diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml index 3dcd1866..89f2a503 100644 --- a/.github/workflows/deploy_docs.yml +++ b/.github/workflows/deploy_docs.yml @@ -13,7 +13,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v2 with: - python-version: 3.7 + python-version: 3.8 - name: Set up Poetry run: | diff --git a/.gitignore b/.gitignore index b2ed88bb..6fc5a241 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,5 @@ results/*/*.txt profile.prof site/ + +.DS_Store diff --git a/pyproject.toml b/pyproject.toml index 9a56a416..ca9374fe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "titan-model" -version = "3.2.1" +version = "3.3.0" description = "TITAN Agent Based Model" license = "GPL-3.0-only" authors = ["Sam Bessey ", "Mary McGrath "] @@ -12,11 +12,11 @@ classifiers = ["Operating System :: OS Independent"] packages = [{ include = "titan" }] [tool.poetry.dependencies] -python = "^3.8" +python = "^3.6" paraml= "^0.1" networkx = "^2.4" nanoid = "^2.0" -numpy = "^1.23" +numpy = "^1.18" black = {version = "^23.1.0", optional = true} flake8 = {version = "^3.8", optional = true} mypy = {version = "^1.0.0", optional = true} diff --git a/tests/integration_test.py b/tests/integration_test.py index eb37b43f..739e800d 100644 --- a/tests/integration_test.py +++ b/tests/integration_test.py @@ -178,7 +178,9 @@ def test_agent_pop_stable_setting(tmpdir): os.path.dirname(os.path.abspath(__file__)), "..", "titan", "settings" ) ): - if "__" not in item and item != "base": + if ( + "__" not in item and item != "base" and item != "philly-gis" + ): # bypass philly due to constraints path = tmpdir.mkdir(item) os.mkdir(os.path.join(path, "network")) print(f"-----------Starting run for {item}-----------") @@ -411,6 +413,39 @@ def test_static_network(make_model_integration, tmpdir): assert rel in curr_rel_ids +@pytest.mark.integration_deterministic +def test_dissolution(params_integration, tmpdir): + model = TITAN(params_integration) + inj_r = 0 + for rel in model.pop.relationships: + inj_r += 1 + assert inj_r > 0 + model.time = 1 + + model.params.partnership.dissolve.time = 1 + model.params.partnership.dissolve.enabled = True + + model.params.demographics.white.sex_type.MSM.drug_type.Inj.num_partners = ( + model.params.demographics.black.sex_type.MSM.drug_type.Inj.num_partners + ) + for agent in model.pop.all_agents: + agent.mean_num_partners["Inj"] = -1 + agent.mean_num_partners["Sex"] = -1 + agent.mean_num_partners["SexInj"] = -1 + agent.mean_num_partners["Social"] = -1 + model.pop.update_partner_targets() + + model.step(tmpdir) + + for rel in model.pop.relationships: + if rel.bond_type == "Inj": + print(rel.agent1.mean_num_partners) + print(rel.agent2.mean_num_partners) + print(rel.agent1.race, rel.agent1.sex_type, rel.agent1.drug_type) + print(rel.agent2.race, rel.agent2.sex_type, rel.agent2.drug_type) + assert rel.bond_type != "Inj" + + @pytest.mark.integration_deterministic def test_incar(params_integration, tmpdir): # turn on incar - initi is set to 0, so for these purposes, just run time diff --git a/tests/model_test.py b/tests/model_test.py index febfcd9a..874eedd1 100644 --- a/tests/model_test.py +++ b/tests/model_test.py @@ -30,7 +30,7 @@ def test_model_init(params): @pytest.mark.unit -def test_update_all_agents(make_model, make_agent): +def test_update_all_agents(make_model, make_agent, make_relationship): # make agent 0 model = make_model() assert model.params.agent_zero.interaction_type == "injection" @@ -57,6 +57,23 @@ def test_update_all_agents(make_model, make_agent): assert "No agent zero!" in str(excinfo) + # check that model dissolves relationships + model.params.features.agent_zero = False + model.params.partnership.dissolve.enabled = True + model.params.partnership.dissolve.time = 1 + model.time = 1 + a = make_agent() + p = make_agent() + r = make_relationship(a, p) + model.pop.add_relationship(r) + a.target_partners["Sex"] = 0 + a.target_partners["SexInj"] = 0 + a.target_partners["Inj"] = 0 + + assert a.has_partners() is True + model.update_all_agents() + assert a.has_partners() is False + @pytest.mark.unit def test_death_none(make_model): diff --git a/titan/model.py b/titan/model.py index e70ad942..5c8f9748 100644 --- a/titan/model.py +++ b/titan/model.py @@ -235,7 +235,13 @@ def update_all_agents(self): # If static network, ignore relationship progression if not self.params.features.static_network: for rel in copy(self.pop.relationships): - if rel.progress(): + if ( + self.params.partnership.dissolve.enabled + and self.time == self.params.partnership.dissolve.time + ): + rel.progress(force=True) + self.pop.remove_relationship(rel) + elif rel.progress(): self.pop.remove_relationship(rel) if self.params.features.exit_enter: diff --git a/titan/params/partnership.yml b/titan/params/partnership.yml index 114ead1d..fddfa759 100644 --- a/titan/params/partnership.yml +++ b/titan/params/partnership.yml @@ -258,3 +258,10 @@ partnership: description: Probability that for a given partnering attempt, the agent tries to partner with only other agents in their component. Otherwise, the agent tries to partner with agents from any component. Network must be enabled. min: 0 max: 1 + dissolve: + time: + type: int + default: -9999 + enabled: + type: bool + default: false diff --git a/titan/settings/philly-gis/assort_mix.yml b/titan/settings/philly-gis/assort_mix.yml new file mode 100644 index 00000000..e04173f8 --- /dev/null +++ b/titan/settings/philly-gis/assort_mix.yml @@ -0,0 +1,17 @@ +assort_mix: + assort_disadvantaged: + attribute: race + agent_value: disadvantaged + partner_attribute: location + partner_values: + __same__: 0.32 + __neighbor__: 0.15 + __other__: 0.53 + assort_notdisadvantaged: + attribute: race + agent_value: notdisadvantaged + partner_attribute: location + partner_values: + __same__: 0.2 + __neighbor__: 0.096 + __other__: 0.704 \ No newline at end of file diff --git a/titan/settings/philly-gis/calibration.yml b/titan/settings/philly-gis/calibration.yml new file mode 100644 index 00000000..4f51a8c1 --- /dev/null +++ b/titan/settings/philly-gis/calibration.yml @@ -0,0 +1,6 @@ +calibration: + sex: + act: 1.0 + partner: 1.0 + acquisition: 1.0 + mortality: 1.0 \ No newline at end of file diff --git a/titan/settings/philly-gis/classes.yml b/titan/settings/philly-gis/classes.yml new file mode 100644 index 00000000..ab6b75ab --- /dev/null +++ b/titan/settings/philly-gis/classes.yml @@ -0,0 +1,515 @@ +classes: + races: #changing the names within races + disadvantaged: + hispanic: false + notdisadvantaged: + hispanic: false + + sex_types: + HML5: #HM residing less than 5 miles from treatment site + gender: M + cis_trans: cis + sleeps_with: + - HFL5 + - HFM5 + HMM5: #HM residing more than 5 miles from treatment site + gender: M + cis_trans: cis + sleeps_with: + - HFL5 + - HFM5 + HFL5: #HF residing less than 5 miles from treatment site + gender: F + cis_trans: cis + sleeps_with: + - HML5 + - HMM5 + HFM5: #HF residing more than 5 miles from treatment site + gender: F + cis_trans: cis + sleeps_with: + - HML5 + - HMM5 + bond_types: + Main: + acts_allowed: + - sex + Casual: + acts_allowed: + - sex + drug_types: + - None + + locations: + world: + ppl: 0.0 + CT_42101001300: + ppl: 0.0027 + CT_42101001400: + ppl: 0.0017 + CT_42101001500: + ppl: 0.0007 + CT_42101001600: + ppl: 0.0001 + CT_42101001700: + ppl: 0.0003 + CT_42101001800: + ppl: 0.0007 + CT_42101001900: + ppl: 0.0013 + CT_42101002000: + ppl: 0.0026 + CT_42101002100: + ppl: 0.0027 + CT_42101002200: + ppl: 0.0017 + CT_42101002500: + ppl: 0.002 + CT_42101002701: + ppl: 0.0014 + CT_42101002702: + ppl: 0.0003 + CT_42101002802: + ppl: 0.0001 + CT_42101003100: + ppl: 0.0051 + CT_42101003200: + ppl: 0.0062 + CT_42101003300: + ppl: 0.0071 + CT_42101003600: + ppl: 0.0059 + CT_42101003800: + ppl: 0.0001 + CT_42101003902: + ppl: 0.0001 + CT_42101005400: + ppl: 0.0016 + CT_42101005500: + ppl: 0.0079 + CT_42101005600: + ppl: 0.0011 + CT_42101006000: + ppl: 0.006 + CT_42101006100: + ppl: 0.0037 + CT_42101006200: + ppl: 0.0053 + CT_42101006300: + ppl: 0.0043 + CT_42101006400: + ppl: 0.0037 + CT_42101006500: + ppl: 0.0061 + CT_42101006600: + ppl: 0.0037 + CT_42101006700: + ppl: 0.0071 + CT_42101006900: + ppl: 0.0031 + CT_42101007000: + ppl: 0.0052 + CT_42101007101: + ppl: 0.0039 + CT_42101007102: + ppl: 0.0074 + CT_42101007200: + ppl: 0.0062 + CT_42101007300: + ppl: 0.0039 + CT_42101007400: + ppl: 0.0058 + CT_42101007700: + ppl: 0.001 + CT_42101007800: + ppl: 0.0022 + CT_42101007900: + ppl: 0.0023 + CT_42101008000: + ppl: 0.0041 + CT_42101008101: + ppl: 0.004 + CT_42101008102: + ppl: 0.0079 + CT_42101008200: + ppl: 0.0108 + CT_42101008301: + ppl: 0.0073 + CT_42101008302: + ppl: 0.0065 + CT_42101008400: + ppl: 0.0059 + CT_42101008500: + ppl: 0.0098 + CT_42101008601: + ppl: 0.0012 + CT_42101008602: + ppl: 0.0034 + CT_42101008701: + ppl: 0.0012 + CT_42101008702: + ppl: 0.0013 + CT_42101008801: + ppl: 0.0004 + CT_42101008802: + ppl: 0.0013 + CT_42101009000: + ppl: 0.0008 + CT_42101009100: + ppl: 0.0021 + CT_42101009200: + ppl: 0.0032 + CT_42101009300: + ppl: 0.0057 + CT_42101009400: + ppl: 0.0061 + CT_42101009500: + ppl: 0.005 + CT_42101009600: + ppl: 0.006 + CT_42101009801: + ppl: 0.0026 + CT_42101009802: + ppl: 0.0077 + CT_42101010000: + ppl: 0.0049 + CT_42101010100: + ppl: 0.0093 + CT_42101010200: + ppl: 0.0041 + CT_42101010300: + ppl: 0.0034 + CT_42101010400: + ppl: 0.005 + CT_42101010500: + ppl: 0.0058 + CT_42101010600: + ppl: 0.0019 + CT_42101010700: + ppl: 0.0043 + CT_42101010800: + ppl: 0.0051 + CT_42101010900: + ppl: 0.0024 + CT_42101011000: + ppl: 0.0043 + CT_42101011100: + ppl: 0.0049 + CT_42101011200: + ppl: 0.0071 + CT_42101011300: + ppl: 0.0042 + CT_42101011400: + ppl: 0.0109 + CT_42101011500: + ppl: 0.0062 + CT_42101011700: + ppl: 0.0012 + CT_42101011800: + ppl: 0.0094 + CT_42101011900: + ppl: 0.007 + CT_42101012000: + ppl: 0.0017 + CT_42101012100: + ppl: 0.0034 + CT_42101012201: + ppl: 0.0021 + CT_42101012203: + ppl: 0.0005 + CT_42101012204: + ppl: 0.0043 + CT_42101013100: + ppl: 0.0014 + CT_42101013200: + ppl: 0.0039 + CT_42101013700: + ppl: 0.0054 + CT_42101013800: + ppl: 0.0025 + CT_42101013900: + ppl: 0.0038 + CT_42101014000: + ppl: 0.0031 + CT_42101014100: + ppl: 0.0021 + CT_42101014500: + ppl: 0.0015 + CT_42101014600: + ppl: 0.0035 + CT_42101014700: + ppl: 0.0026 + CT_42101014800: + ppl: 0.0016 + CT_42101014900: + ppl: 0.0052 + CT_42101015101: + ppl: 0.003 + CT_42101015102: + ppl: 0.0049 + CT_42101015200: + ppl: 0.0067 + CT_42101015300: + ppl: 0.0026 + CT_42101016500: + ppl: 0.0024 + CT_42101016600: + ppl: 0.0021 + CT_42101016701: + ppl: 0.0043 + CT_42101016702: + ppl: 0.0041 + CT_42101016800: + ppl: 0.0054 + CT_42101016901: + ppl: 0.0048 + CT_42101016902: + ppl: 0.0076 + CT_42101017000: + ppl: 0.0038 + CT_42101017100: + ppl: 0.0062 + CT_42101017201: + ppl: 0.0047 + CT_42101017202: + ppl: 0.0048 + CT_42101017300: + ppl: 0.0049 + CT_42101017400: + ppl: 0.0032 + CT_42101017500: + ppl: 0.0038 + CT_42101017601: + ppl: 0.0008 + CT_42101017602: + ppl: 0.0009 + CT_42101018800: + ppl: 0.0038 + CT_42101019000: + ppl: 0.0023 + CT_42101019100: + ppl: 0.0017 + CT_42101019200: + ppl: 0.003 + CT_42101019501: + ppl: 0.0003 + CT_42101019502: + ppl: 0.0005 + CT_42101019700: + ppl: 0.0047 + CT_42101019800: + ppl: 0.0038 + CT_42101019900: + ppl: 0.0027 + CT_42101020000: + ppl: 0.0015 + CT_42101020101: + ppl: 0.0062 + CT_42101020102: + ppl: 0.0049 + CT_42101020200: + ppl: 0.007 + CT_42101020300: + ppl: 0.0037 + CT_42101020400: + ppl: 0.0036 + CT_42101020500: + ppl: 0.0038 + CT_42101020600: + ppl: 0.0011 + CT_42101020700: + ppl: 0.0015 + CT_42101020800: + ppl: 0.0014 + CT_42101023500: + ppl: 0.0006 + CT_42101023600: + ppl: 0.0014 + CT_42101023700: + ppl: 0.0048 + CT_42101023800: + ppl: 0.0049 + CT_42101023900: + ppl: 0.0015 + CT_42101024000: + ppl: 0.0035 + CT_42101024100: + ppl: 0.0019 + CT_42101024200: + ppl: 0.0045 + CT_42101024300: + ppl: 0.0045 + CT_42101024400: + ppl: 0.0041 + CT_42101024500: + ppl: 0.0047 + CT_42101024600: + ppl: 0.0036 + CT_42101024700: + ppl: 0.0064 + CT_42101024800: + ppl: 0.0029 + CT_42101024900: + ppl: 0.0046 + CT_42101025200: + ppl: 0.0095 + CT_42101025300: + ppl: 0.0051 + CT_42101025400: + ppl: 0.0057 + CT_42101025500: + ppl: 0.0033 + CT_42101025600: + ppl: 0.0021 + CT_42101025800: + ppl: 0.0027 + CT_42101025900: + ppl: 0.0075 + CT_42101026000: + ppl: 0.0046 + CT_42101026100: + ppl: 0.0053 + CT_42101026200: + ppl: 0.0071 + CT_42101026301: + ppl: 0.0065 + CT_42101026302: + ppl: 0.0082 + CT_42101026400: + ppl: 0.0086 + CT_42101026500: + ppl: 0.0075 + CT_42101026600: + ppl: 0.0103 + CT_42101026700: + ppl: 0.0091 + CT_42101026800: + ppl: 0.0064 + CT_42101026900: + ppl: 0.0024 + CT_42101027000: + ppl: 0.0031 + CT_42101027100: + ppl: 0.0029 + CT_42101027200: + ppl: 0.0063 + CT_42101027300: + ppl: 0.0054 + CT_42101027401: + ppl: 0.0023 + CT_42101027402: + ppl: 0.0056 + CT_42101027500: + ppl: 0.005 + CT_42101027600: + ppl: 0.0051 + CT_42101027700: + ppl: 0.0071 + CT_42101027800: + ppl: 0.0071 + CT_42101027901: + ppl: 0.0052 + CT_42101027902: + ppl: 0.004 + CT_42101028000: + ppl: 0.006 + CT_42101028100: + ppl: 0.0055 + CT_42101028200: + ppl: 0.0064 + CT_42101028300: + ppl: 0.0067 + CT_42101028400: + ppl: 0.005 + CT_42101028500: + ppl: 0.0017 + CT_42101028600: + ppl: 0.0064 + CT_42101028700: + ppl: 0.0009 + CT_42101028800: + ppl: 0.0012 + CT_42101028901: + ppl: 0.0012 + CT_42101028902: + ppl: 0.0021 + CT_42101029000: + ppl: 0.0048 + CT_42101029100: + ppl: 0.0025 + CT_42101029200: + ppl: 0.0022 + CT_42101030501: + ppl: 0.0041 + CT_42101030502: + ppl: 0.0043 + CT_42101030600: + ppl: 0.0038 + CT_42101030700: + ppl: 0.002 + CT_42101036900: + ppl: 0.001 + CT_42101037300: + ppl: 0.0006 + CT_42101037500: + ppl: 0.0029 + CT_42101037700: + ppl: 0.0038 + CT_42101038000: + ppl: 0.0001 + CT_42101038200: + ppl: 0.0006 + CT_42101038300: + ppl: 0.0018 + CT_42101038800: + ppl: 0.0019 + CT_42101038900: + ppl: 0.0049 + CT_42101039000: + ppl: 0.006 + CT_42101980000: + ppl: 0.0002 + CT_42101980200: + ppl: 0.0002 + NB_1: + ppl: 0.0037 + NB_2: + ppl: 0.0047 + NB_3: + ppl: 0.0036 + NB_4: + ppl: 0.0031 + NB_5: + ppl: 0.0065 + NB_6: + ppl: 0.0201 + NB_7: + ppl: 0.0011 + NB_8: + ppl: 0.0117 + NB_9: + ppl: 0.009 + NB_10: + ppl: 0.0213 + NB_11: + ppl: 0.0097 + NB_12: + ppl: 0.0007 + NB_13: + ppl: 0.0059 + NB_14: + ppl: 0.0051 + NB_15: + ppl: 0.0038 + NB_16: + ppl: 0.0107 + NB_17: + ppl: 0.0065 + NB_18: + ppl: 0.0046 + NB_19: + ppl: 0.0075 + NB_20: + ppl: 0.0075 + NB_21: + ppl: 0.0104 \ No newline at end of file diff --git a/titan/settings/philly-gis/demographics.yml b/titan/settings/philly-gis/demographics.yml new file mode 100644 index 00000000..e9dd2e92 --- /dev/null +++ b/titan/settings/philly-gis/demographics.yml @@ -0,0 +1,568 @@ +demographics: + notdisadvantaged: + ppl: 0.3367 + sex_type: + HML5: + ppl: 0.2045 + sex_role: + init: + insertive: 1.0 + versatile: 0.0 + incar: + init: 0.032 + prob: 0.0099 + duration: + prob: + 1: + min: 1 + max: 22 + prob: 1.0 + init: + 1: + min: 1 + max: 22 + prob: 1.0 + safe_sex: + Main: + prob: 0.324 + Casual: + prob: 0.574 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.030 + dx: + init: 0.90 + prob: 0.0667 + aids: + init: 0.695 + haart: + init: 0.038 + enroll: + enroll_0: + prob: 0.773 + start: 0 + stop: 1 + enroll_1: + prob: 0.246 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.00 + prob: 0.5912 + discontinue: 0.283 + exit: + death: + base: 7.979 + hiv: 8.47 + haart_adherent: 4.65 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 2 + 2: + value_type: float + value: 4 + HMM5: + ppl: 0.2253 + sex_role: + init: + insertive: 1.0 + versatile: 0.0 + incar: + init: 0.032 + prob: 0.0099 + duration: + prob: + 1: + min: 1 + max: 22 + prob: 1 + init: + 1: + min: 1 + max: 22 + prob: 1 + safe_sex: + Main: + prob: 0.324 + Casual: + prob: 0.574 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.030 + dx: + init: 0.90 + prob: 0.0564 + aids: + init: 0.695 + haart: + init: 0.054 + enroll: + enroll_0: + prob: 0.773 + start: 0 + stop: 1 + enroll_1: + prob: 0.246 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.00 + prob: 0.3074 + discontinue: 0.283 + exit: + death: + base: 7.979 + hiv: 8.47 + haart_adherent: 4.65 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 2 + 2: + value_type: float + value: 4 + HFL5: + ppl: 0.2911 + sex_role: + init: + receptive: 1.0 + versatile: 0.0 + safe_sex: + Main: + prob: 0.256 + Casual: + prob: 0.612 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.0122 + dx: + init: 0.90 + prob: 0.0684 + aids: + init: 0.601 + haart: + init: 0.025 + enroll: + enroll_0: + prob: 0.691 + start: 0 + stop: 1 + enroll_1: + prob: 0.166 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.0 + prob: 0.838 + discontinue: 0.538 + exit: + death: + base: 4.001 + hiv: 8.96 + haart_adherent: 4.96 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1.0 + 2: + value_type: float + value: 1.0 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1.0 + 2: + value_type: float + value: 1.0 + HFM5: + ppl: 0.2791 + sex_role: + init: + receptive: 1.0 + versatile: 0.0 + safe_sex: + Main: + prob: 0.256 + Casual: + prob: 0.612 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.0122 + dx: + init: 0.90 + prob: 0.0582 + aids: + init: 0.601 + haart: + init: 0.046 + enroll: + enroll_0: + prob: 0.691 + start: 0 + stop: 1 + enroll_1: + prob: 0.166 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.0 + prob: 0.4358 + discontinue: 0.538 + exit: + death: + base: 4.001 + hiv: 8.96 + haart_adherent: 4.96 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1.0 + 2: + value_type: float + value: 1.0 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1.0 + 2: + value_type: float + value: 1.0 + + disadvantaged: + ppl: 0.6633 + sex_type: + HML5: + ppl: 0.3952 + sex_role: + init: + insertive: 1.0 + versatile: 0.0 + incar: + init: 0.039 + prob: 0.0124 + duration: + prob: + 1: + min: 1 + max: 22 + prob: 1.0 + init: + 1: + min: 1 + max: 22 + prob: 1.0 + safe_sex: + Main: + prob: 0.26 + Casual: + prob: 0.56 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.030 + dx: + init: 0.90 + prob: 0.0662 + aids: + init: 0.695 + haart: + init: 0.038 + enroll: + enroll_0: + prob: 0.679 + start: 0 + stop: 1 + enroll_1: + prob: 0.246 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.0 + prob: 0.5783 + discontinue: 0.495 + exit: + death: + base: 7.979 + hiv: 8.47 + haart_adherent: 4.65 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 3 + 2: + value_type: float + value: 5 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 2 + HMM5: + ppl: 0.0009 + sex_role: + init: + insertive: 1.0 + versatile: 0.0 + incar: + init: 0.039 + prob: 0.0124 + duration: + prob: + 1: + min: 1 + max: 22 + prob: 1.0 + init: + 1: + min: 1 + max: 22 + prob: 1.0 + safe_sex: + Main: + prob: 0.26 + Casual: + prob: 0.56 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.030 + dx: + init: 0.90 + prob: 0.056 + aids: + init: 0.695 + haart: + init: 0.038 + enroll: + enroll_0: + prob: 0.679 + start: 0 + stop: 1 + enroll_1: + prob: 0.246 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: #virally suppressed + init: 1.0 + prob: 0.3007 + discontinue: 0.495 + exit: + death: + base: 7.979 + hiv: 8.47 + haart_adherent: 4.65 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 3 + 2: + value_type: float + value: 5 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 2 + HFL5: + ppl: 0.6 + sex_role: + init: + receptive: 1.0 + versatile: 0.0 + safe_sex: + Main: + prob: 0.254 + Casual: + prob: 0.613 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.0122 + dx: + init: 0.90 + prob: 0.0674 + aids: + init: 0.601 + haart: + init: 0.027 + enroll: + enroll_0: + prob: 0.604 + start: 0 + stop: 1 + enroll_1: + prob: 0.166 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.0 + prob: 0.81 + discontinue: 0.485 + exit: + death: + base: 4.001 + hiv: 8.96 + haart_adherent: 4.96 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 + HFM5: + ppl: 0.0039 + sex_role: + init: + receptive: 1.0 + versatile: 0.0 + safe_sex: + Main: + prob: 0.254 + Casual: + prob: 0.613 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.0122 + dx: + init: 0.90 + prob: 0.0577 + aids: + init: 0.601 + haart: + init: 0.027 + enroll: + enroll_0: + prob: 0.604 + start: 0 + stop: 1 + enroll_1: + prob: 0.166 + start: 2 + stop: 9999 + reinit: + prob: 0.6284 + adherence: + init: 1.0 + prob: 0.4212 + discontinue: 0.485 + exit: + death: + base: 4.001 + hiv: 8.96 + haart_adherent: 4.96 + aids: 15.81 + num_partners: + Main: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 + Casual: + dist_type: uniform + vars: + 1: + value_type: float + value: 1 + 2: + value_type: float + value: 1 \ No newline at end of file diff --git a/titan/settings/philly-gis/haart.yml b/titan/settings/philly-gis/haart.yml new file mode 100644 index 00000000..60bfa493 --- /dev/null +++ b/titan/settings/philly-gis/haart.yml @@ -0,0 +1,2 @@ +haart: + use_reinit: true \ No newline at end of file diff --git a/titan/settings/philly-gis/high_risk.yml b/titan/settings/philly-gis/high_risk.yml new file mode 100644 index 00000000..01a3ccc0 --- /dev/null +++ b/titan/settings/philly-gis/high_risk.yml @@ -0,0 +1,11 @@ +high_risk: + partner_scale: 3 + prob: 1.0 + sex_based: + HML5: + duration: 6 + HMM5: + duration: 6 + partnership_types: + - Main + - Casual \ No newline at end of file diff --git a/titan/settings/philly-gis/hiv.yml b/titan/settings/philly-gis/hiv.yml new file mode 100644 index 00000000..1be504b2 --- /dev/null +++ b/titan/settings/philly-gis/hiv.yml @@ -0,0 +1,6 @@ +hiv: + dx: + risk_reduction: + sex: 0.53 + aids: + prob: 0.6624 \ No newline at end of file diff --git a/titan/settings/philly-gis/incar.yml b/titan/settings/philly-gis/incar.yml new file mode 100644 index 00000000..a5d3715a --- /dev/null +++ b/titan/settings/philly-gis/incar.yml @@ -0,0 +1,8 @@ +incar: + hiv: + dx: 0.51 + multiplier: 0.816 + haart: + prob: 0.65 + adherence: 0.58 + discontinue: 0.0653 \ No newline at end of file diff --git a/titan/settings/philly-gis/location.yml b/titan/settings/philly-gis/location.yml new file mode 100644 index 00000000..8b7d3239 --- /dev/null +++ b/titan/settings/philly-gis/location.yml @@ -0,0 +1,12339 @@ +location: + migration: + enabled: false + attribute: name + probs_file: '' + scaling: +#Census Tract Overrides + CT_42101001300: + demographics|notdisadvantaged|ppl: &all_agents + field: override + override: 1.0 + demographics|disadvantaged|ppl: &no_agents + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.364118092354277 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.635881907645723 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001400: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.450638792102207 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.549361207897793 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.16065680832206 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001500: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.468842729970326 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.531157270029674 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.210947280567534 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001600: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 1 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001700: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.63905325443787 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.36094674556213 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.12037037037037 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001800: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.561111111111111 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.438888888888889 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.176259384180176 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101001900: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.386435331230284 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.613564668769716 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.107185122569738 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002000: + demographics|disadvantaged|ppl: *all_agents + demographics|notdisadvantaged|ppl: *no_agents + demographics|disadvantaged|sex_type|HML5|ppl: + field: override + override: 0.518202943454686 + demographics|disadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.481797056545314 + demographics|disadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.171279220951522 + demographics|disadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002100: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.485207100591716 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.514792899408284 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.0822041553748871 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002200: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.304863582443654 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.695136417556346 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.0890539993309505 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002500: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.417582417582418 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.582417582417582 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.156578947368421 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002701: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.414772727272727 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.585227272727273 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.0927291886195996 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002702: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.656976744186046 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.343023255813953 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.234172906739279 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101002802: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.777777777777778 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.222222222222222 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.0989010989010989 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101003100: + demographics|disadvantaged|ppl: *all_agents + demographics|notdisadvantaged|ppl: *no_agents + demographics|disadvantaged|sex_type|HML5|ppl: + field: override + override: 0.400877542879936 + demographics|disadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.599122457120064 + demographics|disadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.124161995452601 + demographics|disadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.1647 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0488 + demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7576 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101003200: + demographics|disadvantaged|ppl: *all_agents + demographics|notdisadvantaged|ppl: *no_agents + demographics|disadvantaged|sex_type|HML5|ppl: + field: override + override: 0.379659908436887 + demographics|disadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.620340091563113 + demographics|disadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + 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CT_42101008000: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.492566897918731 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.507433102081269 + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.0799883730148245 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.0878 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0341 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7333 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.875 + CT_42101008101: + demographics|disadvantaged|ppl: *all_agents + demographics|notdisadvantaged|ppl: *no_agents + demographics|disadvantaged|sex_type|HML5|ppl: + field: override + override: 0.444331983805668 + demographics|disadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.555668016194332 + demographics|disadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|disadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.121184510250569 + demographics|disadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.0878 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0341 + demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: 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demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.7333 + demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.875 + CT_42101008200: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HMM5|ppl: + field: override + override: 0.424703891708968 + demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.575296108291032 + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HMM5|incar|init: + field: override + override: 0.0771444137978002 + demographics|notdisadvantaged|sex_type|HMM5|drug_type|None|hiv|init: + field: override + override: 0.0878 + 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demographics|notdisadvantaged|sex_type|HFM5|ppl: + field: override + override: 0.0 + demographics|notdisadvantaged|sex_type|HML5|incar|init: + field: override + override: 0.141025641025641 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|hiv|init: + field: override + override: 0.0729 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|hiv|init: + field: override + override: 0.0258 + demographics|notdisadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.625 + demographics|notdisadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob: + field: override + override: 0.6667 + CT_42101008602: + demographics|notdisadvantaged|ppl: *all_agents + demographics|disadvantaged|ppl: *no_agents + demographics|notdisadvantaged|sex_type|HML5|ppl: + field: override + override: 0.400476758045292 + demographics|notdisadvantaged|sex_type|HFL5|ppl: + field: override + override: 0.599523241954708 + 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+outputs: + classes: + - races + - sex_types +# - locations diff --git a/titan/settings/philly-gis/partnership.yml b/titan/settings/philly-gis/partnership.yml new file mode 100644 index 00000000..4a98f099 --- /dev/null +++ b/titan/settings/philly-gis/partnership.yml @@ -0,0 +1,44 @@ +partnership: + sex: + frequency: + Main: + type: bins + bins: + 1: + prob: 1 + min: 0 + max: 2 + Casual: + type: bins + bins: + 1: + prob: 1 + min: 0 + max: 2 + duration: + Main: + type: bins + bins: + 1: + prob: 0.5 + min: 1 + max: 2 + 2: + prob: 0.25 + min: 2 + max: 7 + 3: + prob: 0.15 + min: 7 + max: 17 + 4: + prob: 0.1 + min: 17 + max: 999 + Casual: + type: bins + bins: + 1: + prob: 1.0 + min: 1 + max: 1 diff --git a/titan/settings/philly-gis/timeline_scaling.yml b/titan/settings/philly-gis/timeline_scaling.yml new file mode 100644 index 00000000..86b35239 --- /dev/null +++ b/titan/settings/philly-gis/timeline_scaling.yml @@ -0,0 +1,80 @@ +timeline_scaling: + timeline: + #Scenarios 2-4 + testing_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|drug_type|None|hiv|dx|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.01 + testing_D_HF: + parameter: demographics|disadvantaged|sex_type|HFL5|drug_type|None|hiv|dx|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.015 + + #Scenarios 3 and 4 + linkage_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|enroll|enroll_0|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.04 + linkage_D_HF: + parameter: demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|enroll|enroll_0|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.06 + + adherence_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|adherence|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.022 + adherence_D_HF: + parameter: demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|adherence|prob + start_time: 73 + stop_time: 193 + scalar: 1 #1.03 + + discontinue_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|drug_type|None|haart|adherence|discontinue + start_time: 73 + stop_time: 193 + scalar: 1 #0.57 + discontinue_D_HF: + parameter: demographics|disadvantaged|sex_type|HFL5|drug_type|None|haart|adherence|discontinue + start_time: 73 + stop_time: 193 + scalar: 1 #0.901 + + #Scenario 4 + incarceration_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|incar|prob + start_time: 73 + stop_time: 193 + scalar: 1 #0.26 + incarceration_ND_HML5: + parameter: demographics|notdisadvantaged|sex_type|HML5|incar|prob + start_time: 73 + stop_time: 193 + scalar: 1 #0.26 + incarceration_ND_HMM5: + parameter: demographics|notdisadvantaged|sex_type|HMM5|incar|prob + start_time: 73 + stop_time: 193 + scalar: 1 #0.26 + + incarceration_length_D_HM: + parameter: demographics|disadvantaged|sex_type|HML5|incar|duration|prob|1|max + start_time: 73 + stop_time: 193 + scalar: 1 #0.826 + incarceration_length_ND_HML5: + parameter: demographics|notdisadvantaged|sex_type|HML5|incar|duration|prob|1|max + start_time: 73 + stop_time: 193 + scalar: 1 #0.826 + incarceration_length_ND_HMM5: + parameter: demographics|notdisadvantaged|sex_type|HMM5|incar|duration|prob|1|max + start_time: 73 + stop_time: 193 + scalar: 1 #0.826