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Dlaydon/add quarantined not sick #383

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38 changes: 28 additions & 10 deletions src/CovidSim.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -3909,7 +3909,7 @@ void SaveSummaryResults(void) //// calculates and saves summary results (called
sprintf(outname, "%s.severity.xls", OutFile);

if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open severity output file\n");
fprintf(dat, "t\tPropSocDist\tRt\tTG\tSI\tS\tI\tR\tincI\tincC\tMild\tILI\tSARI\tCritical\tCritRecov\tSARIP\tCriticalP\tCritRecovP\tincMild\tincILI\tincSARI\tincCritical\tincCritRecov\tincSARIP\tincCriticalP\tincCritRecovP\tincDeath\tincDeath_ILI\tincDeath_SARI\tincDeath_Critical\tcumMild\tcumILI\tcumSARI\tcumCritical\tcumCritRecov\tcumDeath\tcumDeath_ILI\tcumDeath_SARI\tcumDeath_Critical\t");
fprintf(dat, "t\tPropSocDist\tRt\tTG\tSI\tS\tI\tR\tincI\tincC\tMild\tILI\tSARI\tCritical\tCritRecov\tSARIP\tCriticalP\tCritRecovP\tprevQuarNotInfected\tprevQuarNotSymptomatic\tincMild\tincILI\tincSARI\tincCritical\tincCritRecov\tincSARIP\tincCriticalP\tincCritRecovP\tincDeath\tincDeath_ILI\tincDeath_SARI\tincDeath_Critical\tcumMild\tcumILI\tcumSARI\tcumCritical\tcumCritRecov\tcumDeath\tcumDeath_ILI\tcumDeath_SARI\tcumDeath_Critical\t");
fprintf(dat, "PropSocDist_v\tRt_v\tTG_v\tSI_v\tS_v\tI_v\tR_v\tincI_v\tincC_v\tMild_v\tILI_v\tSARI_v\tCritical_v\tCritRecov_v\tincMild_v\tincILI_v\tincSARI_v\tincCritical_v\tincCritRecov_v\tincDeath_v\tincDeath_ILI_v\tincDeath_SARI_v\tincDeath_Critical_v\tcumMild_v\tcumILI_v\tcumSARI_v\tcumCritical_v\tcumCritRecov_v\tcumDeath_v\tcumDeath_ILI_v\tcumDeath_SARI_v\tcumDeath_Critical_v\n");
double SARI, Critical, CritRecov, incSARI, incCritical, incCritRecov, sc1, sc2,sc3,sc4; //this stuff corrects bed prevalence for exponentially distributed time to test results in hospital
sc1 = (P.Mean_TimeToTest > 0) ? exp(-1.0 / P.Mean_TimeToTest) : 0.0;
Expand All @@ -3935,9 +3935,10 @@ void SaveSummaryResults(void) //// calculates and saves summary results (called
CritRecov = TSMean[i].CritRecov * sc4;
}

fprintf(dat, "%.10f\t%.10f\t%.10f\t%.17f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t",
fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.17f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t",
c* TSMean[i].t, c* TSMean[i].PropSocDist, c* TSMean[i].Rdenom, c* TSMean[i].meanTG, c* TSMean[i].meanSI, c* TSMean[i].S, c* TSMean[i].I, c* TSMean[i].R, c* TSMean[i].incI, c* TSMean[i].incC,
c* TSMean[i].Mild, c* TSMean[i].ILI, c* TSMean[i].SARI,c* TSMean[i].Critical, c* TSMean[i].CritRecov,c* (TSMean[i].SARI - SARI), c* (TSMean[i].Critical - Critical), c* (TSMean[i].CritRecov - CritRecov),
c * TSMean[i].prevQuarNotInfected, c * TSMean[i].prevQuarNotSymptomatic,
c * TSMean[i].incMild, c * TSMean[i].incILI, c * TSMean[i].incSARI, c * TSMean[i].incCritical, c * TSMean[i].incCritRecov, c * incSARI, c * incCritical, c * incCritRecov, c * TSMean[i].incD,
c * TSMean[i].incDeath_ILI, c * TSMean[i].incDeath_SARI, c * TSMean[i].incDeath_Critical,
c * TSMean[i].cumMild, c * TSMean[i].cumILI, c * TSMean[i].cumSARI, c * TSMean[i].cumCritical, c * TSMean[i].cumCritRecov, c*TSMean[i].D,
Expand Down Expand Up @@ -4585,19 +4586,18 @@ void UpdateEfficaciesAndComplianceProportions(double t)
// for (int PlaceNum = ThreadNum; PlaceNum < P.Nplace[PlaceType]; PlaceNum += P.NumThreads)
// DoPlaceOpen(PlaceType, PlaceNum, ts, ThreadNum);

P.PlaceCloseSpatialRelContact = P.PC_SpatialEffects_OverTime [ChangeTime]; //// spatial
P.PlaceCloseHouseholdRelContact = P.PC_HouseholdEffects_OverTime[ChangeTime]; //// household
P.PlaceCloseSpatialRelContact = P.PC_SpatialEffects_OverTime [ChangeTime]; //// spatial
P.PlaceCloseHouseholdRelContact = P.PC_HouseholdEffects_OverTime[ChangeTime]; //// household
for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
{
P.PlaceCloseEffect[PlaceType] = P.PC_PlaceEffects_OverTime[ChangeTime][PlaceType]; //// place
P.PlaceCloseEffect[PlaceType] = P.PC_PlaceEffects_OverTime[ChangeTime][PlaceType]; //// place
P.PlaceClosePropAttending[PlaceType] = P.PC_PropAttending_OverTime[ChangeTime][PlaceType]; //// place
}

P.PlaceCloseIncTrig = P.PC_IncThresh_OverTime [ChangeTime]; //// global incidence threshold
P.PlaceCloseFracIncTrig = P.PC_FracIncThresh_OverTime [ChangeTime]; //// fractional incidence threshold
P.PlaceCloseCellIncThresh = P.PC_CellIncThresh_OverTime [ChangeTime]; //// cell incidence threshold
P.PlaceCloseDuration = P.PC_Durs_OverTime [ChangeTime]; //// duration of place closure

P.PlaceCloseIncTrig = P.PC_IncThresh_OverTime [ChangeTime]; //// global incidence threshold
P.PlaceCloseFracIncTrig = P.PC_FracIncThresh_OverTime [ChangeTime]; //// fractional incidence threshold
P.PlaceCloseCellIncThresh = P.PC_CellIncThresh_OverTime [ChangeTime]; //// cell incidence threshold
P.PlaceCloseDuration = P.PC_Durs_OverTime [ChangeTime]; //// duration of place closure

//// reset place close time start - has been set to 9e9 in event of no triggers. m
if(P.PlaceCloseTimeStart<1e10) P.PlaceCloseTimeStart = t;
Expand Down Expand Up @@ -4648,7 +4648,22 @@ void RecordAdminAgeBreakdowns(int t_int)
// Record incidence. Need new total minus old total. Add new total
TimeSeries[t_int].incInf_age_adunit[AgeGroup][AdUnit] += (double)(State.cumInf_age_adunit[AgeGroup][AdUnit]);
}
}

void RecordQuarNotInfected(int n, unsigned short int ts)
{
int QuarNotInfected = 0, QuarNotSymptomatic = 0;
#pragma omp parallel for schedule(static,1) reduction(+:QuarNotInfected, QuarNotSymptomatic)
for (int thread_no = 0; thread_no < P.NumThreads; thread_no++)
for (int Person = thread_no; Person < P.PopSize; Person += P.NumThreads)
if (HOST_QUARANTINED(Person))
{
if (Hosts[Person].inf == InfStat_Susceptible || abs(Hosts[Person].inf) == InfStat_Recovered) QuarNotInfected++;
if (Hosts[Person].inf > 0) QuarNotSymptomatic++;
}

TimeSeries[n].prevQuarNotInfected = (double) QuarNotInfected;
TimeSeries[n].prevQuarNotSymptomatic = (double) QuarNotSymptomatic;
}

void RecordSample(double t, int n)
Expand Down Expand Up @@ -4822,8 +4837,11 @@ void RecordSample(double t, int n)
if (P.DoAdUnits && P.OutputAdUnitAge)
RecordAdminAgeBreakdowns(n);

RecordQuarNotInfected(n, ts);

if (P.DoSeverity)
{

//// Record incidence. (Must be done with old State totals)
TimeSeries[n].incMild = (double)(cumMild - State.cumMild );
TimeSeries[n].incILI = (double)(cumILI - State.cumILI );
Expand Down
25 changes: 14 additions & 11 deletions src/InfStat.h
Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,21 @@

//// Infection Status definitons / labels (generally positive value indicates asymptomatic infection, negative value indicates symptomatic infection).
enum InfStat {
InfStat_Susceptible = 0, //// Susceptible
InfStat_Latent = 1, //// E or L (neither infectious nor symptomatic).
InfStat_InfectiousAlmostSymptomatic =-1, //// Infectious and about to become a case.

//// Note - DO NOT CHANGE these definitions without accounting for "Quarantined not Infected" / "Quarantined not symptomatic" calculation: relies on value below being negative for symptomatic people.

InfStat_Susceptible = 0, //// Susceptible
InfStat_Latent = 1, //// E or L (neither infectious nor symptomatic).
InfStat_InfectiousAlmostSymptomatic = -1, //// Infectious and about to become a case.
InfStat_InfectiousAsymptomaticNotCase = 2, //// Not just asymptomatic, but also will not become symptomatic (i.e. a case.)
InfStat_Case = -2, //// case. Infectious and symptomatic.
InfStat_RecoveredFromAsymp = 3, //// Recovered from asymptomatic infection
InfStat_RecoveredFromSymp = -3, //// Recovered from symptomatic infection
InfStat_Recovered = 3, //// InfStat_Recovered (will use this for abs() values) so code reads correctly
InfStat_ImmuneAtStart = 4, //// Immune at start of epidemic - used to model partially immune population. Distinct therefore from recovered, who recovered during runtime. Doesn't take negative values.
InfStat_Dead_WasAsymp = 5, //// Dead was asymptomatic
InfStat_Dead_WasSymp = -5, //// Dead was symptomatic
InfStat_Dead = 5 //// Dead (will use this for abs() values) so code reads correctly
InfStat_Case = -2, //// case. Infectious and symptomatic.
InfStat_RecoveredFromAsymp = 3, //// Recovered from asymptomatic infection
InfStat_RecoveredFromSymp = -3, //// Recovered from symptomatic infection
InfStat_Recovered = 3, //// InfStat_Recovered (will use this for abs() values) so code reads correctly
InfStat_ImmuneAtStart = 4, //// Immune at start of epidemic - used to model partially immune population. Distinct therefore from recovered, who recovered during runtime. Doesn't take negative values.
InfStat_Dead_WasAsymp = 5, //// Dead was asymptomatic
InfStat_Dead_WasSymp = -5, //// Dead was symptomatic
InfStat_Dead = 5 //// Dead (will use this for abs() values) so code reads correctly
};

// SeverityClass defintions / labels (numbers arbitrary but must be different to each other).
Expand Down
1 change: 1 addition & 0 deletions src/Model.h
Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,7 @@ struct Results
double incDeath_ILI_age[NUM_AGE_GROUPS], incDeath_SARI_age[NUM_AGE_GROUPS], incDeath_Critical_age[NUM_AGE_GROUPS]; // tracks incidence of death from ILI, SARI & Critical severities
double cumDeath_ILI_age[NUM_AGE_GROUPS], cumDeath_SARI_age[NUM_AGE_GROUPS], cumDeath_Critical_age[NUM_AGE_GROUPS]; // tracks cumulative deaths from ILI, SARI & Critical severities

double prevQuarNotInfected, prevQuarNotSymptomatic; // Which people are under quarantine but not themselves infected/sypmtomatic?

/////// possibly need quantities by age (later)
//// state variables (S, L, I, R) and therefore (Mild, ILI) etc. changed in i) SetUpModel (initialised to zero); ii)
Expand Down
12 changes: 6 additions & 6 deletions tests/uk-input/results.checksums.txt
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ mt-results-int.01100.bmp 5376098c7da8a8fdcfbaf0588debc7f
mt-results-int.avNE.age.xls 528b9d5cf7d108365818e418af8fa84a9f582728eb9974714e305af9e40169d50f39a5290acabe480b38a0ee06e94bfdc822f7c170cdf7191b86a489f88b8ecd
mt-results-int.avNE.severity.adunit.xls 28212050773c57107b6ae7de7e5962da6a1c706499c75d0d7ab5453d3d3cb8beafd0fdb0cfdeadd95a6e1209bce13fb645c3255443b6b7176c14c2b4c4aa35a3
mt-results-int.avNE.severity.age.xls 159184e954eaf4ce56f46c806bbf02afaa7507465085d6931ce4cd4f112fef0e8a18c38cf09e804b2be9e949763f12a52222a11481f7ac10c504ea5591786ad9
mt-results-int.avNE.severity.xls 9c7385144b1cc6ad8c5b49a78a0a089db29fd53f6111e2b1f9220245bd9406e93981f99f328357fa9375d3a95794b04fd6f8ab82aa2a86ade194df03eb7af221
mt-results-int.avNE.severity.xls e633e380480c687e18b797fb7e5a49c9f175d05e169a10990fc6ce569a773d9aa8ed6c1e9d8cb0e0e7fe0942a1e282137906fbab7a15ca2eb46d24f6e1ecc7c1
mt-results-noint-repeat.00000.bmp 59c39fb51cca2ea8a5469c02e65359de2b82cbc0ad3166a3b236cda0a38e00db331bb00d9f490565028c11408ddf515f631f3c5f5954b2511252ef8117217b5a
mt-results-noint-repeat.00100.bmp 215f64e8f265ef6d1f9494b15cc57eab37bb693aeb6701482a1cc38fef1ffb12b1c6f90f9f2f02aecc7eb4202fad4234f401d88c041cfb4b3e4d81b933be0ed3
mt-results-noint-repeat.00200.bmp 3de2b93bb8a6402c87f194aa8988b0c3dda6762c3f4b80bd952461e4ce786b3513f0b64d98534a87950f92513a7d6b6462e7945a7e14b3242ff34a848f5ab1b2
Expand All @@ -30,7 +30,7 @@ mt-results-noint-repeat.01200.bmp af71826dacb8930f906099dd325423f
mt-results-noint-repeat.avNE.age.xls 035b014df97c2edba0a5e6f1f5d7e27e65b2ca8c88623eed998846124bc43b7838fd0e28d2d46961d13612bc4863f4bc8ad4866732860ce3b763cbc2a80d798f
mt-results-noint-repeat.avNE.severity.adunit.xls 3e4b945dbd8782c24b76d2e9dcfff6aa20deae7b684c79c35740c3ca537bedb3e37ba9c12bf576dcc8c6d6e5468af0559ed78634ecbb165b9810e919ee8f8ce0
mt-results-noint-repeat.avNE.severity.age.xls 084058390eee3ef33ca0cb15d794f361c717b4e90d437d895e5483eb1d3e723a0954e39b8928663b7cda7e23f9441aed17be6074605aba207e158e7a15cf34be
mt-results-noint-repeat.avNE.severity.xls 87d547386d2f282ff50156475542add3c8e59ee01659cc1585b420b49e98f421d7ad88f50a8e94e4f41e7f61f7dab36c3dc3316060eedf2b26e0d30549eb79a0
mt-results-noint-repeat.avNE.severity.xls a6512707e06831c4728dd4dfd6e7f434f6e31441aa06f57263172ec0dbf8597e500c522535c0de1965f2cf560e72b91abdafae022b1b61964bbac376f50c8d83
mt-results-noint.00000.bmp 59c39fb51cca2ea8a5469c02e65359de2b82cbc0ad3166a3b236cda0a38e00db331bb00d9f490565028c11408ddf515f631f3c5f5954b2511252ef8117217b5a
mt-results-noint.00100.bmp 215f64e8f265ef6d1f9494b15cc57eab37bb693aeb6701482a1cc38fef1ffb12b1c6f90f9f2f02aecc7eb4202fad4234f401d88c041cfb4b3e4d81b933be0ed3
mt-results-noint.00200.bmp 3de2b93bb8a6402c87f194aa8988b0c3dda6762c3f4b80bd952461e4ce786b3513f0b64d98534a87950f92513a7d6b6462e7945a7e14b3242ff34a848f5ab1b2
Expand All @@ -47,7 +47,7 @@ mt-results-noint.01200.bmp af71826dacb8930f906099dd325423f
mt-results-noint.avNE.age.xls 035b014df97c2edba0a5e6f1f5d7e27e65b2ca8c88623eed998846124bc43b7838fd0e28d2d46961d13612bc4863f4bc8ad4866732860ce3b763cbc2a80d798f
mt-results-noint.avNE.severity.adunit.xls 3e4b945dbd8782c24b76d2e9dcfff6aa20deae7b684c79c35740c3ca537bedb3e37ba9c12bf576dcc8c6d6e5468af0559ed78634ecbb165b9810e919ee8f8ce0
mt-results-noint.avNE.severity.age.xls 084058390eee3ef33ca0cb15d794f361c717b4e90d437d895e5483eb1d3e723a0954e39b8928663b7cda7e23f9441aed17be6074605aba207e158e7a15cf34be
mt-results-noint.avNE.severity.xls 87d547386d2f282ff50156475542add3c8e59ee01659cc1585b420b49e98f421d7ad88f50a8e94e4f41e7f61f7dab36c3dc3316060eedf2b26e0d30549eb79a0
mt-results-noint.avNE.severity.xls a6512707e06831c4728dd4dfd6e7f434f6e31441aa06f57263172ec0dbf8597e500c522535c0de1965f2cf560e72b91abdafae022b1b61964bbac376f50c8d83
st-results-int.00000.bmp a2bcacff67edd59711f7948a496167bbc6c11e73e923138af4133e2d2401b50142c85014889aba52b8aa19107d85afb81ccb0f25fea8cce5491060aeae81e056
st-results-int.00100.bmp 1477d7e220515c9fe3f5295ae9ad89f27d6d62b1272bd948a6d2cfe6d96438cb010bc53dc412fcabaa1e228472d2a666d5b66a92e0170801c75242eea8348fe1
st-results-int.00200.bmp e84630b773cf63d4f9ed0db3ec0ed12ab3d280907c8504f5e011a53048e42e38522b0ce04d669f5ddb6e4b6e8bc3add8f989a2f56f237684b568870514a89ae5
Expand All @@ -74,7 +74,7 @@ st-results-int.02200.bmp bc988e06e4156172c47afde9c1e8340
st-results-int.avNE.age.xls 5e2b951120cddfd458bdd030b33ecc8e99ceedce9c80b12c04f3147202ab70d2779cc06794cec788868ecb33371e62be08f0aff3ef8b37659e748b6d38b16115
st-results-int.avNE.severity.adunit.xls d322225f9c7c36a314e9ea9558c2cfd6b838a5f5e2686f158de2b7619641a80c6efc0629df4b0f8e3f5e2054f54883d10e9d0007fad521b3c4a34f597d6d5247
st-results-int.avNE.severity.age.xls d9f635d793e958bc42596ecfc862811760c0283ef72316db3fd9ea9c2195140ed5baa13839d067480d6e577761329b5c28ad5536d1300cb3155851839caa810e
st-results-int.avNE.severity.xls 5b9fc2ee5ba69cf1274a7765e4dbd08127353c01cdb8644f006075a639ec27a1a010fb0d21d4e7e96484183bd93d3b9678950a7800b3b5be164445df67d43a51
st-results-int.avNE.severity.xls a1167807c84e584be24e7068d75ea057800be5f6d9d4f8e5b7d65aac68047d7093a14895e2b1508048b6a50e20267b3e358582baba94b2911fb31154f2a6992f
st-results-noint-repeat.00000.bmp a2bcacff67edd59711f7948a496167bbc6c11e73e923138af4133e2d2401b50142c85014889aba52b8aa19107d85afb81ccb0f25fea8cce5491060aeae81e056
st-results-noint-repeat.00100.bmp 1477d7e220515c9fe3f5295ae9ad89f27d6d62b1272bd948a6d2cfe6d96438cb010bc53dc412fcabaa1e228472d2a666d5b66a92e0170801c75242eea8348fe1
st-results-noint-repeat.00200.bmp 0781ba1ee7133bbdbf2617cfcb10847be7f54095e80449f281bbd125e73b14b90299f9239e5e660666b77528efec362d1eeb3eb28cb57c2bb58a705bc212b453
Expand Down Expand Up @@ -107,7 +107,7 @@ st-results-noint-repeat.02800.bmp 9614fd0ea5aad1a7d8801b1369dcf43
st-results-noint-repeat.avNE.age.xls 44ca8f8874f1637a6d7d330685b09a55d9210af024bb656ebc7f2d7cb8ef133fa1c5c439ef64c73b99bcaae1511b6a9cbf1dd1d8f974dd2b4ce5e13401980b80
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st-results-noint-repeat.avNE.severity.age.xls 4dcdb254fe2a9f713ca9a0bccde5c3c05d4355123387e8774120e0d285775f0a844be3f31e2f5eac8acef7662545742d281bc938aaed71bf3f223dbefa3f7651
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st-results-noint-repeat.avNE.severity.xls a22600bffbd6a4352654ca9d839637c8e1312b8b1326117638b1be8d405c9ff154a86e57a319a4cbe8ceb643d357b79d51d30272fbe3c08542802551cd7a0c87
st-results-noint.00000.bmp a2bcacff67edd59711f7948a496167bbc6c11e73e923138af4133e2d2401b50142c85014889aba52b8aa19107d85afb81ccb0f25fea8cce5491060aeae81e056
st-results-noint.00100.bmp 1477d7e220515c9fe3f5295ae9ad89f27d6d62b1272bd948a6d2cfe6d96438cb010bc53dc412fcabaa1e228472d2a666d5b66a92e0170801c75242eea8348fe1
st-results-noint.00200.bmp 0781ba1ee7133bbdbf2617cfcb10847be7f54095e80449f281bbd125e73b14b90299f9239e5e660666b77528efec362d1eeb3eb28cb57c2bb58a705bc212b453
Expand Down Expand Up @@ -140,4 +140,4 @@ st-results-noint.02800.bmp 9614fd0ea5aad1a7d8801b1369dcf43
st-results-noint.avNE.age.xls 44ca8f8874f1637a6d7d330685b09a55d9210af024bb656ebc7f2d7cb8ef133fa1c5c439ef64c73b99bcaae1511b6a9cbf1dd1d8f974dd2b4ce5e13401980b80
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st-results-noint.avNE.severity.xls a22600bffbd6a4352654ca9d839637c8e1312b8b1326117638b1be8d405c9ff154a86e57a319a4cbe8ceb643d357b79d51d30272fbe3c08542802551cd7a0c87
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