Module specification

THIS IS DEPRECATED. GO TO HopkinsIDD/COVID19_Minimal

R interface basics

The python code will call your R scripts, setting some variable in the environment:

• from_python: truthy boolean, test for this to know if your code is run automatically.
• ti_str, tf_str model start and end as a string
• foldername the folder that contains everything related to the setup. You'll have to load geodata.csv from there. It include the / at the end.

if (!from_python) {         # or whatever values you use to test.
    ti_str <- '2020-01-31'
    tf_str <- '2020-08-31'
    foldername <- 'west-coast/'      
}
# write code here that uses what is above and can load more files.

The code is run from the root folder of the repository.

Setup

A setup has a name, and this name is a also folder that contains file geodata.csv (see below).

Modules

(and status if the current R implementation respect the specification)

Mobility (WIP)

• From R: dataframe named mobility with columns: from, to, amount. Relationships not specified will be set to zero. You can set different value for A -> B and B -> A (if you only specified A -> B, we'll assume B -> A = 0).
• From file: matrix to be imported with numpy as it is. Dimension: (nnodes, nnnodes) (may have a third dimension if time varying). First index is from, second is to, diagonal is zero (mobility[ori, dest])
• From python: numpy matrix as file.

Population (DONE)

• From file: geodata.csv : specification of the spatial nodes, with at least column for the zero based index, the geoid or name, the population.

Importation (TODO)

• From R: dataframe named importation with column date, to, amount where date is a string, to contains a geoid and amount contains an integer.

NPI (DONE)

Different R scripts define the Nonpharmaceutical Intervention (NPI) to apply in the simulation. Based on the following system arguments, an R script will be called that generates the appropriate intervention. The start and end dates for each NPI needs to be specified (YYYY-MM-DD).

• None: No intervention, R0 reduction is 0
• SchoolClosure: School closure, counties randomly assigned an R0 reduction ranging from 16-30% (Jackson, M. et al., medRxiv, 2020)
• Influenza1918: Influenza social distancing as observed in 1918 Influenza. Counties are randomly assigned an R reduction value ranging from 44-65% (the most intense social distancing R0 reduction values from Milwaukee) (Bootsma & Ferguson, PNAS, 2007)
• Wuhan: Counties randomly assigned an R0 reduction based on values reported in Wuhan before and after travel ban during COVID-19 outbreak (R0 reduction of 81-88%) (Zhang, B., Zhou, H., & Zhou F. medRxiv, 2020; Mizumoto, R., Kagaya, K., & Chowell, G., medRxiv, 2020)
• TestIsolate: This intervention represents rapid testing and isolation of cases, similar to what was done in Wuhan at the beginning of the outbreak. It reduces R0 by 45-96%.
• Mild: This intervention has two sequential interventions: School closures, followed by a period of Wuhan-style lockdown followed by nothing.
• Mid: This intervention has three sequential interventions: School closures, followed by a period of Wuhan-style lockdown, followed by social distancing practices used during the 1918 Influenza pandemic
• Severe: This intervention has three sequential interventions: School closures, followed by a Wuhan-style lockdown, followed by rapid testing and isolation.

Transmission parameters (TODO)