Exploratory data analysis in environmental health

ENV-444

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Course summary

Introduction

This course is taught by Dr Mayssam Nehme, head of the Unit of Population Epidemiology  (UEP) at Geneva University Hospitals, and Dr Stéphane Joost (GEOME-LGB group at EPFL). It explains how to apply exploratory spatial data analysis to health data (link to the course booklet). Teaching focuses on the basics of exploratory spatial statistics and of how to apply these methods to epidemiological data with a geographic component.  The course proposes a context to analyse geodatasets making it possible to study the relationship between health and the environment. It consists of:
  1. Theoretical lectures, including a section dedicated to the writing/structure of scientific articles
  2. Practical exercises
  3. A semester project, consisting in the writing of a scientific article (work in groups)


Keywords: Exploratory spatial data analysis; Geocomputation; EDA; ESDA; Geovisualization; GIS; Geoda; Thematic mapping; Semiology of graphics; Spatial statistics; Principal Component Analysis; Rate smoothing; Spatial regression; Logistic regression; Scientific paper writing; Open access; Open source

Software used: Geoda (v1.22) and QGIS (v3.34 LTR), RStudio (version communicated later)

Organization: components of the course are:

  • Theoretical lectures
  • Exercises in the room GRB330 on personal computers (only open source and free software will be used) and/or in the IT/TP room GRB001. 
  • Semester project: scientific article (work in groups)

  • Technical questions can be asked continuously by means of the Forum on ED. 
  • Questions related to organizational and administrative elements of the course can be asked directly by email to Stéphane Joost.

Content
Each week's lecture (in class lectures and video sequences) will present the basics of spatial exploratory data analysis and important notions in spatial epidemiology and environmental health. Then the exercises proposed will allow the concepts presented previously to be put into practice. The data used are provided by current research case studies (spatial epidemiology in urban environments) jointly investigated by Geneva University Hospitals (HUG) and EPFL. Tasks to be carried out consist in data exploration, geovisualization, geocomputation, but also in thematic mapping. In parallel, the data provided and the approaches taught will be used to write a scientific paper.


Evaluation: continuous control during the semester.
  • 7/9 exercises on exploratory data analysis/spatial statistics/theoretical content  (individual short reports or "comptes-rendus") = 20% of the final grade
  • 1 scientific article (semester project, group work) = 40%
  • Oral presentation of the semester project (content of the scientific article) = 40%.
    Each group of 5 students will present its semester project - Each student will be graded individually on his/her oral performance. Precise requirements will be transmitted.

Important dates
  • Submission of the scientific article (semester project): January 5 (Monday), 2025, at 23h59
  • Oral presentation of semester projects: Monday 15.12.2025, 08h15 to 12h15

Work in groups

Indications as regards the composition of groups will be given by teachers after week 4 on the basis of the total number of students.
Groups will have to produce:

  1. A project proposal, i.e. the description of the content of the scientific article (semester project) to be produced. It will contain the idea of the research to be carried out to verify working hypotheses related to a topic defined by the group (examples: relationship between obesity and road traffic nightnoise, relationship between Body Mass Index and green areas; relationship between the frequency intake of sugar sweetened beverages and estimated soil temperature, etc.).
  2. The scientific article (8-10 pages max.)

Data
The main data to elaborate the semester projects will be presented during the initial part of the semester.
  1. Environmental variables that each student will produce in the context of an exercise and that will constitute an open dataset of reference;
  2. Data on mental health in the Lausanne area.

Students will have the opportunity to download additional data to characterize the territory in the area of Lausanne.

Documentation - Course material

  1. Geoda Workbook
  2. Slides of the theoretical lectures (distributed through corresponding weeks herunder)

Examples of good scientific articles carried by previous ENV-444 students

Week 1

Week 2

For the exercises, in case you do not want to install the software on your computer (Geoda, QGIS, RStudio), you can use the ENAC-SSIE virtual environment (https://vdi.epfl.ch/portal/webclient/#/home).

Exercise 2b is a tutorial so that you learn how to use several among Geoda exploratory tools. Thus you will receive no Solution file for this part.

Lundi du Jeûne fédéral

Week 3

Week 4

Week 5

Vacances

Week 6


Week 7

Week 8


Week 9

Week 10

Week 11

At 9h15 we will have a presentation by Dr Anaïs Ladoy, responsible for geographic information at the Pôle santé numérique et qualité of the Direction Générale de la Santé of the Vaud canton. She will give a talk about how geographic information can be used in the domain of public health policies application and elaboration.

Week 12

Week 13