Merge pull request #8 from synthetichealth/canada

Canada

README.md

@@ -45,7 +45,7 @@ Other Issues:
 
 # License
 
-Copyright 2020 The MITRE Corporation
+Copyright 2020 - 2021 The MITRE Corporation
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

ca/readme.md

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+# Canada
+
+This folder contains the configuration files for Canada.
+
+Data was sourced from Statistics Canada websites.
+
+Specifically the 2016 census data (https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/prof/details/download-telecharger/comp/GetFile.cfm?Lang=E&FILETYPE=CSV&GEONO=044)
+and the Open Database of Healthcare Facilities (https://www.statcan.gc.ca/eng/lode/databases/odhf).
+
+The timezone data, zip/postal codes, and latitude/longitude data are functional, but should be viewed with suspicion.

ca/src/main/resources/geography/timezones_ca.csv

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+STATE,ST,TIMEZONE,TZ
+Alberta,AB,Mountain Standard Time,MST
+British Columbia,BC,Pacific Standard Time,PST
+Manitoba,MB,Central Standard Time,CST
+New Brunswick,NB,Eastern Standard Time,EST
+Newfoundland and Labrador,NL,Newfoundland Standard Time,NST
+Nova Scotia,NS,Atlantic Standard Time,AST
+Northwest Territories,NT,Mountain Standard Time,MST
+Nunavut,NU,Eastern Standard Time,EST
+Ontario,ON,Eastern Standard Time,EST
+Prince Edward Island,PE,Newfoundland Standard Time,NST
+Quebec,QC,Eastern Standard Time,EST
+Saskatchewan,SK,Central Standard Time,CST
+Yukon,YT,Pacific Standard Time,PST

ca/src/main/resources/payers/insurance_companies_ca.csv

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+,id,name,address,city,state_headquartered,zip,phone,states_covered,services_covered,deductible,default_coinsurance,default_copay,monthly_premium,ownership
+0,10001,Alberta Health Care Insurance Plan,1 Main Street,Edmonton,Alberta,T5B,1-800-622-6232,Alberta,*,0,0,0,0,Government
+1,10002,Medical Services of British Columbia,1 Main Street,Victoria,British Columbia,V9E,1-800-622-6232,British Columbia,*,0,0,0,0,Government
+2,10003,Manitoba Health,1 Main Street,Winnipeq,Manitoba,R3A,1-800-622-6232,Manitoba,*,0,0,0,0,Government
+3,10004,New Brunswick Health Care,1 Main Street,Fredericton,New Brunswick,E3B,1-800-622-6232,New Brunswick,*,0,0,0,0,Government
+4,10005,Newfoundland and Labrador Medical Care Plan,1 Main Street,St. John's,Newfoundland and Labrador,A1A,1-800-622-6232,Newfoundland and Labrador,*,0,0,0,0,Government
+5,10006,NWT Health Care Insurance Plan,1 Main Street,Yellowknife,Northwest Territories,X1A,1-800-622-6232,Northwest Territories,*,0,0,0,0,Government
+6,10007,Medical Service Insurance,1 Main Street,Halifax,Nova Scotia,B3K,1-800-622-6232,Nova Scotia,*,0,0,0,0,Government
+7,10008,Nunavut Health Care Plan,1 Main Street,Iqaluit,Nunavut,1H0,1-800-622-6232,Nunavut,*,0,0,0,0,Government
+8,10009,Ontario Health Insurance Plan,1 Main Street,Toronto,Ontario,M5A,1-800-622-6232,Ontario,*,0,0,0,0,Government
+9,10010,Prince Edward Island Hospital and Medical Services Plan,1 Main Street,Charlottetown,Prince Edward Island,C1A,1-800-622-6232,Prince Edward Island,*,0,0,0,0,Government
+10,10011,R�gie de l'assurance maladie du Qu�bec,1 Rue principale,Quebec City,Quebec,G1A,1-800-622-6232,Quebec,*,0,0,0,0,Government
+11,10012,Saskatchewan Medical Care Insurance Plan,1 Main Street,Regina,Saskatchewan,S4M,1-800-622-6232,Saskatchewan,*,0,0,0,0,Government
+12,10013,Yukon Health Care Insurance Plan,1 Main Street,Whitehorse,Yukon,Y1A,1-800-622-6232,Yukon,*,0,0,0,0,Government

ca/src/main/resources/synthea.properties

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+# Starting with a properties file because it requires no additional dependencies
+
+exporter.baseDirectory = ./output/
+exporter.use_uuid_filenames = false
+exporter.subfolders_by_id_substring = false
+# number of years of history to keep in exported records, anything older than this may be filtered out
+# set years_of_history = 0 to skip filtering altogether and keep the entire history
+exporter.years_of_history = 10
+# split records allows patients to have one record per provider organization
+exporter.split_records = false
+exporter.split_records.duplicate_data = false
+exporter.ccda.export = false
+exporter.fhir.export = true
+exporter.fhir_stu3.export = false
+exporter.fhir_dstu2.export = false
+exporter.fhir.use_shr_extensions = false
+exporter.fhir.use_us_core_ig = false
+exporter.fhir.transaction_bundle = true
+exporter.fhir.bulk_data = false
+exporter.groups.fhir.export = false
+exporter.hospital.fhir.export = true
+exporter.hospital.fhir_stu3.export = false
+exporter.hospital.fhir_dstu2.export = false
+exporter.practitioner.fhir.export = true
+exporter.practitioner.fhir_stu3.export = false
+exporter.practitioner.fhir_dstu2.export = false
+exporter.encoding = UTF-8
+exporter.csv.export = false
+# if exporter.csv.append_mode = true, then each run will add new data to any existing CSVs. if false, each run will clear out the files and start fresh 
+exporter.csv.append_mode = false
+# if exporter.csv.folder_per_run = true, then each run will have CSVs placed into a unique subfolder. if false, each run will only use the top-level csv folder
+exporter.csv.folder_per_run = false
+# included_files and excluded_files list out the files to include/exclude in the csv exporter
+# only one of these may be set at a time, if both are set then both will be ignored
+# if neither is set, then all files will be included
+# see list of files at: https://github.com/synthetichealth/synthea/wiki/CSV-File-Data-Dictionary
+# include filenames separated with a comma, ex: patients.csv,procedures.csv,medications.csv
+# NOTE: the csv exporter does not actively delete files, so if Run 1 you included a file, then Run 2 you exclude that file, the version from Run 1 will still be present
+exporter.csv.included_files = 
+exporter.csv.excluded_files = 
+
+exporter.cpcds.export = false
+exporter.cpcds.append_mode = false
+exporter.cpcds.folder_per_run = false
+exporter.cpcds.single_payer = false
+exporter.cdw.export = false
+exporter.text.export = false
+exporter.text.per_encounter_export = false
+exporter.clinical_note.export = false
+
+# parameters for symptoms export
+exporter.symptoms.csv.export = false
+# selection mode of conditions or symptom export: 0 = conditions according to  exporter.years_of_history. other values = all conditions (entire history)
+exporter.symptoms.mode = 0
+# if exporter.symptoms.csv.append_mode = true, then each run will add new data to any existing CSVs. if false, each run will clear out the files and start fresh
+exporter.symptoms.csv.append_mode = false
+# if exporter.symptoms.csv.folder_per_run = true, then each run will have CSVs placed into a unique subfolder. if false, each run will only use the top-level csv folder
+exporter.symptoms.csv.folder_per_run = false
+exporter.symptoms.text.export = false
+
+# the number of patients to generate, by default
+# this can be overridden by passing a different value to the Generator constructor
+generate.default_population = 1
+
+generate.log_patients.detail = simple
+# options are "none", "simple", or "detailed" (without quotes). defaults to simple if another value is used
+# none = print nothing to the console during generation
+# simple = print patient names once they are generated.
+# detailed = print patient names, atributes, vital signs, etc..  May slow down processing
+
+generate.timestep = 604800000
+# time is in ms
+# 1000 * 60 * 60 * 24 * 7 = 604800000
+
+# default demographics is every city in the US
+generate.demographics.default_file = geography/demographics_ca.csv
+generate.geography.zipcodes.default_file = geography/zipcodes_ca.csv
+generate.geography.country_code = CA
+generate.geography.timezones.default_file = geography/timezones_ca.csv
+generate.geography.foreign.birthplace.default_file = geography/foreign_birthplace.json
+
+# Lookup Table Folder location
+generate.lookup_tables = modules/lookup_tables/
+
+# Set to true if you want every patient to be dead.
+generate.only_dead_patients = false
+# Set to true if you want every patient to be alive.
+generate.only_alive_patients = false
+# If both only_dead_patients and only_alive_patients are set to true,
+# It they will both default back to false
+
+# if true, tracks and prints out details of transition tables for each module upon completion
+# note that this may significantly slow down processing, and is intended primarily for debugging
+generate.track_detailed_transition_metrics = false
+
+# If true, person names have numbers appended to them to make them more obviously fake
+generate.append_numbers_to_person_names = true
+
+# if true, the entire population will use veteran prevalence data
+generate.veteran_population_override = false
+
+# these should add up to 1.0
+# weighting and categories are inspired by the following but there are no specific hard numbers to point to
+# http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1694190/pdf/amjph00543-0042.pdf
+# http://www.ncbi.nlm.nih.gov/pubmed/8122813
+generate.demographics.socioeconomic.weights.income = 0.2
+generate.demographics.socioeconomic.weights.education = 0.7
+generate.demographics.socioeconomic.weights.occupation = 0.1
+
+generate.demographics.socioeconomic.score.low = 0.0
+generate.demographics.socioeconomic.score.middle = 0.25
+generate.demographics.socioeconomic.score.high = 0.66
+
+generate.demographics.socioeconomic.education.less_than_hs.min = 0.0
+generate.demographics.socioeconomic.education.less_than_hs.max = 0.5
+generate.demographics.socioeconomic.education.hs_degree.min = 0.1
+generate.demographics.socioeconomic.education.hs_degree.max = 0.75
+generate.demographics.socioeconomic.education.some_college.min = 0.3
+generate.demographics.socioeconomic.education.some_college.max = 0.85
+generate.demographics.socioeconomic.education.bs_degree.min = 0.5
+generate.demographics.socioeconomic.education.bs_degree.max = 1.0
+
+generate.demographics.socioeconomic.income.poverty = 11000
+generate.demographics.socioeconomic.income.high = 75000
+
+generate.birthweights.default_file = birthweights.csv
+generate.birthweights.logging = false
+
+# in Massachusetts, the individual insurance mandate became law in 2006
+# in the US, the Affordable Care Act become law in 2010,
+# and individual and employer mandates took effect in 2014.
+# mandate.year will determine when individuals with an occupation score above mandate.occupation
+# receive employer mandated insurance (aka "private" insurance).
+# prior to mandate.year, anyone with income greater than the annual cost of an insurance plan
+# will purchase the insurance.
+generate.insurance.mandate.year = 1984
+generate.insurance.mandate.occupation = 0.0
+
+# Default Costs, to be used for pricing something that we don't have a specific price for
+# -- $500 for procedures is completely invented
+generate.costs.default_procedure_cost = 500.00
+# -- $255 for medications - also invented
+generate.costs.default_medication_cost = 255.00
+# -- Encounters billed using avg prices from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096340/
+# -- Adjustments for initial or subsequent hospital visit and level/complexity/time of encounter
+# -- not included. Assume initial, low complexity encounter (Tables 4 & 6)
+generate.costs.default_encounter_cost = 125.00
+# -- https://www.nytimes.com/2014/07/03/health/Vaccine-Costs-Soaring-Paying-Till-It-Hurts.html
+# -- currently all vaccines cost $136.
+generate.costs.default_immunization_cost = 136.00
+
+# Providers
+generate.providers.hospitals.default_file = providers/hospitals_ca.csv
+generate.providers.longterm.default_file = providers/longterm_ca.csv
+generate.providers.nursing.default_file = providers/nursing_ca.csv
+generate.providers.rehab.default_file = providers/rehab.csv
+generate.providers.hospice.default_file = providers/hospice.csv
+generate.providers.dialysis.default_file = providers/dialysis.csv
+generate.providers.homehealth.default_file = providers/home_health_agencies.csv
+generate.providers.veterans.default_file = providers/va_facilities_ca.csv
+generate.providers.urgentcare.default_file = providers/urgent_care_facilities_ca.csv
+generate.providers.primarycare.default_file = providers/primary_care_facilities_ca.csv
+
+# Provider selection behavior
+# How patients select a provider organization:
+#  nearest - select the closest provider. See generate.providers.maximum_search_distance
+#  quality - select the best provider if quality is known. Otherwise nearest.
+#  random  - select randomly.
+#  network - select the nearest provider in your insurance network. same as random except it changes every time the patient switches insurance provider.
+generate.providers.selection_behavior = nearest
+
+# minimum number of providers linked per patient
+# if this number is not met it re-runs the simulation
+generate.providers.minimum = 1
+
+# maximum distance to look for a provider for a given patient, in km
+# set to 10 degrees lat/lon to support the model that veterans only seek care at VA facilities
+generate.providers.maximum_search_distance = 100
+
+# Payers
+generate.payers.insurance_companies.default_file = payers/insurance_companies_ca.csv
+generate.payers.insurance_companies.medicare = Medicare
+generate.payers.insurance_companies.medicaid = Medicare
+generate.payers.insurance_companies.dual_eligible = Medicare
+
+# Payer selection behavior
+# How patients select a payer:
+#  best_rates - select insurance with best rates for person's existing conditions and medical needs
+#  random  - select randomly.
+generate.payers.selection_behavior = random
+
+# Experimental feature. Patients will miss care if true, but side-effects of missing that care
+# are not handled. Additionally, the path the disease module might take may no longer make sense.
+# It might assume things occurred that haven't actually happened it. Use with care.
+generate.payers.loss_of_care = false
+
+# Add a FHIR terminology service URL to enable the use of ValueSet URIs within code definitions.
+# generate.terminology_service_url = https://r4.ontoserver.csiro.au/fhir
+
+# Quit Smoking
+lifecycle.quit_smoking.baseline = 0.01
+lifecycle.quit_smoking.timestep_delta = -0.01
+lifecycle.quit_smoking.smoking_duration_factor_per_year = 1.0
+
+# Quit Alcoholism
+lifecycle.quit_alcoholism.baseline = 0.001
+lifecycle.quit_alcoholism.timestep_delta = -0.001
+lifecycle.quit_alcoholism.alcoholism_duration_factor_per_year = 1.0
+
+# Adherence
+lifecycle.adherence.baseline = 0.05
+
+# set this to true to enable randomized "death by natural causes"
+# highly recommended if "only_dead_patients" is true
+lifecycle.death_by_natural_causes = false
+
+# set this to enable "death by loss of care" or missed care,
+# e.g. not covered by insurance or otherwise unaffordable.
+# only functional if "generate.payers.loss_of_care" is also true.
+lifecycle.death_by_loss_of_care = false
+
+# Use physiology simulations to generate some VitalSigns
+physiology.generators.enabled = false
+
+# Allow physiology module states to be executed
+# If false, all Physiology state objects will immediately redirect to the state defined in
+# the alt_direct_transition field
+physiology.state.enabled = false
+
+# set to true to introduce errors in height, weight and BMI observations for people
+# under 20 years old
+growtherrors = false

ca/src/test/resources/test.properties

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+# comment
+test.foo.bar = true
+test.foo.baz = false
+
+test.bar = 42
+
+# another comment
+foo = string value
+
+test_state.default = Ontario
+test_state.alternative = Ontario
+
+test_town.default = Ottawa
+test_town.alternative = Ottawa