Reproducibility with R short workshop 2015 ioslides presentation. PDF File generated with knitr

1. Reproducible R coding
CMEC R-Group
Martin Jung
12.02.2015

2. Goals of reproducible programming?
Make your code readible by you and others
Group your code and functionalize
Embrace collaboration, version control and automation

3. First step - readibility
1. Writing cleaner code

4. Writing cleaner R code | Names
Keep new filenames descriptive and meaningful
"helper-functions.R"
# or for sequences of processing work
"01_Download.R"
"02_Preprocessing.R"
#...
Use CamelCase or Snake_case for variables
"spatial_data"
"ModelFit"
"regression.results"
Avoid predetermined names like c or plot

5. Writing cleaner R code | Spacing
Use Spacing just as in the english language
# Good
model.fit <- lm(age ~ circumference, data = Orange)
# Bad
f1=lm(Orange$age~Orange$circumference)
Don’t be afraid of using new lines
model.results <- data.frame(Type = sample(letters, 10),
Data = NA,
SampleSize = 10 )
# Same goes for loops
# And don't forget good documentation

6. More on writing clean code
Google R Style Guide
Hadley Wickhams Style Guide
RopenSci Guide
And there even is a r-package to clean up your code:
formatR

7. Further ways to improve reproduciability
Ideally attach your code + data to publications
Open-access hoster (DataDryad, Figshare, Zenodo)
Restructuring of workflow with RMarkdown / LaTeX / HTML

8. Functionalize!
Many R users are tempted to write their code very specialized
and non-reusable
Number 1 rule for clear coding :
DRY - Don't repeat yourself!
Simple example: We want to fit a linear model to test if in an
orange orchard the circumference (mm) increases with age (age of
trees). If so we want to quantify and display the
Root-Mean-Square-Error (RMSE) of this fit for each individual
orange tree in the dataset (N = 5).

9. Normal way:
# Linear model
model.fit <- lm(age ~ circumference, data = Orange)
model.resid <- residuals( model.fit )
model.fitted <- fitted( model.fit )
rmse <- sqrt( mean( (model.resid - model.fitted)^2 ))
tapply(model.resid - model.fitted, Orange$Tree,
function(x) sqrt( mean( (x)^2 )))

10. 3 1 5 2 4
0200400600800100012001400

11. Defining your functions
Essentially most r-packages are just a compilation of useful
functions that users have written.
# We want to get the RMSE of a linear model
rmse <- function(fit, groups = NULL, ...)
{
f.resid <- residuals(fit);f.fitted <- fitted(fit)
if(! is.null( groups )) {
tapply((f.resid-f.fitted), groups, function(x) sqrt(mea
} else {
sqrt(mean((f.resid-f.fitted)^2, ...))
}
}

12. model.fit <- lm(age ~ circumference, data = Orange)
# This function is more flexible, can be further customized
# applied in other situations
rmse(model.fit)
## [1] 1041.809
rmse(model.fit, Orange$Tree)
## 3 1 5 2 4
## 602.4244 688.8896 929.9055 1319.1573 1408.7033

13. (very) short intro into pipes
Pipes (|) are a common tool in the linux / programming world that
can be used to chain inputs and outputs of functions together. In R
there are two packages, namely dplyr and magrittr that enable
general piping between all functions
Goal:
Solve complex problems by combining simple pieces
(Hadley Wickham)

14. library(dplyr)
model.rmse <- Orange %>%
lm(age ~ circumference, data=.) %>%
rmse(., Orange$Tree) %>%
barplot
OR like this (Correlation within Iris dataset)
iris %>% group_by(Species) %>%
summarize(count = n(), pear_r = cor(Sepal.Length, Petal.L
arrange(desc(pear_r))
## Source: local data frame [3 x 3]
##
## Species count pear_r
## 1 virginica 50 0.8642247
## 2 versicolor 50 0.7540490
## 3 setosa 50 0.2671758

15. Outsource your functions
# Put your function into an extra files
# At the beginning of your main processing script
# you simply load them via source
source("outsourced.rmse.R")

16. Easy package writing
Open RStudio
Install the devtools and roxygen2 package
Create a new package project and use the existing function as
basis
Create the documentation for it
Update the package metadata and build your package
library(roxygen2)
library(devtools)
# Build your package with two simple commands
# Has to be within your package project
document() # Update the namespace
install() # Install.package

17. However package development has multiple facets and options.
More detailed info on Package development with RStudio.
Higher acceptance for method papers and analysis code. Make
it citable with a DOI

18. Software management and collaboration with Github
Git is one of the most commonly used revision control systems
Originally developed for the Linux kernel by Linus Torvalds

20. Github is web-based software repository service offering
distributed revision control
Californian Startup, now the largest code hoster in the
world
Offers public repositories for free, private for money and a
nice snippet exchange service called gists

21. How to Git with rstudio (do it later)
1. Setup an account with a git repository hoster like Github
2. Install RStudio and git for your platform (http://www.
rstudio.com/ide/docs/version_control/overview)
3. Link to the git executable within the RStudio options
4. Create a new repository on Github and a new project in
RStudio -> Version Control git
5. Clone your empty project (pull), add new files/changes to it
(commit) and (push)

22. Idea for CMEC R Users:
Create a Github organization (like a repository basecamp)

23. Further developments
There are now packages to push gists and normal git updates
directly from within R. In order to use them you need a github api
key (instructions on the websites below) rgithub
To detailed to show here, but have a look at the gistr package:
gistr