第7次课

SD/20240321_0_R实践课程/index.qmd

@@ -150,5 +150,4 @@ author: 姓名
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
-
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240321_1_R语言介绍/index.qmd

@@ -218,4 +218,4 @@ devtools::install_github("kjhealy/socviz")
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240321_2_R语言语法基础/index.qmd

@@ -792,4 +792,4 @@ names(Y) <- c("colA", "colB", "colC")
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240321_3_Excel基础/index.qmd

@@ -130,4 +130,4 @@ require(learnr)
 ## 欢迎讨论！{.center}
 
 
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`

SD/20240326_1_codestyle/_extensions

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

SD/20240326_1_codestyle/index.qmd

@@ -0,0 +1,157 @@
+---
+title: "代码编写规则"
+subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
+author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
+date: today
+lang: zh
+format:
+  revealjs:
+    theme: dark
+    slide-number: true
+    chalkboard:
+      buttons: true
+    preview-links: auto
+    lang: zh
+    toc: true
+    toc-depth: 1
+    toc-title: 大纲
+    logo: ./_extensions/inst/img/ucaslogo.png
+    css: ./_extensions/inst/css/revealjs.css
+    pointer:
+      key: "p"
+      color: "#32cd32"
+      pointerSize: 18
+revealjs-plugins:
+  - pointer
+filters:
+  - d2
+---
+
+
+```{r}
+#| echo: false
+knitr::opts_chunk$set(echo = TRUE)
+# source("../../coding/_common.R")
+library(tidyverse)
+library(nycflights13)
+```
+
+
+## tidy data
+
+```{r}
+knitr::include_graphics("../../image/tidy-1.png", dpi = 270)
+```
+
+
+## pipe（管道） |>
+
+```{r}
+#| eval: false
+require(patchwork)
+plot(1:10)
+1:10 |> plot()
+plot(x = 1:10, y = sin(1:10))
+1:10 |> plot(y = sin(1:10))
+
+```
+
+```{r}
+#| echo: false
+#| layout-nrow: 1
+#| fig-width: 4
+#| fig-height: 3
+#| out-height: 90%
+require(patchwork)
+plot(1:10)
+1:10 |> plot()
+plot(x = 1:10, y = sin(1:10))
+1:10 |> plot(y = sin(1:10))
+
+```
+
+
+
+## pipe（管道）：%>%
+
+```{r}
+#| eval: false
+#| layout-nrow: 1
+#| fig-width: 3
+#| fig-height: 4
+#| out-height: 125%
+require(magrittr)
+1:10 %>% plot()
+1:10 %>% plot(y = sin(1:10))
+sin(1:10) %>% plot(1:10, .)
+sin(1:10) |> plot(x = 1:10, y = _)
+
+```
+
+```{r}
+#| echo: false
+#| layout-nrow: 1
+#| fig-width: 3
+#| fig-height: 4
+#| out-height: 125%
+require(magrittr)
+1:10 %>% plot()
+1:10 %>% plot(y = sin(1:10))
+sin(1:10) %>% plot(1:10, .)
+sin(1:10) |> plot(x = 1:10, y = _)
+
+```
+
+
+
+
+
+
+## 代码编写规则
+
+```{r}
+#| eval: false
+
+# Strive for:
+short_flights <- flights |> filter(air_time < 60)
+# Avoid:
+SHORTFLIGHTS <- flights |> filter(air_time < 60)
+
+# Strive for
+z <- (a + b)^2 / d
+# Avoid
+z<-( a + b ) ^ 2/d
+
+# Strive for
+mean(x, na.rm = TRUE)
+# Avoid
+mean (x ,na.rm=TRUE)
+```
+
+## 练习
+
+```{r}
+#| eval: false
+flights|>filter(dest=="IAH")|>
+  group_by(year,month,day)|>summarize(n=n(),
+delay=mean(arr_delay,na.rm=TRUE))|>filter(n>10)
+
+flights|>filter(carrier=="UA",
+  dest%in%c("IAH","HOU"),sched_dep_time>
+0900,sched_arr_time<2000)|>group_by(flight)|>
+  summarize(delay=mean(
+arr_delay,na.rm=TRUE),cancelled=sum(is.na(arr_delay)),
+    n=n())|>filter(n>10)
+```
+
+
+## quarto
+
+![](../../image/quarto-flow.png) 
+
+
+## 欢迎讨论！{.center}
+
+
+`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "../")`
+

SD/20240326_1_datavisualize/_extensions/authors-block/_extension.yml

@@ -1,13 +0,0 @@
-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
-

SD/20240326_1_datavisualize/_extensions/authors-block/authors-block.lua

@@ -1,64 +0,0 @@
---[[
-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

SD/20240326_1_datavisualize/_extensions/authors-block/from_author_info_blocks.lua

@@ -1,197 +0,0 @@
--- 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

SD/20240326_1_datavisualize/_extensions/authors-block/from_scholarly_metadata.lua

@@ -1,59 +0,0 @@
---[[
-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

SD/20240326_1_datavisualize/_extensions/authors-block/utils.lua

@@ -1,62 +0,0 @@
---[[
-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

SD/20240326_1_datavisualize/_extensions/bootstrap/googlefonts.css

@@ -1,225 +0,0 @@
-/* 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;
-}

SD/20240326_1_datavisualize/_extensions/d2/_extension.yml

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

SD/20240326_1_datavisualize/_extensions/d2/d2.lua

@@ -1,272 +0,0 @@
--- 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

SD/20240326_1_datavisualize/_extensions/inst/css/revealjs.css

@@ -1,345 +0,0 @@
-: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;
-}
-
-li:hover {
-  font-weight: bold;
-}
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SD/20240326_1_datavisualize/_extensions/inst/tex/american-chemical-society.csl

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-    <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>
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-    <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">
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SD/20240326_1_datavisualize/_extensions/inst/tex/china-national-standard-gb-t-7714-2015-numeric.csl

@@ -1,435 +0,0 @@
-<?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"/>
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-        <names variable="container-author"/>
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-    </names>
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-  <!-- 专著题名 -->
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-        <choose>
-          <if variable="container-title">
-            <text variable="container-title"/>
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-          <else>
-            <text variable="event"/>
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-        <text macro="book-volume"/>
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-          <date variable="event-date" form="text"/>
-          <text variable="event-place"/>
-        </if>
-      </choose>
-    </group>
-  </macro>
-  <!-- 版本项 -->
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-    <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>
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-      <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>

SD/20240326_1_datavisualize/_extensions/inst/tex/cv.tex

@@ -1,240 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% 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}

SD/20240326_1_datavisualize/_extensions/inst/tex/els.tex

@@ -1,426 +0,0 @@
-$-- Keeping in template layout for backward compatibility
-\documentclass[$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{%
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SD/20240326_1_datavisualize/_extensions/inst/tex/elsevier-harvard.csl

@@ -1,239 +0,0 @@
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SD/20240326_1_datavisualize/_extensions/inst/tex/nature-biotechnology.csl

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-<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-GB">
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-    <link href="http://www.nature.com/nbt/pdf/gta.pdf" rel="documentation"/>
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-    <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>
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SD/20240326_1_datavisualize/_extensions/inst/tex/nature.csl

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-    <updated>2022-07-02T13:18:26+00:00</updated>
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SD/20240326_1_datavisualize/_extensions/inst/tex/supp.tex

@@ -1,432 +0,0 @@
-$-- Keeping in template layout for backward compatibility
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-%%% Begin My package additions %%%%%%%%%%%%%%%%%%%
-\usepackage[hyphens]{url}
-$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}

SD/20240326_1_datavisualize/_extensions/inst/tex/the-isme-j.csl

@@ -1,181 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
-  <info>
-    <title>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>

SD/20240326_1_datavisualize/_extensions/martinomagnifico/simplemenu/_extension.yml

@@ -1,21 +0,0 @@
-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

SD/20240326_1_datavisualize/_extensions/martinomagnifico/simplemenu/simplemenu.css

@@ -1,190 +0,0 @@
-.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);
-}

SD/20240326_1_datavisualize/_extensions/martinomagnifico/simplemenu/simplemenu.js

@@ -1,644 +0,0 @@
-
-/*****************************************************************
- * @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;
-
-}));

SD/20240326_1_datavisualize/_extensions/mloubout/critic-markup/_extension.yml

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

SD/20240326_1_datavisualize/_extensions/mloubout/critic-markup/critic-markup.lua

@@ -1,174 +0,0 @@
-
-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}}

SD/20240326_1_datavisualize/_extensions/mloubout/critic-markup/critic.css

@@ -1,131 +0,0 @@
-.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
-    }
-}

SD/20240326_1_datavisualize/_extensions/pandoc-ext/abstract-section/_extension.yaml

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

SD/20240326_1_datavisualize/_extensions/pandoc-ext/abstract-section/abstract-section.lua

@@ -1,59 +0,0 @@
---[[
-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

SD/20240326_1_datavisualize/_extensions/pandoc-ext/author-info-blocks/_extension.yaml

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

SD/20240326_1_datavisualize/_extensions/pandoc-ext/author-info-blocks/author-info-blocks.lua

@@ -1,179 +0,0 @@
-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,
-	},
-}

SD/20240326_1_datavisualize/_extensions/pandoc-ext/scholarly-metadata/_extension.yaml

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

SD/20240326_1_datavisualize/_extensions/pandoc-ext/scholarly-metadata/scholarly-metadata.lua

@@ -1,197 +0,0 @@
---[[
-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,
-	},
-}

SD/20240326_1_datavisualize/_extensions/quarto-ext/latex-environment/_extension.yml

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

SD/20240326_1_datavisualize/_extensions/quarto-ext/latex-environment/latex-environment.lua

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

SD/20240326_1_datavisualize/_extensions/quarto-ext/pointer/_extension.yml

@@ -1,15 +0,0 @@
-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

SD/20240326_1_datavisualize/_extensions/quarto-ext/pointer/pointer.css

@@ -1 +0,0 @@
-.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;}

SD/20240326_1_datavisualize/_extensions/quarto-ext/pointer/pointer.js

@@ -1 +0,0 @@
-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}}}}();

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/_extension.yml

@@ -1,19 +0,0 @@
-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

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/bib/elsevier-harvard.csl

@@ -1,239 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="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>

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/elsevier.lua

@@ -1,166 +0,0 @@
--- 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,
-
-  }
-}

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/partials/_two-column-longtable.tex

@@ -1,20 +0,0 @@
-\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

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/partials/before-body.tex

@@ -1,41 +0,0 @@
-\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}
-

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/partials/revision.tex

@@ -1,66 +0,0 @@
-\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}}
-

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/partials/title.tex

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

SD/20240326_1_datavisualize/_extensions/quarto-journals/elsevier/styles/elsevier.scss

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

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/_extension.yml

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

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/resources/css/add_header.css

@@ -1,67 +0,0 @@
-/*@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; }
-}

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/resources/css/grid_htext.css

@@ -1,50 +0,0 @@
-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; }
-}

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/resources/css/grid_no_htext.css

@@ -1,50 +0,0 @@
-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; }
-}

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/resources/js/add_header.js

@@ -1,130 +0,0 @@
-/**
- * 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();
-});

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/resources/js/sc_sb_title.js

@@ -1,93 +0,0 @@
-/**
- * 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();
-});
-
-
-

SD/20240326_1_datavisualize/_extensions/shafayetShafee/reveal-header/reveal-header.lua

@@ -1,117 +0,0 @@
---[[
-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

SD/20240326_1_datavisualize/index.qmd

@@ -1,541 +0,0 @@
----
-title: "数据可视化"
-subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
-author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
-date: today
-lang: zh
-format:
-  revealjs:
-    theme: dark
-    slide-number: true
-    chalkboard:
-      buttons: true
-    preview-links: auto
-    lang: zh
-    toc: true
-    toc-depth: 1
-    toc-title: 大纲
-    logo: ./_extensions/inst/img/ucaslogo.png
-    css: ./_extensions/inst/css/revealjs.css
-    pointer:
-      key: "p"
-      color: "#32cd32"
-      pointerSize: 18
-revealjs-plugins:
-  - pointer
-filters:
-  - d2
----
-
-```{r}
-#| echo: false
-knitr::opts_chunk$set(echo = TRUE)
-source("../../coding/_common.R")
-library(tidyverse)
-library(palmerpenguins)
-library(ggthemes)
-```
-
-
-
-## 查看数据
-
-```{r}
-penguins
-```
-
-## 查看数据
-
-```{r}
-glimpse(penguins)
-```
-
-## 效果
-
-```{r}
-#| echo: false
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins, with a
-#|   best fit line of the relationship between these two variables 
-#|   overlaid. The plot displays a positive, fairly linear, and relatively 
-#|   strong relationship between these two variables. Species (Adelie, 
-#|   Chinstrap, and Gentoo) are represented with different colors and 
-#|   shapes. The relationship between body mass and flipper length is 
-#|   roughly the same for these three species, and Gentoo penguins are 
-#|   larger than penguins from the other two species.
-penguins |>
-  ggplot(aes(x = flipper_length_mm, y = body_mass_g)) +
-geom_point(aes(color = species, shape = species)) +
-geom_smooth(method = "lm") +
-labs(
-  title = "Body mass and flipper length",
-  subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
-  x = "Flipper length (mm)",
-  y = "Body mass (g)",
-  color = "Species",
-  shape = "Species"
-) +
-scale_color_colorblind()
-```
-
-## 分层展示
-
-```{r}
-#| fig-alt: |
-#|   A blank, gray plot area.
-
-ggplot(data = penguins)
-```
-
-## 分层展示
-
-```{r}
-#| fig-alt: |
-#|   The plot shows flipper length on the x-axis, with values that range from 
-#|   170 to 230, and body mass on the y-axis, with values that range from 3000 
-#|   to 6000.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-)
-```
-
-## 分层展示
-
-```{r}
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. The plot 
-#|   displays a positive, linear, and relatively strong relationship between 
-#|   these two variables.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point()
-```
-
-## 分层展示
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. The plot 
-#|   displays a positive, fairly linear, and relatively strong relationship 
-#|   between these two variables. Species (Adelie, Chinstrap, and Gentoo) 
-#|   are represented with different colors.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g, color = species)
-) +
-  geom_point()
-```
-
-## 分层展示
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. Overlaid 
-#|   on the scatterplot are three smooth curves displaying the 
-#|   relationship between these variables for each species (Adelie, 
-#|   Chinstrap, and Gentoo). Different penguin species are plotted in 
-#|   different colors for the points and the smooth curves.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g, color = species)
-) +
-  geom_point() +
-  geom_smooth(method = "lm")
-```
-
-## 分层展示
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. Overlaid 
-#|   on the scatterplot is a single line of best fit displaying the 
-#|   relationship between these variables for each species (Adelie, 
-#|   Chinstrap, and Gentoo). Different penguin species are plotted in 
-#|   different colors for the points only.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point(mapping = aes(color = species)) +
-  geom_smooth(method = "lm")
-```
-
-## 分层展示
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. Overlaid 
-#|   on the scatterplot is a single line of best fit displaying the 
-#|   relationship between these variables for each species (Adelie, 
-#|   Chinstrap, and Gentoo). Different penguin species are plotted in 
-#|   different colors and shapes for the points only.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point(mapping = aes(color = species, shape = species)) +
-  geom_smooth(method = "lm")
-```
-
-## 分层展示
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins, with a 
-#|   line of best fit displaying the relationship between these two variables 
-#|   overlaid. The plot displays a positive, fairly linear, and relatively 
-#|   strong relationship between these two variables. Species (Adelie, 
-#|   Chinstrap, and Gentoo) are represented with different colors and 
-#|   shapes. The relationship between body mass and flipper length is 
-#|   roughly the same for these three species, and Gentoo penguins are 
-#|   larger than penguins from the other two species.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point(aes(color = species, shape = species)) +
-  geom_smooth(method = "lm") +
-  labs(
-    title = "Body mass and flipper length",
-    subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
-    x = "Flipper length (mm)", y = "Body mass (g)",
-    color = "Species", shape = "Species"
-  ) +
-  scale_color_colorblind()
-```
-
-
-## 分层展示
-
-```{r}
-#| echo: false
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins, colored 
-#|   by bill depth. A smooth curve of the relationship between body mass 
-#|   and flipper length is overlaid. The relationship is positive, 
-#|   fairly linear, and moderately strong.
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point(aes(color = bill_depth_mm)) +
-  geom_smooth()
-```
-
-## 分层展示
-
-```{r}
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g, color = island)
-) +
-  geom_point() +
-  geom_smooth(se = FALSE)
-```
-
-## 分层展示
-
-```{r}
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point() +
-  geom_smooth()
-
-ggplot() +
-  geom_point(
-    data = penguins,
-    mapping = aes(x = flipper_length_mm, y = body_mass_g)
-  ) +
-  geom_smooth(
-    data = penguins,
-    mapping = aes(x = flipper_length_mm, y = body_mass_g)
-  )
-```
-
-## 分层展示
-
-```{r}
-
-ggplot(
-  data = penguins,
-  mapping = aes(x = flipper_length_mm, y = body_mass_g)
-) +
-  geom_point()
-```
-
-## 分层展示
-
-```{r}
-
-ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) + 
-  geom_point()
-```
-
-## 柱状图
-
-```{r}
-#| fig-alt: |
-#|   A bar chart of frequencies of species of penguins: Adelie 
-#|   (approximately 150), Chinstrap (approximately 90), Gentoo 
-#|   (approximately 125).
-
-ggplot(penguins, aes(x = species)) +
-  geom_bar()
-```
-
-## 柱状图
-
-```{r}
-#| fig-alt: |
-#|   A bar chart of frequencies of species of penguins, where the bars are 
-#|   ordered in decreasing order of their heights (frequencies): Adelie 
-#|   (approximately 150), Gentoo (approximately 125), Chinstrap 
-#|   (approximately 90).
-
-ggplot(penguins, aes(x = fct_infreq(species))) +
-  geom_bar()
-```
-
-## 直方图
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A histogram of body masses of penguins. The distribution is unimodal 
-#|   and right skewed, ranging between approximately 2500 to 6500 grams.
-
-ggplot(penguins, aes(x = body_mass_g)) +
-  geom_histogram(binwidth = 200)
-```
-
-## 直方图
-
-```{r}
-#| warning: false
-#| layout-ncol: 2
-#| fig-width: 3
-#| fig-alt: |
-#|   Two histograms of body masses of penguins, one with binwidth of 20 
-#|   (left) and one with binwidth of 2000 (right). The histogram with binwidth 
-#|   of 20 shows lots of ups and downs in the heights of the bins, creating a 
-#|   jagged outline. The histogram  with binwidth of 2000 shows only three bins.
-
-ggplot(penguins, aes(x = body_mass_g)) +
-  geom_histogram(binwidth = 20)
-ggplot(penguins, aes(x = body_mass_g)) +
-  geom_histogram(binwidth = 2000)
-```
-
-## 密度图
-
-```{r}
-#| fig-alt: |
-#|   A density plot of body masses of penguins. The distribution is unimodal 
-#|   and right skewed, ranging between approximately 2500 to 6500 grams.
-
-ggplot(penguins, aes(x = body_mass_g)) +
-  geom_density()
-```
-
-
-
-## 箱图
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   Side-by-side box plots of distributions of body masses of Adelie, 
-#|   Chinstrap, and Gentoo penguins. The distribution of Adelie and 
-#|   Chinstrap penguins' body masses appear to be symmetric with 
-#|   medians around 3750 grams. The median body mass of Gentoo penguins 
-#|   is much higher, around 5000 grams, and the distribution of the 
-#|   body masses of these penguins appears to be somewhat right skewed.
-
-ggplot(penguins, aes(x = species, y = body_mass_g)) +
-  geom_boxplot()
-```
-
-## 分组
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A density plot of body masses of penguins by species of penguins. Each 
-#|   species (Adelie, Chinstrap, and Gentoo) is represented with different 
-#|   colored outlines for the density curves.
-
-ggplot(penguins, aes(x = body_mass_g, color = species)) +
-  geom_density(linewidth = 0.75)
-```
-
-## 分组
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A density plot of body masses of penguins by species of penguins. Each 
-#|   species (Adelie, Chinstrap, and Gentoo) is represented in different 
-#|   colored outlines for the density curves. The density curves are also 
-#|   filled with the same colors, with some transparency added.
-
-ggplot(penguins, aes(x = body_mass_g, color = species, fill = species)) +
-  geom_density(alpha = 0.5)
-```
-
-## 分组
-
-```{r}
-#| fig-alt: |
-#|   Bar plots of penguin species by island (Biscoe, Dream, and Torgersen)
-ggplot(penguins, aes(x = island, fill = species)) +
-  geom_bar()
-```
-
-## 分组
-
-```{r}
-#| fig-alt: |
-#|   Bar plots of penguin species by island (Biscoe, Dream, and Torgersen)
-#|   the bars are scaled to the same height, making it a relative frequencies 
-#|   plot
-
-ggplot(penguins, aes(x = island, fill = species)) +
-  geom_bar(position = "fill")
-```
-
-## 分组
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. The plot 
-#|   displays a positive, linear, relatively strong relationship between 
-#|   these two variables.
-
-ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
-  geom_point()
-```
-
-## 分组
-
-```{r}
-#| warning: false
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. The plot 
-#|   displays a positive, linear, relatively strong relationship between 
-#|   these two variables. The points are colored based on the species of the 
-#|   penguins and the shapes of the points represent islands (round points are 
-#|   Biscoe island, triangles are Dream island, and squared are Torgersen 
-#|   island). The plot is very busy and it's difficult to distinguish the shapes
-#|   of the points.
-
-ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
-  geom_point(aes(color = species, shape = island))
-```
-
-## 分面
-
-```{r}
-#| warning: false
-#| fig-width: 8
-#| fig-asp: 0.33
-#| fig-alt: |
-#|   A scatterplot of body mass vs. flipper length of penguins. The shapes and 
-#|   colors of points represent species. Penguins from each island are on a 
-#|   separate facet. Within each facet, the relationship between body mass and 
-#|   flipper length is positive, linear, relatively strong. 
-
-ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
-  geom_point(aes(color = species, shape = species)) +
-  facet_wrap(~island)
-```
-
-## 分面
-
-```{r}
-#| warning: false
-
-ggplot(
-  data = penguins,
-  mapping = aes(
-    x = bill_length_mm, y = bill_depth_mm, 
-    color = species, shape = species
-  )
-) +
-  geom_point() +
-  labs(color = "Species")
-```
-
-## 练习
-
-```{r}
-#| echo: false
-#| layout-ncol: 2
-
-ggplot(penguins, aes(x = island, fill = species)) +
-  geom_bar(position = "fill")
-ggplot(penguins, aes(x = species, fill = island)) +
-  geom_bar(position = "fill")
-```
-
-## 练习
-
-```{r}
-#| echo: false
-
-ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
-  geom_point()
-```
-
-## 练习
-
-
-```{r}
-#| echo: false
-
-ggplot(mpg, aes(x = class)) + geom_bar()
-```
-
-## 练习
-
-
-```{r}
-#| echo: false
-
-ggplot(mpg, aes(x = cty, y = hwy)) + geom_point()
-```
-
-## 练习
-
-```{r}
-#| echo: false
-
-ggplot(data = mpg) +
-geom_point(mapping = aes(x = displ, y = hwy))
-```
-
-## 欢迎讨论！{.center}
-
-
-`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`
-