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#' @title checkSimPara
#'
#' @description check (and correct) parameter list
#'
#' @param para list: optimization parameters, e.g., generated via \code{\link{babsimHospitalPara}}
#'
#' @return corrected parameter list
#'
#' @examples
#'
#' x0 <- babsimHospitalPara()
#' x <- checkSimPara(x0)
#' @export
checkSimPara <- function(para = babsimHospitalPara()) {
minDays <- 1e-06
maxDays <- 365
minVal <- 1e-06
maxVal <- 1e+06
minProb <- 0
maxProb <- 1
# x1:
para$AmntDaysInfectedToHospital <- ensureRangeOpen(
para$AmntDaysInfectedToHospital,
minDays, maxDays
)
# x2:
para$AmntDaysNormalToHealthy <- ensureRangeOpen(
para$AmntDaysNormalToHealthy,
minDays, maxDays
)
# x3:
para$AmntDaysNormalToIntensive <- ensureRangeOpen(
para$AmntDaysNormalToIntensive,
minDays, maxDays
)
# x4:
para$AmntDaysNormalToVentilation <- ensureRangeOpen(
para$AmntDaysNormalToVentilation,
minDays, maxDays
)
# x5:
para$AmntDaysNormalToDeath <- ensureRangeOpen(
para$AmntDaysNormalToDeath, minDays,
maxDays
)
# x6:
para$AmntDaysIntensiveToAftercare <- ensureRangeOpen(
para$AmntDaysIntensiveToAftercare,
minDays, maxDays
)
# x7:
para$AmntDaysIntensiveToVentilation <- ensureRangeOpen(
para$AmntDaysIntensiveToVentilation,
minDays, maxDays
)
# x8:
para$AmntDaysIntensiveToDeath <- ensureRangeOpen(
para$AmntDaysIntensiveToDeath,
minDays, maxDays
)
# x9:
para$AmntDaysVentilationToIntensiveAfter <- ensureRangeOpen(
para$AmntDaysVentilationToIntensiveAfter,
minDays, maxDays
)
# x10:
para$AmntDaysVentilationToDeath <- ensureRangeOpen(
para$AmntDaysVentilationToDeath,
minDays, maxDays
)
# x11:
para$AmntDaysIntensiveAfterToAftercare <- ensureRangeOpen(
para$AmntDaysIntensiveAfterToAftercare,
minDays, maxDays
)
# x12:
para$AmntDaysIntensiveAfterToDeath <- ensureRangeOpen(
para$AmntDaysIntensiveAfterToDeath,
minDays, maxDays
)
# x13:
para$GammaShapeParameter <- ensureRangeOpen(
para$GammaShapeParameter, minVal,
maxVal
)
# x14:
para$FactorPatientsInfectedToHospital <- ensureRangeOpen(
para$FactorPatientsInfectedToHospital,
minProb, maxProb
)
# x15:
para$FactorPatientsHospitalToIntensive <- ensureRangeOpen(
para$FactorPatientsHospitalToIntensive,
minProb, maxProb
)
# x16:
para$FactorPatientsHospitalToVentilation <- ensureRangeOpen(
para$FactorPatientsHospitalToVentilation,
minProb, maxProb
)
# x17:
para$FactorPatientsNormalToIntensive <- ensureRangeOpen(
para$FactorPatientsNormalToIntensive,
minProb, maxProb
)
# x18:
para$FactorPatientsNormalToVentilation <- ensureRangeOpen(
para$FactorPatientsNormalToVentilation,
minProb, maxProb
)
# x19:
para$FactorPatientsNormalToDeath <- ensureRangeOpen(
para$FactorPatientsNormalToDeath,
minProb, maxProb
)
# x20:
para$FactorPatientsIntensiveToVentilation <- ensureRangeOpen(
para$FactorPatientsIntensiveToVentilation,
minProb, maxProb
)
# x21:
para$FactorPatientsIntensiveToDeath <- ensureRangeOpen(
para$FactorPatientsIntensiveToDeath,
minProb, maxProb
)
# x22:
para$FactorPatientsVentilationToIntensiveAfter <- ensureRangeOpen(
para$FactorPatientsVentilationToIntensiveAfter,
minProb, maxProb
)
# x23:
para$FactorPatientsIntensiveAfterToDeath <- ensureRangeOpen(
para$FactorPatientsIntensiveAfterToDeath,
minProb, maxProb
)
# x24:
para$AmntDaysAftercareToHealthy <- ensureRangeOpen(
para$AmntDaysAftercareToHealthy,
minDays, maxDays
)
# x25:
para$RiskFactorA <- ensureRangeOpen(para$RiskFactorA, minVal, maxVal)
# x26:
para$RiskFactorB <- ensureRangeOpen(para$RiskFactorB, minVal, maxVal)
# Risk based on gender x27:
para$RiskMale <- ensureRangeOpen(para$RiskMale, minVal, maxVal)
# x28:
para$AmntDaysIntensiveAfterToHealthy <- ensureRangeOpen(
para$AmntDaysIntensiveAfterToHealthy,
minDays, maxDays
)
# x29:
para$FactorPatientsIntensiveAfterToHealthy <- ensureRangeOpen(
para$FactorPatientsIntensiveAfterToHealthy,
minProb, maxProb
)
## Repair probabilities:
P <- getMatrixP(para = para)
m <- rep(1, nrow(P))
Q <- P %*% diag(m)
S <- diag(1 / rowSums(Q))
R <- S %*% Q
para <- mapPToPara(P = R, para = para)
return(para)
}
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