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index.Rpres
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Replication and Reproducibility in Social Sciences and Statistics: Overview and Practice
========================================================
author: Lars Vilhuber
date: `r Sys.Date()`
autosize: true
width: 1200
Cornell University
```{r setup, echo=FALSE, include=FALSE, msg = FALSE, eval=FALSE}
pkgTest <- function(x)
{
if (!require(x,character.only = TRUE))
{
install.packages(x,dep=TRUE,repos=" http://cran.us.r-project.org")
if(!require(x,character.only = TRUE)) stop("Package not found")
}
return("OK")
}
pkgTestGit <- function(x)
{
# handle the github notation
x.pkg <- unlist(strsplit(x,split="/"))[2]
if (!require(x.pkg,character.only = TRUE))
{
devtools::install_github(x)
if(!require(x.pkg,character.only = TRUE)) stop("Package not found")
}
return("OK")
}
global.libraries <- c("dplyr","rmarkdown","ggplot2","ggthemes","knitr","devtools")
dev.libraries <- c("hadley/emo")
results <- sapply(as.list(global.libraries), pkgTest)
results.dev <- sapply(as.list(dev.libraries),pkgTestGit)
```
```{r, echo=FALSE}
# shortcuts
check <- emo::ji("heavy_check_mark")
```
Overview
========================================================
- High-level overview (60:00)
- A very concrete example (remainder)
Replication and Reproducibility in Social Sciences and Statistics: Context, Concerns, and Concrete Measures
========================================================
[](https://github.com/labordynamicsinstitute/replicability-presentation2019/raw/v20190328b/Vilhuber-Presentation2019-Paris-2019-03-28.pdf) ([alt](https://github.com/labordynamicsinstitute/replicability-presentation2019))
[](https://doi.org/10.5281/zenodo.2621959)
Goals of this tutorial
==================
- Goal 1: Identify all the elements of a fully reproducible analysis
- Goal 2: Be able to curate the data and code necessary for reproducible analysis
- Goal 3: Robustness and automation - getting close to push-button reproducibility
- Goal 4: Correctly document reproducible research
Requirements
============
## Requirements
- web browser
- some R knowledge (not much)
***
## Sub goals
- show you enough of the toolkit to have you explore more
- recognize (some) of the limitations
- NOT make you a master of this today
Let's get started
=================
type: section
Details: Goal 1: Elements of a fully reproducible analysis
===============
Consider the AEA's suggested README and the Social Science Data Editors' guidance for verification:
- [Template README](https://aeadataeditor.github.io/aea-de-guidance/template-README.html)
- [Verification guidance](https://social-science-data-editors.github.io/guidance/Verification_guidance.html)
***
[](https://social-science-data-editors.github.io/guidance/Verification_guidance.html)
Details: Goal 1
===============
### Elements
- Data (where possible)
- Data provenance
- Instructions
- Code (always*)
- Expected results
- Persistence
Goal 1: Elements: Data (where possible)
=================
- Old method: send the journal a ZIP file
- Source: Your laptop
- Destination: random file on a journal website
***
Questions/ What-ifs:
- the data is not on your laptop?
- too big
- on server
- a database
- the data is not yours to send
- confidentiality
- proprietary
- other licensing issues
Goal 1: Elements: Data (where possible)
=================
- Old method: send the journal a ZIP file
- **Source: Your laptop**
- Destination: random file on a journal website
***
Questions/ What-ifs:
- how did the data get to your laptop?
- how did the data get generated?
These are **provenance** questions.
Goal 1: Elements: Data (where possible)
=================
- Old method: send the journal a ZIP file
- Source: Your laptop
- **Destination: random file on a journal website**
***
Questions/ What-ifs:
- is the ZIP file complete?
- are the ZIP file contents curated (preserved)?
- can the data be re-used?
- can the data be properly attributed to the creator?
- can the data be found independently of the article?
These are **FAIR** questions
FAIR Data Principles
===================
- **F**indable
- **A**ccessible
- **I**nteroperable
- **R**e-Usable
***
The Example
===========
The Census Bureau put out a blog post with data.
- I attempted to replicate it
- The replication itself should be replicable
- Focus here: *my replication* of the blog post
***
http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/
The Context
===========
the original page:
[](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)
***
the replication project page: https://larsvilhuber.github.io/jobcreationblog/README.html
We are going to focus on 1 figure
=================================
Original
***
Replicated
Let's start
===========
type: section
<div style="text-align: center;">
<img src="images/giphy_scan.gif" width="50%" alt="scan" />
</div>
Elements of Goal 1
===============
### Elements
- Data (where possible)
- Data provenance
- Instructions
- Code (always*)
- Expected results
- Persistence
***
### Here:
- Data is small (< 75k) - `r check`
- Data provenance - URL `r check`
- Instructions - RMarkdown file `r check`
- Code - Within Rmd `r check`
- Expected results - Copy of Figure `r check`
- Persistence - Github `r check`
Hold on
===========
type: section
```{r, include=FALSE}
# Image by <a href="https://pixabay.com/users/3D_Maennchen-1553824/?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=1013732">Peggy und Marco Lachmann-Anke</a> from <a href="https://pixabay.com/?utm_source=link-attribution&utm_medium=referral&utm_campaign=image&utm_content=1013732">Pixabay</a>
```
<div style="text-align: center;">
<img src="images/stop-1013732_640.jpg" width="50%" alt="scan" />
</div>
Elements of Goal 1
===============
### Elements
- Data (where possible)
- Data provenance
- Instructions
- Code (always*)
- Expected results
- Persistence
***
### Here:
- Data is small (< 75k) - `r check`
- **Data provenance - URL ??**
- Instructions - RMarkdown file
- Code - Within Rmd
- Expected results - Copy of Figure
- **Persistence - Github ??**
Data provenance
===============
"Data" in this project:
- the blog post
- the underlying data
***
Where available:
- URL
- URL
First problem
=============
incremental: true
the original page: http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/
Safeguarding scientific output
==============================
The role of journals is to provide a **permanent record**
of scientific knowledge.
- how reliable is that record?
- where are journals stored?
- what if the information is not in a journal?
***
Safeguarding scientific output
==============================
- journals disappear, as do websites
- **paper** journals are stored in libraries
- **e-journals** in a system called LOCKSS = *Lots of Copies Keep Stuff Safe*
- **data** should be stored in repositories
***
<!--  -->
These are still fallible
========================
<div style="text-align: center;">
<img src="images/d814ae2e0c47c399afcd93f6e232fb09.jpg" width="50%" alt="scan" />
</div>
What is NOT safeguarded
=============================
- random URLs
- Github repositories
***
Solving the first snag
======================
We use the [Internet Archive](https://www.archive.org)
- <small>[http://researchmatters.blogs.](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)[census.gov/](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)[2016/12/01/how-much-do-startups-](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)[impact-employment-growth-](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)[in-the-u-s/](http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/)</small>
Solving the first snag
======================
to archive websites:
- <small>https://web.archive.org/web/20161229210623/http://researchmatters.blogs.census.gov/2016/12/01/how-much-do-startups-impact-employment-growth-in-the-u-s/</small>
Exercise
========
type: alert
- Pick a random website
- Stephen Fienberg - http://www.stat.cmu.edu/~fienberg/
- CIQSS - https://www.ciqss.org/a-propos
- etc.
- Figure out if there is a Web Archive copy of it
- Useful: [WayBack Machine Firefox Plugin](https://addons.mozilla.org/en-CA/firefox/addon/wayback-machine_new/)
- If not, get the Web Archive (aka WayBack Machine) to create a copy
- Cite the Web Archive version of the page
Do it now
==========
type: section
<div style="text-align: center;">
<img src="images/giphy_scan.gif" width="50%" alt="scan" />
</div>
Result
======
> Goal 2: Be able to curate the data and code necessary for reproducible analysis
<div style="text-align: center;">
<img src="images/partway-768567_640.jpg" width="50%" alt="scan" />
</div>
Let's start... again
===========
type: section
The replication of the original
=======================
the [project page](https://larsvilhuber.github.io/jobcreationblog/README.html):
***
the code behind it: <small>https://github.com/larsvilhuber/jobcreationblog </small>
What is Github?
==============
incremental: true
`git`
Distributed version control system, created by Linus Torvalds in 2005
***
Github.com
> At a high level, GitHub is a website and cloud-based service that helps developers store and manage their code, as well as track and control changes to their code.
[[1](https://kinsta.com/knowledgebase/what-is-github/)]
Also a **collaboration tool** when multiple people (developers, researchers) collaborate in a structured fashion on text/code/programs/etc.
Gitlab? Github? Git? What's up with that?
=========================================
type: warning
<img alt="Gitlab logo" width="45%" style="vertical-align: middle;" src="images/gitlab-logo-gray-rgb.png"/>
<img alt="Gitlab logo" width="10%" style="vertical-align: middle;" src="images/GitHub-Mark-120px-plus.png"/>
<img alt="Gitlab logo" width="25%" style="vertical-align: middle;" src="images/GitHub_Logo.png"/>
> Both GitLab (and GitLab.com) and GitHub (and GitHub.com) are products providing Git repository hosting service. [[1](https://www.quora.com/What-are-the-differences-between-GitHub-GitLab)]
***
Also:
- Bitbucket.com (despite no Git in the name)
- All of these have free plans for
- private (non-public) repositories
- public repositories
at least for academics.
Training for Git
================
Many training opportunities and tutorials out there
- [my own short training](https://github.com/labordynamicsinstitute/replicability-training/blob/master/Fall%202019/Basics_of_Git.md)
- [10 minute read Git Handbook](https://guides.github.com/introduction/git-handbook/)
What Github, Gitlab, etc. are NOT
=================
incremental: true
While these sites make it really easy to publish your code/website/etc.
***
They are **NOT** archives.
Github etc. are transitory
=============================
incremental: true
Github pages, much as private websites, can be unpublished at any time:
***
In fact, the entire code repository can be deleted at any time:
Git(hub,lab) as a tool for reproducible research
================
> Goal 3: Robustness and automation - getting close to push-button reproducibility
(Advanced features of Git(hub,lab) allows us to implement and test that)
***
> Goal 4: Correctly document reproducible research
- Git(hub,lab) allow us to freeze consistent versions of input data, code, and output as "*releases*", "versions", etc., thus making it easy to **document your code**
Git(hub,lab) as a tool for reproducible research
================
> Goal 3: Robustness and automation - getting close to push-button reproducibility
(Advanced features of Git(hub,lab) allows us to implement and test that)
***
> Goal 4: Correctly document reproducible research
- (also respond to thesis advisor, referree, editor, curious journalist asking the question "what has changed")
Getting our hands dirty
=======================
Rather than squint on code on the screen, let's ... replicate my replication. Online. Now.
We will
- Make a copy of the code repository
- Verify that the original code runs, and make any changes necessary
- Make a (permanent) copy of the code
- Address any issues on the way
***
Requirements:
- Rstudio.cloud account (alt: Google, Github)
- Git*** account
- alt Gitlab: Google/ Twitter/ Github / Bitbucket
- alt Github: none
- Zenodo account (alt: Github, ORCID)
You can delete all online materials at the end of the class.
Getting our hands dirty
=======================
Rather than squint on code on the screen, let's ... replicate my replication. Online. Now.
- Go to <a href="https://rstudio.cloud" target="_blank">https://rstudio.cloud</a>
***
<a href="https://rstudio.cloud" target="_blank"><img alt="Rstudio.cloud" src="images/Screenshot_2019-04-23_RStudio_Cloud.png" /></a>
First task: Make a copy
=====================
Source: <small>https://github.com/larsvilhuber/jobcreationblog </small>
***
Destination:
<a href="https://gitlab.com"><img alt="Gitlab logo" width="45%" style="vertical-align: middle;" src="images/gitlab-logo-gray-rgb.png"/>
<img alt="Gitlab logo" width="10%" style="vertical-align: middle;" src="images/GitHub-Mark-120px-plus.png"/></a>
<a href="https://github.com"><img alt="Gitlab logo" width="25%" style="vertical-align: middle;" src="images/GitHub_Logo.png"/></a>
Using Gitlab: Two options
=========================
incremental: true
**Import** project from Git
***
**Fork** an existing Gitlab project:
**GITLAB**<small>.com/larsvilhuber/jobcreationblog </small>
Your own Gitlab "jobcreationblog" repo
=====================================
incremental: true
> Goal 2: Be able to curate the data and code necessary for reproducible analysis
<div style="text-align: center;">
<img src="images/giphy_success.gif" width="60%" alt="scan" />
</div>
Next step: Rstudio.cloud
============
type: alert
<div style="text-align: center;">
<img alt="Rstudio.cloud" src="images/Screenshot_2019-04-23_RStudio_Cloud.png" width="60%"/>
</div>
Logging on to the Rstudio.cloud server
=======================
incremental: true
***
While you do that
=================
Other cloud-based compute environments:
## [Rstudio.cloud](https://rstudio.cloud)
- R-focused
## [MyBinder.org](https://mybinder.org)
- Origins with Jupyter
- Julia, Python, and R
- different approach
***
## https://codeocean.com
- Software-agnostic
- R
- Python
- Stata !
- Matlab !
- others
- but always scripted
- integrated versioning of the entire compute capsule
Creating a new project
=======================
incremental: true
***
Creating a new project from Gitlab
==================================
## https://gitlab.com/larsvilhuber/jobcreationblog
(replace "**larsvilhuber**" with your own Gitlab name space, or your Github clone URL)
***
Creating a new project from Gitlab
==================================
<div style="text-align: center;">
<img src="images/RStudio_Cloud_457.png" width="80%" alt="scan" />
</div>
Creating a new project from Gitlab
==================================
<div style="text-align: center;">
<img src="images/RStudio_Cloud_458.png" width="80%" alt="scan" />
</div>
Notes
=====
## You could have done the same thing on your laptop
- you might not have (the same version of) **[Rstudio](https://www.rstudio.com)** installed (free)
- you might not have (the same version of) **[R](https://www.r-project.org/)** installed (free)
- you might have a Mac/ Windows/ **Linux**/ old / brand new machine
***
## All of these are issues affecting computational reproducibility
However, they do not solve everything...
Open the README document
========================
<div style="text-align: center;">
<img src="images/RStudio_Cloud_459.png" width="60%" alt="scan" />
</div>
A (solved) problem of dependencies
==================================
<div style="text-align: center;">
<img src="images/RStudio_Cloud_460.png" width="80%" alt="scan" />
</div>
Issues of dependencies (new)
=======================
## You could have done the same thing on your laptop
- you might not have (the same version of) **[Rstudio](https://www.rstudio.com)** installed (free)
- you might not have (the same version of) **[R](https://www.r-project.org/)** installed (free)
- you might have a Mac/ Windows/ **Linux**/ old / brand new machine
- <span style="color: red;">you might not have (the same version of) **packages** installed</span>
Rstudio solves that for you
==================================
<div style="text-align: center;">
<h2>Go ahead, click on "install"</h2>
<img src="images/RStudio_Cloud_460.png" width="80%" alt="scan" />
</div>
Solving dependencies
====================
The problem is not just in R:
- SSC or Stata Journal packages in Stata
- libraries or compilers in Fortran
- Modules (paid!) in SPSS or SAS
- packages in Python (and versions of Python!)
***
[](https://xkcd.com/1987/)
Solving dependencies (R)
====================
- use `packrat` or `checkpoint` functionality
- declare dependencies explicitly [[1](https://gist.github.com/larsvilhuber/85026976027b58714c00420d75f04281)]
<small>
```{r libs,eval=FALSE}
####################################
# global libraries used everywhere #
####################################
# Package lock in - optional
MRAN.snapshot <- "2019-01-01"
options(repos = c(CRAN = paste0("https://mran.revolutionanalytics.com/snapshot/",MRAN.snapshot)))
pkgTest <- function(x)
{
if (!require(x,character.only = TRUE))
{
install.packages(x,dep=TRUE)
if(!require(x,character.only = TRUE)) stop("Package not found")
}
return("OK")
}
global.libraries <- c("dplyr","devtools","rprojroot","tictoc")
results <- sapply(as.list(global.libraries), pkgTest)
```
</small>
Solving dependencies (Stata)
===========================
- install packages locally [[1](https://gist.github.com/larsvilhuber/8ead0ba85119e4085e71ab3062760190)]
- commit as part of the repository
<small>
```{stata, eval=FALSE}
// Make a path local to the project
// Also see my related config.do at
// https://gist.github.com/larsvilhuber/6bcf4ff820285a1f1b9cfff2c81ca02b
local pwd "/c/path/to/project"
capture mkdir `pwd'/ado
sysdir set PERSONAL `pwd'/ado/personal
sysdir set PLUS `pwd'/ado/plus
sysdir set SITE `pwd'/ado/site
/* Now install them */
/*--- SSC packages ---*/
foreach pkg in outreg esttab someprog {
ssc install `pkg'
}
```
</small>
Result
======
type: alert
> Goal 3: Robustness and automation - getting close to push-button reproducibility
By solving dependencies explicitly, robustness is improved.
By doing so with a dynamic function, automation is possible.
***
> Goal 4: Correctly document reproducible research
Documenting dependencies is a critical part of reproducible research.
Packages installed?
==================
incremental: true
Add text to the document:
```{r, eval=FALSE}
# hidden dependency, will install packages that are needed
source("global-config.R",echo=FALSE)
```
and adjust `global-config.R` to also list `knitcitations`
***
## Click on "Knit"
Dependencies again
=================
<div style="text-align: center;">
<img src="images/RStudio_Cloud_464.png" width="60%" alt="scan" />
</div>
And another problem (maybe)
=======================
Enable popups for this site:
<div style="text-align: center;">
<img src="images/popup-blocker.png" width="60%" alt="scan" />
</div>
Problem solved NOW?
===================
## You should have seen a pop-up window with the compiled text
- do the graphs look the same?
- does the text look the same?
***
Question:
========
type: prompt
incremental: true
## Are we done?
***
## Not quite...
### Important
- record any changes (**Goal 4**)
- how permanent is the data we are using? (**Goal 2**)
- how permanent is my document? (**Goal 2**)
### Useful
- how can others easily see my latest version? (**Goal 3**)
Next steps
==========
## Recording and documenting changes
- using Git**b!
## Making the data permanent
- using Zenodo again
***
## Making the page more permanent
- Using [Zenodo](zenodo.html)
## Making the page more accessible
- [on Github](github-pages.html)
- on Gitlab
Recording changes
=================
type: section
Your almost there
=================
Because we used Git**b, we have the changes already under control:
<div style="text-align: center;">
<img alt="Rstudio top right" src="images/RStudio_Cloud_top_right.png" width="60%" />
</div>
Commit all the changes
===================
<div style="text-align: center;">
<img alt="Rstudio git" src="images/RStudio_Cloud_git.png" width="60%" />
</div>
Commit all the changes
===================
<div style="text-align: center;">
<img alt="Rstudio git boxes checked" src="images/RStudio_Cloud_git_checked.png" width="60%" />
</div>
Review the changes
==================
<div style="text-align: center;">
<img alt="Rstudio review" src="images/RStudio_Cloud_git_review_changes.png" width="60%" />
</div>
Push back to repository
======================
<div style="text-align: center;">
<img alt="Rstudio git push" src="images/RStudio_Cloud_git_push.png" width="60%" />
</div>