README.md

Introduction { .unnumbered }

This Tinderbox file supports creating a book, manuscript (beta), revealjs with Quarto.

Tinderbox file for Quarto (Web version)

You can easily make qmd files and _quarto.yml with it. Here is an example of books created with Quarto.

• R for Data Science (2e)(@Wickham2016Data)

You can preview Rchunk and Graphs (Mermaid Flowchart and Graphviz) in Tinderbox.

My Workflow is @fig-workflow-graphviz.

//| label: fig-workflow-graphviz
//| fig-cap: Tinderbox Work Flow with Quarto. ( Graphviz version )
//| fig-width: 5
digraph {
    layout=dot
    compound=true
    graph [charset = "UTF-8" splines = "spline" ];
subgraph cluster_A{
                label="Applications"
                spline="curved"
                color="#000000"
                penwidth="1"
                style="filled"
                fillcolor="#e7f3e7"
                fontcolor="#000000"
        A B 

        subgraph cluster_B{
                    label="Tinderbox"
                    color="#000000"
                    penwidth="1"
                    style="filled"
                    fillcolor="#f6e04d"
                    fontcolor="#000000"
                    URL="https://www.eastgate.com/Tinderbox/"


        subgraph cluster_C{
                        label="Demo_TBX_for_Quarto.tbx"
                        color="#000000"
                        penwidth="1"
                        style="filled"
                        fillcolor="#ffffff"
                        fontcolor="#000000"
                        URL="https://github.com/fryagbye/tinderboxwithquarto"
        C D E 
}

}

}

subgraph cluster_D{
                label="Quarto"
                color="#000000"
                penwidth="1"
                style="filled"
                fillcolor="#fff4e6"
                fontcolor="#000000"
        F G H 
}

subgraph cluster_E{
                label="Output"
                color="#000000"
                penwidth="1"
                style="filled"
                fillcolor="#ffffff"
                fontcolor="#000000"
        I J K 
}


A [ style="filled"  label="Bookends" color="#000000", penwidth="1", fillcolor="#fcbd63", fontcolor="#000000", URL="https://www.sonnysoftware.com/bookends-for-mac"]
B [ style="filled"  label="Snippety" color="#990000", penwidth="1", fillcolor="#5c9dfe", fontcolor="#000000", URL="https://snippety.app/"]
C [ style="filled"  label="Mermaid" color="#000000", penwidth="1", fillcolor="#c735e9", fontcolor="#ffffff", URL="https://mermaid.js.org/"]
D [ style="filled"  label="Graphviz" color="#000000", penwidth="1", fillcolor="#30638d", fontcolor="#ffffff", URL="https://graphviz.org/"]
E [ style="filled"  label="Preview \nwith Rscript" ]
F [ style="filled"  label="R Studio" color="#000000", penwidth="1", fillcolor="#80a9d7", fontcolor="#000000", URL="https://posit.co/products/open-source/rstudio/"]
G [ style="filled"  label="RMarkdown ( .qmd )" color="#000000", penwidth="1", fillcolor="#74bbff", fontcolor="#000000"]
H [ style="filled"  label="quarto CLI" color="#000000", penwidth="1", fillcolor="#74bbff", fontcolor="#000000", URL="https://quarto.org/"]
I [ style="filled"  label="Book" color="#000000", penwidth="1", fillcolor="#93dd93", fontcolor="#000000"]
J [ style="filled"  label="Manuscript" color="#000000", penwidth="1", fillcolor="#93dd93", fontcolor="#000000"]
K [ style="filled"  label="revealjs" color="#d53f8c", penwidth="1", fillcolor="#f2e142", fontcolor="#000000"]

A -> C [fillcolor="#cbd9d7" fontcolor="#000000" lhead = "cluster_C" ltail = "cluster_A" ]
B -> E [fillcolor="#cbd9d7" fontcolor="#000000" lhead = "cluster_C" ]
D -> G [fillcolor="#cbd9d7" fontcolor="#000000" lhead = "cluster_D" ltail = "cluster_C" ]
F -> H [label = "Call" fillcolor="#cbd9d7" fontcolor="#000000" ]
G -> F [label = "Read qmd files" fillcolor="#cbd9d7" fontcolor="#000000" ]
G -> H [label = "Call" fillcolor="#cbd9d7" fontcolor="#000000" ]
H -> I [label = "Export" fillcolor="#cbd9d7" fontcolor="#000000" ]
H -> J [label = "Export" fillcolor="#cbd9d7" fontcolor="#000000" ]
H -> K [label = "Export" fillcolor="#cbd9d7" fontcolor="#000000" ]
}

Usage environment {#sec-usage-environment }

Please refer to the output results of quato check.

• Quarto is using the released version 1.7.13 (pre-release)¹.

• R is version 4.4.2.

• I use luaLatex for output in Japanese. I have installed MacTex because TinyTex doesn't include it.

• It may be better to uninstall TinyTex.

• I have set it to use the lightbox extension ( included in Quarto v1.4+.).

*I have set it to use the quarto-live extension for revealjs. (quarto live)

quarto check

# Quarto check output
Quarto 1.7.13

[✓] Checking environment information...

      Quarto cache location: /Users/tk4o2ka/Library/Caches/quarto

[✓] Checking versions of quarto binary dependencies...

      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK

[✓] Checking versions of quarto dependencies......OK


[✓] Checking Quarto installation......OK

      Version: 1.7.13
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK

      Chromium: 869685
      TinyTeX: (not installed)

[✓] Checking LaTeX....................OK

      Using: Installation From Path
      Path: /usr/local/texlive/2024/bin/universal-darwin
      Version: 2024

[✓] Checking Chrome Headless....................OK

      Using: Chrome found on system
      Path: /Applications/Google Chrome.app/Contents/MacOS/Google Chrome
      Source: MacOS known location

[✓] Checking basic markdown render....OK


[✓] Checking Python 3 installation....OK

      Version: 3.13.2
      Path: /opt/homebrew/opt/python@3.13/bin/python3.13
      Jupyter: (None)
      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter
      There is an unactivated Python environment in .venv. Did you forget to activate it?

[✓] Checking R installation...........OK

      Version: 4.4.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
      knitr: 1.49
      rmarkdown: 2.29

[✓] Checking Knitr engine render......OK

Installed packages {#sec-installed-packages }

#| echo: false
#| message: false
pacman::p_load(tidyverse, gt)
installed.packages() |> 
  as_tibble() |> 
  select(Package, Version, Built) |> 
  gt::gt()

Package List

Name	Version	Built
askpass	1.2.0	4.4.0
backports	1.4.1	4.4.0
base	4.4.0	4.4.0
base64enc	0.1-3	4.4.0
bigD	0.2.0	4.4.0
bit	4.0.5	4.4.0
bit64	4.0.5	4.4.0
bitops	1.0-7	4.4.0
blob	1.2.4	4.4.0
boot	1.3-30	4.4.0
brew	1.0-10	4.4.0
brio	1.1.5	4.4.0
broom	1.0.5	4.4.0
bslib	0.7.0	4.4.0
cachem	1.0.8	4.4.0
callr	3.7.6	4.4.0
cellranger	1.1.0	4.4.0
class	7.3-22	4.4.0
cli	3.6.2	4.4.0
clipr	0.8.0	4.4.0
cluster	2.1.6	4.4.0
codetools	0.2-20	4.4.0
collections	0.3.7	4.4.0
colorspace	2.1-0	4.4.0
commonmark	1.9.1	4.4.0
compiler	4.4.0	4.4.0
conflicted	1.2.0	4.4.0
cpp11	0.4.7	4.4.0
crayon	1.5.2	4.4.0
curl	5.2.1	4.4.0
cyclocomp	1.1.1	4.4.0
data.table	1.15.4	4.4.0
datasets	4.4.0	4.4.0
DBI	1.2.2	4.4.0
dbplyr	2.5.0	4.4.0
desc	1.4.3	4.4.0
digest	0.6.35	4.4.0
downlit	0.4.3	4.4.0
dplyr	1.1.4	4.4.0
dtplyr	1.3.1	4.4.0
ellipsis	0.3.2	4.4.0
evaluate	0.23	4.4.0
fansi	1.0.6	4.4.0
farver	2.1.1	4.4.0
fastmap	1.1.1	4.4.0
fontawesome	0.5.2	4.4.0
forcats	1.0.0	4.4.0
foreign	0.8-86	4.4.0
fs	1.6.4	4.4.0
gargle	1.5.2	4.4.0
generics	0.1.3	4.4.0
ggplot2	3.5.1	4.4.0
gitcreds	0.1.2	4.4.0
glue	1.7.0	4.4.0
googledrive	2.1.1	4.4.0
googlesheets4	1.1.1	4.4.0
graphics	4.4.0	4.4.0
grDevices	4.4.0	4.4.0
grid	4.4.0	4.4.0
gt	0.10.1	4.4.0
gtable	0.3.5	4.4.0
gtExtras	0.5.0	4.4.0
haven	2.5.4	4.4.0
highr	0.10	4.4.0
hms	1.1.3	4.4.0
htmltools	0.5.8.1	4.4.0
htmlwidgets	1.6.4	4.4.0
httr	1.4.7	4.4.0
ids	1.0.1	4.4.0
isoband	0.2.7	4.4.0
jquerylib	0.1.4	4.4.0
jsonlite	1.8.8	4.4.0
juicyjuice	0.1.0	4.4.0
kableExtra	1.4.0	4.4.0
KernSmooth	2.23-22	4.4.0
knitr	1.46	4.4.0
labeling	0.4.3	4.4.0
languageserver	0.3.16	4.4.0
lattice	0.22-6	4.4.0
lazyeval	0.2.2	4.4.0
lifecycle	1.0.4	4.4.0
lintr	3.1.2	4.4.0
lubridate	1.9.3	4.4.0
magrittr	2.0.3	4.4.0
markdown	1.12	4.4.0
MASS	7.3-60.2	4.4.0
Matrix	1.7-0	4.4.0
memoise	2.0.1	4.4.0
methods	4.4.0	4.4.0
mgcv	1.9-1	4.4.0
mime	0.12	4.4.0
modelr	0.1.11	4.4.0
munsell	0.5.1	4.4.0
nlme	3.1-164	4.4.0
nnet	7.3-19	4.4.0
nvimcom	0.9.42	4.4.0
openssl	2.1.2	4.4.0
pacman	0.5.1	4.4.0
paletteer	1.6.0	4.4.0
parallel	4.4.0	4.4.0
pillar	1.9.0	4.4.0
pkgbuild	1.4.4	4.4.0
pkgconfig	2.0.3	4.4.0
pkgload	1.3.4	4.4.0
prettyunits	1.2.0	4.4.0
prismatic	1.1.2	4.4.0
processx	3.8.4	4.4.0
progress	1.2.3	4.4.0
ps	1.7.6	4.4.0
purrr	1.0.2	4.4.0
R.cache	0.16.0	4.4.0
R.methodsS3	1.8.2	4.4.0
R.oo	1.26.0	4.4.0
R.utils	2.12.3	4.4.0
R6	2.5.1	4.4.0
ragg	1.3.0	4.4.0
rappdirs	0.3.3	4.4.0
RColorBrewer	1.1-3	4.4.0
Rcpp	1.0.12	4.4.0
reactable	0.4.4	4.4.0
reactR	0.5.0	4.4.0
readr	2.1.5	4.4.0
readxl	1.4.3	4.4.0
rematch	2.0.0	4.4.0
rematch2	2.1.2	4.4.0
remotes	2.5.0	4.4.0
reprex	2.1.0	4.4.0
rex	1.2.1	4.4.0
rlang	1.1.3	4.4.0
rmarkdown	2.26	4.4.0
roxygen2	7.3.1	4.4.0
rpart	4.1.23	4.4.0
rprojroot	2.0.4	4.4.0
rstudioapi	0.16.0	4.4.0
rvest	1.0.4	4.4.0
sass	0.4.9	4.4.0
scales	1.3.0	4.4.0
selectr	0.4-2	4.4.0
spatial	7.3-17	4.4.0
splines	4.4.0	4.4.0
stats	4.4.0	4.4.0
stats4	4.4.0	4.4.0
stringi	1.8.3	4.4.0
stringr	1.5.1	4.4.0
styler	1.10.3	4.4.0
survival	3.5-8	4.4.0
svglite	2.1.3	4.4.0
sys	3.4.2	4.4.0
systemfonts	1.0.6	4.4.0
tcltk	4.4.0	4.4.0
textshaping	0.3.7	4.4.0
tibble	3.2.1	4.4.0
tidyr	1.3.1	4.4.0
tidyselect	1.2.1	4.4.0
tidyverse	2.0.0	4.4.0
timechange	0.3.0	4.4.0
tinytex	0.50	4.4.0
tools	4.4.0	4.4.0
tzdb	0.4.0	4.4.0
utf8	1.2.4	4.4.0
utils	4.4.0	4.4.0
uuid	1.2-0	4.4.0
V8	4.4.2	4.4.0
vctrs	0.6.5	4.4.0
viridisLite	0.4.2	4.4.0
vroom	1.6.5	4.4.0
withr	3.0.0	4.4.0
xfun	0.43	4.4.0
xml2	1.3.6	4.4.0
xmlparsedata	1.0.5	4.4.0
yaml	2.3.8	4.4.0

RStudio Session information {#sec-session-information }

#| echo: false
sessionInfo()

Platform: aarch64-apple-darwin20 Running under: macOS 15.1.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo tzcode source: internal attached base packages:

[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):

[1] compiler_4.4.0 tools_4.4.0

Setting {#sec-setting }

1. Setting up with "TBXConfig" note

   You need to change the values of the following "TBXConfig" attributes for configuration.

• $Indent_Charactor → Set the symbol representing the depth of indentation. ( default value = ★ )

• $ExList → List of notes excluded from cross-reference search ( default value = "List and Agent etc" )

• $ProjectContainer → Book Project Path for CrossRef Search and Label Lists

{#fig-projectcontaierexample fig-alt="Project Contaier Example" fig-align="left" width=80%}

• $ExportFolder → Path of exported files.

{#fig-exportfoldersetting fig-alt="Export Folder Setting" fig-align="left" width=50%}

• $ToggleTOC → Toggle for Generating TOC. ( default value = false ) You can use quarto option for TOC in _quarto.yml.

• $Q_TableOfContainsNote → $Name of TOC note. ( default value = Table of Contents )

• $Rename_in → translate-shell option setting `[SOURCES]:[TAGETS]. ( default value = ja:en )

• $Q_PDFEngine → Setting for pdf engine This file is tested only with lualatex. ( default value = lualatex )

• $OutlineBaseControl → Adjustment of section levels in Markdown. ( default = 1 )

  $OutlineBaseControl is enabled in Manuscript and revealjs project. This attribute is used in pSubfolderManuscript and pSubfolderRevealjs note. e.g.

  • $OutlineBaseControl = 1 → ## Title

  • $OutlineBaseControl = 1 → # Title

• $RScriptLibraryPath → R Library Resource Path ( default Value )

  {#fig-rscript-libpath fig-alt="Rscript Library Path" fig-align="left" width=80%}

2. Making a _quarto.yml

   You can change the values of attributes of the "_quarto" note to change quarto options. The quarto options are attributes that start with "Q" in this file. The initial setting specified in _quarto.yml is for Japanese output. Please refer to Quarto Book Structure and PDF Basics in detail. If you use Custom Translations, you need to make $Q_Has_Language_YML true and set $Q_Language_YML for the filename. The "_language" note in this file is for translating to Japanese.

3. Changing the _common.R file. ( optional )

   You can set up knitr package options for R chunk.

Book format {#sec-book-format }

Make notes {#sec-make-notes }

1. Make notes with Prototype pNote and pSubnote

   pNote is for Sections and pSubnote is for Subsections. Please set the Prototype of pNote to level 1 and pSubnote below level.

• When creating a note, please enter "#pNote" or "#pSubnote" following the title. (or apply the pNote Prototype or pSubnote to notes you make )

  e.g. Note title -> わが輩は猫である#pSubnote

  • The note title ($Name) is the header for pNote or pSubnote.

• Depending on the hierarchy level, the level of the header also changes.

  e.g. If the title of pSubnote in level 2 depth is "わが輩は猫である", it will be output as follows when exporting.

  ## わが輩は猫である

2. Index.qmd

   In the quarto book format, only one index.qmd is required, $IsIndexqmd of the index.qmd is set to true. You can make the note for index.qmd with the pIndexQmd Prototype.

Special Notes Prototype

1. pReferenceQmd

   This prototype is inherited from pNote and $Text has a div with id refs to call a works cited list (below). (Quarto Bibliography Generation) ::: {#refs} :::

2. pAppendixQmd

   This prototype is inherited from pNote and $IsAppendix is true.

Chunks and Graphs {#sec-chunks-and-graphs }

1. R chunk and Python chunk notes

You can create a pRChunk for an R chunk and a pPChunk for a Python chunk. The “Chunk & Graph: Make Chunk List” stamp generates a tag like ＜Lang:Tag Label➡️Figure Label＞. These tags can be used to reference R chunks, Python chunks, Mermaid diagrams, or Graphviz code. Please do not insert tags in the middle of a sentence.

If tags called in your notes are changed or deleted, the warning is shown. you can suppress the warning with $SuppresTagDetectWaring in the project container note.

2. Rendered Preview in Text Pane(R chunks, Mermaid diagrams, and Graphviz only)

You can check the results of the code executed within an R chunk in the Preview screen. Similarly, the results of Mermaid and Graphviz code can also be displayed. However, this is not possible for Python.

Rename HTMLExportFileName of a note with translation {#sec-translate-and-rename }

There is a stamp "Notes: Tranlate Section Labels" that translates the Japanese title ($Name) into English and automatically sets $HTMLExportFileName ². and you can set $SectionLabel with stamp "Set: Section Label". The labels of the section cannot be duplicated, so please modify them manually if necessary. In addition, you can change the language to be translated with $Rename_in in the TBX configuration note (TBXConfig). ( By default, from Japanese to English).

> brew install translate-shell

Part in Book format {#sec-part-in-book-format }

For Part, please refer to Quarto's "Book Structure" reference. pNote is compatible with quarto's Part or Chapter. If pNote is at the bottom of pNote, the top pNote will be Part (Part ○), and the lower pNote will be Chapter (Chapter ○). You can place pNote at hierarchical level 2 only if you are under pNote of hierarchy level 1. In this case, the hierarchy level and header level are different, so the header level is set based on the user attribute $OutlineDepthBase. pNote, which is treated as a Part, is turned on (true) for $Is_Part_qmd. The lower pNote contains the export file name (e.g. filename.qmd) of the pNote, which is Part, in $Part_file. If a Part note is empty, only the title ($Name) of the note is reflected in _quarto.yml, as shown in the "Dice" in the example below. If the dice.qmd is not empty, the part title (as a level one header) as well as some introductory content for the part.

#_quarto.yml
chapters:
  - index.qmd
  - preface.qmd
  - part: "Dice" # if $Text("Dice").wordCount == 0 
  chapters: 
    - basics.qmd
    - packages.qmd

#_quarto.yml
chapters:
  - index.qmd
  - preface.qmd
  - part: dice.qmd # if $Text("Dice").wordCount >0 
    chapters: 
      - basics.qmd
      - packages.qmd

The figure below shows the export example when Part is supported and the output result of _quarto.yml.

Cross-Reference using Ziplink {#sec-cross-reference-using-ziplink }

In Quarto, labeled diagrams, tables, etc., can be mutually quoted. Label Lists are collected automatically (or manually). ³

Convert it to a quotable title (citation name starting with @) and create a note for the corresponding part. Tinderbox's Ziplink function ⁴ is a function for easily pasting links to notebooks. It is diverted to make it easy to enter the quoted name. This makes it relatively easy to find and enter the quoted label even if the number increases.

How to set the label of the diagram {#sec-how-to-set-the-label }

Image link in markdown format {#sec-image-link-in-markdown-format }

Recognize and collect labels in a format that extends the markdown. {#fig-test fig-alt="test" fig-align="left" width=100%}

{#fig-test fig-alt="test" fig-align="left" width=100%}

R chunk {#sec-r-chunk }

Automatically recognize and collect R chunk labels in the following format (#| label: fig-xxx-ooo, etc.). The method of specifying a label in the curly bracket ({r fig-xxx-ooo}) is not supported. In the following example, you can quote @fig-airquality.

#| warning: false
#| label: fig-airquality
#| fig-cap: Temperature and ozone level.
#| fig-width: 5
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess")

Python chunk

#| label: fig-numpy
#| fig-width: 5
import numpy as np
a = np.arange(15).reshape(3, 5)
a

#| label: fig-matplotlib
#| fig-width: 5
import matplotlib.pyplot as plt
fig = plt.figure()
x = np.arange(10)
y = 2.5 * np.sin(x / 20 * np.pi)
yerr = np.linspace(0.05, 0.2, 10)

plt.errorbar(x, y + 3, yerr=yerr, label='both limits (default)')
plt.errorbar(x, y + 2, yerr=yerr, uplims=True, label='uplims=True')
plt.errorbar(x, y + 1, yerr=yerr, uplims=True, lolims=True,
             label='uplims=True, lolims=True')

upperlimits = [True, False] * 5
lowerlimits = [False, True] * 5
plt.errorbar(x, y, yerr=yerr, uplims=upperlimits, lolims=lowerlimits,
             label='subsets of uplims and lolims')

plt.legend(loc='lower right')
plt.show(fig)

How to set the label of the table {#sec-how-to-set-the-label-of-the-table }

There are multiple ways to specify labels, but they are only supported if it is a table in markdown format and the label name is above, as shown in the example below.⁵

:明度・彩度の修飾子 {#tbl-brightness-saturation}

 
|項目|効果|
|----|------------|
|dark|暗くする|
|darker|より暗くする|
|darkest|最も暗くする|
|light| 明るくする|

:明度・彩度の修飾子 {#tbl-brightness-saturation}

項目	効果
dark	暗くする
darker	より暗くする
darkest	最も暗くする
light	明るくする

Equations {#sec-equations }

Equation Example Black-Scholes (@eq-black-scholes) is a mathematical model that seeks to explain

$$ ma^{2} \mathrm S^{2} \frac{\partial^{2} \mathrm C}{\partial \mathrm S^2} + \mathrm r \mathrm S \frac{\partial \mathrm C}{\partial \mathrm S}\ = \mathrm r \mathrm C $$

$$
ma^{2} \mathrm S^{2}
\frac{\partial^{2} \mathrm C}{\partial \mathrm S^2}  + \mathrm r \mathrm S \frac{\partial \mathrm C}{\partial \mathrm S}\ =  \mathrm r \mathrm C 
$$

How to quote {#sec-how-to-quote }

If you enter two square brackets "[[", the list will be displayed, so please enter a part of the label name. As the candidates are narrowed down, select the citation label you want to enter.

:How to quote

Types of quotations	Lable	Quote
Chapters, Sections etc.	#sec-	@sec-
Figures	#fig- #| label:fig- %%| label:fig- //| label:fig-	@fig-
Charts	#tbl-	@tbl-
Equations	#eq-	@eq-

Dummy links for cross-reference {#sec-add-dummy-links-to-cross-ref }

You can create dummy links showing where each cross-reference, starting with the @ symbol in the section, figure, and table label lists, is cited.

1. execute the "Labels: Make Dummy Link Data For Cross-Reference" stamp

2. select cross-ref label notes ( start with "@" ) and execute the "Labels: Dummy Link between Reference and Selected notes" stamp.

Restrictions on quoted labels {#sec-restrictions-on-quoted-labels }

• The label before change or deletion remains because it cannot be detected even if the quoted label name is changed or deleted.

• Cross-ref detection is carried out by regular expression. If it is executed in the middle of input, it will be duplicated with a short label.

In this case, if necessary, delete the quoted label name in Stamp and perform the detection manually by following the steps below.

1. Labels: Clear Cross-Reference List（Delete all citation labels under the Reference List.）

2. Labels: Make Cross-Reference List（Re-detect the quoted label.）

Export and Render {#sec-export }

1. Export _quarto.yml

You can change the output format to "pdf" or "html" with the stamp "Change quarto.yml template". If you use a _language.yml, you export "_language" note (optional. See @sec-setting Setting)

2. Export .qmd files ( pNote notes only)

The pSubnote at the bottom of pNote at the time of output is all output as one qmd file in the state contained when pNote is exported. Therefore, it is OK to export by selecting only pNote to output. In addition, pSubnote does not require output, but if you export, it is set to output as a text file (extension .txt). If you select the pNote notes below "Export Agent" and output it, then execute the "Move qmd files" stamp, you can overwrite the qmd file directly to ./output (=$HTMLExportFileName of the your project folder) ( @fig-after ). This is a method to avoid having to consider the folder structure when referencing image files with a relative path.

{#fig-before}

{#fig-after}

qmd files are moved to the project path by stamp

3. Preview HTML output.

# preview for only html output
> quarto preview projectname

4. Render pdf or html.

> quarto render

You can use RStudio for preview and render.

Example {#sec-example }

Example PDF

Manuscript format {#sec-manuscript-format }

Make sub-project folder {#sec-make-manuscript-subproject }

Make a note for the sub-project with pSubfolderManuscript like this ( _quarto_manuscript ).

Make notes

The manuscript has only one qmd file. The qmd file name is set in _quarto.yml (_quarto_manuscript).

Front Matter and Subnote

1. pFrontmatterManuscript

   This is a qmd file that contains a Front Matter. When you export, it has contents of descendants. You can set data for author(s) with the path of note with pAuther notes. ( like Authors )

2. pSubnoteManuscript

   This is a dummy file for pFrontmatterManuscript. The markdown level depends on the indent level and $OutlineBaseControl of of the subproject folder.

$OutlineDepthBase * "#"  + $OutlineBaseControl(collect(ancestors,$Path)[-1]))

Export and Render {#sec-export }

1. Export _quarto.yml

You can change the output format to "pdf" or "html" with the stamp "Change quarto.yml template". If you use a _language.yml, you export "_language" note (optional. See @sec-setting Setting)

2. Export .qmd files ( pNote notes only)

The pSubnote at the bottom of pNote at the time of output is all output as one qmd file in the state contained when pNote is exported. Therefore, it is OK to export by selecting only pNote to output. In addition, pSubnote does not require output, but if you export, it is set to output as a text file (extension .txt). If you select the pNote notes below "Export Agent" and output it, then execute the "Move qmd files" stamp, you can overwrite the qmd file directly to ./output (=$HTMLExportFileName of the your project folder) ( @fig-after ). This is a method to avoid having to consider the folder structure when referencing image files with a relative path.

{#fig-before}

{#fig-after}

qmd files are moved to the project path by stamp

3. Preview HTML output.

# preview for only html output
> quarto preview projectname

4. Render pdf or html.

> quarto render

You can use RStudio for preview and render.

revealjs format {#sec-revealjs-format }

Make sub-project folder {#sec-make-manuscript-subproject }

Make a note for the sub-project with pSubfolderManuscript like this ( _quarto_manuscript ).

Make notes

The manuscript has only one qmd file. The qmd file name is set in _quarto.yml (_quarto_manuscript).

Front Matter and Subnote

1. pFrontmatterManuscript

   This is a qmd file that contains a Front Matter. When you export, it has contents of descendants. You can set data for author(s) with the path of note with pAuther notes. ( like Authors )

2. pSubnoteManuscript

   This is a dummy file for pFrontmatterManuscript. The markdown level depends on the indent level and $OutlineBaseControl of of the subproject folder.

$OutlineDepthBase * "#"  + $OutlineBaseControl(collect(ancestors,$Path)[-1]))

Mermaid flowchart (optional) {#sec-mermaid-flowchart }

This file can generate Mermaid flowchart from notes, links.

• Container notes -> Subgraphs ( pMFSubgraph )

• Non Container notes -> Nodes ( pMFNode)

Work Flow is a sample of Mermaid flowchart.
Please check it in Map view. You need to use pre-release version ⁶

How to use {#sec-how-to-use-mermaid }

1. You make a container noto for Flowchart and set pMFContainer.

2. You make notes ( pMFNode) and links.

3. You choose a direction for drawing like TD or LR.($M_Direction)

4. Run the stamp ( Mermaid: Make a Flowchart ).

5. Prototypes of container notes has a child note change from pMFNode to pMFContainer automatically by the stamp.

6. The note (pMFContainer) has the code for mermaid flowchart.

Supported shapes {#sec-supported-shapes }

• rectangle (<- normal and other shapes)

• rounded

• oval

• lozenge

• diamond

• hex

Supported line types (Priority) {#sec-supported-line-types-priority }

• normal --> (4th)

• bold ==> (3rd)

• dotted -.-> (2nd)

• invisible ~~~ (1st)

Supported arrow types {#sec-supported-arrow-types }

• arrow only

Example {#sec-mermaid-example }

%%| label: fig-flowchart
%%| fig-width: 5
flowchart TB
    A["Christmas"] -->|"Get money"| B["Go shopping"]
    B["Go shopping"] -->  Sub1["Let me think"]
    C["Laptop"]
    D["iPhone"]
    E["Car"]
 subgraph Sub1["Let me think"]
    C
    D
    E
end 
 subgraph Sub2["Subgraph"]
    A
    B
    Sub1
end 
    Sub1["Let me think"] -->|"One"| C["Laptop"]
    Sub1["Let me think"] -->|"Two"| D["iPhone"]
    Sub1["Let me think"] -->|"Three"| E["Car"]
%% Styles & Links
    style Sub2 fill:#eeebe9,color:#000000,stroke:#dc490b,stroke-width:2px

Graphviz β version (optional) {#sec-graphviz-optional }

How to use {#sec-how-to-use-graphviz }

1. You make a container noto for the graph and set pGContainer.

2. You make notes ( pGNode) and links. You can't make links to cluster (subgraph).

3. You choose a direction for drawing like TB or LR.($GG_Rankdir)

4. You can choose a Layout Engin like dot, neato, fdp and so on.

5. Change attributes for Graphviz.

   • Attributes starting with GG_ are for the Subgraph ( cluster ) options

   • Attributes starting with GN_ are for the Note options

   • Attributes starting with GE_ are for the Edge options

6. Run the stamp ( Graphviz: Make a Dot graph ).

7. Prototypes of container notes have a child note change from pGNode to pGContainer automatically by the stamp.

8. The note (pGContainer) has the code for Graphviz.

Example {#sec-graphviz-example }

@fig-workflow-graphviz and @fig-Test.

//| label: fig-Test
//| fig-cap: Graphviz Test
//| fig-width: 5
digraph {
    layout=dot
    compound=true
    graph [charset = "UTF-8" ];
subgraph cluster_A{
                label="Cluster B"
                color="#000000"
                penwidth="1"
                style="filled"
                fillcolor="#ffffff"
                fontcolor="#000000"
        "node2" "node4" "node6" "node8" 
}

subgraph cluster_B{
                label="Cluster A"
                color="#000000"
                penwidth="1"
                style="filled"
                fillcolor="#ffffff"
                fontcolor="#000000"
        "node1" "node3" "node5" "node7" 
}


"node2" [ style="filled" ]
"node4" [ style="filled" ]
"node6" [ style="filled" ]
"node8" [ style="filled" ]
"node1" [ style="filled" ]
"node3" [ style="filled" ]
"node5" [ style="filled" ]
"node7" [ style="filled" ]

"node1" -> "node2" [label = "1" fillcolor="#ffffff" fontcolor="#000000" ]
"node3" -> "node4" [label = "2" fillcolor="#ffffff" fontcolor="#000000" ltail = "cluster_B" ]
"node5" -> "node6" [label = "3" fillcolor="#ffffff" fontcolor="#000000" lhead = "cluster_A" ]
"node7" -> "node8" [label = "4" fillcolor="#ffffff" fontcolor="#000000" lhead = "cluster_A" ltail = "cluster_B" ]
}

References {#sec-references }

Anderson, Mark. 2024. “A Tinderbox Reference File.” 2024. Wickham, Hadley, and Garrett Grolemund. 2016. R for Data Science: Import, Tidy, Transform, Visualize, and Model Data. “O’Reilly Media, Inc.”

Restrictions { .appendix }

It seems that the section label customization function cannot be used in the latest release ref. Cross-references on unnumbered pages fail (PDF) or are mislabeled (HTML). If you turn on $IsUnnumbered and $HasSectionLabel, the display of the quote will be fixed to the number + title, so please turn off $IsUnnumbered. Please do not use parentheses in note titles. The section label list is not being generated correctly.

Footnotes

1. Since the old headless mode has been removed from Chrome 132, Quarto v1.7.13 or later is required. ↩

2. Translate-shell installation required. ↩

3. The diagrams and tables are extracted in regular expressions. ↩

4. Please refer to "Text link creation via the Ziplinking method" in A Tinderbox Reference File.(@Anderson2024Tinde) ↩

5. For other formats, please refer to quarto cross-reference. ↩

6. Since the old headless mode has been removed from Chrome 132, Quarto v1.7.13 or later is required.(Transition to Chrome new headless mode · Issue #10532 · quarto-dev/quarto-cli) ↩