jatotterdell/AIR-COPD

AIR

AIR: Adaptive clinical trial Investigating GLA-targeted therapies in the Respiratory disease COPD

Background

The aim for AIR is to evaluate multiple novel interventions against a shared control group. The primary outcome is neutraphil elastase (NE) at D28 (i.e. 28 days after randomisation).

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Scripts

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

AIR

To (locally) reproduce this project, do the following:

1. Download this code base. Notice that raw data are typically not included in the git-history and may need to be downloaded independently.

2. Open a Julia console and do:

   julia> using Pkg
   julia> Pkg.add("DrWatson") # install globally, for using `quickactivate`
   julia> Pkg.activate("path/to/this/project")
   julia> Pkg.instantiate()

This will install all necessary packages for you to be able to run the scripts and everything should work out of the box, including correctly finding local paths.

Run Simulation

To run a simulation file using multi-threading, call for example

julia -t auto scripts/run_simulations.jl

or with auto replaced with the number of threads.

Alternatively, if sysimage has been created can instead use

julia -t auto --sysimage=AIRproject.so scripts/run_simulations.jl

Tests

Some basic tests implemented in test/ which can be run via

pkgs> activate .
(AIR) pkg> test