Merge pull request #31 from TrishC/TrishC-patch-1

Trish has contributed a great case study from her PhD.

src/SUMMARY.md

@@ -71,6 +71,7 @@
 - [Case studies](case-studies/README.md)
   - [Fixing a bug in pypfilt](case-studies/moss-pypfilt-earlier-states.md)
   - [Incorrect data in a pre-print figure](case-studies/moss-incorrect-data-pre-print.md)
+  - [Pen and paper version control](case-studies/campbell-pen-and-paper-version-control.md)
 
 -----------
 

src/case-studies/campbell-pen-and-paper-version-control.md

@@ -0,0 +1,29 @@
+# Pen and paper - a less user-friendly form of version control than Git
+
+Author: Trish Campbell (`[email protected]`)
+
+Project: Pertussis modelling
+
+## The problem
+
+In this project, I developed a compartmental model of pertussis to determine appropriate vaccination strategies.
+While plotting some single model simulations, I noticed anomalies in the modelled output for two experiments.
+The first experiment had an order of magnitude more people in the infectious compartments than in the second experiment, even though there seemed to be far fewer infections occurring.
+This scenario did not fit with the parameter values that were being used.
+In the differential equation file for my model, in addition to extracting the state of the model (i.e. the population in each compartment at each time step), for ease of analysis I also extracted the cumulative number of infections up to that time step.
+The calculation for this extraction of cumulative incidence was incorrect.
+
+## The solution
+
+The error occurred because susceptible people in my model were not all equally susceptible, and I failed to account for this when I calculated the cumulative number of infections at each time step.
+I identified that this was the problem by running some targeted test parameter sets and observing the changes in model output.
+The next step was to find out how long this bug had existed in the code and which analyses had been affected.
+While I was using version control, I tended to make large infrequent commits.
+I did, however, keep extensive hand-written notes in lab books, which played the role of a detailed history of commits.
+Searching through my historical lab books, I identified that I had introduced this bug into the code two years earlier.
+I was able to determine which parts of my results would have been affected by the bug and made the decision that all experiments needed to be re-run.
+
+## How version control helped
+
+Using a **pen and paper** form of version control enabled me to pinpoint the introduction of the error and identify the affected analyses, but it was a tedious process.
+While keeping an immaculate record of changes that I had made was invaluable, imagine how much simpler and faster the process would have been if I had been a regular user of an electronic version control system such as Git! 

src/contributors.md

@@ -5,3 +5,4 @@ Here is a list of the contributors who have helped develop these materials:
 - Rob Moss ([robmoss](https://github.com/robmoss))
 - Eamon Conway ([EamonConway](https://github.com/EamonConway))
 - James Ong ([jomonman537](https://github.com/jomonman537))
+- Trish Campbell ([TrishC](https://github.com/TrishC))