Fully rename parameters and decide hospitalization when symptoms appear

docs/source/usage/utilities.rst

@@ -36,11 +36,11 @@ Data is either written as an ``int`` or a ``real``.
 
   - Real data:
 
-    - ``incubation_period``: (currently misleadingly named) Latent period length, i.e. time between exposure and infectiousness.
+    - ``latent_period``: Latent period length, i.e. time between exposure and infectiousness.
 
     - ``infectious_period``: Infections period length, i.e. time during which agent can spread disease
 
-    - ``symptomdev_period``: Symptom development period length (known as incubation period in some contexts), i.e. time between exposure and symptoms appearing.
+    - ``incubation_period``: Symptom development period length (known as incubation period in some contexts), i.e. time between exposure and symptoms appearing.
 
 - Every day (time-varying)
 

etc/plot_infected.ipynb

@@ -22,11 +22,11 @@
     "never = []\n",
     "with open(\"agent_data/run_9_cases.out\") as f:\n",
     "    for line in f:\n",
-    "        if line.startswith(\"Never infected: \"):\n",
+    "        if line.startswith(\"Susceptible: \"):\n",
     "            never.append(int(line.strip().split()[-1]))\n",
     "        if line.startswith(\"Infected: \"):\n",
     "            infected.append(int(line.strip().split()[1]))\n",
-    "        if line.startswith(\"Immune: \"):\n",
+    "        if line.startswith(\"Recovered: \"):\n",
     "            immune.append(int(line.strip().split()[1]))"
    ]
   },
@@ -53,7 +53,7 @@
     "ax = plt.gca()\n",
     "ax.set_xlabel(\"Day\")\n",
     "ax.set_ylabel(\"Number\")\n",
-    "plt.legend((\"Never infected\", \"Infected\", \"Immune\"))\n",
+    "plt.legend((\"Susceptible\", \"Infected\", \"Recovered\"))\n",
     "\n",
     "plt.savefig(\"infected_9_cases\")"
    ]

src/AgentContainer.cpp

@@ -495,9 +495,9 @@ void AgentContainer::infectAgents ()
 
                 auto counter_ptr           = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::disease_counter).data();
                 auto prob_ptr              = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::prob).data();
-                auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
+                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 symptomdev_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::symptomdev_period).data();
+                auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
 
                 auto* lparm = m_d_parm[d];
 
@@ -510,9 +510,9 @@ void AgentContainer::infectAgents ()
                         if (amrex::Random(engine) < prob_ptr[i]) {
                             status_ptr[i] = Status::infected;
                             counter_ptr[i] = 0.0_rt;
-                            incubation_period_ptr[i] = amrex::RandomNormal(lparm->latent_length_mean, lparm->latent_length_std, engine);
+                            latent_period_ptr[i] = amrex::RandomNormal(lparm->latent_length_mean, lparm->latent_length_std, engine);
                             infectious_period_ptr[i] = amrex::RandomNormal(lparm->infectious_length_mean, lparm->infectious_length_std, engine);
-                            symptomdev_period_ptr[i] = amrex::RandomNormal(lparm->incubation_length_mean, lparm->incubation_length_std, engine);
+                            incubation_period_ptr[i] = amrex::RandomNormal(lparm->incubation_length_mean, lparm->incubation_length_std, engine);
                             return;
                         }
                     }

src/AgentDefinitions.H

@@ -29,9 +29,9 @@ struct RealIdxDisease
         treatment_timer = 0,    /*!< Timer since hospital admission */
         disease_counter,        /*!< Counter since start of infection */
         prob,                   /*!< Probability of infection */
-        incubation_period,      /*!< Time until infectious */
+        latent_period,          /*!< Time until infectious */
         infectious_period,      /*!< Length of time infectious */
-        symptomdev_period,      /*!< Time until symptoms would develop */
+        incubation_period,      /*!< Time until symptoms would develop */
         nattribs                /*!< number of real-type attribute*/
     };
 };
@@ -163,7 +163,7 @@ bool notInfectiousButInfected ( const int      a_idx, /*!< Agent index */
 {
     return (    (a_ptd.m_runtime_idata[i0(a_d)+IntIdxDisease::status][a_idx] == Status::infected)
              && (a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::disease_counter][a_idx]
-                 <= a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::incubation_period][a_idx]) );
+                 <= a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::latent_period][a_idx]) );
 }
 
 /*! \brief Is an agent infectious? */
@@ -175,7 +175,7 @@ bool isInfectious ( const int      a_idx, /*!< Agent index */
 {
     return (   (a_ptd.m_runtime_idata[i0(a_d)+IntIdxDisease::status][a_idx] == Status::infected)
             && (a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::disease_counter][a_idx]
-                >= a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::incubation_period][a_idx]) );
+                >= a_ptd.m_runtime_rdata[r0(a_d)+RealIdxDisease::latent_period][a_idx]) );
 }
 
 /*! \brief Is an agent susceptible? */

src/CensusData.cpp

@@ -889,9 +889,9 @@ int infect_random_community (AgentContainer& pc, /*!< Agent container (particle
         auto status_ptr = soa.GetIntData(i_RT+i0(d_idx)+IntIdxDisease::status).data();
 
         auto counter_ptr           = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::disease_counter).data();
-        auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::incubation_period).data();
+        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 symptomdev_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::symptomdev_period).data();
+        auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d_idx)+RealIdxDisease::incubation_period).data();
 
         //auto unit_arr = pc.m_unit_mf[mfi].array();
         auto comm_arr = censusData.comm_mf[mfi].array();
@@ -932,9 +932,9 @@ int infect_random_community (AgentContainer& pc, /*!< Agent container (particle
                 } else {
                     status_ptr[pindex] = Status::infected;
                     counter_ptr[pindex] = 0;
-                    incubation_period_ptr[pindex] = amrex::RandomNormal(lparm->latent_length_mean, lparm->latent_length_std, engine);
+                    latent_period_ptr[pindex] = amrex::RandomNormal(lparm->latent_length_mean, lparm->latent_length_std, engine);
                     infectious_period_ptr[pindex] = amrex::RandomNormal(lparm->infectious_length_mean, lparm->infectious_length_std, engine);
-                    symptomdev_period_ptr[pindex] = amrex::RandomNormal(lparm->incubation_length_mean, lparm->incubation_length_std, engine);
+                    incubation_period_ptr[pindex] = amrex::RandomNormal(lparm->incubation_length_mean, lparm->incubation_length_std, engine);
                     ++ni;
                 }
             }

src/DiseaseStatus.H

@@ -63,7 +63,7 @@ class DiseaseStatus
     + If agent status is #Status::never or #Status::susceptible, do nothing
     + If agent status is #Status::infected, then
       + Increment its counter by 1 day
-      + If counter is within incubation period, do nothing more
+      + If counter is within latent period, do nothing more
       + Else, use hospitalization probabilities (by age group)
         to decide if agent is hospitalized. If yes, use age group to set hospital timer. Also, use
         age-group-wise probabilities to move agent to ICU and then to ventilator. Adjust timer
@@ -72,7 +72,7 @@ class DiseaseStatus
         status (using the agent's home community)
       + Else (beyond 3 days), count down hospital timer if agent is hospitalized. At end of hospital
         stay, determine if agent is #Status dead or #Status::immune. For non-hospitalized agents,
-        set them to #Status::immune after incubation length + infection length days.
+        set them to #Status::immune after latent length + infection length days.
 
     The input argument is a MultiFab with 4 components corresponding to "hospitalizations", "ICU",
     "ventilator", and "death". It contains the cumulative totals of these quantities for each
@@ -140,9 +140,9 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
                 auto timer_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::treatment_timer).data();
                 auto counter_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::disease_counter).data();
                 auto prob_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::prob).data();
-                auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
+                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 symptomdev_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::symptomdev_period).data();
+                auto incubation_period_ptr = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
 
                 auto* disease_parm_d = a_agents.getDiseaseParameters_d(d);
                 auto* disease_parm_h = a_agents.getDiseaseParameters_h(d);
@@ -175,7 +175,7 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
                                 symptomatic_ptr[i] = SymptomStatus::presymptomatic;
                             }
                         }
-                        if (counter_ptr[i] == Math::floor(symptomdev_period_ptr[i])) {
+                        if (counter_ptr[i] == Math::floor(incubation_period_ptr[i])) {
                             if (symptomatic_ptr[i] != SymptomStatus::asymptomatic) {
                                 symptomatic_ptr[i] = SymptomStatus::symptomatic;
                             }
@@ -184,31 +184,28 @@ void DiseaseStatus<AC,ACT,ACTD,A>::updateAgents(AC& a_agents, /*!< Agent contain
                                 &&  (Random(engine) < symptomatic_withdraw_compliance)) {
                                 withdrawn_ptr[i] = 1;
                             }
-                        }
-                        if (counter_ptr[i] < incubation_period_ptr[i]) {
-                            // incubation phase
-                            return;
-                        }
-                        if (counter_ptr[i] == Math::ceil(incubation_period_ptr[i])) {
-                            int flag_ICU_i = 0, flag_vent_i = 0;
-                            Real num_days = 0;
-                            disease_parm_d->check_hospitalization( num_days,
-                                                                   flag_ICU_i,
-                                                                   flag_vent_i,
-                                                                   age_group_ptr[i],
-                                                                   u50frac,
-                                                                   engine );
-                            timer_ptr[i] = ParticleReal(num_days);
-                            if (timer_ptr[i] > 0) { flag_hosp_ptr[i] = 1; }
-                            if (flag_ICU_i) { flag_ICU_ptr[i] = 1; }
-                            if (flag_vent_i) { flag_vent_ptr[i] = 1; }
-                        } else {
-                            if (!isHospitalized(i,ptd)) {
-                                if (counter_ptr[i] >= (incubation_period_ptr[i] + infectious_period_ptr[i])) {
-                                    status_ptr[i] = Status::immune;
-                                    counter_ptr[i] = amrex::RandomNormal(immune_length_mean, immune_length_std, engine);
-                                    symptomatic_ptr[i] = SymptomStatus::presymptomatic;
-                                    withdrawn_ptr[i] = 0;
+
+                            if (symptomatic_ptr[i] == SymptomStatus::symptomatic) {
+                                int flag_ICU_i = 0, flag_vent_i = 0;
+                                Real num_days = 0;
+                                disease_parm_d->check_hospitalization( num_days,
+                                                                       flag_ICU_i,
+                                                                       flag_vent_i,
+                                                                       age_group_ptr[i],
+                                                                       u50frac,
+                                                                       engine );
+                                timer_ptr[i] = ParticleReal(num_days);
+                                if (timer_ptr[i] > 0) { flag_hosp_ptr[i] = 1; }
+                                if (flag_ICU_i) { flag_ICU_ptr[i] = 1; }
+                                if (flag_vent_i) { flag_vent_ptr[i] = 1; }
+                            } else {
+                                if (!isHospitalized(i,ptd)) {
+                                    if (counter_ptr[i] >= (latent_period_ptr[i] + infectious_period_ptr[i])) {
+                                        status_ptr[i] = Status::immune;
+                                        counter_ptr[i] = amrex::RandomNormal(immune_length_mean, immune_length_std, engine);
+                                        symptomatic_ptr[i] = SymptomStatus::presymptomatic;
+                                        withdrawn_ptr[i] = 0;
+                                    }
                                 }
                             }
                         }

src/HospitalModel.H

@@ -88,13 +88,13 @@ void HospitalModel<AC,ACT,ACTD,A>::treatAgents(AC& a_agents, /*!< Agent containe
             int r_RT = RealIdx::nattribs;
 
             GpuArray<int*,ExaEpi::max_num_diseases> status_ptrs, symptomatic_ptrs;
-            GpuArray<ParticleReal*,ExaEpi::max_num_diseases> counter_ptrs, timer_ptrs, incub_per_ptrs;
+            GpuArray<ParticleReal*,ExaEpi::max_num_diseases> counter_ptrs, timer_ptrs, latent_per_ptrs;
             for (int d = 0; d < n_disease; d++) {
                 status_ptrs[d] = soa.GetIntData(i_RT+i0(d)+IntIdxDisease::status).data();
                 symptomatic_ptrs[d] = soa.GetIntData(i_RT+i0(d)+IntIdxDisease::symptomatic).data();
                 counter_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::disease_counter).data();
                 timer_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::treatment_timer).data();
-                incub_per_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::incubation_period).data();
+                latent_per_ptrs[d] = soa.GetRealData(r_RT+r0(d)+RealIdxDisease::latent_period).data();
             }
 
             Gpu::DeviceVector<int> is_alive;
@@ -139,7 +139,7 @@ void HospitalModel<AC,ACT,ACTD,A>::treatAgents(AC& a_agents, /*!< Agent containe
                         // agent is not in hospital
                         return;
                     }
-                    if (counter_ptrs[d][i] == Math::ceil(incub_per_ptrs[d][i])) {
+                    if (counter_ptrs[d][i] == Math::ceil(latent_per_ptrs[d][i])) {
                         // agent just started treatment
                         return;
                     }

src/IO.cpp

@@ -126,9 +126,9 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
             real_varnames.push_back("treatment_timer"); write_real_comp.push_back(1);
             real_varnames.push_back("disease_counter"); write_real_comp.push_back(1);
             real_varnames.push_back("infection_prob"); write_real_comp.push_back(1);
-            real_varnames.push_back("incubation_period"); write_real_comp.push_back(static_cast<int>(step==0));
+            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("symptomdev_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));
             int_varnames.push_back ("status"); write_int_comp.push_back(1);
             int_varnames.push_back ("strain"); write_int_comp.push_back(static_cast<int>(step==0));
             int_varnames.push_back ("symptomatic"); write_int_comp.push_back(1);
@@ -137,9 +137,9 @@ void writePlotFile (const AgentContainer& pc, /*!< Agent (particle) container */
                 real_varnames.push_back(disease_names[d]+"treatment_timer"); write_real_comp.push_back(1);
                 real_varnames.push_back(disease_names[d]+"_disease_counter"); write_real_comp.push_back(1);
                 real_varnames.push_back(disease_names[d]+"_infection_prob"); write_real_comp.push_back(1);
-                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]+"_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]+"_symptomdev_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));
                 int_varnames.push_back (disease_names[d]+"_status"); write_int_comp.push_back(1);
                 int_varnames.push_back (disease_names[d]+"_strain"); write_int_comp.push_back(static_cast<int>(step==0));
                 int_varnames.push_back (disease_names[d]+"_symptomatic"); write_int_comp.push_back(1);

src/InteractionModHome.H

@@ -118,11 +118,11 @@ class InteractionModHome : public InteractionModel<AC,ACT,ACTD,A>
       + Find its bin and the range of indices in the bin-sorted array for agents in its bin
       + If the agent is #Status::immune, do nothing.
       + If the agent is #Status::infected with the number of days infected (RealIdxDisease::disease_counter)
-        less than the incubation length, do nothing.
+        less than the latent length, do nothing.
       + Else, for each agent *j* in the same bin:
         + If the agent is #Status::immune, do nothing.
         + If the agent is #Status::infected with the number of days infected (RealIdxDisease::disease_counter)
-          less than the incubation length, do nothing.
+          less than the latent length, do nothing.
         + Else if *i* is not infected and *j* is infected, compute probability of *i* getting infected
           from *j* (see below).
 

src/InteractionModNborhood.H

@@ -111,11 +111,11 @@ class InteractionModNborhood : public InteractionModel<AC,ACT,ACTD,A>
       + Find its bin and the range of indices in the bin-sorted array for agents in its bin
       + If the agent is #Status::immune, do nothing.
       + If the agent is #Status::infected with the number of days infected (RealIdxDisease::disease_counter)
-        less than the incubation length, do nothing.
+        less than the latent length, do nothing.
       + Else, for each agent *j* in the same bin:
         + If the agent is #Status::immune, do nothing.
         + If the agent is #Status::infected with the number of days infected (RealIdxDisease::disease_counter)
-          less than the incubation length, do nothing.
+          less than the latent length, do nothing.
         + Else if *i* is not infected and *j* is infected, compute probability of *i* getting infected
           from *j* (see below).