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Refactor DigitalContactTracingSweep #417

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Refactor DigitalContactTracingSweep #417

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b425066
Refactor DigitalContactTracingSweep
DavidVernest Jun 23, 2020
8bd1853
cleanup Dct functions
DavidVernest Jun 23, 2020
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129 changes: 72 additions & 57 deletions src/Sweep.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,11 @@
#include "Sweep.h"
#include "Update.h"

// DigitalContractTracing helper functions
static void GetDctStartEndTimes(int infector, int contact, unsigned short contact_time, unsigned short& dct_start_time,
unsigned short& dct_end_time);
static void UpdateDctQueue(int j, int i, int k, int contact, int infector, unsigned short contact_time);
static void StopDct(int contact);

void TravelReturnSweep(double t)
{
Expand Down Expand Up @@ -1107,44 +1112,10 @@ void DigitalContactTracingSweep(double t)
int infector = StateT[j].dct_queue[i][k].index;
int contact = StateT[j].dct_queue[i][k].contact;
unsigned short int contact_time = StateT[j].dct_queue[i][k].contact_time;

unsigned short int dct_start_time, dct_end_time;
//this condition is only ever met when a symptomatic case is detected in DoDetectedCase and is not already an index case. If they have already
//been made an index case due to testing, then this won't occur again for them.
if (infector==-1)
{
//i.e. this is an index case that has been detected by becoming symptomatic and added to the digital contact tracing queue
dct_start_time = Hosts[contact].dct_trigger_time; //trigger time for these cases is set in DoIncub and already accounts for delay between onset and isolation
dct_end_time = dct_start_time + (unsigned short int)(P.LengthDigitalContactIsolation * P.TimeStepsPerDay);

}
else //We are looking at actual contact events between infectious hosts and their contacts.
{
//trigger times are either set in DoDetectedCase or in the loop below (for asymptomatic and presymptomatic cases that are picked up via testing
//If the contact's index case has a trigger time that means that they have been detected, and we can calculate start and end isolation times for the contact.
if (Hosts[infector].dct_trigger_time < (USHRT_MAX - 1))
{
if (contact_time > Hosts[infector].dct_trigger_time)
{
//if the contact time was made after host detected, we should use the later time
dct_start_time = contact_time + (unsigned short int) (P.DigitalContactTracingDelay * P.TimeStepsPerDay);
}
else
{
//if the contact time was made before or at the same time as detection, use the trigger time instead
dct_start_time = Hosts[infector].dct_trigger_time + (unsigned short int) (P.DigitalContactTracingDelay * P.TimeStepsPerDay);
}
dct_end_time = dct_start_time + (unsigned short int)(P.LengthDigitalContactIsolation * P.TimeStepsPerDay);
}
else
{
dct_start_time = USHRT_MAX - 1; //for contacts of asymptomatic or presymptomatic cases - they won't get added as their index case won't know that they are infected (unless explicitly tested)
//but we keep them in the queue in case their index case is detected as the contact of someone else and gets their trigger time set
//set dct_end_time to recovery time of infector, in order to remove from queue if their infector isn't detected before they recover.
dct_end_time = Hosts[infector].recovery_or_death_time;
}
}

unsigned short int dct_start_time;
unsigned short int dct_end_time;
GetDctStartEndTimes(infector, contact, contact_time, dct_start_time, dct_end_time);

//if we've reached the start time for isolation
if (dct_start_time == ts)
{
Expand Down Expand Up @@ -1180,9 +1151,7 @@ void DigitalContactTracingSweep(double t)
//if false negative, remove from queue by setting the end time to the test time
if ((P.SensitivityDCT == 0) || ((P.SensitivityDCT < 1) && (ranf_mt(tn) >= P.SensitivityDCT)))
{
Hosts[contact].dct_end_time = Hosts[contact].dct_test_time;
//set index_dct_flag to 2 to indicate that contacts should be removed, if we are removing based on negative test result of index case
if (P.RemoveContactsOfNegativeIndexCase) Hosts[contact].index_case_dct = 2;
StopDct(contact);
}
}
//if host is non-infectious)
Expand All @@ -1192,8 +1161,7 @@ void DigitalContactTracingSweep(double t)
if ((P.SpecificityDCT == 1) || ((P.SpecificityDCT > 0) && (ranf_mt(tn) < P.SpecificityDCT)))
{
//again mark them to be removed from list at test time rather than end_time, and change index_case_dct flag
Hosts[contact].dct_end_time = Hosts[contact].dct_test_time;
if (P.RemoveContactsOfNegativeIndexCase) Hosts[contact].index_case_dct = 2;
StopDct(contact);
}
}
}
Expand Down Expand Up @@ -1222,9 +1190,7 @@ void DigitalContactTracingSweep(double t)
StateT[tn].cumDCT++;

//now remove this case from the queues
StateT[j].dct_queue[i][k] = StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1];
StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1] = { contact,infector,contact_time };
StateT[j].ndct_queue[i]--;
UpdateDctQueue(j, i, k, contact, infector, contact_time);
}
else
{
Expand All @@ -1251,9 +1217,7 @@ void DigitalContactTracingSweep(double t)
//if false negative, remove from
if ((P.SensitivityDCT == 0) || ((P.SensitivityDCT < 1) && (ranf_mt(tn) >= P.SensitivityDCT)))
{
Hosts[contact].dct_end_time = Hosts[contact].dct_test_time;
//set index_dct_flag to 2 to indicate that contacts should be removed
if (P.RemoveContactsOfNegativeIndexCase) Hosts[contact].index_case_dct = 2;
StopDct(contact);
}
}
//if host is non-infectious
Expand All @@ -1263,8 +1227,7 @@ void DigitalContactTracingSweep(double t)
if ((P.SpecificityDCT == 1) || ((P.SpecificityDCT > 0) && (ranf_mt(tn) < P.SpecificityDCT)))
{
//again mark them to be removed from list at test time rather than end_time, and change index_case_dct flag
Hosts[contact].dct_end_time = Hosts[contact].dct_test_time;
if (P.RemoveContactsOfNegativeIndexCase) Hosts[contact].index_case_dct = 2;
StopDct(contact);
}
}
}
Expand All @@ -1288,18 +1251,14 @@ void DigitalContactTracingSweep(double t)

}
//now remove this case from the queue
StateT[j].dct_queue[i][k] = StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1];
StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1] = { contact,infector,contact_time };
StateT[j].ndct_queue[i]--;
UpdateDctQueue(j, i, k, contact, infector, contact_time);
}
}
//if contact of an asymptomatic host has passed the recovery time of their asymptomatic index, they would no longer be identified by testing of their index case - remove from the queue so they don't stay here forever
else if ((dct_start_time == (USHRT_MAX - 1)) && (dct_end_time == ts))
{
//now remove this case from the queue
StateT[j].dct_queue[i][k] = StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1];
StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1] = { contact,infector,contact_time };
StateT[j].ndct_queue[i]--;
UpdateDctQueue(j, i, k, contact, infector, contact_time);
}
else
{
Expand Down Expand Up @@ -2006,3 +1965,59 @@ int TreatSweep(double t)

return (f > 0);
}

static void GetDctStartEndTimes(int infector, int contact, unsigned short contact_time, unsigned short& dct_start_time,
unsigned short& dct_end_time)
{
//this condition is only ever met when a symptomatic case is detected in DoDetectedCase and is not already an index case. If they have already
//been made an index case due to testing, then this won't occur again for them.
if (infector == -1)
{
//i.e. this is an index case that has been detected by becoming symptomatic and added to the digital contact tracing queue
dct_start_time = Hosts[contact].dct_trigger_time; //trigger time for these cases is set in DoIncub and already accounts for delay between onset and isolation

//i.e. this is an index case that has been detected by becoming symptomatic and added to the digital contact tracing queue
dct_end_time = dct_start_time + (unsigned short int)(P.LengthDigitalContactIsolation * P.TimeStepsPerDay);

}
else //We are looking at actual contact events between infectious hosts and their contacts.
{
//trigger times are either set in DoDetectedCase or in the loop below (for asymptomatic and presymptomatic cases that are picked up via testing
//If the contact's index case has a trigger time that means that they have been detected, and we can calculate start and end isolation times for the contact.
if (Hosts[infector].dct_trigger_time < (USHRT_MAX - 1))
{
if (contact_time > Hosts[infector].dct_trigger_time)
{
//if the contact time was made after host detected, we should use the later time
dct_start_time = contact_time + (unsigned short int) (P.DigitalContactTracingDelay * P.TimeStepsPerDay);
}
else
{
//if the contact time was made before or at the same time as detection, use the trigger time instead
dct_start_time = Hosts[infector].dct_trigger_time + (unsigned short int) (P.DigitalContactTracingDelay * P.TimeStepsPerDay);
}
dct_end_time = dct_start_time + (unsigned short int)(P.LengthDigitalContactIsolation * P.TimeStepsPerDay);
}
else
{
dct_start_time = USHRT_MAX - 1; //for contacts of asymptomatic or presymptomatic cases - they won't get added as their index case won't know that they are infected (unless explicitly tested)
//but we keep them in the queue in case their index case is detected as the contact of someone else and gets their trigger time set
//set dct_end_time to recovery time of infector, in order to remove from queue if their infector isn't detected before they recover.
dct_end_time = Hosts[infector].recovery_or_death_time;
}
}
}

static void UpdateDctQueue(int j, int i, int k, int contact, int infector, unsigned short contact_time)
{
StateT[j].dct_queue[i][k] = StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1];
StateT[j].dct_queue[i][StateT[j].ndct_queue[i] - 1] = { contact,infector,contact_time };
StateT[j].ndct_queue[i]--;
}

static void StopDct(int contact)
{
Hosts[contact].dct_end_time = Hosts[contact].dct_test_time;
//set index_dct_flag to 2 to indicate that contacts should be removed, if we are removing based on negative test result of index case
if (P.RemoveContactsOfNegativeIndexCase) Hosts[contact].index_case_dct = 2;
}