Rticles: template for technical documents using bookdown

Features

Thesis and articles template
Export word and html document
Word improved template
Bibliography citation
R workflow for data analysis
Scientific graphic quality

Example: https://flavjack.github.io/rticles/

Softwars to install

It is recommended install and create an account if is needed for the following apps, all are free and can be complemented with reproducible research.

R https://cran.rstudio.com/
Rstudio https://rstudio.com/products/rstudio/download/
Git https://git-scm.com/
Zotero https://www.zotero.org/download/
Google account: Gsuit

How to use the template

Use the template or clone the repository

You can use "rticles" as template from GitHub: https://github.com/Flavjack/rticles

You can clone the "rticles" repository using the terminal in Rstudio, for windows user using bash (install Git)

bash
prj="project_name"
info="project info"
gituser="Flavjack"
repo="https://github.com/Flavjack/rticles"
cd
mkdir git
cd git
git clone $repo.git $prj
cd $prj
mv 'rticles.Rproj' $prj.Rproj
curl -u $gituser https://api.github.com/user/repos -d "{\"name\":\"$prj\", \"description\": \"$info\", \"private\": \"true\"}"
git remote rm origin
git commit -m "starting rticles"
git remote add origin https://github.com/$gituser/$prj.git
git push -u origin master
open $prj.Rproj
open .

Document Setup

Run the first chunk in the "index.Rmd" called "setup" and all the packages will be installed automatically.
If all packages are installed correctly shoul be appear the "Build" button in the Rstudio IDE (Integrated Development Environment).
Play the "Build" button and wait until compile the document and if all is okay pop-up window will be appeare with the html version of the document.
You can modify the document changing the text and code in the "index.Rmd" file.
Now you are ready to go and produce your first document!

Folders and files

Type	Name	Removable	Description
folder	cnfg	NO	Contains all document settings.
file	index.Rmd	NO	File that produce the article (code/figures/tables).
file	rticle.Rproj	NO	Rename the file according your repository name.
file	.gitignore	NO	System options.
file	_bookdown.yml	YES	Options to compile the document.
file	_output.yml	YES	html options for the web page.
file	README.rmd	YES	It is the repository description!
folder	files	YES	Images and files that are included in the document.
folder	docs	YES	Files for deploy the web page using github pages).

About the docuent

The document is building with Lorem Ipsum text, and the dataset, examples and tables used are from GerminaR package.

Dataset

The dataset is a germination data example* with a completely randomized design with four replications per treatment under laboratory conditions. The first factor corresponds to five levels of sodium chloride (NaCl) (0, 0.5, 1.0, 1.5 and 2 MPa), and the second factor corresponds to four levels of temperature (25°C, 30°C, 35°C and 40°C).

Source: https://docs.google.com/spreadsheets/d/1QziIXGOwb8cl3GaARJq6Ez6aU7vND_UHKJnFcAKx0VI/edit#gid=137089581

*Lozano-Isla, Flavio, Omar E. Benites-Alfaro, and Marcelo F. Pompelli, ‘GerminaR: An R Package for Germination Analysis with the Interactive Web Application “GerminaQuant for R”’, Ecological Research, 34.2 (2019), 339–46 https://doi.org/10.1111/1440-1703.1275

Bookdown configuration

Thesis cover page yaml

title:  |-  
  Universidad Nacional  
  Facultad de  
  Carrera Profesional de  
  `r if (!knitr:::is_html_output()) knitr::include_graphics('cnfg/icons/logo.png')`  
subtitle:  |-  
  __________________________________________________________  
  TITLE  
  __________________________________________________________  
  *Tesis para Optar el Título *  
author: "Nombres y Apelidos"
date:  |-  
  `r if (knitr:::is_html_output()) {format(Sys.time(), '%d %b %Y %X')}`
  Lugar-País  
  2020

Include section only in the html document

`r if (knitr:::is_html_output()) '# Figures'`

Include section only in the word document

`r if (!knitr:::is_html_output()) '# Figures'`

Blocks

<!-- caution - important - note - tip - warning -->

Texto!

Markdown cheatsheet

# Cita textual

@CiteKey

# Cita contextual

[@CiteKey]

# Fonts

**negrita**

*italica*

upper^indice^

sub~indice~

# Page 

# Salto de página

\newpage 

# Linea horizonatal

***

Import data from Gsheets to R

source("cnfg/setup.r")
sheets_auth(T)
url <- "googlehseet_url"
gs <- as_sheets_id(url)
# browseURL(url)
xl <- gs %>% drive_download("files/fieldbook.xlsx", overwrite = T) %>% pluck(2)
fb <- xl %>% readxl::read_excel("fb")

Insert figure

Create a Gsheet with tabname "fig". The tab should be 3 colums:

figure: name to identify the figure ("chunk_name")
description: title caption
url: image url

fig <- opts_current$get('label')
sheet <- "fig"
title <- xl %>% 
  read_excel(sheet) %>% 
  filter(figure == fig) %>%
  select(description) %>% 
  as_vector()
xl %>% 
  read_excel(sheet) %>% 
  filter(figure == fig) %>%
  select(url) %>% 
  as_vector() %>% 
  include_graphics()
knitr::opts_knit$set(eval.after = 'fig.cap')
# \@ref(fig:)

Cite figure:

@ref(fig:figure_name)

Insert table

Create a Gsheet with tabname "tab". The tab should be 3 colums:

table: tab name with the table ("chunk_name")
description: title caption
note: sub title caption

tab <- opts_current$get("label")
sheet <- "tab"
title <- xl %>% 
  read_excel(sheet) %>% 
  filter(table == tab) %>%
  select(description) %>% 
  as_vector()
note <- xl %>% 
  read_excel(sheet) %>% 
  filter(table == tab) %>%
  select(note) %>% 
  as_vector()
xl %>% 
  read_excel(tab) %>% 
  kable(caption = title) %>% 
  add_footnote(notation = "symbol", label = note)
# \@ref(tab:)

Cite table:

@ref(tab:chunk_name)

Include references

`r if (knitr::is_html_output()){'
# References 
<div id="refs"></div>'}`

`r if (!knitr::is_html_output()){'
# References
<div id="refs"></div>'}`

Include another Rmd file

Include pdf

<embed src="files/file_name.pdf" width="100%" height="500" alt="pdf" pluginspage="http://www.adobe.com/products/acrobat/readstep2.html">

Include video or slides

<iframe width="100%" height="450" src="https://www.youtube.com/embed/video_id" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

Git useful codes

# Import changes from origen
git pull

# Push changes to origen
git add .
git commit -m "message"
git push 

# re-write local files from origen
git fetch --all
git reset --hard origin/master
git pull origin master

# Force push to origen
git push -f origin master

# Undoing Multiple Commits
git reset --hard <commit>

omarbenites/rticles