Towards Streamlined Scientific Reporting: Rmarkdown and Shiny Templates for Scientists

Highly customizable rmarkdown theme

Built to maximize efficiency, whitespace and style

# install

# load library

Example output:

Take 2, a rebuild of sciRmdTheme

Example .Rmd

title: “Scientific Report Example”
highlighter: “dracula” # code theme
codelang: “r” #default is R, you may add js php python and so on
themecolor: brown #specify a theme color
author: “Obinna Obianom”
date: “r Sys.Date()
toc: TRUE
self_contained: TRUE
link-citations: yes
summaryslide: TRUE # whether to show summary slide on top
lightsummaryslide: FALSE # whether to make summary slide light
- Fusce id velit ut tortor pretium viverra. Lectus urna duis convallis convallis tellus id interdum.
- Erat imperdiet sed euismod nisi porta lorem. Sed viverra tellus in hac habitasse platea dictumst.
- Turpis egestas integer eget aliquet nibh praesent tristique. Ultricies integer quis auctor elit.
- Dictum varius duis at consectetur lorem donec massa. Convallis aenean et tortor at risus viverra.
- Egestas tellus rutrum tellus pellentesque eu tincidunt tortor aliquam nulla. Aliquet bibendum enim facilisis gravida neque.
- Porta lorem mollis aliquam ut porttitor leo a diam. Sit amet mattis vulputate enim nulla aliquet porttitor lacus.
- Vestibulum rhoncus est pellentesque elit ullamcorper dignissim. Risus feugiat in ante metus dictum.


Sample text implemented in LaTeX and HTML/CSS

{r, message=FALSE} library(ggplot2) mtcars2 <- mtcars mtcars2$am <- factor( mtcars$am, labels = c('automatic', 'manual') ) ggplot(mtcars2, aes(hp, mpg, color = am)) + geom_point() + geom_smooth() + theme(legend.position = 'bottom')


Highlighter options (Enlighterjs)

Enlighter (enlighter, standard) - Enlighter`s default Theme
Classic (classic) - SyntaxHighlighter inspired
Bootstrap (bootstrap4) - Bootstrap 4 inpired themes, high contrast
Beyond (beyond) - BeyondTechnology Theme
Godzilla (godzilla) - A MDN inspired Theme
Eclipse (eclipse) - Eclipse inspired
MooTwo (mootwo) - Inspired by the MooTools Website
Droide (droide) - Modern, minimalistic
Minimal (minimal) - Bright, High contrast
Atomic (atomic) - Dark, Colorful
Dracula (dracula) - Dark, using official draculatheme colorscheme
Rowhammer (rowhammer) - Light, Transparent, divided rows

Languages for codelang

ABAP (abap)
Apache HTTPD (apache)
Assembly (assembly, asm)
AVR Assembly (avrassembly, avrasm)
Windows Batch/Bat (bat,batch,cmd)
C/C++ (c,cpp, c++)
C# (csharp)
CSS (css)
Cython (cython)
CordPro (cordpro)
diff (diff)
Dockerfile (docker, dockerfile)
Generic (generic, standard) - default highlighting scheme
Groovy (groovy)
Go (go, golang)
HTML (html)
Ini (ini, conf)
Java (java)
Javascript (js, javascript, jquery, mootools, ext.js)
JSON (json)
JSX (jsx)
Kotlin (kotlin)
LATEX (latex)
LESS (less)
lighttpd (lighttpd)
LUA (lua)
MariaDB (mariadb)
Markdown (gfm, md, markdown)
Matlab/Octave (octave, matlab)
MSSQL (mssql)
NGINX (nginx)
NSIS (nsis)
Oracle Database (oracledb)
PHP (php)
Powerhsell (powershell)
Prolog (prolog)
Python (py, python)
PureBasic (purebasic, pb)
QML (qml)
R (r)
RAW (raw) - raw code without highlighting with EnlighterJS container styles!
RouterOS/SwitchOS (routeros)
Ruby (ruby)
Rust (rust)
Scala (scala)
SCSS (scss, sass)
Shellscript (shell, bash)
Generic SQL (sql)
Squirrel (squirrel)
Swift (swift)
Typescript (typescript)
VHDL (vhdl)
VisualBasic (visualbasic, vb)
Verilog (verilog)
XML (xml, html)
YAML (yaml)