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---
title: Reproducible computing: An initial walkthrough
layout: page
---

make a new directory and cd into it

mkdir BBSRC-git-demo cd BBSRC-git-demo

create a new git repository

git init git status

create a file called somecode.R containing the following lines:

this will load the data from the Lewandowsky et al. study

(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075637)

df=read.table('http://data.bris.ac.uk/datasets/swyt56qr4vaj17op9cw3sag7d/LskyetalPLOSONE.csv', header=TRUE,sep=',') head(df)

run the R script using the "source" button in Rstudio

This worked, so let's check our file into the repo

git status git add somecode.R git status git commit -m"initial add" git status

let's run a linear regression model to see if

performance is related to age

- add the following code and source the file:

lm.result=lm(conspiracist_avg~age,data=df) summary(lm.result)

this should also complete. Let's go ahead and check in again

git add somecode.R git commit -m"adding lm"

let's put this into a repository on github so that we can

share it with others

  1. log into github.com
  2. create a new repository (+ sign at top right)
  • give it the same name as your directory (BBSRC-git-demo)
  • just use the defaults (it should be public) and click "create repository"
  1. There will be a set of commands in the section titled "…or push an existing repository from the command line"
  • copy those and paste them into the terminal inside the directory with your git repository - somethign like:

git remote add origin git@github.com:poldrack/BBSRC-git-demo.git git push -u origin master

Click on the repository link at the top of the page to go to the main repo page. you should see "somecode.R" in the list.

let's go ahead and set up circleci to automatically

run a smoke test for us

create a file called circle.yml and add the following lines:

dependencies: pre: - sudo apt-get update && sudo apt-get -y install r-base test: override: - Rscript somecode.R

then add to repo and commit and push to github

git add circle.yml git commit -m"initial add" git push origin master

next we have to hook this up to the circleci system

  1. go to circleci.com and log in using your github account
  2. click on the "Projects" button (with the + sign) Choose your github account, and then click on the "build project" button for your repo It will then take you to a page showing the status of the build. for an overview, click on the "builds" button which will take you to a list of builds.

after a couple of minutes it should show that the build succeeded

look at the log to see what we've done so far

git log

we are a bit surprised that there is no relation

between age and performance, so let's have a look

add the following code and source the file

plot(df$age,df$performance)

git add somecode.R git commit -m"adding plot"

let's say that we decided that we don't want the

plot in the file. We can go back to the previous commit:

git revert

the change in the file should show up immediately in the RStudio editor window

#it's clear from the plot that something is wrong

there is an outlier in the age distribution

let's first add a test to check for age outliers

in this study, subjects were supposed to be between

20 and 60

add the following code above the lm command:

stopifnot(max(df$age)<60) stopifnot(min(df$age)>20)

when you source the file, you should see an error.

let's see what happens when we push this to github

git add somecode.R git commit -m"adding assertion test" git push origin master

a few seconds later, you will see that the automated

test starts on circleci

you will see that the test fails due to the error

let's add some code to clean up the outliers

above the assertion tests, add:

df=subset(df,age>20&age<60)

run the code again - this time it succeeds

and we now see a strong effect of age

push it back to github and check circleci again

git add somecode.R git commit -m"adding outlier removal" git push origin master

add a fancy badge to your github page to show off

  • go to the builds page and click the gear next to your repo
  • click on "status badges" and copy the text under "embed code" CircleCI
  • add this into a README file on github