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Helminthiases

The Soil Transmitted Helminths Project

Project Flow


Table of contents

  1. Flow Diagram
  2. A Brief Guide to Running the Project’s Programs


Flow Diagram


The contents, repositories page outlines the functions of the repositories of the Helminthiases hub.   The flow diagram below outlines data flows - data dependencies - between repositories.   It also outlines the project’s external data sources.

The diagram’s icons have links; beware of the diagram key, bottom left.   Clicking on a GitHub repository icon takes you to the repository in question, clicking on a data storage point leads to the storage point in question, etc.   Additionally, some items - icons & text elements - have tooltips, which are observable/readable by hovering over an item.


The acronyms are → ESPEN: Expanded Special Project for Elimination of Tropical Diseases. IHME: Institute for Health Metrics and Evaluation, WaSH: water, sanitation, and hygiene. SEDAC: socioeconomic data & application centre. SRTM: Shuttle Radar Topography Mission.



A Brief Guide to Running the Project’s Programs


In relation to top directory hub wherein all the repositories reside, the program

  cd infections
  python src/main.py

runs the programs of infections.   Subsequently,

  cd ../spatial
  source(file = 'spatial/R/main.R')

which additionally depends on the outputs of infections, runs the programs of spatial; spatial will search for the outputs at infections/warehouse.   In terms of modelling

  cd ../modelling
  source(file = 'R/main.R')

runs all the modelling related programs.   It depends on the outputs of spatial, which reside within spatial/warehouse.


Missing Data Analysis

In contrast to the previous programs, the programs of this section access the outputs of another repository locally.

As the flow diagram illustrates, the programs of preliminary depend on the outputs of the infections & spatial repositories.

  cd preliminary
  python src/main.py

Finally, association depends on the outputs of preliminary.

  cd ../association
  source(file = 'R/main.R')