# knitr showcase

# Examples from other users

### 2013-03-11

Below are links related to **knitr** in other websites and applications (if you have more, or you do not like your links to be listed here, please feel free to let me know).

## Websites

- RPubs: Easy web publishing from R
- knitr in a knutshell, a short tutorial by Karl Broman
- R learning resources at UCLA by Joshua Wiley et al (dynamically built with
**knitr**) - knitr on ShareLaTeX (an online LaTeX editor)
- Rcpp Gallery: Articles and code examples for the
**Rcpp**package - Slidify: reproducible HTML5 slides made easy
- One Page R Literate Data Science by Graham Williams
- Reproducible graphics with R and ggplot2 by Baptiste Auguié
- ML/stats notes by John Myles White
- A French introduction to R by Julien Barnier (also see CRAN)
- Applications of R in Business Contest (knitr’s entry; announcement)

## Book Reviews

Below is a list of the book reviews on Dynamic Documents with R and knitr.

- A book review in the
*Journal of Statistical Software*by Amelia McNamara - A book review in
*MAA Reviews*by Peter Rabinovitch - A book review on TUGboat by Boris Veytsman
- A book review on RPubs by RK
- A book review in
*The American Statistician*by Quan Zhang

## Solutions

- a knitr Howto page in Vanderbilt Biostatistics Wiki
- Plain Text, Papers, Pandoc by Kieran Healy
- R Markdown output formats for Tufte-style handouts by Michael Sachs
- Blogging with Rmarkdown, knitr, and Jekyll by Brendan Rocks
- Blog with Knitr and Jekyll by Jason C Fisher
- Creating HTML5 slides with RStudio, knitr and pandoc by Gaston Sanchez
- A framework to create bootstrap styled HTML reports from knitr Rmarkdown by Jim Hester (a preview)
- Creating a Business Dashboard in R by Bart Smeets
- Carl Boettiger has cool blog posts demonstrating how to publish a post to Wordpress.com with knitr and RWordPress purely in R, with images uploaded to Imgur and Flickr respectively
- knitr + cactus + TwitterBootstrap + Jquery by Barry Rowlingson (includes a smart use of jQuery to add links to R functions)
- Interactive reports in R with knitr and RStudio and Interactive HTML presentation with R, googleVis, knitr, pandoc and slidy by Markus Gesmann
- Stacked bar plots with several descriptive nodes by ADP
- Blogging from R to Wordpress by William K. Morris
- A demo on using
`tidy=TRUE`

or the listings environment so code chunks can stay inside page margins (link to StackExchange) - How to Use Knitr with a Rakefile by Lincoln A. Mullen
- Reproducible Research with Word? by Eric P. Green
- knitr, slidify, and Popcorn.js by Ramnath Vaidyanathan (#466)
- Transparent, reproducible blogging with nanoc and knitr by Charles Hogg
- Using knitr and R to make instructor/student handout versions by Luke Miller
- Thesis template to generate LaTeX files using R with knitr by Alexis Sarda

## R Packages

- The Github Wiki of the cda package by Baptiste Auguie
- website of ggbio package by Tengfei Yin
- The sampSurf Package by Jeffrey H. Gove
- the RHadoop Wiki by Revolution Analytics
- The ggmcmc package examples by Xavier Fernández-i-Marín
- tabplot: Tableplot, a visualization of large datasets by Martijn Tennekes and Edwin de Jonge (see its PDF vignette)
- the ggplot2 transition guide to version 0.9.0 by Dennis Murphy et al
- a few packages on Bioconductor: ReportingTools and RGalaxy
- the dendextend package by Tal Galili
- An Introduction to CHNOSZ vignette by Jeffrey M. Dick using Tufte style

## Courses

Below is a lecture on **knitr** kindly shared by Roger Peng for the Coursera
course *Computing for Data Analysis*:

And below are some other courses related to **knitr**:

- BMI 826-003 (Tools for Reproducible Research) by Karl Broman, University of Wisconsin-Madison
- Reproducible Research by Roger Peng, Coursera
- Introduction to data science by Mahbubul Majumder, University of Nebraska at Omaha
- BIOS 301 (Introduction to Statistical Computing) by Chris Fonnesbeck, Vanderbilt University
- Math 344 (Probability and Statistics) by Randall Pruim, Calvin College
- Stat 506 (Advanced Regression) by Jim Robison-Cox, Montana State University
- STT 3820 by Alan T. Arnholt, Appalachian State University
- Math 747 (Topics in math biology) by Ben Bolker, McMaster University
- STAT 319 (Applied Statistics in Science) by Yuan Huang, Penn State University (also see the tutorial Create Dynamic R Statistical Reports Using R Markdown)
- some notes on reproducible research by Aedin Culhane, Harvard University
- STAT 622 (Bayesian Data Analysis) by Marina Vannucci, Rice University
- STA613/CBB540 (Statistical methods in computational biology) by Barbara Engelhardt, Duke University
- Stat 590 (Statistical Computing) by Erik Erhardt, University of New Mexico
- STAT 497C (Topics in R Statistical Language) by Eric Nord, Penn State University
- CSSS-Stat 567 (Statistical Analysis of Social Networks) by Peter Hoff, University of Washington
- Math 15 (Statistics) by David Arnold, College of the Redwoods
- STAT 545A Exploratory Data Analysis by Jennifer Bryan, University of British Columbia
- STAT545 Introduction to Computational Statistics, by Vinayak Rao, Purdue University
- Sta 101 Data Analysis and Statistical Inference, by Mine Çetinkaya-Rundel, Duke University
- GEOL 6370 Data Analysis in the Geosciences, by Steven M. Holland, University of Georgia

## Workshops and Presentations

Below is a tutorial kindly made and shared by Joshua Wiley:

More text versions of presentations:

- New tools and workflows for data analysis by Jennifer Bryan (video)
- Geospatial Data in R and Beyond by Barry Rowlingson
- Broom Spatial R Class by Frank Davenport (PDF)
- Visualizing Categorical Data by Michael Friendly
- ggplot2 workshop notes by Josef Fruehwald for AVML 2012
- R Introduction for UCL PhDs by Florian Oswald at University College London
- Introduction to R lectures for ECPR Winter School 2013 by Zoltán Fazekas, University of Southern Denmark
- R for the brave by Will Pearse
- Introduction to knitr: The R Markdown (Rmd) format by L. Collado Torres for JHSPH Biostat computing club
- Stop Clicking, Start typing by Matt Frost
- そろそろRStudioの話でもしてみようと思う by 和田 計也
- Introduction to Data Analysis and Visualization using R by Vinayak Hedge
- Creating publication quality graphics using R by Tim Salabim
- Reproducible Research Using Knitr/R by Keith Hughitt

## Books

- The Analysis of Data by Guy Lebanon (written with R Markdown)
- Dynamic Report Generation with R and knitr by Yihui Xie (written with LyX + the
`knitr`

module) - Text Analysis with R for Students of Literature by Matthew L. Jockers
- Data Analysis for the Life Sciences by Rafael Irizarry and Michael Love
- Using R for Introductory Statistics, Second Edition by John Verzani
- Learning R: A Step-by-Step Function Guide to Data Analysis by Richard Cotton (written with AsciiDoc +
`knitr`

) - Introductory Fisheries Analysis with R by Derek H. Ogle
- The Statistical Sleuth In R by Nicholas Horton, Kate Aloisio, and Ruobing Zhang (
`knitr`

+ LaTeX) - Regression Modeling Strategies (
`knitr`

+ LaTeX) - Latent Variable Modeling using R: A Step-By-Step Guide
- Biolostatistical Design and Analysis using R
- Statistics for Experimental Economists: Elegant Analysis with R by Mark A. Olson
- R과 Knitr를 활용한 데이터 연동형 문서 만들기
- El arte de programar en R: un lenguaje para la estadística by Julio Sergio Santana and Efraín Mateos Farfán
- PH525x series - Biomedical Data Science by Rafael Irizarry and Michael Love
- Data Science for Fundraising: Build Data-Driven Solutions Using R by Ashutosh Nandeshwar and Rodger Devine

## Papers and reports

- Our path to better science in less time using open data science tools by Julia S. Stewart Lowndes
*et al*, Nature Ecology & Evolution**1**, Article number: 0160 (2017) - Eglen, SJ; Weeks, M; Jessop, M; Simonotto, J; Jackson, T; Sernagor, E. A data repository and analysis framework for spontaneous neural activity recordings in developing retina. GigaScience 2014, 3:3 http://dx.doi.org/10.1186/2047-217X-3-3
- plus an interview to the first author
- Q&A on dynamic documents

- Programming tools: Adventures with R by Sylvia Tippmann,
*Nature***517**, 109–110 (01 January 2015) doi:10.1038/517109a - Rebooting review,
*Nature Biotechnology***33**, 319 (2015) - Rule rewrite aims to clean up scientific software,
*Nature***520**, 276–277 (2015) - A Guide to Reproducible Code (Guides to Better Science), by the British Ecological Society
- 2017 Employer Health Benefits Survey by Kaiser Family Foundation (2017)
- Referenced by the New York Times article “While Premiums Soar Under Obamacare, Costs of Employer-Based Plans Are Stable“

- Irregularities in LaCour (2014) by David Broockman, Joshua Kalla, and Peter Aronow, a rebuttal paper with retraction letter from Donald P. Green
- LaCour, Michael J. & Donald P. Green. 2014. “When contact changes minds: An experiment on transmission of support for gay equality[2].” Science 346(6215): 1366.

- Piwowar HA, Vision TJ. (2013) Data reuse and the open data citation advantage. PeerJ 1:e175 http://dx.doi.org/10.7717/peerj.175
- Some great short courses on R, generalized additive models, and machine learning, etc, by Michael Clark, Center for Social Research, Notre Dame
- An Introduction to Mediation Analysis by Joshua F. Wiley
- ORANGE REPORT: Annual Report of the Swedish Pension System by the Swedish Pensions Agency
- 2011 Census Open Atlas Project by Alex Singleton
- openWAR: An Open Source System for Evaluating Overall Player Performance in Major League Baseball
- Design and Analysis of Bar-seq Experiments by Robinson et al., 2014
- Data and program code for meta-analyses of population health and health services research questions by Tim Churches
- Genomic analysis using R and knitr by Konrad Rudolph
- Assessing the 2016 Budget reforms by John Daley and Brendan Coates
- CFPB Data Point: Becoming Credit Visible by the CFPB Office of Research
- A parametric texture model based on deep convolutional features closely matches texture appearance for humans by Wallis et al.
- Revisiting the effect of red on competition in humans (supplementary information) by Laura Fortunato and Aaron Clauset

## Wrappers in other languages

- knitr-ruby: a Ruby wrapper
- Flask-FlatPages-Knitr: Knitr preprocessing for Flask-FlatPages

## Blog posts

- Using knitr and pandoc to create reproducible scientific reports by Peter Humburg
- Reproducible research, training wheels, and knitr by Jerzy Wieczorek
- Don’t R alone! A guide to tools for collaboration with R by Noam Ross
- Getting Started with R Markdown, knitr, and Rstudio 0.96, How to Convert Sweave LaTeX to knitr R Markdown and Converting Sweave LaTeX to knitr LaTeX: A case study by Jeromy Anglim
- Tools for making a paper by Will Lowe
- Integrate data and reporting on the Web with knitr by me as a guest blog post on Revolution Analytics
- knitr: A flexible R authoring tool (HTML5 slides) by Josef Fruehwald
- Planting seeds of reproducibility with knitr and markdown by Mine Çetinkaya-Rundel (the Citizen-Statistician blog)
- A closer look at “How economists get tripped up by statistics” by Laurie Samuels
- Latex Allergy Cured by knitr
- knitr Performance Report-Attempt 1
- Easier literate programming with R by Christophe Lalanne
- knitR - eine Alternative zu Sweave? by Christian B.
- Better R support in pygments by monkey patching SLexer by f3lix
- 被knitr包给震撼到了 by @xccds
- Reproducible Research by Tom Torsney-Weir (on Vim and Marked)
- 为什么Markdown+R有较大概率成为科技写作主流？ by 阳志平
- Governance Indicators by Russell Shepherd
- Petrol prices adjusted for inflation by Matt Cooper
- Creating beautiful reports from R with knitr by David Smith
- An R-based Research Notebook by Tom Torsney-Weir
- knitR, Markdown, and Your Homework by Jarrett Byrnes
- Color Palettes in HCL Space by Trestle Technology, LLC
- Introduction to R and Biostatistics by Leonardo Collado Torres
- Reproducible Research using R and Bioconductor by Paolo Sonego
- Bioinformaticians Need Lab Notebooks Too by Nacho Caballero
- From OpenOffice noob to control freak: A love story with R, LaTeX and knitr by Christoph Molnar
- Including an interactive 3D rgl graphic in a html report with knitr by Stéphane Laurent
- Create HTML or PDF Files with R, Knitr, MiKTeX, and Pandoc by Justin Meyer
- Reproducible research with R, Knitr, Pandoc and Word by Rolf Fredheim
- Visualizing Farmers’ Markets Geo Data using googleVis, plyr, knitr and Markdown using R by Peter Chen
- 2013 NSF Graduate Research Fellowship statistics by Elson Liu
- Ben Bolker’s notes on workflows, pipelines, reproducible research, etc. by Steve C Walker
- Playing with R, ggplot2 and knitr by Mladen Jovanović
- A simple bootstrap-based knitr template by Sean Davis
- Automated Blogging by Romain François
- How to avoid scandals using knitr by Mango Solutions
- Fast-track publishing using knitr: Part I, Part II, Part III by Max Gordon
- Basic data-frame manipulations in R by THE ROSTRUM
- Reproducibility is not just for researchers by Kevin Markham
- Tools for statistical writing and reproducible research by Bill Gardner
- knitr ではじめるデータ分析レポート作成 ~基礎編~ by Yu ISHIKAWA
- Starting data analysis/wrangling with R: Things I wish I’d been told by Stian Håklev
- Knitr’s best hidden gem: spin by Dean Attali
- Why use KnitR for scientific publishing? by Rob Les Davidson
- From Code to Reports with knitr & Markdown by Andrew Brooks
- Top 10 data mining algorithms in plain R by Ray Li
- Knotes on Knitr by Jon Zelner
- A reproducibility horror story
- Reproducible Analytical Pipeline by Matt Upson
- Composing reproducible manuscripts using R Markdown by Chris Hartgerink, Tilburg University