🤔 Find sources on how to model multiwave dynamics

jonjoncardoso commented 3 years ago

How do we explicitly model this?

This is an exploratory task, whatever we decide in terms of new equations will become new tasks.

References:

P.1. lineage in Manaus: https://science.sciencemag.org/content/sci/372/6544/815.full.pdf
Cacciapaglia 2020: Second wave COVID‑19 pandemics in Europe: a temporal playbook https://www.nature.com/articles/s41598-020-72611-5.pdf
Cacciapaglia 2021: Multiwave pandemic dynamics explained: how to tame the next wave of infectious diseases https://www.nature.com/articles/s41598-021-85875-2.pdf
Identifying Bayesian Mixture Models | Michael Betancourt | https://mc-stan.org/users/documentation/case-studies/identifying_mixture_models.html

Should we translate Cacciapaglia2021 to stan equations?

What are other relevant sources?

jonjoncardoso commented 3 years ago

cc @phcavelar you're welcome if you want to venture in this modelling adventure with us

jonjoncardoso commented 3 years ago

Some other relevant sources I found:

Sub-epidemics

Chowell et al 2019

Chowell, G., Tariq, A. & Hyman, J.M. A novel sub-epidemic modeling framework for short-term forecasting epidemic waves. BMC Med 17, 164 (2019). https://doi.org/10.1186/s12916-019-1406-6

From the conclusion: "We have introduced a sub-epidemic wave modeling framework based on the premise that overlapping and regular sub-epidemics, which are often unobserved, can determine the shape of the trajectory of epidemic waves that are observed at larger spatial scales"

Metrics-based

Xu et al 2020

Bo Xu, Jun Cai, Daihai He, Gerardo Chowell, Bing Xu. 2020. Journal of Theoretical Biology. Mechanistic modelling of multiple waves in an influenza epidemic or pandemic. https://www.sciencedirect.com/science/article/pii/S0022519319304394

Hoen et al 2015

Hoen et al 2015. Journal of Medical Internet Research. Epidemic Wave Dynamics Attributable to Urban Community Structure: A Theoretical Characterization of Disease Transmission in a Large Network https://www.jmir.org/2015/7/e169

SIR (or other compartimental) models adapted to multiwaves

Kaxiras & Neofotistos 2020

Kaxiras & Neofotistos 2020. Journal of Medical Internet Research. Multiple Epidemic Wave Model of the COVID-19 Pandemic: Modeling Study. https://www.jmir.org/2020/7/e20912

Shao et al 2018

Shi Zhao, Yijun Lou, Alice P.Y. Chiu, Daihai He. 2018. Journal of Theoretical Biology Modelling the skip-and-resurgence of Japanese encephalitis epidemics in Hong Kong.

jonjoncardoso commented 3 years ago

A little off-topic but related to Hoen2015: City size and the spreading of COVID-19 in Brazil

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239699

jonjoncardoso commented 3 years ago

Theoretical TODOs spanning from these references:

[ ] Study the application of Chowell et al 2019 to our model
[ ] Study the application of Shao et al 2018 to our model

jonjoncardoso commented 3 years ago

Add multiple variants to the model

[ ] Add an integer list variants to the data section
[ ] Break mu distribution into two distributions: for variant in variants: mu[variant] ~ ....
[ ] Rt should be indexed by variants as well. ex: Rt[i, m, v]
[ ] prediction becomes the sum of the products between different Rts and each variant convolution
[ ] How to include a binary variable in the model to "choose" which variant is available and when

Data-Science-Brigade / modelo-epidemiologico-sc