# 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

- Cut the tyranny of copy-and-paste with these coding tools by Jeffrey M. Perkel,
*Nature*603, 191-192 (2022) - 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.

- Granger-causality analysis of integrated-model outputs, a tool to assess external drivers in fishery by Margarita Rincón, Rachele Corti, Bjarki Elvarsson, Fernando Ramos, and Javier Ruiz.
- Harry Alastair V., Butcher Paul A., Macbeth William G., Morgan Jess A. T., Taylor Stephen M., Geraghty Pascal T. (2019) Life history of the common blacktip shark, Carcharhinus limbatus, from central eastern Australia and comparative demography of a cryptic shark complex. Marine and Freshwater Research. https://doi.org/10.1071/MF18141
- 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
- Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets by Jayaram Kancherla, Alexander Zhang, Brian Gottfried, and Hector Corrada Bravo

## 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