3.3 Synthesis: elr_synthesis.Rmd

This report compiles results of all WHO regions, defines ELR for the countries, and stores the main results into an xlsx file.

3.3.1 Inputs

The report compiles the latest results obtained for the different WHO regions stored in asmodee_outputs/rds/.

3.3.2 Outputs

Based on the metrics used in the pinplots, countries are assigned an ELR using the algorithm summarised in figure 3.2. The report provides complementary informations including trend plots (ASMODEE results) for the countries with Medium risk or higher, and some additional information on Testing Positivity Rates (TPR) and vaccination coverage.

Algorithm to define Epi Level of Risk (**ELR**). This diagram summarises the algorithm used to define a risk level (*Low* / *Medium* / *High* / *Very High*) based on values of the daily growth rates, weekly incidence, and signs of acceleration in transmission. Grey squares indicate *Minimal* risk. *Intel adjustments* represent the possibility for other sources of information (e.g. status of the healthcare system) to shift ELR by one level (or more in extreme cases) right or left.

Figure 3.2: Algorithm to define Epi Level of Risk (ELR). This diagram summarises the algorithm used to define a risk level (Low / Medium / High / Very High) based on values of the daily growth rates, weekly incidence, and signs of acceleration in transmission. Grey squares indicate Minimal risk. Intel adjustments represent the possibility for other sources of information (e.g. status of the healthcare system) to shift ELR by one level (or more in extreme cases) right or left.

Besides the html version of the report, other outputs include:

  • dynamics_synthesis.xlsx: and Excel spreadsheet providing the ELR for each country alongside the different metrics used in the algorithm as well as additional information on TPR and vaccination coverage

  • excluded_countries.txt: a text file listing all countries that were excluded from the analysis alongside the reason for their exclusion

3.3.3 Parameters

The report does not accept parameters.

3.3.4 Example compilation

The following instructions will compile the report: