def add_scenario_reports(cb,
include_summary=True,
include_inset=True,
include_bednet_events_in_counter=False):
if include_summary:
add_summary_report(cb, age_bins=summary_age_bins, start=365)
events_to_count = [
"Received_Treatment", "Received_Test", "Received_Campaign_Drugs",
"Received_RCD_Drugs", "Received_SMC", "Received_Ivermectin",
"Received_Primaquine"
]
if include_bednet_events_in_counter:
events_to_count += [
"Bednet_Discarded", "Bednet_Got_New_One", "Bednet_Using"
]
add_event_counter_report(cb, event_trigger_list=events_to_count)
# drug_events = ["Received_Treatment", "Diagnostic_Survey_0", "Received_Test", "Received_RCD_Drugs",
# "Received_Campaign_Drugs"]
# cb.set_param("Listed_Events", drug_events)
# cb.set_param("Custom_Individual_Events", drug_events)
if include_inset:
cb.set_param("Enable_Default_Reporting", 1)
else:
cb.set_param("Enable_Default_Reporting", 0)
def iver_sweep(cb, intervention_df_dict, vc_pack, drug_pack, vc_coverage, mda_coverage, ivm_duration, restricted_ivm=False):
add_hs(cb, intervention_df_dict["hs"])
event_trigger_list = ["Received_Treatment"]
if vc_pack == "none":
pass
elif vc_pack == "ITN only":
itn_events = intervention_df_dict["itn"]
itn_events["cov_all"] = vc_coverage
add_itn(cb, itn_events)
elif vc_pack == "IRS only":
irs_events = intervention_df_dict["irs"]
irs_events["cov_all"] = vc_coverage
add_irs(cb, irs_events)
elif vc_pack == "ITN and IRS":
itn_events = intervention_df_dict["itn"]
itn_events["cov_all"] = vc_coverage
irs_events = intervention_df_dict["irs"]
irs_events["cov_all"] = vc_coverage
add_itn(cb, itn_events)
add_irs(cb, irs_events)
# Is there a DP component to the MDA?
if mda_coverage > 0:
mda_events = intervention_df_dict["mda"]
mda_events["cov_all"] = mda_coverage
if drug_pack != "Pure IVM MDA": # MDA includes DP
event_trigger_list.append('Received_Campaign_Drugs')
add_mda(cb, mda_events)
elif drug_pack == "Pure IVM MDA": # MDA with only IVM and no DP
event_trigger_list.append('Received_Ivermectin')
add_pure_ivm_mda(cb, mda_events, ivm_duration, restricted_ivm=restricted_ivm)
if drug_pack == "MDA with IVM":
event_trigger_list.append('Received_Ivermectin')
if not restricted_ivm:
add_ivermectin(cb, box_duration=ivm_duration, coverage=1.0, start_days=[1],
trigger_condition_list=['Received_Campaign_Drugs'], target_residents_only=False)
else:
target_groups = [{'agemin': 5, 'agemax': 200, 'gender': 'Male'},
{'agemin': 51, 'agemax': 200, 'gender': 'Female'},
{'agemin': 5, 'agemax': 12, 'gender': 'Female'}]
for tg in target_groups:
add_ivermectin(cb, box_duration=ivm_duration, coverage=1.0, start_days=[1],
trigger_condition_list=['Received_Campaign_Drugs'], target_residents_only=False,
target_group=tg)
add_event_counter_report(cb, event_trigger_list=event_trigger_list)
return {"vc_pack": vc_pack,
"drug_pack": drug_pack,
"vc_coverage": vc_coverage,
"mda_coverage": mda_coverage,
"ivm_duration": ivm_duration}
def add_all_reports(cb):
add_event_counter_report(cb, event_trigger_list=["Received_Treatment"])
add_filtered_spatial_report(cb, channels=["Population", "True_Prevalence"])
# Filtered report just for work node, and just for catchment:
regional_EIR_node_label = 100000
# Quick and dirty way to get sorted, unique list of grid cells in catchment:
df = pd.read_csv("./inputs/grid_all_healthseek_events.csv")
catch_node_ids = list(set(list(df["grid_cell"])))
add_filtered_report(cb,
nodes=[regional_EIR_node_label],
description='Work')
add_filtered_report(cb, nodes=catch_node_ids, description='Catchment')
def add_burnin_reports(cb, include_inset=False):
add_summary_report(cb, start=45 * 365)
if include_inset:
cb.set_param("Enable_Default_Reporting", 1)
else:
cb.set_param("Enable_Default_Reporting", 0)
events_to_count = [
"Bednet_Discarded", "Bednet_Got_New_One", "Bednet_Using",
"Received_Treatment", "Received_SMC"
]
add_event_counter_report(cb,
event_trigger_list=events_to_count,
duration=365 * 50)
def __call__(self, cb):
from malaria.reports.MalariaReport import add_event_counter_report
return add_event_counter_report(cb,
self.channels,
start=self.start,
duration=self.duration,
nodes=self.nodes,
description=self.description)
def add_standard_reports(cb):
add_event_counter_report(cb,
event_trigger_list=[
"Received_Treatment", "Received_Test",
"Received_Campaign_Drugs",
"Received_RCD_Drugs"
],
start=start,
duration=duration)
cb.update_params({
"Listed_Events": [
"Received_Treatment", "Diagnostic_Survey_0", "Received_Test",
"Received_RCD_Drugs", "Received_Campaign_Drugs"
]
})
# Replace InsetChart with a filtered report
cb.update_params({"Enable_Default_Reporting": 0})
add_filtered_report(cb, start=365 * 3, description="Final_Year")
def add_reports_for_likelihood_analyzers(self,
cb,
catch,
filter_duration_days=3650):
filter_end = self.sim_duration_days
filter_start = self.sim_duration_days - filter_duration_days
add_filtered_spatial_report(cb,
start=filter_start,
end=filter_end,
channels=[
'Population', 'True_Prevalence',
"Blood_Smear_Parasite_Prevalence"
]) # 'New_Clinical_Cases','New_Infections'
# Now add report for is for HF-level incidence likelihood analyzer.
add_event_counter_report(
cb,
# event_trigger_list=['Received_Treatment', 'Received_IRS', 'Received_Campaign_Drugs', 'Received_RCD_Drugs', 'Bednet_Got_New_One', 'Received_Test'],
event_trigger_list=[
'Received_Treatment'
], #, 'Received_Test', 'TestedPositive', 'Received_Campaign_Drugs'],
start=filter_start,
duration=filter_duration_days)
# Get list of cells that correspond to this catchment:
catch_nodes = catchment_grid_cells(catch, as_list=True)
add_filtered_report(cb,
start=filter_start,
end=filter_end,
nodes=catch_nodes)
# Add a similar report for the migration node
add_filtered_report(cb,
start=filter_start,
end=filter_end,
nodes=[100000],
description='Work')
from simtools.ExperimentManager.ExperimentManagerFactory import ExperimentManagerFactory
from simtools.SetupParser import SetupParser
from dtk.interventions.incidence_counter import add_incidence_counter
from dtk.interventions.irs import add_node_IRS
from malaria.reports.MalariaReport import add_event_counter_report # you need to isntall the malaria package
# This block will be used unless overridden on the command-line
# this means that simtools.ini local block will be used
SetupParser.default_block = 'LOCAL'
cb = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb, 'Namawala')
# event counter can help you keep track of events that are happening
add_event_counter_report(
cb,
["HappyBirthday", "Party", "PartyHarder", "IRS_Blackout_Event_Trigger"])
# adding an incidence counter, which starts on day 20, and counts "Happy Birthday" events for 30 days. the default
# thresholds are 10 and 100 event counts and default events being sent out when the threshold is reached are Action1 and Action2
add_incidence_counter(
cb,
start_day=20,
count_duration=30,
count_triggers=['HappyBirthday'],
threshold_type=
'COUNT', #this is the default, we can also look at % per eligible population
thresholds=[13, 254],
triggered_events=['Party', 'PartyHarder'])
add_incidence_counter(cb,
start_day=50,
def add_interventions_and_reports(cb, sim_time_dict):
sim_start_year = sim_time_dict["sim_start_year"]
sim_length_years = sim_time_dict["sim_length_years"]
sim_filter_start_time = sim_time_dict["sim_filter_start_time"]
sim_filter_duration = sim_time_dict["sim_filter_duration"]
mozamb_exp.start_year = sim_start_year
mozamb_exp.sim_length_years = sim_length_years
mozamb_exp.implement_baseline_healthseeking(
cb
) #fixme In future, pass start_year and sim_length_years to avoid race conditions
mozamb_exp.implement_interventions(cb, True, True, False, True, True)
all_nodes = list(mozamb_exp.desired_cells)
if importation_version == 0:
cb.update_params({
'x_Regional_Migration': 0.03,
})
add_migration_event(
cb,
nodeto=100000,
coverage=0.5,
repetitions=500,
tsteps_btwn=30,
duration_of_stay=3,
duration_before_leaving_distr_type='UNIFORM_DURATION',
duration_before_leaving=0,
duration_before_leaving_2=30,
nodesfrom={
'class': 'NodeSetNodeList',
'Node_List': all_nodes
},
ind_property_restrictions=[{
'TravelerStatus': 'IsTraveler'
}])
elif importation_version == 1:
cb.update_params({
'x_Regional_Migration': 0.0405,
})
# Add specific reports that we want (have to do it here because we need to know what times to filter for):
# Add filter report that has same length for both burn-in and non-burn-in runs (2010-2020).
# This version is for grid-level prevalence comparison
add_filtered_spatial_report(
cb,
start=sim_filter_start_time,
end=(sim_filter_start_time + sim_filter_duration),
# channels=['Population', 'New_Diagnostic_Prevalence'])
channels=['Population',
'True_Prevalence']) # 'New_Clinical_Cases','New_Infections'
# Add filter that has same length for both burn-in and non-burn-in runs (2010-2020)
# This version is for HF-level incidence comparison. Add a similar report for the migration node
add_filtered_report(cb,
start=sim_filter_start_time,
end=(sim_filter_start_time + sim_filter_duration),
nodes=all_nodes)
add_filtered_report(cb,
start=sim_filter_start_time,
end=(sim_filter_start_time + sim_filter_duration),
nodes=[EIR_node_label],
description='Work')
# # Add filter report for prevalence in each bairro
foo = bairro_df.groupby('bairro')
for (bairro_num, df) in foo:
add_filtered_report(cb,
start=sim_filter_start_time,
end=(sim_filter_start_time + sim_filter_duration),
nodes=[int(x) for x in df['grid_cell'].values],
description=str(int(bairro_num)))
# Add counter report for clinical incidence
add_event_counter_report(cb,
event_trigger_list=[
'Received_Treatment', 'Received_IRS',
'Received_Campaign_Drugs',
'Received_RCD_Drugs', 'Bednet_Got_New_One',
'Received_Test'
],
start=sim_filter_start_time,
duration=sim_filter_duration)
# you will need to install malaria package for use with dtk-tools:
# use > dtk get_package malaria -v HEAD
# This block will be used unless overridden on the command-line
# this means that simtools.ini local block will be used
# change this to 'LOCAL' to run it on just your machine.
#SetupParser('HPC')
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM')
cb.update_params({"Genome_Markers": []})
cb.update_params({"Base_Population_Scale_Factor": 0.001}),
configure_site(cb, "Matsari")
# event counter can help you keep track of events that are happening that you're interested in.
add_event_counter_report(cb, ["Took_Dose", "NewClinicalCase"])
# run_sim_args is what the `dtk run` command will look for
run_sim_args = {
'exp_name': 'Matsari_Malaria_Adherence_Drug_Example',
'config_builder': cb
}
# There are defaults for all the variables except the config_builder that gets passed in
# you could, if you wanted to, create this interventions with
# add_adherent_drug(cb)
# You'll want to define the configuration for the usage/waning of the drug separately and pass the whole thing
# to adherence_config variable - there is a default, which is the following, in which the any user takes all the drugs
# { # the default is for person to take everything not matter what age
# "class": "WaningEffectMapLinearAge",
####################
# Reports and logs #
####################
add_summary_report(cb, age_bins=summary_age_bins, start=365)
events_to_count = [
"Received_Treatment", "Received_Test", "Received_Campaign_Drugs_Term_1",
"Received_Campaign_Drugs_Term_2", "Received_Campaign_Drugs_Term_3",
"Received_RCD_Drugs", "Received_SMC", "Received_Ivermectin",
"Received_Primaquine"
]
events_to_count += ["Bednet_Discarded", "Bednet_Got_New_One", "Bednet_Using"]
add_event_counter_report(cb, event_trigger_list=events_to_count)
cb.set_param("Enable_Default_Reporting", 1)
###############################
# Submission/COMPs parameters #
###############################
comps_experiment_name = "southern_sac_ipt_iver_withheld_from_term"
comps_priority = "AboveNormal"
# comps_priority = "Highest"
comps_coreset = "emod_abcd"
# comps_coreset = "emod_32cores"
##################
# Job submission #
add_summary_report(cb,
age_bins=summary_age_bins,
start=365,
duration_days=sim_duration)
cb.set_param("Enable_Demographics_Reporting", 1)
events_to_count = [
"Received_Treatment", "Received_Test", "Received_Campaign_Drugs",
"Received_RCD_Drugs", "Received_SMC", "Received_Ivermectin",
"Received_Primaquine"
]
events_to_count += ["Bednet_Discarded", "Bednet_Got_New_One", "Bednet_Using"]
add_event_counter_report(cb,
event_trigger_list=events_to_count,
duration=sim_duration)
cb.set_param("Enable_Default_Reporting", 1)
###############################
# Submission/COMPs parameters #
###############################
comps_experiment_name = "sahel_smc_with_transmission_blocking"
comps_priority = "Normal"
# comps_priority = "Highest"
comps_coreset = "emod_abcd"
# comps_coreset = "emod_32cores"
##################
}])
add_filtered_report(cb, nodes=all_nodes, description='Catchment')
add_filtered_report(cb, nodes=[100000], description='Work')
# Add counter report for clinical incidence
# add_event_counter_report(cb,
# event_trigger_list=['Received_Treatment', 'Received_IRS', 'Received_Campaign_Drugs', 'Received_RCD_Drugs', 'Bednet_Got_New_One', 'Received_Test'])
# Add counter for new infections in work node vs all other nodes:
add_event_counter_report(
cb,
event_trigger_list=['NewInfectionEvent'],
description='WorkInfections',
# start=sim_filter_start_time,
# duration=sim_filter_duration,
nodes={
'Node_List': all_nodes,
"class": "NodeSetNodeList"
})
add_event_counter_report(
cb,
event_trigger_list=['NewInfectionEvent'],
description='NonworkInfections',
# start=sim_filter_start_time,
# duration=sim_filter_duration,
nodes={
'Node_List': [100000],
"class": "NodeSetNodeList"
})
def add_intervention(cb, intervention, coverage, target, ivm_duration) :
IPR = [{'HomeVillage' : 'Village1'}] if target == 'vill1' else None
if intervention == 'ivermectin_to_forest' :
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage, start_days=[365],
trigger_condition_list=['Immigrating'],
nodeIDs=forest_nodes,
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_to_forest' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365],
repetitions=1,
trigger_condition_list=['Immigrating'],
nodeIDs=forest_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_MDA' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365 + 152],
repetitions=3, tsteps_btwn_repetitions=30,
nodeIDs=village_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
elif intervention == 'drug_ivermectin_MDA' :
add_drug_campaign(cb, 'MDA', 'DP', coverage=coverage, start_days=[365 + 152],
repetitions=3, tsteps_btwn_repetitions=30,
nodeIDs=village_nodes,
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
nodeIDs=village_nodes,
target_residents_only=False
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 51, 'agemax': 200, 'gender': 'Female'},
nodeIDs=village_nodes,
target_residents_only=False
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=1, start_days=[365],
trigger_condition_list=['Received_Campaign_Drugs'],
target_group={'agemin': 5, 'agemax': 12, 'gender': 'Female'},
nodeIDs=village_nodes,
target_residents_only=False
)
elif intervention == 'ivermectin_MDA' :
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 5, 'agemax': 200, 'gender': 'Male'},
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 51, 'agemax': 200, 'gender': 'Female'},
target_residents_only=False,
ind_property_restrictions=IPR
)
add_ivermectin(cb, box_duration=ivm_duration, coverage=coverage,
start_days=[365 + 152 + 30 * x for x in range(3)],
nodeIDs=village_nodes,
target_group={'agemin': 5, 'agemax': 12, 'gender': 'Female'},
target_residents_only=False,
ind_property_restrictions=IPR
)
forest_HS_coverage = coverage if intervention == 'forest_HS' else 0.4
add_health_seeking(cb, start_day=0,
drug=['Artemether', 'Lumefantrine'],
nodes=village_nodes,
targets=[
{'trigger': 'NewClinicalCase', 'coverage': forest_HS_coverage, 'seek': 1, 'rate': 0.2}],
ind_property_restrictions=[{'ForestGoing': 'LovesForest'}]
)
event_trigger_list=['Received_Treatment']
if 'ivermectin' in intervention :
event_trigger_list.append('Received_Ivermectin')
if 'drug' in intervention :
event_trigger_list.append('Received_Campaign_Drugs')
add_event_counter_report(cb, event_trigger_list=event_trigger_list)
return { 'intervention' : intervention,
'coverage' : coverage,
'target' : target,
'IVM duration' : ivm_duration}
