SCH Simulation Model

To run the SCH simulation model, import the SCH_Simulation() function from the helsim_RUN_KK module in the sch_simulation package.

The SCH_Simulation() function requires the following inputs:

• paramFileName: name of the input file with the model parameters. The available files are listed in the following table.

• demogName: name of the demography. The available demographies are listed in the following table.

• numReps: number of simulations. If not provided, the number of simulations is extracted from the parameters file.

The SCH_Simulation() function returns a data frame with the following columns: time, SAC Prevalence, Adult Prevalence, SAC Heavy Intensity Prevalence and Adult Heavy Intensity Prevalence.

The output data frame can be exported in several different formats; see sch_results.json for an example of the results in JSON format.

See also sch_run.py for an example of how to use the SCH_Simulation() function.

How to run

Requires Python 3.9-3.10.

• Install pipenv according to the instructions for your OS (on macOS it's brew install pipenv), then cd to the project directory, check out the branch you want to use, and run:

$ pipenv shell # sets up/runs a per-project python environment ('virtualenv'/'venv')
(ntd-model-sch) $ pip install . # installs python libraries & NTD model inside the venv
(ntd-model-sch) $ python sch_run.py # or could be 'pickle_example.py' - runs the model

Automatic tests

$ pipenv run pytest tests

The file tests/test_single_simulation.py runs a single SCH simulation over 24 years. The resulting yearly prevalence values are compared to reference values stored in tests/data/prevalence_reference.txt.

Reference prevalence data can be automatically updated by running:

pipenv run tests/test_single_simulation --update-ref

Endgame inputs

There are two input files required to run endgame simulations :

• a text file containing the parameters e.g. ascaris_scenario_3a.txt
• a spreadsheet containing the intervention timings and coverage e.g. ascaris_coverage_scenario_3a.xlsx

Text file

The text file must contain the following categories of parameters :

Run time parameters

repNum : number of repetitions \ nYears : number of years to run\ outputEvents : what time intervals should events be outputted at

Underlying biological and epidemiological parameters

species : the species name, e.g. ascaris\ unfertilized : unfertilised marker\ k : shape parameter of assumed negative binomial distribution of worms amongst host\ lambda : Eggs per gram (lambda)\ R0 : Basic reproductive number (R0)\ ReservoirDecayRate : Reservoir decay rate (decay rate of eggs in the environment)\ sigma : Worm death rate (sigma) i.e. 1/worm_life_span, same for all development stages\ gamma : Exponential density dependence of parasite adult stage (gamma) N.B. fecundity parameter z = exp(-gamma)\ k_epg: size parameter of negative binomial for test\ reproFuncNam : name of function for reproduction (a string). Deterministic\ StochSR : Turn SR on or off in the stochastic model. Stochastic\ nHosts : Size of definitive host population (N)\ neverTreated : proportion never treated\ contactAgeBreaks : Contact age group breaks (minus sign necessary to include zero age)\ betaValues : Relative contact rates (Beta)\ rhoValues: Rho, contribution to the reservoir by contact age group

Post-processing parameters

outputBreaks : What are the output age classes? \ highBurdenBreaks : Three categories here \ highBurdenValues : Corresponding values \ mediumThreshold : threshold for medium intensity infection \ heavyThreshold : threshold for heavy intensity infection

Treatment parameters

treatmentBreaks : Minimum age of each treatment group (minus sign necessary to include zero age): Infants; Pre-SAC; SAC; Adults \ drugEff : Drug efficacy drugEff1 : Drug efficacy of old product if more than one drug is used \ drugEff2 : Drug efficacy of new product if more than one drug is used

Currently the coverage and treatment information can be passed either within the .txt file or in the spreadsheet (see section below). If the coverage information is passed in the text file, the following parameters must be specified:

treatInterval1 : interval between treatments in years, pre-COVID \ treatInterval2 : interval between treatments in years, post-COVID \ treatStart1 : Treatment year start, pre-COVID \ treatStart2 :Treatment year start, post-COVID \ nRounds1 : Number of treatment rounds, pre-COVID \ nRounds2 : Number of treatment rounds, post-COVID \ coverage1 : Coverages pre-COVID: Infants; Pre-SAC; SAC; Adults coverage2 : Coverages post-COVID: Infants; Pre-SAC; SAC; Adults

Vaccine parameters

V1sigma : impact of vaccine on worm death rate. Assume worm death rate is v1sigma \ V2lambda : impact of vaccine on eggs per gram Fraction of eggs produced when vaccinated \ v3betaValues : impact of vaccine on contact rates Assume contact rate under vaccination is times v3\ VaccDecayRate: vacc decay rate. rate of vaccine decay = 1/duration of vaccine A vector with value 0 in state 1 and the vacc decay rate for state 2

Currently the vaccine information can be passed either within the .txt file or in the spreadsheet (see section below). If the vaccine information is passed in the text file, the following parameters must be specified:

VaccTreatmentBreaks : age range of the vaccinated group. These are the lower bounds of ranges with width 1, they must be more than one year part \ VaccCoverage : Vaccine coverage of the age group \ VaccTreatStart : Vaccine administration year start\ nRoundsVacc : number of vaccine rounds \ treatIntervalVacc : time interval between vaccine rounds

Survey parameters

timeToFirstSurvey : time of the first survey after simulation starts\ timeToNextSurvey : time between surveys\ surveyThreshold : prevalence threshold for passing survey\ sampleSizeOne : sample size for the first survey\ sampleSizeTwo : sample size for the second survey\ nSamples : how many samples to take from each individual\ minSurveyAge : minimum survey age\ maxSurveyAge : maximum survey age

Spreadsheet

The treatment and vaccination timings and coverages can be passed in a .xlsx file. The spreadsheet consists of two tabs:

• PlatformCoverage
• MarketShare

The PlatformCoverage tab must contain the following columns:

• InterventionType : the type of intervention, Treatment, Vaccine
• min age : the minimum age of the intervention recipients
• max age : the maximum age of the intervention recipients
• Then one column for each time point of application of the intervention, containing the coverage percentage.

Example row:

The columns “Country/Region”, “Platform Type” and “Platform” are currently optional.

The MarketShare tab must contain the following columns:

• Product : one of ‘New Product A’ or ‘Old Product B (SOC)’
• Then one column for each time point of application of mass treatment, containing market share percentage of ‘New Product A’ or ‘Old Product B (SOC)’

Example row:

The columns “Country/Region” and “Platform” are currently optional.