_bookdown.yml

output_dir: "html_outputs"
#book_filename: "hbk_files"   # name of folder in output_dir
language:
  ui:
    chapter_name: ""
#new_session: yes   # does not work with rmd_files option
download: [["index.html", "Offline HTML version"]]  
after_chapter_script: "common.R"
description: "The Epi R Handbook is a R reference manual for applied epidemiology and public health."  
delete_merged_file: FALSE         
rmd_files: [
  # INTRO & CONTRIBUTORS
  "index.Rmd",                              # objectives, how to read, authors, acknowledgements

  # ABOUT BOOK
  "new_pages/cat_about_book.Rmd",           # start of new section
  "new_pages/editorial_style.Rmd",          # editorial style
  "new_pages/data_used.Rmd",                # data used

  # BASICS
  "new_pages/cat_basics.Rmd",               # start of new section
  "new_pages/basics.Rmd",
  "new_pages/transition_to_R.Rmd",
  "new_pages/packages_suggested.Rmd",
  "new_pages/r_projects.Rmd",
  "new_pages/importing.Rmd",

  # DATA MANGEMENT
  "new_pages/cat_data_management.Rmd",      # start of new section
  "new_pages/cleaning.Rmd",
  "new_pages/dates.Rmd",
  "new_pages/characters_strings.Rmd",
  "new_pages/factors.Rmd",
  "new_pages/pivoting.Rmd",
  "new_pages/grouping.Rmd",
  "new_pages/joining_matching.Rmd",
  "new_pages/deduplication.Rmd",
  "new_pages/iteration.Rmd",


  # ANALYSIS
  "new_pages/cat_analysis.Rmd",                 # start of new section
  "new_pages/tables_descriptive.Rmd",
  "new_pages/stat_tests.Rmd",
  "new_pages/regression.Rmd",
  "new_pages/missing_data.Rmd",
  "new_pages/standardization.Rmd",
  "new_pages/moving_average.Rmd",
  "new_pages/time_series.Rmd",
  "new_pages/epidemic_models.Rmd",
  "new_pages/contact_tracing.Rmd",
  "new_pages/survey_analysis.Rmd",
  "new_pages/survival_analysis.Rmd",
  "new_pages/gis.Rmd",


  # DATA VIZ
  "new_pages/cat_data_viz.Rmd",             # start of new section
  "new_pages/tables_presentation.Rmd",
  "new_pages/ggplot_basics.Rmd",
  #"new_pages/plot_continuous.Rmd",
  #"new_pages/plot_discrete.Rmd",
  "new_pages/ggplot_tips.Rmd",
  "new_pages/epicurves.Rmd",
  "new_pages/age_pyramid.Rmd",
  "new_pages/heatmaps.Rmd",
  "new_pages/diagrams.Rmd",
  "new_pages/combination_analysis.Rmd",
  #"new_pages/transmission_chains.Rmd",
  "new_pages/phylogenetic_trees.Rmd",
  "new_pages/interactive_plots.Rmd",

  # REPORTS AND DASHBOARDS
  "new_pages/cat_reports_dashboards.Rmd",                 # start of new section
  "new_pages/rmarkdown.Rmd",
  "new_pages/reportfactory.Rmd",
  "new_pages/flexdashboard.Rmd",
  "new_pages/shiny_basics.Rmd",


  # MISCELLANEOUS
  "new_pages/cat_misc.Rmd",                 # start of new section
  "new_pages/writing_functions.Rmd",
  "new_pages/directories.Rmd",
  "new_pages/collaboration.Rmd",
  "new_pages/errors.Rmd",
  "new_pages/help.Rmd",
  #"new_pages/relational_databases.Rmd",
  "new_pages/network_drives.Rmd",
  "new_pages/data_table.Rmd" #,
  #"new_pages/rstudio_advanced.Rmd"
]


# OLD YAML FOR ARCHIVE
# 
# title:  |
#   ![](../images/R Handbook Logo.png)
# author: "Version 1.0.0"
# date: "Produced `r format(Sys.time(), '%A %d %B %Y')`"
# output:s
#   html_document:
#     code_folding: show
#     highlight: zenburn
#     number_sections: no
#     theme: sandstone
#     toc: yes
#     toc_collapse: no
#     toc_depth: 3
#     toc_float: yes
# params:
#   run_page_ind: TRUE
# 
# 
# book_filename: "chapter"
# language:
#   ui:
#     chapter_name: ""
# output_dir: "docs"
# delete_merged_file: FALSE
# rmd_files: [
#   "index.Rmd",
#   "raw_pages/deduplication.Rmd",
# 
# ]
#