defined in slide body none
+    document.querySelectorAll('div.header').forEach(el => {
+      el.style.display = 'none';
+    });
+    
+    
+    // change the header if currently loaded slide has the header div defined
+    // which won't be captured by slidechanged event unless we change slides.
+    let dynamic_header = Reveal.getCurrentSlide().querySelector('div.header p');
+    change_header(dynamic_header, header_text, header_inner_html);
+    
+    Reveal.on( 'slidechanged', event => {
+      let dyn_header = event.currentSlide.querySelector('div.header p');
+      change_header(dyn_header, header_text, header_inner_html);
+    });
+    
+    /************** header text in title slide if title or ***********************/
+    /*************  subtitle is used as header text        ***********************/
+    
+    var title_text = document.querySelector('.reveal-header .title-text p');
+    if (title_text != null) {
+      title_text.style.visibility = 'hidden';
+      hide_from_title_slide(title_text);
+    };
+    
+    /*************** hide header text and logo on title slide ********************/
+    
+    var hide_header_text = document.querySelector('.header-text').getAttribute('data-hide-from-titleslide');
+    var hide_header_logo = document.querySelector('.header-logo').getAttribute('data-hide-from-titleslide');
+    
+    if (hide_header_text == 'true') {
+      header_text.style.visibility = 'hidden';
+      hide_from_title_slide(header_text);
+    }
+    
+    if (hide_header_logo == 'true') {
+      logo_img.style.visibility = 'hidden';
+      hide_from_title_slide(logo_img);
+    } 
+    
+  }; 
+};
+
+
+window.addEventListener("load", (event) => {
+  header();
+});

_extensions/shafayetShafee/reveal-header/resources/js/sc_sb_title.js

@@ -0,0 +1,93 @@
+/**
+ * reveal-header
+ * A filter that adds header text and logo.
+ * 
+ * MIT License
+ * Copyright (c) 2023 Shafayet Khan Shafee.
+ */
+ 
+ function add_sc_sb_title() {
+   
+   function get_title() {
+    var h1_arr = [];
+    var h2_arr = [];
+  
+    Reveal.getSlides().forEach(el => {
+      if (!el.matches('#title-slide')) {
+       var h1 = el.querySelector('.title-slide h1')?.innerText;
+       var h2 = el.querySelector('.title-slide h2')?.innerText;
+       h1_arr.push(h1);
+       h2_arr.push(h2);
+      };
+    });
+    
+    return [h1_arr, h2_arr]
+  };
+    
+  function fill_array(ar) {
+    let last_val = ar[0] || " ";
+    for (let i = 1; i < ar.length; i++) {
+      if (typeof ar[i] === 'undefined') {
+        ar[i] = last_val;
+      } else {
+        last_val = ar[i];
+      }
+    }
+    return ar
+  };
+  
+  
+  if (Reveal.isReady()) {
+  
+    if (document.querySelector('div.reveal-header img').getAttribute('src').length == 0) {
+      document.querySelector('div.reveal-header').classList.add('no-logo')
+    }
+  
+    var [h1_array, h2_array] = get_title();
+    var filled_h1_array = fill_array(h1_array);
+    var filled_h2_array = fill_array(h2_array);
+    
+    Reveal.getSlides().forEach((el, idx) => {
+      if (!el.matches('#title-slide')) {
+        el.setAttribute('data-sc-title', filled_h1_array[(idx - 1)])
+        el.setAttribute('data-sb-title', filled_h2_array[(idx - 1)])
+      }
+    });
+  
+    Reveal.on( 'slidechanged', event => {
+      let sp = Reveal.getSlidesElement().querySelector('.stack.present');
+      
+      if (sp != null) {
+        let header = document.querySelector("div.reveal-header");
+        
+        // handling h1 section title (`.sc-title`)
+        var section_text = event.currentSlide.getAttribute('data-sc-title') || " ";
+        if (event.currentSlide.matches('.title-slide.level1')) {
+          header.querySelector('.sc-title p').innerText = ""; 
+        } else if (event.currentSlide.matches('.title-slide.level2')) {
+          header.querySelector('.sc-title p').innerText = section_text;  
+        } else {
+          header.querySelector('.sc-title p').innerText = section_text;
+        };
+        
+        // handling h2 section title (`.sb-title`)
+        var sbsection_text = event.currentSlide.getAttribute('data-sb-title') || " ";
+        if (event.currentSlide.matches('.title-slide.level1')) {
+          header.querySelector('.sb-title p').innerText = "";
+        } else if (event.currentSlide.matches('.title-slide.level2')) {
+          header.querySelector('.sb-title p').innerText = "";
+        } else {
+          header.querySelector('.sb-title p').innerText = sbsection_text;
+        };
+      };
+    });
+  };
+};
+
+
+window.addEventListener("load", (event) => {
+  add_sc_sb_title();
+});
+
+
+

_extensions/shafayetShafee/reveal-header/reveal-header.lua

@@ -0,0 +1,117 @@
+--[[
+MIT License
+
+Copyright (c) 2023 Shafayet Khan Shafee
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+]]--
+
+
+local function ensureHtmlDeps()
+  quarto.doc.add_html_dependency({
+    name = "reveal-header",
+    version = "1.0.0",
+    scripts = {
+        { path = "resources/js/add_header.js", attribs = {defer = "true"}}
+      },
+    stylesheets = {"resources/css/add_header.css"}
+  })
+end
+
+local function sc_sb_title()
+  quarto.doc.add_html_dependency({
+    name = "sc-sb-title",
+    version = "1.0.0",
+    scripts = {
+        { path = "resources/js/sc_sb_title.js", attribs = {defer = "true"}}
+      }
+  })
+end
+
+local function grid_htext()
+  quarto.doc.add_html_dependency({
+  name = "grid-htext",
+  version = "1.0.0",
+  stylesheets = {"resources/css/grid_htext.css"}
+})
+end
+
+local function grid_no_htext()
+  quarto.doc.add_html_dependency({
+  name = "grid-no-htext",
+  version = "1.0.0",
+  stylesheets = {"resources/css/grid_no_htext.css"}
+})
+end
+
+
+if quarto.doc.is_format('revealjs') then
+  -- Ensuring the dependencies got loaded before proceeding
+  ensureHtmlDeps()
+  function Pandoc(doc)
+    local blocks = doc.blocks
+    local str = pandoc.utils.stringify
+    local meta = doc.meta
+    if meta['sc-sb-title'] then
+      sc_sb_title()
+    end
+    if meta['header'] then
+      grid_htext()
+    else
+      grid_no_htext()
+    end
+    local header_text = meta['header'] and str(meta['header']) or " "
+    local header_para_class = {class = "header-text"}
+    if meta['title-as-header'] then
+      header_text = meta['title']
+      header_para_class = {class = "header-text title-text"}
+    end
+    if meta['subtitle-as-header'] then
+      header_text = meta['subtitle']
+      header_para_class = {class = "header-text title-text"}
+    end
+    -- make divs structure for holding text and logo.
+    local header_logo = meta['header-logo'] and str(meta['header-logo']) or ""
+    local header_img = pandoc.Div(pandoc.Image("", header_logo, ""), {class = "header-logo"})
+    local header_section = pandoc.Div(pandoc.Para(" "), {class = "sc-title"})
+    local header_sbsection = pandoc.Div(pandoc.Para(" "), {class = "sb-title"})
+    local header_para = pandoc.Div(pandoc.Para(header_text), header_para_class)
+    if meta['hide-from-titleSlide'] then
+      local hide = str(meta['hide-from-titleSlide'])
+      if hide == "text" then
+        header_para.attributes['hide-from-titleslide'] = "true"
+      elseif hide == "logo" then
+        header_img.attributes['hide-from-titleslide'] = "true"
+      elseif hide == "all" then
+        header_para.attributes['hide-from-titleslide'] = "true"
+        header_img.attributes['hide-from-titleslide'] = "true"
+      end
+    end
+    local div = pandoc.Div(
+      {
+        header_img,
+        header_section,
+        header_para,
+        header_sbsection
+      }, 
+      {class = 'reveal-header'})
+    table.insert(blocks, div)
+    return doc
+  end
+end