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Finished making two new output files
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@RobertManningSmith
RobertManningSmith committed Sep 16, 2024
1 parent 2ab6265 commit f28adef
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Showing 3 changed files with 169 additions and 19 deletions.
173 changes: 158 additions & 15 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/Logging.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,17 +14,21 @@

public class Logging {
// set up commonly used variables to avoid repetition
// age boundaries to format log files
private final static List <Integer> upper_age_range = Arrays.asList(1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 120);
private final static List <Integer> lower_age_range = Arrays.asList(0, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95);
private final static List <Integer> birthrate_upper_age_range = Arrays.asList(20, 25, 30, 35, 40, 45, 50);
private final static List <Integer> birthrate_lower_age_range = Arrays.asList(15, 20, 25, 30, 35, 40, 45);
private final static String age_categories = "<1" + "\t" + "1_4" + "\t" + "5_9" + "\t" + "10_14" + "\t" + "15_19" + "\t" + "20_24" + "\t" + "25_29" +
"\t" + "30_34" + "\t" + "35_39" + "\t" + "40_44" + "\t" + "45_49" + "\t" + "50_54" + "\t" + "55_59" + "\t" + "60_64" + "\t" + "65_69" + "\t" +
"70_74" + "\t" + "75_79" + "\t" + "80_84" + "\t" + "85_89" + "\t" + "90_94" + "\t" + "95<";
// tab shortcut
private final static String t = "\t";
// age sex breakdown header
private final static String age_sex_categories = t + "sex" + age_categories + "\n";

// set up commonly used functions to avoid repetition
// get those alive of given age and sex
private static Map<SEX, Map<Integer, Map<Boolean, Long>>> age_sex_alive_map(WorldBankCovid19Sim world) {
Map<SEX, Map<Integer, Map<Boolean, Long>>> age_sex_alive_map = world.agents.stream().collect(
Collectors.groupingBy(
Expand All @@ -41,7 +45,7 @@ private static Map<SEX, Map<Integer, Map<Boolean, Long>>> age_sex_alive_map(Worl
return age_sex_alive_map;
}


// get those who alive with COVID of given age and sex
private static Map<SEX, Map<Integer, Map<Boolean, Map<Boolean, Long>>>> age_sex_has_covid_map(
WorldBankCovid19Sim world) {
Map<SEX, Map<Integer, Map<Boolean, Map<Boolean, Long>>>> age_sex_map_has_covid = world.agents.stream().collect(
Expand All @@ -62,10 +66,11 @@ private static Map<SEX, Map<Integer, Map<Boolean, Map<Boolean, Long>>>> age_sex_
return age_sex_map_has_covid;
}

// get number of those alive of age and sex
private static ArrayList <Integer> get_number_of_alive(WorldBankCovid19Sim world, SEX sex) {
ArrayList <Integer> alive_ages = new ArrayList<Integer>();
Map<SEX, Map<Integer, Map<Boolean, Long>>> age_sex_alive_map_copy = age_sex_alive_map(world);
// We now iterate over the age ranges, create a variable to keep track of the iterations
// We now iterate over the age ranges, create a variable to keep track of the iterations
Integer idx = 0;
for (Integer val: upper_age_range) {
// for each age group we begin to count the number of people who fall into each category, create variables
Expand All @@ -89,6 +94,8 @@ private static ArrayList <Integer> get_number_of_alive(WorldBankCovid19Sim world
}
return alive_ages;
}

// get those alive with COVID of age
private static ArrayList <Integer> get_covid_counts_by_age(WorldBankCovid19Sim world, SEX sex) {
Integer idx = 0;
ArrayList <Integer> covid_by_ages = new ArrayList<Integer>();
Expand Down Expand Up @@ -120,6 +127,8 @@ private static ArrayList <Integer> get_covid_counts_by_age(WorldBankCovid19Sim w
}
return covid_by_ages;
}

// get those who died of COVID of age
private static ArrayList <Integer> get_covid_death_counts_by_age(WorldBankCovid19Sim world, SEX sex) {
Integer idx = 0;
ArrayList <Integer> covid_death_by_ages = new ArrayList<Integer>();
Expand Down Expand Up @@ -165,6 +174,8 @@ private static ArrayList <Integer> get_covid_death_counts_by_age(WorldBankCovid1
}
return covid_death_by_ages;
}

// get those alive at location
private static Map<Boolean, Map<String, List<Person>>> get_alive_at_location(WorldBankCovid19Sim world) {
// create a function to group the population by who is alive at this admin zone
Map<Boolean, Map<String, List<Person>>> aliveAtLocation = world.agents.stream().collect(
Expand All @@ -178,6 +189,39 @@ private static Map<Boolean, Map<String, List<Person>>> get_alive_at_location(Wor
return aliveAtLocation;
}

// get those alive with COVID at location
private static Map<Boolean, Map<String, Map<Boolean, List<Person>>>> get_covid_at_location(
WorldBankCovid19Sim world) {
Map<Boolean, Map<String, Map<Boolean, List<Person>>>> covidAtLocation = world.agents.stream().collect(
Collectors.groupingBy(
Person::isAlive,
Collectors.groupingBy(
Person::getCurrentAdminZone,
Collectors.groupingBy(
Person::hasCovid
)
)
)
);
return covidAtLocation;
}

// get those who died of COVID at location
private static Map<String, Map<Boolean, Map<Boolean, List<Person>>>> get_dead_from_covid_at_location(
WorldBankCovid19Sim world) {
Map<String, Map<Boolean, Map<Boolean, List<Person>>>> covidDeathsAtLocation = world.agents.stream().collect(
Collectors.groupingBy(
Person::getCurrentAdminZone,
Collectors.groupingBy(
Person::isDeadFromCovid,
Collectors.groupingBy(
Person::getDeathLogged
)
)
)
);
return covidDeathsAtLocation;
}
// =============================== Demographic information logging =============================================================================
// output for birthRateOutputFilename
public class BirthRateReporter implements Steppable{
Expand Down Expand Up @@ -828,17 +872,7 @@ public void step(SimState arg0) {

Map<Boolean, Map<String, List<Person>>> aliveAtLocation = get_alive_at_location(world);
// create a function to group the population by who is alive in each admin zone and has covid
Map<Boolean, Map<String, Map<Boolean, List<Person>>>> covidAtLocation = world.agents.stream().collect(
Collectors.groupingBy(
Person::isAlive,
Collectors.groupingBy(
Person::getCurrentAdminZone,
Collectors.groupingBy(
Person::hasCovid
)
)
)
);
Map<Boolean, Map<String, Map<Boolean, List<Person>>>> covidAtLocation = get_covid_at_location(world);

// get a list of admin zone to iterate over
List <String> adminZones = ((WorldBankCovid19Sim)arg0).params.adminZoneNames;
Expand Down Expand Up @@ -981,6 +1015,114 @@ public void step(SimState arg0) {
};
}

// output for adminZonePercentCovidCasesFatalOutputFilename
public static Steppable ReportPercentOfCovidCasesThatAreFatalPerAdminZone(WorldBankCovid19Sim world) {
return new Steppable() {

@Override
public void step(SimState arg0) {
// create a function to group the population by who is alive in each admin zone and has covid
Map<Boolean, Map<String, Map<Boolean, List<Person>>>> covidAtLocation = get_covid_at_location(world);
Map<String, Map<Boolean, Map<Boolean, List<Person>>>> covidDeathsAtLocation = get_dead_from_covid_at_location(
world);
// get a list of admin zone to iterate over
List <String> adminZones = ((WorldBankCovid19Sim)arg0).params.adminZoneNames;
// format the output file for population counts
int time = (int) (arg0.schedule.getTime() / world.params.ticks_per_day);
// create a list to store the number of people and who has covid in each admin zone
ArrayList <Float> adminZonePercentCovidCasesFatal = new ArrayList<Float>();
// iterate over each admin zone
for (String place: adminZones) {
// get population counts in each admin zone
try {
// numerator = number of people at location who have died from covid, but have not had their deaths recorded
int numerator = covidDeathsAtLocation.get(place).get(true).get(false).size();
// denominator = number of people at location who currently are alive with covid plus those at location who have died from covid but not had their deaths recorded
int denominator = covidAtLocation.get(true).get(place).get(true).size() + numerator;
adminZonePercentCovidCasesFatal.add((float) numerator / denominator);
}
catch (Exception e) {
// age wasn't present in the population, skip
adminZonePercentCovidCasesFatal.add(0f);
}
}
// format log file
String percent_covid_death_per_admin = "";

if (time == 0) {
percent_covid_death_per_admin += "day" + t;
for (String place: adminZones) {
percent_covid_death_per_admin += place + t;
}
percent_covid_death_per_admin += "\n" + String.valueOf(time);
}
else {
percent_covid_death_per_admin += "\n" + String.valueOf(time);
}
// calculate the percentage in the admin zone with covid
for (float percent: adminZonePercentCovidCasesFatal) {;
percent_covid_death_per_admin += t + percent;
}
// export the file
ImportExport.exportMe(world.adminZonePercentCovidCasesFatalOutputFilename, percent_covid_death_per_admin, world.timer);
}
};
}

// output for adminZonePercentCovidCasesFatalOutputFilename
public static Steppable adminZonePercentDiedFromCovidOutputFilename(WorldBankCovid19Sim world) {
return new Steppable() {

@Override
public void step(SimState arg0) {
// create a function to group the population by who is alive in each admin zone and has covid
Map<Boolean, Map<String, List<Person>>> aliveAtLocation = get_alive_at_location(world);
// create a function to group the population by who died from covid at each admin zone
Map<String, Map<Boolean, Map<Boolean, List<Person>>>> covidDeathsAtLocation = get_dead_from_covid_at_location(
world);
// get a list of admin zone to iterate over
List <String> adminZones = ((WorldBankCovid19Sim)arg0).params.adminZoneNames;
// format the output file for population counts
int time = (int) (arg0.schedule.getTime() / world.params.ticks_per_day);
// create a list to store the number of people and who has covid in each admin zone
ArrayList <Float> adminZonePercentCovidFatal = new ArrayList<Float>();
// iterate over each admin zone
for (String place: adminZones) {
// get population counts in each admin zone
try {
// numerator = number of people at location who have died from covid, but have not had their deaths recorded
int numerator = covidDeathsAtLocation.get(place).get(true).get(false).size();
// denominator = number of people at location who currently are alive with covid plus those at location who have died from covid but not had their deaths recorded
int denominator = aliveAtLocation.get(true).get(place).size() + numerator;
adminZonePercentCovidFatal.add((float) numerator / denominator);
}
catch (Exception e) {
// age wasn't present in the population, skip
adminZonePercentCovidFatal.add(0f);
}
}
// format log file
String percent_covid_death_per_admin = "";

if (time == 0) {
percent_covid_death_per_admin += "day" + t;
for (String place: adminZones) {
percent_covid_death_per_admin += place + t;
}
percent_covid_death_per_admin += "\n" + String.valueOf(time);
}
else {
percent_covid_death_per_admin += "\n" + String.valueOf(time);
}
// calculate the percentage in the admin zone with covid
for (float percent: adminZonePercentCovidFatal) {;
percent_covid_death_per_admin += t + percent;
}
// export the file
ImportExport.exportMe(world.adminZonePercentDiedFromCovidOutputFilename, percent_covid_death_per_admin, world.timer);
}
};
}
// =============================== Non-spatial disease logging ================================================================================

// output for covidIncDeathOutputFilename
Expand All @@ -992,7 +1134,7 @@ public static Steppable ReportCovidIncidenceOfDeath(WorldBankCovid19Sim world) {
public void step(SimState arg0) {
int time = (int) (arg0.schedule.getTime() / world.params.ticks_per_day);

// calculate incidence of death in each age group by cause
// calculate incidence of death in each age group by cause
// covid deaths, incidence in age groups 0-1, 1-4, 5-9, 10-14, ..., 95+
// create a list to define our age group search ranges

Expand Down Expand Up @@ -1269,7 +1411,7 @@ public void step(SimState arg0) {

// =============================== Reset the properties to avoid counting the same thing multiple times ====================================

public static Steppable ResetLogedProperties(WorldBankCovid19Sim world) {
public static Steppable ResetLoggedProperties(WorldBankCovid19Sim world) {
return new Steppable() {
@Override
public void step(SimState arg0) {
Expand Down Expand Up @@ -1301,4 +1443,5 @@ public void step(SimState arg0) {
};
}


}
1 change: 1 addition & 0 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/SingleRun.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ public static void main(String [] args) {

// Set how long the simulation should run for
mySim.targetDuration = numDays;
mySim.params.infection_beta = 0.3;
// Begin the simulation
mySim.start();
// Update the file names of where we will import the infecitons output and the general simulation information output
Expand Down
14 changes: 10 additions & 4 deletions Protecs/src/main/java/uk/ac/ucl/protecs/sim/WorldBankCovid19Sim.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ public class WorldBankCovid19Sim extends SimState {
public String infections_export_filename;
public String adminZoneCovidPrevalenceOutputFilename;
public String adminZonePercentDiedFromCovidOutputFilename;
public String adminZonePercenCovidCasesFatalOutputFilename;
public String adminZonePercentCovidCasesFatalOutputFilename;
public String adminZonePopBreakdownOutputFilename;
public String sim_info_filename;
public String covidCountsOutputFilename;
Expand Down Expand Up @@ -92,7 +92,7 @@ public WorldBankCovid19Sim(long seed, Params params, String outputFilename) {
this.covidCountsOutputFilename = outputFilename + "_Age_Gender_Demographics_Covid.txt";
this.covidByEconOutputFilename = outputFilename + "_Economic_Status_Covid.txt";
this.adminZonePercentDiedFromCovidOutputFilename = outputFilename + "_Percent_In_Admin_Zone_Died_From_Covid.txt";
this.adminZonePercenCovidCasesFatalOutputFilename = outputFilename + "_Percent_Covid_Cases_Fatal_In_Admin_Zone.txt";
this.adminZonePercentCovidCasesFatalOutputFilename = outputFilename + "_Percent_Covid_Cases_Fatal_In_Admin_Zone.txt";
}

public void start(){
Expand Down Expand Up @@ -240,8 +240,14 @@ public void step(SimState arg0) {
// Report on the number of COVID counts in each occupation (covidByEconOutputFilename)
schedule.scheduleRepeating(Logging.ReportCovidCountsByOccupation(this), this.param_schedule_reporting, params.ticks_per_day);

// Schedule the resetting of COVID reporting properties in the agents
schedule.scheduleRepeating(Logging.ResetLogedProperties(this), this.param_schedule_reporting_reset, params.ticks_per_day);
// Report on the percent of COVID cases that are fatal per admin zone (adminZonePercentCovidCasesFatalOutputFilename)
schedule.scheduleRepeating(Logging.ReportPercentOfCovidCasesThatAreFatalPerAdminZone(this), this.param_schedule_reporting, params.ticks_per_day);

// Report on the prevalence of COVID death per admin zone (adminZonePercentDiedFromCovidOutputFilename)
schedule.scheduleRepeating(Logging.adminZonePercentDiedFromCovidOutputFilename(this), this.param_schedule_reporting, params.ticks_per_day);

// Schedule the resetting of COVID reporting properties in the agents
schedule.scheduleRepeating(Logging.ResetLoggedProperties(this), this.param_schedule_reporting_reset, params.ticks_per_day);

// SCHEDULE LOCKDOWNS
Steppable lockdownTrigger = new Steppable() {
Expand Down

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