Epidemiology Modeling Workflows

In brief

This Raku Perl 6 package has grammar classes and action classes for the parsing and interpretation of spoken commands that specify epidemiology modeling workflows.

It is envisioned that the interpreters (actions) are going to target different programming languages: R, WL, Python, etc.

In the first version(s) the workflows targeted are Epidemiology Compartmental Modeling workflows, [AAr1, AAr2].

Installation

From Zef Ecosystem:

zef install DSL::English::EpidemiologyModelingWorkflows

From GitHub:

zef install https://github.com/antononcube/Raku-DSL-English-EpidemiologyModelingWorkflows.git

Examples

Here an epidemiology model simulation workflow is specified and translated to R code with the package ECMMon-R, [AAr2] :

use DSL::English::EpidemiologyModelingWorkflows;

say ToEpidemiologyModelingWorkflowCode('
     create with SEI2HR;
     assign 100000 to total population;
     set infected normally symptomatic population to be 0;
     set infected severely symptomatic population to be 1;
     assign 0.56 to contact rate of infected normally symptomatic population;
     assign 0.58 to contact rate of infected severely symptomatic population;
     assign 0.1 to contact rate of the hospitalized population;
     simulate for 240 days;
     plot results;
', 'R-ECMMon');

# ECMMonUnit( model = SEI2HRModel()) %>%
# ECMMonAssignInitialConditions( initConds = c(TPt = 100000) ) %>%
# ECMMonAssignInitialConditions( initConds = c(INSPt = 0) ) %>%
# ECMMonAssignInitialConditions( initConds = c(ISSPt = 1) ) %>%
# ECMMonAssignRateValues( rateValues = c(contactRateINSP = 0.56) ) %>%
# ECMMonAssignRateValues( rateValues = c(contactRateISSP = 0.58) ) %>%
# ECMMonAssignRateValues( rateValues = c(contactRateHP = 0.1) ) %>%
# ECMMonSimulate(maxTime = 240) %>%
# ECMMonPlotSolutions()

Versions

The original version of this Raku package was developed/hosted at [ AA3 ].

A dedicated GitHub repository was made in order to make the installation with Raku's zef more direct. (As shown above.)

References

[AAr1] Anton Antonov, Coronavirus-propagation-dynamics, (2020), SystemModeling at GitHub.

[AAr2] Anton Antonov, Epidemiology Compartmental Modeling Monad in R, (2020), ECMMon-R at GitHub.

[AA3] Anton Antonov, Epidemiology Modeling Workflows Raku Package, (2020), ConversationalAgents at GitHub.