.github/workflows/example.R

In SwissTPH/r-openMalariaUtilities: Helper functions to provide easier usage of Open Malaria from R

## Generate and simulate the original OpenMalaria example.

## TODO Instead of relying on raw input, use our functions to generation list
##      sections.

devtools::load_all()

testExp <- list(
  ## Mandatory
  expName = "exp_test",
  ## Optional
  ## subDir = "example_test",
  ## Optional
  ## country = "GHA",
  ## Mandatory
  OMVersion = 44L,
  ## Optional
  ## analysisNo = 1L,
  ## Optional
  ## xmlBasename = "meppa_base",
  ## Mandatory
  demography = list(
    maximumAgeYrs = 90,
    name = "Ifakara",
    popSize = "@pop@",
    ageGroup = list(
      lowerbound = 0,
      group = list(poppercent = 3.474714994, upperbound = 1),
      group = list(poppercent = 12.76004028, upperbound = 5),
      group = list(poppercent = 14.52151394, upperbound = 10),
      group = list(poppercent = 12.75565434, upperbound = 15),
      group = list(poppercent = 10.83632374, upperbound = 20),
      group = list(poppercent = 8.393312454, upperbound = 25),
      group = list(poppercent = 7.001421452, upperbound = 30),
      group = list(poppercent = 5.800587654, upperbound = 35),
      group = list(poppercent = 5.102136612, upperbound = 40),
      group = list(poppercent = 4.182561874, upperbound = 45),
      group = list(poppercent = 3.339409351, upperbound = 50),
      group = list(poppercent = 2.986112356, upperbound = 55),
      group = list(poppercent = 2.555766582, upperbound = 60),
      group = list(poppercent = 2.332763433, upperbound = 65),
      group = list(poppercent = 1.77400255, upperbound = 70),
      group = list(poppercent = 1.008525491, upperbound = 75),
      group = list(poppercent = 0.74167341, upperbound = 80),
      group = list(poppercent = 0.271863401, upperbound = 85),
      group = list(poppercent = 0.161614642, upperbound = 90)
    )
  ),
  monitoring = list(
    name = "Quarterly Surveys",
    ## Mandatory, different from OM schema
    startDate = "2000-01-01",
    continuous = list(
      period = "1",
      option = list(name = "input EIR", value = "true"),
      option = list(name = "simulated EIR", value = "true"),
      option = list(name = "human infectiousness", value = "true"),
      option = list(name = "N_v0", value = "true"),
      option = list(name = "immunity h", value = "true"),
      option = list(name = "immunity Y", value = "true"),
      option = list(name = "new infections", value = "true"),
      option = list(name = "num transmitting humans", value = "true"),
      option = list(name = "ITN coverage"),
      option = list(name = "GVI coverage"),
      option = list(name = "alpha", value = "true"),
      option = list(name = "P_B", value = "false"),
      option = list(name = "P_C*P_D", value = "false")
    ),
    SurveyOptions = monitoringSurveyOptionsGen(
      options = list(
        name = c("nHost", "nPatent", "nUncomp", "nSevere", "nDirDeaths", "inputEIR", "simulatedEIR"),
        value = c("true", "true", "true", "true", "false", "true", "true")
      )
    ),
    surveys = list(
      detectionLimit = 40,
      surveyTime = list(repeatStep = "1y", repeatEnd = "20.027y", "1t"),
      surveyTime = list(repeatStep = "1y", repeatEnd = "20.027y", "19t"),
      surveyTime = list(repeatStep = "1y", repeatEnd = "20.027y", "37t"),
      surveyTime = list(repeatStep = "1y", repeatEnd = "20.027y", "55t")
    ),
    ageGroup = surveyAgeGroupsGen(0, c(5,90))
  ),
  interventions = list(
    name = "test",
    human = list(
      component = list(
        id = "GVI",
        name = "DDT test",
        GVI = list(
          decay = list(
            L = "0.5",
            "function" = "exponential"
          ),
          anophelesParams = list(
            mosquito = "gambiae_ss", propActive = "1",
            deterrency = list(value = "0.56"),
            preprandialKillingEffect = list(value = "0"),
            postprandialKillingEffect = list(value = "0.24")
          )
        )
      ),
      deployment = list(
        name = "DDT test",
        component = list(id = "GVI"),
        timed = list(
          deploy = list(coverage = "0.9", time = "10y")
        )
      )
    )
  ),
  healthSystem = list(
    ImmediateOutcomes = list(
      name = "Tanzania ACT",
      drugRegimen = list(
        firstLine = "ACT",
        inpatient = "QN",
        secondLine = "ACT"
      ),
      initialACR = list(
        ACT = list(value = 0.85),
        QN = list(value = 0.998),
        selfTreatment = list(value = 0.63)
      ),
      compliance = list(
        ACT = list(value = 0.9),
        selfTreatment = list(value = 0.85)
      ),
      nonCompliersEffective = list(
        ACT = list(value = 0),
        selfTreatment = list(value = 0)
      ),
      treatmentActions = list(
        ACT = list(
          name = "clear blood-stage infections",
          clearInfections = list(
            stage = "blood",
            timesteps = "1"
          )
        ),
        QN = list(
          name = "clear blood-stage infections",
          clearInfections = list(
            stage = "blood",
            timesteps = "1"
          )
        )
      ),
      pSeekOfficialCareUncomplicated1 = list(value = 0.04),
      pSelfTreatUncomplicated = list(value = 0.01),
      pSeekOfficialCareUncomplicated2 = list(value = 0.04),
      pSeekOfficialCareSevere = list(value = 0.48)
    ),
    CFR = list(
      group = list(lowerbound = 0, value = 0.09189),
      group = list(lowerbound = 0.25, value = 0.0810811),
      group = list(lowerbound = 0.75, value = 0.0648649),
      group = list(lowerbound = 1.5, value = 0.0689189),
      group = list(lowerbound = 2.5, value = 0.0675676),
      group = list(lowerbound = 3.5, value = 0.0297297),
      group = list(lowerbound = 4.5, value = 0.0459459),
      group = list(lowerbound = 7.5, value = 0.0945946),
      group = list(lowerbound = 12.5, value = 0.1243243),
      group = list(lowerbound = 15, value = 0.1378378)
    ),
    ## Mandatory
    pSequelaeInpatient = list(
      interpolation = "none",
      group = list(lowerbound = "0.0", value = 0.0132),
      group = list(lowerbound = "5.0", value = 0.005)
    )
  ),
  entomology = list(
    mode = "dynamic", name = "Namawala",
    vector = list(
      anopheles = list(
        mosquito = "gambiae_ss", propInfected = 0.078, propInfectious = "0.021",
        seasonality = list(
          annualEIR = "16", input = "EIR",
          fourierSeries = list(
            EIRRotateAngle = "0",
            coeffic = list(
              a = "0.8968", b = "2.678"
            ),
            coeffic = list(a = "-0.4551", b = "2.599")
          )
        ),
        mosq = list(
          minInfectedThreshold = "0.001",
          mosqRestDuration = list(value = "3"),
          extrinsicIncubationPeriod = list(value = "11"),
          mosqLaidEggsSameDayProportion = list(value = "0.313"),
          mosqSeekingDuration = list(value = "0.33"),
          mosqSurvivalFeedingCycleProbability = list(value = "0.623"),
          availability = list(distr = "const"),
          mosqProbBiting = list(mean = "0.95", variance = "0"),
          mosqProbFindRestSite = list(mean = "0.95", variance = "0"),
          mosqProbResting = list(mean = "0.99", variance = "0"),
          mosqProbOvipositing = list(value = "0.88"),
          mosqHumanBloodIndex = list(value = "0.939")
        ),
        nonHumanHosts = list(
          name = "unprotectedAnimals",
          mosqRelativeEntoAvailability = list(value = "1.0"),
          mosqProbBiting = list(value = "0.95"),
          mosqProbFindRestSite = list(value = "0.95"),
          mosqProbResting = list(value = "0.99")
        )
      ),
      nonHumanHosts = list(name = "unprotectedAnimals", number = "1.0")
    )
  ),
  model = list(
    ModelOptions = list(
      option = list(name = "LOGNORMAL_MASS_ACTION", value = "true"),
      option = list(name = "NO_PRE_ERYTHROCYTIC", value = "true"),
      option = list(name = "INNATE_MAX_DENS", value = "false"),
      option = list(name = "INDIRECT_MORTALITY_FIX", value = "false"),
      option = list(name = "NON_MALARIA_FEVERS", value = "true")
    ),
    clinical = list(
      healthSystemMemory = "6",
      NonMalariaFevers = list(
        incidence = list(
          group = list(lowerbound = "0", value = "0.322769924518357"),
          group = list(lowerbound = "0", value = "0.308520194304172"),
          group = list(lowerbound = "1", value = "0.279441774808493"),
          group = list(lowerbound = "2", value = "0.250431781111273"),
          group = list(lowerbound = "3", value = "0.223285859756841"),
          group = list(lowerbound = "4", value = "0.199298352451799"),
          group = list(lowerbound = "5", value = "0.179376872365614"),
          group = list(lowerbound = "6", value = "0.163623659390782"),
          group = list(lowerbound = "7", value = "0.152227726923469"),
          group = list(lowerbound = "8", value = "0.145022785567758"),
          group = list(lowerbound = "9", value = "0.141493087461765"),
          group = list(lowerbound = "10", value = "0.140473293219353"),
          group = list(lowerbound = "11", value = "0.141109775159515"),
          group = list(lowerbound = "12", value = "0.142644475217328"),
          group = list(lowerbound = "13", value = "0.144335079395766"),
          group = list(lowerbound = "14", value = "0.145964032924869"),
          group = list(lowerbound = "15", value = "0.147708915135714"),
          group = list(lowerbound = "16", value = "0.149731543445568"),
          group = list(lowerbound = "17", value = "0.151887428568276"),
          group = list(lowerbound = "18", value = "0.154060663485195"),
          group = list(lowerbound = "19", value = "0.156179169710494"),
          group = list(lowerbound = "20", value = "0.158135015380583"),
          group = list(lowerbound = "21", value = "0.159704766482219"),
          group = list(lowerbound = "22", value = "0.160807788387655"),
          group = list(lowerbound = "23", value = "0.161427976448279"),
          group = list(lowerbound = "24", value = "0.161620429119137"),
          group = list(lowerbound = "25", value = "0.16144021875986"),
          group = list(lowerbound = "26", value = "0.160943264630612"),
          group = list(lowerbound = "27", value = "0.160217573697398"),
          group = list(lowerbound = "28", value = "0.159422614374451"),
          group = list(lowerbound = "29", value = "0.158542519631641"),
          group = list(lowerbound = "30", value = "0.157501217628248"),
          group = list(lowerbound = "31", value = "0.156175160594841"),
          group = list(lowerbound = "32", value = "0.154402302191411"),
          group = list(lowerbound = "33", value = "0.152102040636481"),
          group = list(lowerbound = "34", value = "0.14921450014676"),
          group = list(lowerbound = "35", value = "0.145714433541659"),
          group = list(lowerbound = "36", value = "0.141800502067518"),
          group = list(lowerbound = "37", value = "0.137916853907569"),
          group = list(lowerbound = "38", value = "0.134503529382102"),
          group = list(lowerbound = "39", value = "0.131746276580642"),
          group = list(lowerbound = "40", value = "0.12969902537497"),
          group = list(lowerbound = "41", value = "0.128398077347679"),
          group = list(lowerbound = "42", value = "0.127864136551891"),
          group = list(lowerbound = "43", value = "0.12804497197004"),
          group = list(lowerbound = "44", value = "0.128894055047661"),
          group = list(lowerbound = "45", value = "0.130350838992718"),
          group = list(lowerbound = "46", value = "0.132286605622701"),
          group = list(lowerbound = "47", value = "0.134599921072495"),
          group = list(lowerbound = "48", value = "0.137212726976988"),
          group = list(lowerbound = "49", value = "0.140035253913284"),
          group = list(lowerbound = "50", value = "0.142934573453621"),
          group = list(lowerbound = "51", value = "0.145830221511879"),
          group = list(lowerbound = "52", value = "0.148674810561069"),
          group = list(lowerbound = "53", value = "0.151497963594518"),
          group = list(lowerbound = "54", value = "0.15438856687865"),
          group = list(lowerbound = "55", value = "0.157403790093505"),
          group = list(lowerbound = "56", value = "0.16059513222516"),
          group = list(lowerbound = "57", value = "0.16402433342886"),
          group = list(lowerbound = "58", value = "0.16770481415944"),
          group = list(lowerbound = "59", value = "0.171626873047865"),
          group = list(lowerbound = "60", value = "0.175748327054247"),
          group = list(lowerbound = "61", value = "0.180030857856799"),
          group = list(lowerbound = "62", value = "0.184411365583771"),
          group = list(lowerbound = "63", value = "0.188816421789366"),
          group = list(lowerbound = "64", value = "0.19316997803338"),
          group = list(lowerbound = "65", value = "0.197435603275487"),
          group = list(lowerbound = "66", value = "0.201578808813379"),
          group = list(lowerbound = "67", value = "0.205556806881398"),
          group = list(lowerbound = "68", value = "0.209307183457343"),
          group = list(lowerbound = "69", value = "0.212783260344084"),
          group = list(lowerbound = "70", value = "0.215944154621391"),
          group = list(lowerbound = "71", value = "0.218749275266548"),
          group = list(lowerbound = "72", value = "0.221187990639016"),
          group = list(lowerbound = "73", value = "0.223361260399378"),
          group = list(lowerbound = "74", value = "0.225363436789592"),
          group = list(lowerbound = "75", value = "0.227254280093211"),
          group = list(lowerbound = "76", value = "0.229084576349576"),
          group = list(lowerbound = "77", value = "0.230891971097789"),
          group = list(lowerbound = "78", value = "0.232690225166173"),
          group = list(lowerbound = "79", value = "0.234484973338876"),
          group = list(lowerbound = "80", value = "0.236276361586796"),
          group = list(lowerbound = "81", value = "0.238064394629696"),
          group = list(lowerbound = "82", value = "0.239849077182917"),
          group = list(lowerbound = "83", value = "0.241630413957381"),
          group = list(lowerbound = "84", value = "0.243408409659591"),
          group = list(lowerbound = "85", value = "0.245183068991633"),
          group = list(lowerbound = "86", value = "0.246954396651183"),
          group = list(lowerbound = "87", value = "0.248722397331501"),
          group = list(lowerbound = "88", value = "0.250487075721441"),
          group = list(lowerbound = "89", value = "0.252248436505447"),
          group = list(lowerbound = "90", value = "0.253127874257909")
        )
      )
    ),
    human = list(
      availabilityToMosquitoes = list(
        group = list(lowerbound = "0", value = "0.7076"),
        group = list(lowerbound = "0", value = "0.8538"),
        group = list(lowerbound = "5", value = "1.0"),
        group = list(lowerbound = "5", value = "1.0")
      )
    ),
    parameters = list(
      interval = "5", iseed = "1", latentp = "3",
      parameter = list(include = "false", name = "'-ln(1-Sinf)'", number = "1", value = "0.050736"),
      parameter = list(include = "false", name = "Estar", number = "2", value = "0.03247"),
      parameter = list(include = "false", name = "Simm", number = "3", value = "0.138161050830301"),
      parameter = list(include = "false", name = "Xstar_p", number = "4", value = "1514.385853233699891"),
      parameter = list(include = "false", name = "gamma_p", number = "5", value = "2.03692533424484"),
      parameter = list(include = "false", name = "sigma2i", number = "6", value = "10.173598698525799"),
      parameter = list(include = "false", name = "CumulativeYstar", number = "7", value = "35158523.31132510304451"),
      parameter = list(include = "false", name = "CumulativeHstar", number = "8", value = "97.334652723897705"),
      parameter = list(include = "false", name = "'-ln(1-alpha_m)'", number = "9", value = "2.33031045876193"),
      parameter = list(include = "false", name = "decay_m", number = "10", value = "2.53106547375805"),
      parameter = list(include = "false", name = "sigma2_0", number = "11", value = "0.655747311168152"),
      parameter = list(include = "false", name = "Xstar_v", number = "12", value = "0.916181104713054"),
      parameter = list(include = "false", name = "Ystar2", number = "13", value = "6502.26335600001039"),
      parameter = list(include = "false", name = "alpha", number = "14", value = "142601.912520000012591"),
      parameter = list(include = "false", name = "Density bias (non Garki)", number = "15", value = "0.177378570987455"),
      parameter = list(include = "false", name = "        sigma2        ", number = "16", value = "0.05"),
      parameter = list(include = "false", name = "log oddsr CF community", number = "17", value = "0.736202"),
      parameter = list(include = "false", name = "Indirect risk cofactor", number = "18", value = "0.018777338"),
      parameter = list(include = "false", name = "Non-malaria infant mortality", number = "19", value = "49.539046599999999"),
      parameter = list(include = "false", name = "Density bias (Garki)", number = "20", value = "4.79610772546704"),
      parameter = list(include = "false", name = "Severe Malaria Threshhold", number = "21", value = "784455.599999999976717"),
      parameter = list(include = "false", name = "Immunity Penalty", number = "22", value = "1"),
      parameter = list(include = "false", name = "Immune effector decay", number = "23", value = "0"),
      parameter = list(include = "false", name = "comorbidity intercept", number = "24", value = "0.0968"),
      parameter = list(include = "false", name = "Ystar half life", number = "25", value = "0.275437402"),
      parameter = list(include = "false", name = "Ystar1", number = "26", value = "0.596539864"),
      parameter = list(include = "false", name = "Asexual immunity decay", number = "27", value = "0"),
      parameter = list(include = "false", name = "Ystar0", number = "28", value = "296.302437899999973"),
      parameter = list(include = "false", name = "Idete multiplier", number = "29", value = "2.797523626"),
      parameter = list(include = "false", name = "critical age for comorbidity", number = "30", value = "0.117383")
    )
  )
)

## Setup dirs
setupDirs(experimentName = "exp_test", replace = TRUE)

## Copy necessary Open Malaria files.
setupOM()

## Create base XML file
createBaseXml(testExp, replace = TRUE)

scenarios <- data.frame(
  pop = 1000L,
  futLSMcov = "none"
)
scenarios <- finalizeScenarios(scenarios)

setupScenarios(scenarios = scenarios)

storeScenarios(scenarios)

## Manually store survey times in cache
dates <- .xmlMonitoringTimeRegularSeq(
  startDate = "2000-01-01",
  "2020-04-01", daysFilter = 5, dateFilter = "quarterly"
)
putCache(
  x = "surveyTimes",
  value = data.table::data.table(number = seq.int(nrow(dates)), dates)
)

## Run simulations
runSimulations(scenarios = scenarios)

collectResults(
  expDir =  getCache("experimentDir"), dbName = "test", replace = TRUE,
  verbose = TRUE)

## Inspect results
con <- DBI::dbConnect(RSQLite::SQLite(), "test.sqlite")
db_tables <- DBI::dbListTables(con)
for (t in db_tables) {
  tbl <- data.table::as.data.table(DBI::dbReadTable(con, t))
  print(tbl)
}
DBI::dbDisconnect(con)