Packages to install

In order to follow along today and to be kind to the WeWork wifi, please run the following commands in your RStudio:

install.packages("devtools")
install.packages("revealjs")
library(devtools)
install_github("ismayc/izzyuntappd")
install_github("ismayc/chemistr")
install_github("ismayc/reedoilabs")
install_github("ismayc/reedtemplates")
install_github("ismayc/thesisdown")

Slides available at http://bit.ly/rmd-pdx-talk

Humble beginnings

George Idea GIF

Slides available at http://bit.ly/rmd-pdx-talk

The Preminaries

RStudio and R Markdown

• Nice user interface
• RStudio in Desktop and Server versions
• Reproducible research using R Markdown

Slides available at http://bit.ly/rmd-pdx-talk

Copy-and-paste never works like this…

Slides available at http://bit.ly/rmd-pdx-talk

To the beeR!

Slides available at http://bit.ly/rmd-pdx-talk

My Untappd ratings

Slides available at http://bit.ly/rmd-pdx-talk

My Untappd R data package

https://github.com/ismayc/izzyuntappd

Slides available at http://bit.ly/rmd-pdx-talk

DEMO 1

install.packages("devtools")
devtools::install_github("ismayc/izzyuntappd")

File -> New File -> R Markdown ->

From Template -> walkthrough

Slides available at http://bit.ly/rmd-pdx-talk

Talking about templates via templates

Slides available at http://bit.ly/rmd-pdx-talk

Slides made via template

install.packages("revealjs")

File -> New File -> R Markdown -> From Template ->

Reveal.js Presentation (HTML)

Slides available at http://bit.ly/rmd-pdx-talk

DEMO 2

Creating your own template package

eCOTS presentation

Creating a basic template package in R

Slides available at http://bit.ly/rmd-pdx-talk

Distributing files

chemistr package for Chem 101/102 at Reed

install.packages("devtools")
devtools::install_github("ismayc/chemistr")

File -> New File -> R Markdown -> From Template -> .

Slides available at http://bit.ly/rmd-pdx-talk

Distributing files

reedoilabs package for MATH 141 at Reed

install.packages("devtools")
devtools::install_github("ismayc/reedoilabs")

MATH 141 Labs from Spring 2016

File -> New File -> R Markdown -> From Template -> .

Slides available at http://bit.ly/rmd-pdx-talk

Distributing files

R version of the JMP lab manual for Bio 101/102 at Reed

install.packages("devtools")
devtools::install_github("ismayc/reedtemplates")

File -> New File -> R Markdown ->

From Template -> Bio 101/102 RStudio Manual

Slides available at http://bit.ly/rmd-pdx-talk

A snazzy template

install.packages("devtools")
devtools::install_github("ismayc/reedtemplates")

File -> New File -> R Markdown ->

From Template -> Package Loader

Slides available at http://bit.ly/rmd-pdx-talk

The Beasts!

(old) R Markdown Senior Thesis Template

install.packages("devtools")
devtools::install_github("ismayc/reedtemplates")

File -> New File -> R Markdown ->

From Template -> Reed Senior Thesis

Slides available at http://bit.ly/rmd-pdx-talk

The Beasts!

(BRAND NEW) R Markdown Senior Thesis Template

install.packages("devtools")
devtools::install_github("ismayc/thesisdown")

File -> New File -> R Markdown ->

From Template -> Thesis

Slides available at http://bit.ly/rmd-pdx-talk

BONUS

Parameterized Reports

• Download the Rmd file from http://bit.ly/rmd-par.
• Make a new package and turn this Rmd file into an R Markdown template.

Slides available at http://bit.ly/rmd-pdx-talk

Useful links

Document Templates

A bookdown book about creating books with bookdown

Shameless plugs

Creating a basic template package in R

Getting used to R, RStudio, and R Markdown gitbook

Resulting gitbook for Reed Thesis template

Slides available at http://bit.ly/rmd-pdx-talk

Thanks!

• Code for slide creation on my GitHub page

• Slides available at https://ismayc.github.io/workshops/rmd-pdx.html

• Feedback is welcomed and encouraged:
  • Google Form: http://bit.ly/rmd-pdx
  • Twitter: @old_man_chester
  • email: chester.ismay@gmail.com

• Let’s go have beer!

sessionInfo()

## R version 3.3.0 (2016-05-03)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.12 (unknown)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] revealjs_0.7       rmarkdown_1.0.9002 knitr_1.14         ggplot2_2.1.0      dplyr_0.5.0       
## [6] needs_0.0.3       
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.6      digest_0.6.10    assertthat_0.1   plyr_1.8.4       grid_3.3.0      
##  [6] R6_2.1.2         gtable_0.2.0     DBI_0.5          formatR_1.4      magrittr_1.5    
## [11] scales_0.4.0     evaluate_0.9     stringi_1.1.1    tools_3.3.0      stringr_1.0.0   
## [16] munsell_0.4.3    yaml_2.1.13      colorspace_1.2-6 htmltools_0.3.5  tibble_1.1