---
title: "mindr"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{mindr}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Overview

The **mindr** package provides two functions for generating mind maps or generating other things from mind maps.

1. The `mm()` function converts a character vector (input) into a desired format (output). 
2. The `mmm()` function converts a file (input) into a desired format (output).

The input can be markdown, Freemind mindmap, R script, or directory. The output can be HTML widget, Freemind mindmap, markdown, R script, directory, Mermaid mindmap.

```{r setup, eval=TRUE}
library(mindr)
```

# From Markdown

## Convert

```{r}
input <- system.file('examples/mindr-md.Rmd', package = 'mindr')
input_txt <- readLines(input, encoding = 'UTF-8')
mm_output <- mm(input_txt, output_type = c('mindmap', 'markdown', 'R', 'widget', 'mermaid'))
```

## Markdown headings

```{r}
mm_output$markdown
```

## FreeMind mind map

```{r, eval=FALSE}
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".mm")
writeLines(mm_output$mindmap, output, useBytes = TRUE)
file.show(output) # Open the output file with the default program, if any
```

## Mermaid mind map

```{r, eval=FALSE}
cat(mm_output$mermaid, sep = '\n')
```

## R script comments

```{r, eval=FALSE}
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".R")
writeLines(mm_output$r, output, useBytes = TRUE)
```

## HTML widget

```{r}
mm_output$widget
# output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".html")
# htmlwidgets::saveWidget(mm_output$widget, file = output)
```

## Generate nested directories

```{r, eval=FALSE}
temp_dir <- file.path(tempdir(), 'mindr')
mm_output <- mm(input_txt, output_type = 'dir', root = 'mindr',
                md_list = TRUE, md_braces = TRUE, md_bookdown = TRUE,
                dir_to = temp_dir)
system2('open', temp_dir) # Open the generated directory
```

# From FreeMind mind map

```{r, eval=FALSE}
## Source document ####
input <- system.file('examples/mindr-mm.mm', package = 'mindr')

## file.show(input) # Open the input file with the default program, if any
input_txt <- readLines(input, encoding = 'UTF-8')

## Convert markdown outline, R script, and HTML widget ####
mm_output <- mm(input_txt, output_type = c('markdown', 'R', 'widget'))
mm_output

## Save the output texts as files ####

### markdown outline ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".md")
writeLines(mm_output$markdown, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### R script ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".R")
writeLines(mm_output$r, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### Widget ####
# output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".html")
# htmlwidgets::saveWidget(mm_output$widget, file = output)
# file.show(output) # Open the output file with the default program, if any
# message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

## Generate directory according to the source document ####
temp_dir <- file.path(tempdir(), 'mindr')
mm_output <- mm(input_txt, output_type = 'dir', root = 'mindr',
                dir_to = temp_dir)
# system2('open', temp_dir) # Open the generatecd directory
# unlink(temp_dir, recursive = TRUE) # remove the generated directory
```

# From R script

```{r, eval=FALSE}
## Source document ####
input <- system.file('examples/mindr-r.R', package = 'mindr')

## file.show(input) # Open the input file with the default program, if any
input_txt <- readLines(input, encoding = 'UTF-8')

## Convert to mind map text, markdown text,  and HTML widget ####
mm_output <- mm(input_txt, output_type = c('mindmap', 'markdown',  'widget'))
mm_output

## Save the output texts as files ####

### mind map ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".mm")
writeLines(mm_output$mindmap, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program, if any
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### R markdown ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".Rmd")
writeLines(mm_output$markdown, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program, if any
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### Widget ####
# output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".html")
# htmlwidgets::saveWidget(mm_output$widget, file = output)
# file.show(output) # Open the output file with the default program, if any
# message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

## Generate directory according to the source document ####
temp_dir <- file.path(tempdir(), 'mindr')
mm_output <- mm(input_txt, output_type = 'dir', root = 'mindr',
                dir_to = temp_dir)
# system2('open', temp_dir) # Open the generated directory
# unlink(temp_dir, recursive = TRUE) # remove the generated directory
```

# From directory

```{r, eval=FALSE}
## Source directory ####
input <- system.file(package = 'mindr')

## Convert to mind map text, markdown outline, R script, and HTML widget ####
mm_output <- mm(input, output_type = c('mindmap', 'markdown', 'R', 'widget'))
mm_output

## Save the output texts as files ####

### mind map ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".mm")
writeLines(mm_output$mindmap, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program, if any
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### markdown outline ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".md")
writeLines(mm_output$markdown, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program, if any
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### R script ####
output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".R")
writeLines(mm_output$r, output, useBytes = TRUE)
# file.show(output) # Open the output file with the default program, if any
message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

### Widget ####
# output <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".html")
# htmlwidgets::saveWidget(mm_output$widget, file = output)
# file.show(output) # Open the output file with the default program, if any
# message('Input:  ', input, '\nOutput: ', output)
# file.remove(output) # remove the output file

## Clone the source directory ####
temp_dir <- file.path(tempdir(), 'mindr')
mm_output <- mm(input, output_type = 'dir',
                dir_to = temp_dir)
# system2('open', temp_dir) # Open the generated directory
# unlink(temp_dir, recursive = TRUE) # remove the generated directory
```

# From any format

With the help of pandoc, you can display the outline of any documents that pandoc can convert to Markdown.

```{r, eval=FALSE}
# HTML: here we use the R-FQA webpage
myurl <- 'https://cran.r-project.org/doc/FAQ/R-FAQ.html'
input <- tempfile(pattern = "file", tmpdir = tempdir())
markdown_temp <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".md")
download.file(myurl, destfile = input, method = 'curl')
rmarkdown::pandoc_convert(input, from = 'html', to = "markdown", output = markdown_temp)
input_txt <- readLines(markdown_temp, encoding = 'UTF-8')
mindr::mm(input_txt)

# MS Word: here we use a .docx document shipped by the 'officer' package
input <- system.file('doc_examples/example.docx', package = 'officer')
markdown_temp <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".md")
rmarkdown::pandoc_convert(input, to = "markdown", output = markdown_temp)
input_txt <- readLines(markdown_temp, encoding = 'UTF-8')
mindr::mm(input_txt, md_list = TRUE)

# pdf: here we use the pdf files in the R installation
input <- file.path(R.home(), 'doc/manual/R-intro.pdf')
mmm(input)
input <- file.path(R.home(), 'doc/manual/R-data.pdf')
mmm(input, root = 'R-data', md_maxlevel = 2)

# MS Word: here we use a .docx document shipped by the 'officer' package
input <- system.file('doc_examples/example.docx', package = 'officer')
mmm(input)

# HTML: here we use the R-FQA webpage
input <- file.path(R.home(), 'doc/html/rw-FAQ.html')
mmm(input)
```

# Mermaid mind map

Mermaid mind map is the best choice for using **mindr** in reproducible research. 

## Yaml

Using it in a Quarto document:

``` yaml
---
format:
  html:
    mermaid:
      theme: default # default, dark, forest, and neutral
execute: 
  echo: false
---
```

## Chunk

Use the chunk option `results='asis'`, and write R code in a chunk like:

```{r, eval=FALSE}
mdheadings <- c(
  '# Heading 1',
  '## Heading 1.1',
  '## Heading 1.2',
  '## Heading 1.3',
  '# Heading 2',
  '## Heading 2.1',
  '## Heading 2.2',
  '## Heading 2.3'
)
mmd <- mindr::mm(from = mdheadings, 
                 input_type = 'markdown', output_type = 'mermaid',
                 mmd_shape = c('round', 'cloud'),
                 root = 'Demo')
cat(mmd$mermaid, sep = '\n')
```

```{r, eval=FALSE}
mmd <- mindr::mm(from = mdheadings, 
                 input_type = 'markdown', output_type = 'mermaid', 
                 root = 'Demo')
cat(mmd$mermaid, sep = '\n')
```

## Structure of a html book

```{r, eval=FALSE}
myurl <- 'https://yihui.org/litedown/index.html'
temphtml <- tempfile(pattern = "file", tmpdir = tempdir())
tempmd <- tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".md")
download.file(myurl, destfile = temphtml, method = 'curl')
rmarkdown::pandoc_convert(temphtml, from = 'html', to = "markdown", output = tempmd)
input_txt <- readLines(tempmd, encoding = 'UTF-8')
file.remove(temphtml, tempmd)
headings <- mindr::outline(input_txt[-c(1:(grep('^# Preface', input_txt) - 1))], md_maxlevel = 2, md_braces = TRUE, md_bookdown = TRUE)
headings <- gsub('^([#]+) .*\\}([^\\}]+) \\{.*\\}$', '\\1\\2', headings)
headings[(grep('# Appendix', headings) + 1) : length(headings)] <- paste0('#', headings[(grep('# Appendix', headings) + 1) : length(headings)])
mmd <- mindr::mm(from = headings, input_type = 'markdown', output_type = 'mermaid', root = 'litedown')

cat(mmd$mermaid, sep = '\n')
```

## Structure of a pdf book

```{r, eval=FALSE}
pdffile <- 'my-demo.pdf'
mmd <- mindr::mmm(input_file = pdffile, output_type = 'mermaid')
cat(mmd$mermaid, sep = '\n')

mmd <- mindr::mmm(input_file = pdffile, output_type = 'mermaid', md_maxlevel = 2)
cat(mmd$mermaid, sep = '\n')

mmd <- mindr::mmm(input_file = pdffile, output_type = 'mermaid', md_maxlevel = 1, mmd_shape = 'bang')
cat(mmd$mermaid, sep = '\n')
```

## Structure of a docx document

```{r, eval=FALSE}
infile <- 'my-demo.docx'
mmd <- mindr::mmm(input_file = infile, output_type = 'mermaid')
cat(mmd$mermaid, sep = '\n')
```

## Hyperlink 

For hyperlink in mermaid mindmaps, insert a script anywhere in the Quarto document:

``` html
<script src="https://cdnjs.cloudflare.com/ajax/libs/mermaid/11.12.0/mermaid.min.js"></script>
```

Then use the HTML as the text like `<a href="https://github.com/pzhaonet/mindr">mindr</a>`.

<script src="https://cdnjs.cloudflare.com/ajax/libs/mermaid/11.10.0/mermaid.min.js"></script>