micSimParallel: Run microsimulation (parallel computing)

In MicSim: Performing Continuous-Time Microsimulation

Run microsimulation (parallel computing)

Description

The function micSimParallel is a parallelized version of the function micSim. That is, it runs a continuous-time microsimulation simulation distributed, i.e., using more than one CPU core.

Usage

micSimParallel(initPop, immigrPop = NULL, initPopList = c(), immigrPopList = c(), 
  transitionMatrix, absStates = NULL, varInitStates = c(), initStatesProb = c(), 
  fixInitStates = c(), maxAge = 99, simHorizon, fertTr = c(), 
  monthSchoolEnrol=c(), cores=1, seeds=1254)

Arguments

initPop	Either an initial population has to be given as a whole or splitted to be run at the distinct cores, see arguments initPopList. If it is given as a whole it is automatically splitted by MicSim such that the population parts run on the distinct cores are approx. equally sized.
immigrPop	Optionally, a population of migrants entering the virtual population along simulation time can be given, see arguments immigrPopList. This migrants population can either be given as a whole or splitted to be run at the distinct cores. If it is given as a whole it is automatically splitted by MicSim such that the population parts run on the distinct cores are approx. equally sized.
transitionMatrix
absStates
varInitStates
initStatesProb
initPopList	Optional: A list containing the initial population split for the distinct cores.
immigrPopList	Optional: A list containing the immigration population split for the distinct cores.
fixInitStates
maxAge
simHorizon
fertTr
monthSchoolEnrol	See micSim.
cores	Number of CPUs to be used.
seeds	Seeds for pseudo number generators used for parallel computing.

Details

The argument cores must not exceed the number of cores of the computer (cluster) used.

In seeds as many seeds should be given as cores are used. If less are given, the latter are repeated to complete the set of seeds.

Value

The data frame pop contains the whole synthetic population considered during simulation including all events generated. For more details, see micSim.

Author(s)

Sabine Zinn

Examples

# Clean workspace 
rm(list=ls())

# Defining simulation horizon
startDate <- 20140101 # yyyymmdd
endDate   <- 20241231 # yyyymmdd
simHorizon <- c(startDate=startDate, endDate=endDate)

# Seed for random number generator
set.seed(234)

# Definition of maximal age 
maxAge <- 100  

# Defintion of nonabsorbing and absorbing states
sex <- c("m","f")                     
fert <- c("0","1+")           
marital <- c("NM","M","D","W")        
edu <- c("no","low","med","high")   
stateSpace <- expand.grid(sex=sex,fert=fert,marital=marital,edu=edu)
absStates <- c("dead","rest")   

# General month of enrollment to elementary school
monthSchoolEnrol <- 9

# Definition of an initial population (for illustration purposes, create a random population)
N = 10000                                                       
birthDates <- runif(N, min=getInDays(19500101), max=getInDays(20131231)) 
getRandInitState <- function(birthDate){
  age <- trunc((getInDays(simHorizon[1]) - birthDate)/365.25) 
  s1 <- sample(sex,1)
  s2 <- ifelse(age<=18, fert[1], sample(fert,1))
  s3 <- ifelse(age<=18, marital[1], ifelse(age<=22, sample(marital[1:3],1), 
                                           sample(marital,1)))
  s4 <- ifelse(age<=7, edu[1], ifelse(age<=18, edu[2], ifelse(age<=23, sample(edu[2:3],1), 
                                                              sample(edu[-1],1))))
  initState <- paste(c(s1,s2,s3,s4),collapse="/")
  return(initState)
}
initPop <- data.frame(ID=1:N, birthDate=birthDates, initState=sapply(birthDates, getRandInitState))
initPop$birthDate <- getInDateFormat(initPop$birthDate)
range(initPop$birthDate)

# Definition of immigrants entering the population (for illustration purposes, create immigrants 
# randomly)
M = 2000                                                           
immigrDates <- runif(M, min=getInDays(20140101), max=getInDays(20241231)) 
immigrAges <- runif(M, min=15*365.25, max=70*365.25)
immigrBirthDates <- immigrDates - immigrAges
IDmig <- max(as.numeric(initPop[,"ID"]))+(1:M)
immigrPop <- data.frame(ID = IDmig, immigrDate = immigrDates, birthDate=immigrBirthDates, 
                        immigrInitState=sapply(immigrBirthDates, getRandInitState))  
immigrPop$birthDate <- getInDateFormat(immigrPop$birthDate)
immigrPop$immigrDate <- getInDateFormat(immigrPop$immigrDate)

# Definition of initial states for newborns 
varInitStates <- rbind(c("m","0","NM","no"),c("f","0","NM","no")) 
# Definition of related occurrence probabilities
initStatesProb <- c(0.515,0.485)                              

# Definition of (possible) transition rates  
# (1) Fertility rates (Hadwiger mixture model)
fert1Rates <- function(age, calTime, duration){  # parity 1
  b <- ifelse(calTime<=2020, 3.9, 3.3)
  c <- ifelse(calTime<=2020, 28, 29)
  rate <-  (b/c)*(c/age)^(3/2)*exp(-b^2*(c/age+age/c-2))
  rate[age<=15 | age>=45] <- 0
  return(rate)
}
fert2Rates <- function(age, calTime, duration){  # partiy 2+
  b <- ifelse(calTime<=2020, 3.2, 2.8)
  c <- ifelse(calTime<=2020, 32, 33)
  rate <-  (b/c)*(c/age)^(3/2)*exp(-b^2*(c/age+age/c-2))
  rate[age<=15 | age>=45 | duration<0.75] <- 0
  return(rate)
}
# (2) Rates for first marriage (normal density)
marriage1Rates <- function(age, calTime, duration){  
  m <- ifelse(calTime<=2020, 25, 30)
  s <- ifelse(calTime<=2020, 3, 3)
  rate <- dnorm(age, mean=m, sd=s)
  rate[age<=16] <- 0
  return(rate)
}
# (3) Remariage rates (log-logistic model)
marriage2Rates <- function(age, calTime, duration){  
  b <- ifelse(calTime<=2020, 0.07, 0.10)
  p <- ifelse(calTime<=2020, 2.7,2.7)
  lambda <- ifelse(calTime<=1950, 0.04, 0.03)
  rate <- b*p*(lambda*age)^(p-1)/(1+(lambda*age)^p)
  rate[age<=18] <- 0
  return(rate)
}
# (4) Divorce rates (normal density)
divorceRates <- function(age, calTime, duration){
  m <- 40
  s <- ifelse(calTime<=2020, 7, 6)
  rate <- dnorm(age,mean=m,sd=s)
  rate[age<=18] <- 0
  return(rate)
}
# (5) Widowhood rates (gamma cdf)
widowhoodRates <- function(age, calTime, duration){
  rate <- ifelse(age<=30, 0, pgamma(age-30, shape=6, rate=0.06))
  return(rate)
}
# (6) Rates to change educational attainment
# Set rate to `Inf' to make transition for age 7 deterministic.
noToLowEduRates <- function(age, calTime, duration){
  rate <- ifelse(age==7,Inf,0) 
  return(rate)
}
lowToMedEduRates <- function(age, calTime, duration){
  rate <- dnorm(age,mean=16,sd=1)
  rate[age<=15 | age>=25] <- 0
  return(rate)
}
medToHighEduRates <- function(age, calTime, duration){
  rate <- dnorm(age,mean=20,sd=3)
  rate[age<=18 | age>=35] <- 0
  return(rate)
}
# (7) Mortality rates (Gompertz model)
mortRates <- function(age, calTime, duration){
  a <- .00003
  b <- ifelse(calTime<=2020, 0.1, 0.097)
  rate <- a*exp(b*age)
  return(rate)
}
# (8) Emigration rates 
emigrRates <- function(age, calTime, duration){
  rate <- ifelse(age<=18,0,0.0025)
  return(rate)
}

# Transition pattern and assignment of functions specifying transition rates
fertTrMatrix <- cbind(c("0->1+","1+->1+"),                         
  c("fert1Rates", "fert2Rates"))
maritalTrMatrix <- cbind(c("NM->M","M->D","M->W","D->M","W->M"),              
  c("marriage1Rates","divorceRates","widowhoodRates",
 "marriage2Rates","marriage2Rates"))
eduTrMatrix <- cbind(c("no->low","low->med","med->high"),
  c("noToLowEduRates","lowToMedEduRates","medToHighEduRates")) 
allTransitions <- rbind(fertTrMatrix, maritalTrMatrix, eduTrMatrix)
absTransitions <- rbind(c("dead","mortRates"),c("rest","emigrRates"))
transitionMatrix <- buildTransitionMatrix(allTransitions=allTransitions,
  absTransitions=absTransitions, stateSpace=stateSpace)

# Define transitions triggering a birth event
fertTr <- fertTrMatrix[,1]

# Run microsimulation on cluster with three cores (settings depend on cluster used)
## Not run: 
cores <- 3
seeds <- c(1233,1245,265)
initPopList <- list(initPop[1:5000,], initPop[5001:8000,],initPop[8001:nrow(initPop),])
immigrPopList <- list(immigrPop[1:1000,], immigrPop[1001:1500,],immigrPop[1501:nrow(immigrPop),])

pop <- micSimParallel(initPopList=initPopList, immigrPopList=immigrPopList, 
  transitionMatrix=transitionMatrix, absStates=absStates, varInitStates=varInitStates, 
  initStatesProb=initStatesProb, maxAge=maxAge, simHorizon=simHorizon, 
  fertTr=fertTr, monthSchoolEnrol=monthSchoolEnrol, 
  cores=cores, seeds=seeds)

## End(Not run)

MicSim documentation built on Jan. 9, 2023, 5:05 p.m.