Add delay between symptom onset and hospitalization

docs/source/usage/how_to_run.rst

@@ -156,6 +156,12 @@ The following inputs specify the disease parameters:
 * ``disease.incubation_length_beta`` (`float`, default ``0.2``)
     Beta parameter for the incubation length Gamma distribution. The incubation length is the length of time in days after exposure until agents develop symptoms.
     For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2.
+* ``disease.hospital_delay_length_alpha`` (`float`, default ``1.0``)
+    Alpha parameter for the hospital_delay length Gamma distribution. The hospital_delay length is the length of time in days after agents develop symptoms that they seek treatment.
+    For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2.
+* ``disease.hospital_delay_length_beta`` (`float`, default ``1.0``)
+    Beta parameter for the hospital_delay length Gamma distribution. The hospital_delay length is the length of time in days after agents develop symptoms that they seek treatment.
+    For a Gamma distribution, the mean is alpha*beta and the variance is alpha*beta^2.
 * ``disease.hospitalization_days`` (`list of float`, default ``3.0 8.0 7.0``)
     Number of hospitalization days for age groups: under 50, 50-64, 65 and over.
 * ``disease.xmit_comm`` (`list of float`, default ``0.000018125 0.000054375 0.000145 0.000145 0.000145 0.0002175``)

docs/source/usage/utilities.rst

@@ -42,6 +42,8 @@ Data is either written as an ``int`` or a ``real``.
 
     - ``incubation_period``: Symptom development period length (known as incubation period in some contexts), i.e. time between exposure and symptoms appearing.
 
+    - ``hospital_delay``: Delay after symptom appearance for agents to seek treatment.
+
 - Every day (time-varying)
 
   - Int data

examples/inputs.defaults

@@ -107,6 +107,10 @@ disease.infectious_length_beta = 0.17
 disease.incubation_length_alpha = 25.0
 # Beta parameter for the incubation length Gamma distribution. The incubation length is the length in days from the time of infection until symptoms develop.
 disease.incubation_length_beta = 0.2
+# Alpha parameter for the hospital_delay length Gamma distribution. The hospital_delay length is the length in days after developing symptoms that agents seek treatment.
+disease.hospital_delay_length_alpha = 1.0
+# Beta parameter for the hospital_delay length Gamma distribution. The hospital_delay length is the length in days after developing symptoms that agents seek treatment.
+disease.hospital_delay_length_beta = 1.0
 
 # Number of days in hospital for the age groups under 50, 50 to 64 and over 64.
 disease.hospitalization_days = 3 8 7

src/AgentContainer.cpp

@@ -711,6 +711,7 @@ void AgentContainer::infectAgents ()
                 auto latent_period_ptr     = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::latent_period).data();
                 auto infectious_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::infectious_period).data();
                 auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
+                auto hospital_delay_ptr    = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::hospital_delay).data();
 
                 const auto lparm = m_d_parm[d];
 
@@ -722,7 +723,7 @@ void AgentContainer::infectAgents ()
                          status_ptr[i] == Status::susceptible ) {
                         if (amrex::Random(engine) < prob_ptr[i]) {
                             setInfected(&(status_ptr[i]), &(counter_ptr[i]), &(latent_period_ptr[i]), &(infectious_period_ptr[i]),
-                                        &(incubation_period_ptr[i]), engine, lparm);
+                                        &(incubation_period_ptr[i]), &(hospital_delay_ptr[i]), engine, lparm);
                             return;
                         }
                     }

src/AgentDefinitions.H

@@ -32,6 +32,7 @@ struct RealIdxDisease
         latent_period,          /*!< Time until infectious, which could be before symptoms appear */
         infectious_period,      /*!< Length of time infectious */
         incubation_period,      /*!< Time until symptoms appear */
+        hospital_delay,         /*!< Delay after symptom onset until hospital treatment is sought */
         nattribs                /*!< number of real-type attribute*/
     };
 };

src/DiseaseParm.H

@@ -94,6 +94,9 @@ struct DiseaseParm
     Real incubation_length_alpha = Real(25.0);  /*! alpha parameter for gamma distribution*/
     Real incubation_length_beta = Real(0.2);    /*! beta parameter for gamma distribution*/
 
+    Real hospital_delay_length_alpha = Real(1.0);  /*! alpha parameter for gamma distribution*/
+    Real hospital_delay_length_beta = Real(1.0);    /*! beta parameter for gamma distribution*/
+
     /*! number of hospitalization days by age group (#AgeGroups_Hosp); note that the
      *  age groups here are under 50, 50-64, and over 65, and *not* the age groups
      *  used in other parts of the code (#AgeGroups) */
@@ -164,6 +167,7 @@ void setInfected ( int* status,
                    amrex::ParticleReal* latent_period,
                    amrex::ParticleReal* infectious_period,
                    amrex::ParticleReal* incubation_period,
+                   amrex::ParticleReal* hospital_delay,
                    amrex::RandomEngine const& engine,
                    const DiseaseParm* lparm)
 {
@@ -175,9 +179,12 @@ void setInfected ( int* status,
         static_cast<ParticleReal>(amrex::RandomGamma(lparm->infectious_length_alpha, lparm->infectious_length_beta, engine));
     *incubation_period =
         static_cast<ParticleReal>(amrex::RandomGamma(lparm->incubation_length_alpha, lparm->incubation_length_beta, engine));
+    *hospital_delay =
+        static_cast<ParticleReal>(amrex::RandomGamma(lparm->hospital_delay_length_alpha, lparm->hospital_delay_length_beta, engine));
     if (*latent_period < 0) { *latent_period = amrex::Real(0);}
     if (*infectious_period < 0) { *infectious_period = amrex::Real(0);}
     if (*incubation_period < 0) { *incubation_period = amrex::Real(0);}
+    if (*hospital_delay < 0) { *hospital_delay = amrex::Real(0);}
     if (*incubation_period > (*infectious_period + *latent_period)) {
         *incubation_period = std::floor(*infectious_period + *latent_period);
     }

src/DiseaseParm.cpp

@@ -77,10 +77,12 @@ void DiseaseParm::readInputs ( const std::string& a_pp_str /*!< Parmparse string
     pp.query("latent_length_alpha", latent_length_alpha);
     pp.query("infectious_length_alpha", infectious_length_alpha);
     pp.query("incubation_length_alpha", incubation_length_alpha);
+    pp.query("hospital_delay_length_alpha", hospital_delay_length_alpha);
 
     pp.query("latent_length_beta", latent_length_beta);
     pp.query("infectious_length_beta", infectious_length_beta);
     pp.query("incubation_length_beta", incubation_length_beta);
+    pp.query("hospital_delay_length_beta", hospital_delay_length_beta);
 
     pp.query("immune_length_alpha", immune_length_alpha);
     pp.query("immune_length_beta", immune_length_beta);

src/DiseaseStatus.H

@@ -131,6 +131,7 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
                 auto latent_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::latent_period).data();
                 auto infectious_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::infectious_period).data();
                 auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
+                auto hospital_delay_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::hospital_delay).data();
 
                 auto* disease_parm_d = a_agents.getDiseaseParameters_d(d);
                 auto* disease_parm_h = a_agents.getDiseaseParameters_h(d);
@@ -168,6 +169,16 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
                                 if (symptomatic_withdraw_compliance > 0.0_rt && (Random(engine) < symptomatic_withdraw_compliance)) {
                                     withdrawn_ptr[i] = 1;
                                 }
+                                if (Math::floor(hospital_delay_ptr[i]) == 0) {
+                                    disease_parm_d->check_hospitalization(&(timer_ptr[i]),
+                                                                          &(marked_for_ICU_ptr[i]),
+                                                                          &(marked_for_vent_ptr[i]),
+                                                                          age_group_ptr[i],
+                                                                          engine); }
+                                if (timer_ptr[i] > 0) { marked_for_hosp_ptr[i] = 1; }
+                            }
+                        } else if ((Math::floor(hospital_delay_ptr[i]) > 0) && (Math::floor(counter_ptr[i]) == Math::floor(incubation_period_ptr[i]) + Math::floor(hospital_delay_ptr[i]))) {
+                            if (symptomatic_ptr[i] == SymptomStatus::symptomatic) {
                                 disease_parm_d->check_hospitalization(&(timer_ptr[i]),
                                                                       &(marked_for_ICU_ptr[i]),
                                                                       &(marked_for_vent_ptr[i]),

src/IO.cpp

@@ -135,6 +135,7 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
             real_varnames.push_back("latent_period"); write_real_comp.push_back(static_cast<int>(step==0));
             real_varnames.push_back("infectious_period"); write_real_comp.push_back(static_cast<int>(step==0));
             real_varnames.push_back("incubation_period"); write_real_comp.push_back(static_cast<int>(step==0));
+            real_varnames.push_back("hospital_delay"); write_real_comp.push_back(static_cast<int>(step==0));
             int_varnames.push_back ("status"); write_int_comp.push_back(1);
             int_varnames.push_back ("symptomatic"); write_int_comp.push_back(1);
         } else {
@@ -145,6 +146,7 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
                 real_varnames.push_back(disease_names[d]+"_latent_period"); write_real_comp.push_back(static_cast<int>(step==0));
                 real_varnames.push_back(disease_names[d]+"_infectious_period"); write_real_comp.push_back(static_cast<int>(step==0));
                 real_varnames.push_back(disease_names[d]+"_incubation_period"); write_real_comp.push_back(static_cast<int>(step==0));
+                real_varnames.push_back(disease_names[d]+"_hospital_delay"); write_real_comp.push_back(static_cast<int>(step==0));
                 int_varnames.push_back (disease_names[d]+"_status"); write_int_comp.push_back(1);
                 int_varnames.push_back (disease_names[d]+"_symptomatic"); write_int_comp.push_back(1);
             }

src/InitializeInfections.cpp

@@ -81,6 +81,7 @@ static int infect_random_community (AgentContainer& pc, /*!< Agent container (pa
         auto latent_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::latent_period).data();
         auto infectious_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::infectious_period).data();
         auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::incubation_period).data();
+        auto hospital_delay_ptr    = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::hospital_delay).data();
 
         auto comm_arr = comm_mf[mfi].array();
 
@@ -113,7 +114,7 @@ static int infect_random_community (AgentContainer& pc, /*!< Agent container (pa
                     }
                 } else {
                     setInfected(&(status_ptr[pindex]), &(counter_ptr[pindex]), &(latent_period_ptr[pindex]),
-                                &(infectious_period_ptr[pindex]), &(incubation_period_ptr[pindex]), engine, lparm);
+                                &(infectious_period_ptr[pindex]), &(incubation_period_ptr[pindex]), &(hospital_delay_ptr[i]), engine, lparm);
                     ++ni;
                 }
             }