Overview

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

The mm() function converts a character vector (input) into a desired format (output).
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.

library(mindr)

From Markdown

Convert

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

mm_output$markdown
#>  [1] "# (PART) A"                        "# [Chapter 1](https://pzhao.org) "
#>  [3] "## Section 1.1 "                   "## Section 1.2 "                  
#>  [5] "# Chapter 2"                       "## Section 2.1"                   
#>  [7] "## Section 2.2 "                   "# (PART) B"                       
#>  [9] "# Chapter 3"                       "# (APPENDIX) Appendix "           
#> [11] "# a"                               "# b"

FreeMind 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

Mermaid mind map

cat(mm_output$mermaid, sep = '\n')

R script comments

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

HTML widget

mm_output$widget

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

Generate nested directories

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

## 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

## 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

## 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.

# 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:

---
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:

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')

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

Structure of a html book

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

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

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:

<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>.