Adding lateral flow test intervention code.

documentation/parameters/active_intervention_parameters.md

@@ -10,6 +10,7 @@
 | `quarantine_dropout_positive` | 0.01 | - | Daily probability of drop out for an individual quarantining after a positive test result | - |
 | `quarantine_compliance_traced_symptoms` | 0.5 | - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
 | `quarantine_compliance_traced_positive` | 0.9 | - | Fraction of individuals who initially comply with a quarantine notification after their contact tested positive | - |
+| `quarantine_compliance_positive` | 1.0 | - | Fraction of individuals who initially comply with a quarantine after they test positive | - |
 | `test_on_symptoms` | 0 | - | Test individuals who show symptoms (0=no, 1=yes) | - |
 | `test_on_traced` | 0 | - | Test individuals who have been contact-traced (0=no, 1=yes) | - |
 | `test_release_on_negative` | 1 | - | Release individuals following a negative test (0=no, 1=yes) | - |
@@ -34,6 +35,14 @@
 | `test_specificity` | 0.999 | - | Specificity of test (at any time) | - |
 | `test_order_wait` | 1 | - | Minimum number of days to wait to take a test | - |
 | `test_result_wait` | 1 | - | Number of days to wait for a test result | - |
+| `lateral_flow_test_order_wait` | 1 | - | Number of days to wait to receive a set of lateral flow tests | - |
+| `lateral_flow_test_on_symptoms` | 0 | - | Test individuals with Lateral Flow Assay who show symptoms (0=no, 1=yes) | - |
+| `lateral_flow_test_on_traced` | 0 | - | Test individuals with Lateral Flow Assay who have been contact-traced (0=no, 1=yes) | - |
+| `lateral_flow_test_repeat_count` | 7 | - | Number of daily Lateral Flow Assay tests to take in a row | - |
+| `lateral_flow_test_only` | 0 | - | If an individual takes Lateral Flow tests, do not take PCR or quarantine until they receive a test result | - |
+| `lateral_flow_test_fraction` | 0.5 | - | The fraction of individuals who take a Lateral Flow Assay test instead of quarantine if offered | - |
+| `lateral_flow_test_sensitivity` | 0.95 | - | Peak sensitivity of Lateral Flow Assay | - |
+| `lateral_flow_test_specificity` | 0.999 | - | Specificity of Lateral Flow Assay (at any time) | - |
 | `app_users_fraction_0_9` | 0.09 | - | Maximum fraction of the population with smartphones aged 0-9 | OFCOM 3-5 year olds |
 | `app_users_fraction_10_19` | 0.8 | - | Maximum fraction of the population with smartphones aged 10-19 | OFCOM 5-15 year olds |
 | `app_users_fraction_20_29` | 0.97 | - | Maximum fraction of the population with smartphones aged 20-29 | OFCOM 16-55 year olds |

documentation/parameters/parameter_dictionary.md

@@ -136,6 +136,7 @@
 | `quarantine_dropout_positive` | 0.01 | - | Daily probability of drop out for an individual quarantining after a positive test result | - |
 | `quarantine_compliance_traced_symptoms` | 0.5 | - | Fraction of individuals who initially comply with a quarantine notification after their contact reported symptoms | - |
 | `quarantine_compliance_traced_positive` | 0.9 | - | Fraction of individuals who initially comply with a quarantine notification after their contact tested positive | - |
+| `quarantine_compliance_positive` | 1.0 | - | Fraction of individuals who initially comply with a quarantine after they test positive | - |
 | `test_on_symptoms` | 0 | - | Test individuals who show symptoms (0=no, 1=yes) | - |
 | `test_on_traced` | 0 | - | Test individuals who have been contact-traced (0=no, 1=yes) | - |
 | `test_release_on_negative` | 1 | - | Release individuals following a negative test (0=no, 1=yes) | - |
@@ -173,6 +174,14 @@
 | `priority_test_contacts_60_69` | 1000 | - | Number of contacts that triggers priority test for individuals aged 60-69 years old | - |
 | `priority_test_contacts_70_79` | 1000 | - | Number of contacts that triggers priority test for individuals aged 70-79 years old | - |
 | `priority_test_contacts_80` | 1000 | - | Number of contacts that triggers priority test for individuals aged 80+ years old | - |
+| `lateral_flow_test_order_wait` | 1 | - | Number of days to wait to receive a set of lateral flow tests | - |
+| `lateral_flow_test_on_symptoms` | 0 | - | Test individuals with Lateral Flow Assay who show symptoms (0=no, 1=yes) | - |
+| `lateral_flow_test_on_traced` | 0 | - | Test individuals with Lateral Flow Assay who have been contact-traced (0=no, 1=yes) | - |
+| `lateral_flow_test_repeat_count` | 7 | - | Number of daily Lateral Flow Assay tests to take in a row | - |
+| `lateral_flow_test_only` | 0 | - | If an individual takes Lateral Flow tests, do not take PCR or quarantine until they receive a test result | - |
+| `lateral_flow_test_fraction` | 0.5 | - | The fraction of individuals who take a Lateral Flow Assay test instead of quarantine if offered | - |
+| `lateral_flow_test_sensitivity` | 0.95 | - | Peak sensitivity of Lateral Flow Assay | - |
+| `lateral_flow_test_specificity` | 0.999 | - | Specificity of Lateral Flow Assay (at any time) | - |
 | `self_quarantine_fraction` | 0 | - | Proportion of people who self-quarantine upon symptoms | - |
 | `app_users_fraction_0_9` | 0.09 | - | Maximum fraction of the population with smartphones aged 0-9 | OFCOM 3-5 year olds |
 | `app_users_fraction_10_19` | 0.8 | - | Maximum fraction of the population with smartphones aged 10-19 | OFCOM 5-15 year olds |

src/COVID19/default_params/baseline_parameters.csv

@@ -1,2 +1,2 @@
-rng_seed,param_id,n_total,mean_work_interactions_child,mean_work_interactions_adult,mean_work_interactions_elderly,daily_fraction_work,work_network_rewire,mean_random_interactions_child,sd_random_interactions_child,mean_random_interactions_adult,sd_random_interactions_adult,mean_random_interactions_elderly,sd_random_interactions_elderly,random_interaction_distribution,child_network_adults,elderly_network_adults,days_of_interactions,end_time,n_seed_infection,mean_infectious_period,sd_infectious_period,infectious_rate,sd_infectiousness_multiplier,mean_time_to_symptoms,sd_time_to_symptoms,mean_time_to_hospital,mean_time_to_critical,sd_time_to_critical,mean_time_to_recover,sd_time_to_recover,mean_time_to_death,sd_time_to_death,mean_time_to_susceptible_after_shift,time_to_susceptible_shift,fraction_asymptomatic_0_9,fraction_asymptomatic_10_19,fraction_asymptomatic_20_29,fraction_asymptomatic_30_39,fraction_asymptomatic_40_49,fraction_asymptomatic_50_59,fraction_asymptomatic_60_69,fraction_asymptomatic_70_79,fraction_asymptomatic_80,asymptomatic_infectious_factor,mild_fraction_0_9,mild_fraction_10_19,mild_fraction_20_29,mild_fraction_30_39,mild_fraction_40_49,mild_fraction_50_59,mild_fraction_60_69,mild_fraction_70_79,mild_fraction_80,mild_infectious_factor,mean_asymptomatic_to_recovery,sd_asymptomatic_to_recovery,household_size_1,household_size_2,household_size_3,household_size_4,household_size_5,household_size_6,population_0_9,population_10_19,population_20_29,population_30_39,population_40_49,population_50_59,population_60_69,population_70_79,population_80,daily_non_cov_symptoms_rate,relative_susceptibility_0_9,relative_susceptibility_10_19,relative_susceptibility_20_29,relative_susceptibility_30_39,relative_susceptibility_40_49,relative_susceptibility_50_59,relative_susceptibility_60_69,relative_susceptibility_70_79,relative_susceptibility_80,relative_transmission_household,relative_transmission_occupation,relative_transmission_random,hospitalised_fraction_0_9,hospitalised_fraction_10_19,hospitalised_fraction_20_29,hospitalised_fraction_30_39,hospitalised_fraction_40_49,hospitalised_fraction_50_59,hospitalised_fraction_60_69,hospitalised_fraction_70_79,hospitalised_fraction_80,critical_fraction_0_9,critical_fraction_10_19,critical_fraction_20_29,critical_fraction_30_39,critical_fraction_40_49,critical_fraction_50_59,critical_fraction_60_69,critical_fraction_70_79,critical_fraction_80,fatality_fraction_0_9,fatality_fraction_10_19,fatality_fraction_20_29,fatality_fraction_30_39,fatality_fraction_40_49,fatality_fraction_50_59,fatality_fraction_60_69,fatality_fraction_70_79,fatality_fraction_80,mean_time_hospitalised_recovery,sd_time_hospitalised_recovery,mean_time_critical_survive,sd_time_critical_survive,location_death_icu_0_9,location_death_icu_10_19,location_death_icu_20_29,location_death_icu_30_39,location_death_icu_40_49,location_death_icu_50_59,location_death_icu_60_69,location_death_icu_70_79,location_death_icu_80,quarantine_length_self,quarantine_length_traced_symptoms,quarantine_length_traced_positive,quarantine_length_positive,quarantine_dropout_self,quarantine_dropout_traced_symptoms,quarantine_dropout_traced_positive,quarantine_dropout_positive,quarantine_compliance_traced_symptoms,quarantine_compliance_traced_positive,test_on_symptoms,test_on_traced,test_release_on_negative,trace_on_symptoms,trace_on_positive,retrace_on_positive,quarantine_on_traced,traceable_interaction_fraction,tracing_network_depth,allow_clinical_diagnosis,quarantine_household_on_positive,quarantine_household_on_symptoms,quarantine_household_on_traced_positive,quarantine_household_on_traced_symptoms,quarantine_household_contacts_on_positive,quarantine_household_contacts_on_symptoms,quarantined_daily_interactions,quarantine_days,quarantine_smart_release_day,hospitalised_daily_interactions,test_insensitive_period,test_sensitive_period,test_sensitivity,test_specificity,test_order_wait,test_order_wait_priority,test_result_wait,test_result_wait_priority,priority_test_contacts_0_9,priority_test_contacts_10_19,priority_test_contacts_20_29,priority_test_contacts_30_39,priority_test_contacts_40_49,priority_test_contacts_50_59,priority_test_contacts_60_69,priority_test_contacts_70_79,priority_test_contacts_80,self_quarantine_fraction,app_users_fraction_0_9,app_users_fraction_10_19,app_users_fraction_20_29,app_users_fraction_30_39,app_users_fraction_40_49,app_users_fraction_50_59,app_users_fraction_60_69,app_users_fraction_70_79,app_users_fraction_80,app_turn_on_time,lockdown_occupation_multiplier_primary_network,lockdown_occupation_multiplier_secondary_network,lockdown_occupation_multiplier_working_network,lockdown_occupation_multiplier_retired_network,lockdown_occupation_multiplier_elderly_network,lockdown_random_network_multiplier,lockdown_house_interaction_multiplier,lockdown_time_on,lockdown_time_off,lockdown_elderly_time_on,lockdown_elderly_time_off,testing_symptoms_time_on,testing_symptoms_time_off,intervention_start_time,hospital_on,manual_trace_on,manual_trace_time_on,manual_trace_on_hospitalization,manual_trace_on_positive,manual_trace_delay,manual_trace_exclude_app_users,manual_trace_n_workers,manual_trace_interviews_per_worker_day,manual_trace_notifications_per_worker_day,manual_traceable_fraction_household,manual_traceable_fraction_occupation,manual_traceable_fraction_random,relative_susceptibility_by_interaction
-1,1,1000000,10,7,3,0.5,0.1,2,2,4,4,3,3,1,0.2,0.2,10,200,5,5.5,2.14,5.18,0,5.42,2.7,5.14,2.27,2.27,12,5,11.74,8.79,180,10000,0.456,0.412,0.370,0.332,0.296,0.265,0.238,0.214,0.192,0.33,0.533,0.569,0.597,0.614,0.616,0.602,0.571,0.523,0.461,0.72,15,5,7452,9936,4416,4140,1104,552,8054000,7528000,8712000,8835000,8500000,8968000,7069000,5488000,3281000,0.002,0.35,0.69,1.03,1.03,1.03,1.03,1.27,1.52,1.52,2,1,1,0.001,0.006,0.015,0.069,0.219,0.279,0.370,0.391,0.379,0.05,0.05,0.05,0.05,0.063,0.122,0.274,0.432,0.709,0.33,0.25,0.5,0.5,0.5,0.69,0.65,0.88,1,8.75,8.75,18.8,12.21,1,1,0.9,0.9,0.8,0.8,0.4,0.4,0.05,7,14,14,14,0.02,0.04,0.03,0.01,0.5,0.9,0,0,1,0,0,0,0,0.8,0,1,0,0,0,0,0,0,0,7,0,0,3,14,0.8,0.999,1,-1,1,-1,1000,1000,1000,1000,1000,1000,1000,1000,1000,0,0.09,0.8,0.97,0.96,0.94,0.86,0.7,0.48,0.32,10000,0.29,0.29,0.29,0.29,0.29,0.29,1.5,10000,10000,10000,10000,10000,10000,0,0,0,10000,1,0,1,0,300,6,12,1,0.8,0.05,1
+rng_seed,param_id,n_total,mean_work_interactions_child,mean_work_interactions_adult,mean_work_interactions_elderly,daily_fraction_work,work_network_rewire,mean_random_interactions_child,sd_random_interactions_child,mean_random_interactions_adult,sd_random_interactions_adult,mean_random_interactions_elderly,sd_random_interactions_elderly,random_interaction_distribution,child_network_adults,elderly_network_adults,days_of_interactions,end_time,n_seed_infection,mean_infectious_period,sd_infectious_period,infectious_rate,sd_infectiousness_multiplier,mean_time_to_symptoms,sd_time_to_symptoms,mean_time_to_hospital,mean_time_to_critical,sd_time_to_critical,mean_time_to_recover,sd_time_to_recover,mean_time_to_death,sd_time_to_death,mean_time_to_susceptible_after_shift,time_to_susceptible_shift,fraction_asymptomatic_0_9,fraction_asymptomatic_10_19,fraction_asymptomatic_20_29,fraction_asymptomatic_30_39,fraction_asymptomatic_40_49,fraction_asymptomatic_50_59,fraction_asymptomatic_60_69,fraction_asymptomatic_70_79,fraction_asymptomatic_80,asymptomatic_infectious_factor,mild_fraction_0_9,mild_fraction_10_19,mild_fraction_20_29,mild_fraction_30_39,mild_fraction_40_49,mild_fraction_50_59,mild_fraction_60_69,mild_fraction_70_79,mild_fraction_80,mild_infectious_factor,mean_asymptomatic_to_recovery,sd_asymptomatic_to_recovery,household_size_1,household_size_2,household_size_3,household_size_4,household_size_5,household_size_6,population_0_9,population_10_19,population_20_29,population_30_39,population_40_49,population_50_59,population_60_69,population_70_79,population_80,daily_non_cov_symptoms_rate,relative_susceptibility_0_9,relative_susceptibility_10_19,relative_susceptibility_20_29,relative_susceptibility_30_39,relative_susceptibility_40_49,relative_susceptibility_50_59,relative_susceptibility_60_69,relative_susceptibility_70_79,relative_susceptibility_80,relative_transmission_household,relative_transmission_occupation,relative_transmission_random,hospitalised_fraction_0_9,hospitalised_fraction_10_19,hospitalised_fraction_20_29,hospitalised_fraction_30_39,hospitalised_fraction_40_49,hospitalised_fraction_50_59,hospitalised_fraction_60_69,hospitalised_fraction_70_79,hospitalised_fraction_80,critical_fraction_0_9,critical_fraction_10_19,critical_fraction_20_29,critical_fraction_30_39,critical_fraction_40_49,critical_fraction_50_59,critical_fraction_60_69,critical_fraction_70_79,critical_fraction_80,fatality_fraction_0_9,fatality_fraction_10_19,fatality_fraction_20_29,fatality_fraction_30_39,fatality_fraction_40_49,fatality_fraction_50_59,fatality_fraction_60_69,fatality_fraction_70_79,fatality_fraction_80,mean_time_hospitalised_recovery,sd_time_hospitalised_recovery,mean_time_critical_survive,sd_time_critical_survive,location_death_icu_0_9,location_death_icu_10_19,location_death_icu_20_29,location_death_icu_30_39,location_death_icu_40_49,location_death_icu_50_59,location_death_icu_60_69,location_death_icu_70_79,location_death_icu_80,quarantine_length_self,quarantine_length_traced_symptoms,quarantine_length_traced_positive,quarantine_length_positive,quarantine_dropout_self,quarantine_dropout_traced_symptoms,quarantine_dropout_traced_positive,quarantine_dropout_positive,quarantine_compliance_traced_symptoms,quarantine_compliance_traced_positive,quarantine_compliance_positive,test_on_symptoms,test_on_traced,test_release_on_negative,trace_on_symptoms,trace_on_positive,retrace_on_positive,quarantine_on_traced,traceable_interaction_fraction,tracing_network_depth,allow_clinical_diagnosis,quarantine_household_on_positive,quarantine_household_on_symptoms,quarantine_household_on_traced_positive,quarantine_household_on_traced_symptoms,quarantine_household_contacts_on_positive,quarantine_household_contacts_on_symptoms,quarantined_daily_interactions,quarantine_days,quarantine_smart_release_day,hospitalised_daily_interactions,test_insensitive_period,test_sensitive_period,test_sensitivity,test_specificity,test_order_wait,test_order_wait_priority,test_result_wait,test_result_wait_priority,priority_test_contacts_0_9,priority_test_contacts_10_19,priority_test_contacts_20_29,priority_test_contacts_30_39,priority_test_contacts_40_49,priority_test_contacts_50_59,priority_test_contacts_60_69,priority_test_contacts_70_79,priority_test_contacts_80,lateral_flow_test_order_wait,lateral_flow_test_on_symptoms,lateral_flow_test_on_traced,lateral_flow_test_repeat_count,lateral_flow_test_only,lateral_flow_test_fraction,lateral_flow_test_sensitivity,lateral_flow_test_specificity,self_quarantine_fraction,app_users_fraction_0_9,app_users_fraction_10_19,app_users_fraction_20_29,app_users_fraction_30_39,app_users_fraction_40_49,app_users_fraction_50_59,app_users_fraction_60_69,app_users_fraction_70_79,app_users_fraction_80,app_turn_on_time,lockdown_occupation_multiplier_primary_network,lockdown_occupation_multiplier_secondary_network,lockdown_occupation_multiplier_working_network,lockdown_occupation_multiplier_retired_network,lockdown_occupation_multiplier_elderly_network,lockdown_random_network_multiplier,lockdown_house_interaction_multiplier,lockdown_time_on,lockdown_time_off,lockdown_elderly_time_on,lockdown_elderly_time_off,testing_symptoms_time_on,testing_symptoms_time_off,intervention_start_time,hospital_on,manual_trace_on,manual_trace_time_on,manual_trace_on_hospitalization,manual_trace_on_positive,manual_trace_delay,manual_trace_exclude_app_users,manual_trace_n_workers,manual_trace_interviews_per_worker_day,manual_trace_notifications_per_worker_day,manual_traceable_fraction_household,manual_traceable_fraction_occupation,manual_traceable_fraction_random,relative_susceptibility_by_interaction
+1,1,1000000,10,7,3,0.5,0.1,2,2,4,4,3,3,1,0.2,0.2,10,200,5,5.5,2.14,5.18,0,5.42,2.7,5.14,2.27,2.27,12,5,11.74,8.79,180,10000,0.456,0.412,0.370,0.332,0.296,0.265,0.238,0.214,0.192,0.33,0.533,0.569,0.597,0.614,0.616,0.602,0.571,0.523,0.461,0.72,15,5,7452,9936,4416,4140,1104,552,8054000,7528000,8712000,8835000,8500000,8968000,7069000,5488000,3281000,0.002,0.35,0.69,1.03,1.03,1.03,1.03,1.27,1.52,1.52,2,1,1,0.001,0.006,0.015,0.069,0.219,0.279,0.370,0.391,0.379,0.05,0.05,0.05,0.05,0.063,0.122,0.274,0.432,0.709,0.33,0.25,0.5,0.5,0.5,0.69,0.65,0.88,1,8.75,8.75,18.8,12.21,1,1,0.9,0.9,0.8,0.8,0.4,0.4,0.05,7,14,14,14,0.02,0.04,0.03,0.01,0.5,0.9,1.0,0,0,1,0,0,0,0,0.8,0,1,0,0,0,0,0,0,0,7,0,0,3,14,0.8,0.999,1,-1,1,-1,1000,1000,1000,1000,1000,1000,1000,1000,1000,1,0,0,7,0,0.5,0.95,0.999,0,0.09,0.8,0.97,0.96,0.94,0.86,0.7,0.48,0.32,10000,0.29,0.29,0.29,0.29,0.29,0.29,1.5,10000,10000,10000,10000,10000,10000,0,0,0,10000,1,0,1,0,300,6,12,1,0.8,0.05,1

src/COVID19/model.py

@@ -5,6 +5,7 @@
 import pandas as pd
 import pkg_resources
 import sys, time
+import numpy as np
 
 import covid19
 from COVID19.network import Network
@@ -40,12 +41,21 @@ class ModelException(Exception):
     "test_result_wait",
     "test_result_wait_priority",
     "self_quarantine_fraction",
+    "quarantine_compliance_positive",
     "lockdown_on",
     "lockdown_elderly_on",
     "app_turned_on",
     "app_users_fraction",
     "trace_on_symptoms",
     "trace_on_positive",
+    "lateral_flow_test_on_symptoms",
+    "lateral_flow_test_on_traced",
+    "lateral_flow_test_order_wait",
+    "lateral_flow_test_sensitivity",
+    "lateral_flow_test_specificity",
+    "lateral_flow_test_repeat_count",
+    "lateral_flow_test_only",
+    "lateral_flow_test_fraction",
     "lockdown_house_interaction_multiplier",
     "lockdown_random_network_multiplier",
     "lockdown_occupation_multiplier_primary_network",
@@ -1139,6 +1149,20 @@ def one_time_step_results(self):
         results["R_inst_05"] = covid19.calculate_R_instanteous( self.c_model, self.c_model.time, 0.05 )
         results["R_inst_95"] = covid19.calculate_R_instanteous( self.c_model, self.c_model.time, 0.95 )
 
+        results["n_lateral_flow_tests"] = covid19.utils_n_total_by_day(
+            self.c_model, covid19.LATERAL_FLOW_TEST_TAKE, int(self.c_model.time)
+        )
+        if results["n_lateral_flow_tests"] > 0:
+            results["mean_lfa_sensitivity"] = covid19.calculate_mean_lfa_sensitivity( self.c_model, covid19.NO_EVENT )
+            results["mean_lfa_sensitivity_asymptom"] = covid19.calculate_mean_lfa_sensitivity( self.c_model, covid19.ASYMPTOMATIC )
+            results["mean_lfa_sensitivity_symptom_mild"] = covid19.calculate_mean_lfa_sensitivity( self.c_model, covid19.PRESYMPTOMATIC_MILD )
+            results["mean_lfa_sensitivity_symptom"] = covid19.calculate_mean_lfa_sensitivity( self.c_model, covid19.PRESYMPTOMATIC )
+        else:
+            results["mean_lfa_sensitivity"] = np.nan
+            results["mean_lfa_sensitivity_asymptom"] = np.nan
+            results["mean_lfa_sensitivity_symptom_mild"] = np.nan
+            results["mean_lfa_sensitivity_symptom"] = np.nan
+
         return results
 
     def write_output_files(self):