Resources

Developing RECON packages

If you are intersted in developing or contributing to RECON packages, we suggest you explore the rOpenSci Software Peer Review process, as well as the rOpenSci Dev Guide and Epiverse Trace.

Using RECON packages

These resources are archived lectures, tutorials and case studies formerly hosted on RECON Learn.

These resources are not necessarily up-to-date with the current package usage and some have errors or do not complile correctly, however, they still have value.

HTML/pdf/pptx files are lecture slides, while Rmd and md files are either tutorials or contain more details for lectures (regarding authorship etc.).

English

Basic VBD Modelling:

  • Basic Concepts on Vector Borne Disease Modelling by Zulma Cucunuba, Pierre Nouvellet
  • Rmd, html

Compartmental Ebola:

  • Ebola: building few models for Ebola by Zulma Cucunuba, Pierre Nouvellet
  • Rmd, Rmd, md, pdf, pptx

Copenhagen Descriptive:

  • Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 2) by Zhian N. Kamvar, Janetta Skarp, Alexander Spina, Patrick Keating, Thibaut Jombart
  • Rmd, md

Copenhagen Intro:

  • Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 1) by Zhian N. Kamvar, Janetta Skarp, Alexander Spina, Patrick Keating
  • Rmd, md

Copenhagen Stratified:

  • Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 4) by Zhian N. Kamvar, Janetta Skarp, Alexander Spina, Patrick Keating
  • Rmd, md

Copenhagen Univariate:

  • Outbreak of gastroenteritis after a high school dinner in Copenhagen, Denmark,November 2006 (part 3) by Zhian N. Kamvar, Janetta Skarp, Alexander Spina, Patrick Keating
  • Rmd, md

Data Import Short:

Ebola Reconstruction:

  • Ebola simulation part 2: outbreak reconstruction by Thibaut Jombart, Finlay Campbell
  • Rmd, md

Ebola Response:

  • Ebola simulation part 1: early outbreak assessment by Thibaut Jombart, Finlay Campbell
  • Rmd, md

Import Data:

Intro To R:

Intro to R:

  • An introduction to R and RStudio by Zulma M. Cucunuba
  • Rmd, md

Lecture Phylogenetics:

Modelling Public Health:

  • Modelling infectious diseases for public health by Pierre Nouvellet
  • Rmd, pptx

Outbreak Statistics:

  • A primer on statistical outbreak analysis by Thibaut Jombart
  • Rmd, html

Outbreakend:

  • Is this outbreak over? by Michael Höhle
  • Rmd, md

Outbreaker2:

  • Outbreak investigation using outbreaker2 by Thibaut Jombart
  • Rmd, html

Phylogenetics:

  • Phylogenetic tree reconstruction by Thibaut Jombart
  • Rmd, Rmd, md

Projections:

  • Methods for Short Term Projections in epidemics by Pierre Nouvellet
  • Rmd, pdf, pptx

Real Time Response 1:

  • Real-time outbreak analysis: Ebola as a case study - part 1 by Anne Cori, Natsuko Imai, Finlay Campbell, Zhian N. Kamvar, Thibaut Jombart
  • Rmd, md

Real Time Response 2:

  • Real-time outbreak analysis: Ebola as a case study - part 2 by Anne Cori, Natsuko Imai, Finlay Campbell, Zhian N. Kamvar, Thibaut Jombart
  • Rmd, md

Real Time Response 3:

  • Real-time outbreak analysis: Ebola as a case study - part 3 by Anne Cori, Natsuko Imai, Finlay Campbell, Zhian N. Kamvar, Thibaut Jombart
  • Rmd, md

Reproducibility:

  • Reproducibility using R by Thibaut Jombart
  • Rmd, html

Stegen:

  • An outbreak of gastroenteritis in Stegen, Germany, June 1998 by Amrish Baidjoe, Thibaut Jombart, Janetta Skarp, Zhian N. Kamvar, Alexander Spina, Patrick Keating
  • Rmd, md

Stegen Analysis:

  • An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 3) by Janetta Skarp, Zhian N. Kamvar, Alexander Spina, Patrick Keating
  • Rmd, md

Stegen Descriptive:

  • An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 2) by Janetta Skarp, Zhian N. Kamvar, Alexander Spina, Patrick Keating
  • Rmd, md

Stegen Introduction:

  • An outbreak of gastroenteritis in Stegen, Germany, June 1998 (part 1) by Janetta Skarp, Zhian N. Kamvar, Alexander Spina, Patrick Keating
  • Rmd, md

TB:

  • TB: exploring the case of TB elimination with a simple compartmental model by Vesga, Juan
  • Rmd, md

Tools Analytics Pipelines:

Tools Infrastructure:

  • Tools for outbreak analytics infrastructures by Thibaut Jombart
  • Rmd

VBD:

  • VBD: building a simple model for Zika by Zulma Cucunuba, Pierre Nouvellet
  • Rmd, md

Why R:

ggplot2:

Spanish

Intro to R:

  • Una introducción a R y RStudio by Zulma M. Cucunuba, José M. Velasco-España, Andree Valle-Campos
  • Rmd, md

Real Time Response 1:

  • Análisis de brotes en tiempo real: el ébola como estudio de caso - parte 1 by Anne Cori, Natsuko Imai, Finlay Campbell, Zhian N. Kamvar, Thibaut Jombart, José M. Velasco-España
  • Rmd, md

Real Time Response 2:

  • Análisis de brotes en tiempo real: el ébola como estudio de caso - parte 2 by Anne Cori, Natsuko Imai, Finlay Campbell, Zhian N. Kamvar, Thibaut Jombart, José M. Velasco-España
  • Rmd, md

Rmarkdown:

  • Taller R Markdown by Carlos Javier Rincon
  • Rmd, md

Spatial Analysis:

  • Visualización y Análisis de datos espaciales en salud pública by Gabriel Carrasco-Escobar, Antony Barja, Jesus Quispe
  • Rmd, md

VBD:

  • VBD: Construyendo un modelo simple para Zika by Zulma Cucunuba, Pierre Nouvellet, José M. Velasco-España
  • Rmd, md