第7次课

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Ming Su 2024-03-25 21:48:30 +08:00
parent 00c44b652e
commit 04cc6935d6
845 changed files with 120128 additions and 80612 deletions

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@ -150,5 +150,4 @@ author: 姓名
## 欢迎讨论!{.center} ## 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 = "../")`

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@ -218,4 +218,4 @@ devtools::install_github("kjhealy/socviz")
## 欢迎讨论!{.center} ## 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 = "../")`

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@ -792,4 +792,4 @@ names(Y) <- c("colA", "colB", "colC")
## 欢迎讨论!{.center} ## 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 = "../")`

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@ -130,4 +130,4 @@ require(learnr)
## 欢迎讨论!{.center} ## 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 = "../")`

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

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@ -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 = "../")`

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@ -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

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@ -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

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@ -1,197 +0,0 @@
-- https://github.com/pandoc/lua-filters/commit/ca72210b453cc0d045360e0ae36448d019d7dfbf
--[[
affiliation-blocks generate title components
Copyright © 20172021 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

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@ -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

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@ -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

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@ -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;
}

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

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@ -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

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@ -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;
}
.reveal p:hover {
font-weight: bold;
}
.reveal ul li {
line-height: 1.2em;
}
.reveal .thank h2 {
font-size: var(--r-heading1-size);
line-height: var(--r-heading-line-height);
}
.reveal .thank {
text-align: center;
}
.reveal .thank h2:after {
content: " ";
display: block;
border: 3px solid;
border-image: linear-gradient(to right, white, var(--r-heading-color), white)
1;
border-radius: 1px;
}
.panel-tabset [role="tab"] {
border-bottom: 1px solid red;
}
.panel-tabset [role="tab"][aria-selected="true"] {
background-color: #ffdddd;
border-bottom: 1px solid red;
}
.white {
color: #ffffff;
}
.orange {
color: #e09a25;
}
.green {
color: #006e51;
}
.pink {
color: #d13076;
}
.dusty {
color: #ad5d5d;
}
.flame {
color: #ef562d;
}
.kale {
color: #5c7148;
}
.blue {
color: #0c4c8a;
}
.red {
color: #b93a32;
}
.clay {
color: #9e4624;
}
.bodacious {
color: #b76ba3;
}
.serenity {
color: #91a8d0;
}
.cognac {
color: #60413c;
}
.sangria {
color: #760030;
}
.alumium {
color: #75796a;
}
.marsala {
color: #964f4c;
}
.purple {
color: #702fa8;
}
.blank {
background-color: "Yellow";
width: 100%;
color: red;
}
.reveal .slide aside {
position: absolute;
margin: 0 auto;
left: 2%;
font-size: 0.7em;
text-align: end;
max-width: 90%;
width: fit-content;
color: gray;
bottom: -6%;
}
.ref {
position: absolute;
margin: 0 auto;
right: 2%;
font-size: 1em;
text-align: end;
max-width: 90%;
width: fit-content;
color: gray;
bottom: -6%;
}
.con {
position: absolute;
margin: 0 auto;
font-size: 1.4em;
text-align: center;
font-family: inherit;
max-width: 100%;
width: fit-content;
color: #023047;
bottom: -2%;
}
.center {
text-align: center;
}
.tiny {
font-size: 60%;
}
figure > figcaption {
margin-top: -0.5em;
}
.reveal .slide figure > figcaption,
.reveal .slide img.stretch + p.caption,
.reveal .slide img.r-stretch + p.caption {
font-size: 0.9em;
text-align: center;
}
.reveal strong, .reveal b {
font-weight: bold;
color: crimson;
}
.reveal pre code {
background-color: #554433;
line-height: 1.2em;
color: #fff;
font-size: x-large;
}
.reveal pre code:hover{
font-size: xx-large;
line-height: 250%;
}
section#title-slide p.subtitle {
font-size: var(--r-heading3-size);
text-decoration: none;
color: gray;
}
.reveal div.sourceCode pre code {
background-color: #002233;
min-height: 100%;
font-size: x-large;
}
.reveal div.sourceCode pre code:hover {
font-size: xx-large;
}

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

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

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@ -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"/>
<names variable="collection-editor"/>
<names variable="container-author"/>
</substitute>
</names>
</macro>
<!-- 专著题名 -->
<macro name="container-title">
<group delimiter=", ">
<group delimiter=": ">
<choose>
<if variable="container-title">
<text variable="container-title"/>
</if>
<else>
<text variable="event"/>
</else>
</choose>
<text macro="book-volume"/>
</group>
<choose>
<if variable="event-date">
<date variable="event-date" form="text"/>
<text variable="event-place"/>
</if>
</choose>
</group>
</macro>
<!-- 版本项 -->
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition"/>
</else>
</choose>
</macro>
<!-- 电子资源的更新或修改日期 -->
<macro name="issued-date">
<date variable="issued" form="numeric"/>
</macro>
<!-- 出版年 -->
<macro name="issued-year">
<choose>
<if is-uncertain-date="issued">
<date variable="issued" prefix="[" suffix="]">
<date-part name="year" range-delimiter="-"/>
</date>
</if>
<else>
<date variable="issued">
<date-part name="year" range-delimiter="-"/>
</date>
</else>
</choose>
</macro>
<!-- 专著的出版项 -->
<macro name="publishing">
<group delimiter=": ">
<group delimiter=", ">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
<!-- 非电子资源显示“出版年” -->
<choose>
<if variable="publisher page" type="book chapter paper-conference thesis" match="any">
<text macro="issued-year"/>
</if>
<else-if variable="URL DOI" match="none">
<text macro="issued-year"/>
</else-if>
</choose>
</group>
<text variable="page"/>
</group>
<choose>
<!-- 纯电子资源显示“更新或修改日期” -->
<if variable="publisher page" type="book chapter paper-conference thesis" match="none">
<choose>
<if variable="URL DOI" match="any">
<text macro="issued-date" prefix="(" suffix=")"/>
</if>
</choose>
</if>
</choose>
<text macro="accessed-date"/>
</macro>
<!-- 其他责任者 -->
<macro name="secondary-contributor">
<names variable="translator">
<name>
<name-part name="family" text-case="uppercase"/>
<name-part name="given"/>
</name>
<label form="short" prefix=", "/>
</names>
</macro>
<!-- 连续出版物中的析出文献的出处项(年、卷、期等信息) -->
<macro name="periodical-publishing">
<group>
<group delimiter=": ">
<group>
<group delimiter=", ">
<text macro="container-title" text-case="title"/>
<choose>
<if type="article-newspaper">
<text macro="issued-date"/>
</if>
<else>
<text macro="issued-year"/>
</else>
</choose>
<text variable="volume"/>
</group>
<text variable="issue" prefix="(" suffix=")"/>
</group>
<text variable="page"/>
</group>
<text macro="accessed-date"/>
</group>
</macro>
<!-- 题名 -->
<macro name="title">
<group delimiter=", ">
<group delimiter=": ">
<text variable="title"/>
<group delimiter="&#8195;">
<choose>
<if variable="container-title" type="paper-conference" match="none">
<text macro="book-volume"/>
</if>
</choose>
<choose>
<if type="bill legal_case legislation patent regulation report standard" match="any">
<text variable="number"/>
</if>
</choose>
</group>
</group>
<choose>
<if variable="container-title" type="paper-conference" match="none">
<choose>
<if variable="event-date">
<text variable="event-place"/>
<date variable="event-date" form="text"/>
</if>
</choose>
</if>
</choose>
</group>
<text macro="type-code" prefix="[" suffix="]"/>
</macro>
<!-- 文献类型标识 -->
<macro name="type-code">
<group delimiter="/">
<choose>
<if type="article">
<choose>
<if variable="archive">
<text value="A"/>
</if>
<else>
<text value="M"/>
</else>
</choose>
</if>
<else-if type="article-journal article-magazine periodical" match="any">
<text value="J"/>
</else-if>
<else-if type="article-newspaper">
<text value="N"/>
</else-if>
<else-if type="bill collection legal_case legislation regulation" match="any">
<text value="A"/>
</else-if>
<else-if type="book chapter" match="any">
<text value="M"/>
</else-if>
<else-if type="dataset">
<text value="DS"/>
</else-if>
<else-if type="map">
<text value="CM"/>
</else-if>
<else-if type="paper-conference">
<text value="C"/>
</else-if>
<else-if type="patent">
<text value="P"/>
</else-if>
<else-if type="post post-weblog webpage" match="any">
<text value="EB"/>
</else-if>
<else-if type="report">
<text value="R"/>
</else-if>
<else-if type="software">
<text value="CP"/>
</else-if>
<else-if type="standard">
<text value="S"/>
</else-if>
<else-if type="thesis">
<text value="D"/>
</else-if>
<else>
<text value="Z"/>
</else>
</choose>
<choose>
<if variable="URL DOI" match="any">
<text value="OL"/>
</if>
</choose>
</group>
</macro>
<!-- 获取和访问路径以及 DOI -->
<macro name="url-doi">
<group delimiter=". ">
<text variable="URL"/>
<text variable="DOI" prefix="DOI:"/>
</group>
</macro>
<!-- 连续出版物的年卷期 -->
<macro name="year-volume-issue">
<group>
<group delimiter=", ">
<text macro="issued-year"/>
<text variable="volume"/>
</group>
<text variable="issue" prefix="(" suffix=")"/>
</group>
</macro>
<!-- 专著和电子资源 -->
<macro name="monograph-layout">
<group delimiter=". " suffix=".">
<text macro="author"/>
<text macro="title"/>
<text macro="secondary-contributor"/>
<text macro="edition"/>
<text macro="publishing"/>
<text macro="url-doi"/>
</group>
</macro>
<!-- 专著中的析出文献 -->
<macro name="chapter-in-book-layout">
<group delimiter=". " suffix=".">
<text macro="author"/>
<group delimiter="//">
<group delimiter=". ">
<text macro="title"/>
<text macro="secondary-contributor"/>
</group>
<group delimiter=". ">
<text macro="container-author"/>
<text macro="container-title"/>
</group>
</group>
<text macro="edition"/>
<text macro="publishing"/>
<text macro="url-doi"/>
</group>
</macro>
<!-- 连续出版物 -->
<macro name="serial-layout">
<group delimiter=". " suffix=".">
<text macro="author"/>
<text macro="title"/>
<text macro="year-volume-issue"/>
<text macro="publishing"/>
<text variable="URL"/>
<text variable="DOI" prefix="DOI:"/>
</group>
</macro>
<!-- 连续出版物中的析出文献 -->
<macro name="article-in-periodical-layout">
<group delimiter=". " suffix=".">
<text macro="author"/>
<text macro="title"/>
<text macro="periodical-publishing"/>
<text macro="url-doi"/>
</group>
</macro>
<!-- 专利文献 -->
<macro name="patent-layout">
<group delimiter=". " suffix=".">
<text macro="author"/>
<text macro="title"/>
<group>
<text macro="issued-date"/>
<text macro="accessed-date"/>
</group>
<text macro="url-doi"/>
</group>
</macro>
<!-- 正文中引用的文献标注格式 -->
<macro name="citation-layout">
<group>
<text variable="citation-number"/>
</group>
</macro>
<!-- 参考文献表格式 -->
<macro name="entry-layout">
<choose>
<if type="article-journal article-magazine article-newspaper" match="any">
<text macro="article-in-periodical-layout"/>
</if>
<else-if type="periodical">
<text macro="serial-layout"/>
</else-if>
<else-if type="patent">
<text macro="patent-layout"/>
</else-if>
<else-if type="paper-conference" variable="container-title" match="any">
<text macro="chapter-in-book-layout"/>
</else-if>
<else>
<text macro="monograph-layout"/>
</else>
</choose>
</macro>
<citation collapse="citation-number" after-collapse-delimiter=",">
<layout vertical-align="sup" delimiter="," prefix="[" suffix="]">
<text macro="citation-layout"/>
</layout>
</citation>
<bibliography entry-spacing="0" et-al-min="4" et-al-use-first="3" second-field-align="flush">
<!-- 取消这部分注释可以使用 CSL-M 的功能支持双语 -->
<!-- <layout locale="en"><text variable="citation-number" prefix="[" suffix="]"/><text macro="entry-layout"/></layout> -->
<layout>
<text variable="citation-number" prefix="[" suffix="]"/>
<text macro="entry-layout"/>
</layout>
</bibliography>
</style>

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

View File

@ -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{%
\zref@extractdefault{#1}{url}{}%
\zref@ifrefcontainsprop{#1}{anchor}{%
\hashchar\zref@extract{#1}{anchor}}{}}%
{\noexpand\zref{#1}}}\next}
\makeatother
$if(revision)$
% \usepackage{xcolor}
\usepackage{adjustbox}
\usepackage{mdframed}
\newmdenv[topline=false,
leftline=true,
bottomline=false,
rightline=false,
linewidth=3pt,
%backgroundcolor=lightgray,
linecolor=gray!30,
backgroundcolor=gray!5,
skipabove=\topsep,
skipbelow=\topsep,
leftmargin=0pt,
rightmargin=0pt,
innertopmargin=0pt,
innerbottommargin=0pt
]{refquote}
\newmdenv[topline=false,
leftline=true,
bottomline=false,
rightline=false,
linewidth=3pt,
%backgroundcolor=lightgray,
backgroundcolor=red!3!white,
linecolor=red!30!white,
skipabove=\topsep,
skipbelow=\topsep,
leftmargin=0pt,
rightmargin=0pt,
innertopmargin=10pt,
innerbottommargin=10pt
]{question}
\setenumerate{labelsep=*, leftmargin=1.0pc}
% setup hyperlink for page and line number
\def\msname{$if(msname)$$msname$$else$MS$endif$}
\def\smname{$if(smname)$$smname$$else$SM$endif$}
\setenumerate{labelsep=*, leftmargin=1.0pc}
%\zexternaldocument*{ManuscriptNew\veraa}
\zexternaldocument*{\msname}
\zexternaldocument*{\smname}
\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
\linelabel{line:#1}}}
%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
\makeatletter
\newcommand{\clab}[2]{%
\protected@write\@auxout{\let\clab\@secondoftwo}{
\string\newlabel{r:#1}{{#2}{}}}%
\hlabel{#1}#2\hlabel{#1end}}
\makeatother
\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
\zref{line:#1}--\zref{line:#1end}:}\\}}
\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
\renewenvironment{quote}{\begin{question}}{\end{question}}
% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
$endif$
% def default corresponding authors and equal contributing authors variables
\def\hascorr{0}
\def\haseqc{0}
% check if corresponding author(s) and equal contributing authors are available
$for(author)$$if(author.correspondence)$\def\hascorr{1}$endif$$if(author.equalcontribution)$\def\haseqc{1}$endif$ $endfor$
\newcommand{\getcorrauthinfo}{
\subsection{Corresponding Author(s)}
\def\a{} \def\b{} \def\c{}
\hspace{-2.2em}
$for(author)$
$if(author.correspondence)$
\textbf{$author.name$:}
\vspace{-1em}
\begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
$for(author.institute)$ \def\a{$author.institute$}
$for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
\ifx \a\b \item \c; \fi
$endfor$
$endfor$
$if(author.email)$\item email: $author.email$;$endif$
$if(author.orcid)$\item orcid: $author.orcid$;$endif$
$if(author.tel)$\item Tel: $author.tel$;$endif$
$if(author.fax)$\item Fax: $author.fax$$endif$
\end{enumerate}
$endif$
$endfor$
}
\newcommand{\getotherauthinfo}{
\subsection{Author(s)}
\def\a{} \def\b{} \def\c{}
\hspace{-2.2em}
$for(author)$
$if(author.correspondence)$
$else$
\textbf{$author.name$:}
\vspace{-1em}
\begin{enumerate}[labelindent=-12pt,label=\arabic*.,itemindent=0em,leftmargin=!, itemsep = -10pt]
$for(author.institute)$ \def\a{$author.institute$} $for(institute)$ \def\b{$institute.id$} \def\c{$institute.name$}
\ifx \a\b \item \c; \fi
$endfor$
$endfor$
$if(author.email)$\item email: $author.email$;$endif$
$if(author.orcid)$\item orcid: $author.orcid$;$endif$
$if(author.tel)$\item Tel: $author.tel$;$endif$
$if(author.fax)$\item Fax: $author.fax$$endif$
\end{enumerate}
$endif$
$endfor$
}
$preamble$
% remove the two line around Abstract
$if(abstract)$
$else$
\makeatletter
\renewcommand{\MaketitleBox}{%
\resetTitleCounters
\def\baselinestretch{1}%
\begin{center}
\def\baselinestretch{1}%
\large \@title \par
\vskip 18pt
\normalsize\elsauthors \par
\vskip 30pt
\footnotesize \itshape \elsaddress \par
\end{center}
\vskip 12pt
}
\makeatother
$endif$
\begin{document}
$for(include-before)$
$include-before$
$endfor$
\begin{frontmatter}
\title{$title$$if(subtitle)$\\\Large{$subtitle$}$endif$}
$for(author)$\author$if(authorwithinstitute)$[$for(author.institute)$$author.institute$$sep$,$endfor$]$endif${$author.name$$if(author.correspondence)$\corref{corrauth}$endif$$if(author.equalcontribution)$\corref{eqcon}$endif$ $if(author.footnote)$\fnref{$author.footnote$}$endif$}$if(author.email)$\ead{$author.email$}$endif$$endfor$
$if(authorwithinstitute)$ $for(institute)$ \address[$institute.id$]{$institute.name$} $endfor$ $endif$
% generate corresponding authors.
% \StrBehind is from xstring package
\ifnum \hascorr=1
\def\corrauths{
$for(author)$$if(author.correspondence)$and $author.name$ ($author.email$) $endif$$endfor$}
\cortext[corrauth]{Corresponding to \StrBehind*{\corrauths}{and }.}
\fi
% generate equal contributing authors.
\ifnum \haseqc=1
\def\eqa{$for(author)$$if(author.equalcontribution)$and $author.name$ $endif$$endfor$}
\cortext[eqcon]{\StrBehind*{\eqa}{and } are equally contributed to this work.}
\fi
$for(footnote)$
\fntext[$footnote.id$]{$footnote.text$}
$endfor$
$if(abstract)$
\begin{abstract}
$abstract$
\end{abstract}
$if(keywords)$
\begin{keyword}
$for(keywords/allbutlast)$$keywords$ \sep $endfor$
$for(keywords/last)$$keywords$$endfor$
\end{keyword}
$endif$
$endif$
\end{frontmatter}
$body$
$if(authorwithinstitute)$
$else$
\section{Author Information}
\getcorrauthinfo{}
\getotherauthinfo{}
$endif$
$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$bibliography$}
$endif$
$endif$
$for(include-after)$
$include-after$
$endfor$
\end{document}

View File

@ -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>2014-03-04T00:09:00+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="container">
<choose>
<if type="chapter paper-conference" match="any">
<text term="in" prefix=", " suffix=": "/>
<names variable="editor translator" delimiter=", " suffix=", ">
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<label form="short" text-case="capitalize-first" prefix=" (" suffix=")"/>
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<group delimiter=", ">
<text variable="container-title" text-case="title"/>
<text variable="collection-title" text-case="title"/>
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</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>
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$if(author.email)$\item email: $author.email$;$endif$
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$endif$
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$body$
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$else$
\section{Author Information}
\getcorrauthinfo{}
\getotherauthinfo{}
\section{Notes}
The authors declare no competing financial interest.
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@ -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>
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<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>
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<macro name="year-date">
<date variable="issued">
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<citation collapse="citation-number">
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</citation>
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<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>

View File

@ -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

View File

@ -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);
}

View File

@ -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;
}));

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

View File

@ -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}}

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@ -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
}
}

File diff suppressed because one or more lines are too long

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

View File

@ -1,59 +0,0 @@
--[[
abstract-to-meta move an "abstract" section into document metadata
Copyright: © 20172021 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

View File

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

View File

@ -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,
},
}

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

View File

@ -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,
},
}

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@ -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

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@ -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 }
}

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@ -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

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@ -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;}

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@ -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}}}}();

View File

@ -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

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@ -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>

View File

@ -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,
}
}

View File

@ -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

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@ -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}

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@ -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}}

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

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@ -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

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@ -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; }
}

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@ -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; }
}

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@ -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; }
}

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/**
* 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();
});

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@ -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();
});

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@ -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

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@ -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/")`

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