From f58934add79653cb2bbc203595e46637b3e59577 Mon Sep 17 00:00:00 2001 From: sbessey Date: Tue, 22 Jun 2021 12:02:41 -0400 Subject: [PATCH 1/3] refactor(nyc-msm): update calibrated nyc msm setting --- titan/settings/nyc-msm/demographics.yml | 42 ++++++------ titan/settings/nyc-msm/location.yml | 85 ++++++++++++++----------- titan/settings/nyc-msm/model.yml | 31 ++++++--- 3 files changed, 93 insertions(+), 65 deletions(-) diff --git a/titan/settings/nyc-msm/demographics.yml b/titan/settings/nyc-msm/demographics.yml index b866c00b..c72ee936 100644 --- a/titan/settings/nyc-msm/demographics.yml +++ b/titan/settings/nyc-msm/demographics.yml @@ -23,29 +23,29 @@ demographics: None: ppl: 1.0 hiv: - init: 0.315 + init: 0.355 dx: init: 0.920 prob: 0.198 aids: init: 0.500 haart: - init: 0.764 + init: 0.830 enroll: enroll_0: start: 0 - stop: 1 + stop: 2 prob: 0.709 enroll_1: - start: 1 - stop: 3 + start: 2 + stop: 4 prob: 0.212 enroll_2: - start: 3 - stop: 12 + start: 4 + stop: 13 prob: 0.051 enroll_3: - start: 12 + start: 13 stop: 9999 prob: 0.0 reinit: @@ -100,17 +100,17 @@ demographics: None: ppl: 1.0 hiv: - init: 0.166 + init: 0.20 dx: init: 0.920 prob: 0.055 aids: init: 0.487 haart: - init: 0.764 + init: 0.860 enroll: 0: - prob: 0.278 + prob: 0.778 start: 0 stop: 1 1: @@ -184,33 +184,33 @@ demographics: aids: init: 0.471 haart: - init: 0.791 + init: 0.860 enroll: 0: start: 0 - stop: 1 + stop: 2 prob: 0.742 1: - start: 1 - stop: 3 + start: 2 + stop: 4 prob: 0.163 2: - start: 3 - stop: 12 + start: 4 + stop: 13 prob: 0.029 3: - start: 12 + start: 13 stop: 9999 prob: 0.0 reinit: prob: 0.041 adherence: - init: 0.707 - prob: 0.707 + init: 0.790 + prob: 0.790 discontinue: 0.0745 discontinue: 0.00883 death_rate: - base: 0.0696 + base: 0.1 num_partners: Main: dist_type: negative_binomial diff --git a/titan/settings/nyc-msm/location.yml b/titan/settings/nyc-msm/location.yml index 8fc067b0..a6e91277 100644 --- a/titan/settings/nyc-msm/location.yml +++ b/titan/settings/nyc-msm/location.yml @@ -1,55 +1,68 @@ location: scaling: - high_test: - demographics|white|ppl: + high_test_w: + demographics|white|ppl: &all_ags field: override - override: 0.384 + override: 1.0 + demographics|black|ppl: &no_ags + override: 0.0 + field: override + demographics|latino|ppl: *no_ags demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &high_test_prob field: override override: 0.333 - demographics|black|ppl: - field: override - override: 0.278 + high_test_b: + demographics|black|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|latino|ppl: *no_ags demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob - demographics|latino|ppl: - field: override - override: 0.338 + high_test_l: + demographics|latino|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|black|ppl: *no_ags demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob - mid_test: - demographics|white|ppl: + mid_test_w: + demographics|white|ppl: *all_ags + demographics|latino|ppl: *no_ags + demographics|black|ppl: *no_ags + demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: field: override - override: 0.587 - demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob + override: 0.137 + mid_test_b: + demographics|black|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|latino|ppl: *no_ags + demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob field: override override: 0.167 - demographics|black|ppl: - field: override - override: 0.187 - demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob - demographics|latino|ppl: + mid_test_l: + demographics|latino|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|black|ppl: *no_ags + low_test_w: + demographics|white|ppl: *all_ags + demographics|latino|ppl: *no_ags + demographics|black|ppl: *no_ags + demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: field: override - override: 0.226 - demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob - - low_test: - demographics|white|ppl: - field: override - override: 0.605 - demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob + override: 0.022 + low_test_b: + demographics|black|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|latino|ppl: *no_ags + demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob field: override override: 0.042 - demographics|black|ppl: - field: override - override: 0.082 - demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob - demographics|latino|ppl: - field: override - override: 0.313 + low_test_l: + demographics|latino|ppl: *all_ags + demographics|white|ppl: *no_ags + demographics|black|ppl: *no_ags demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob edges: edge_default: - location_1: high_test - location_2: high_test - distance: 0 \ No newline at end of file + location_1: high_test_l + location_2: high_test_l + distance: 0 + \ No newline at end of file diff --git a/titan/settings/nyc-msm/model.yml b/titan/settings/nyc-msm/model.yml index 517c68f0..a8ec9734 100644 --- a/titan/settings/nyc-msm/model.yml +++ b/titan/settings/nyc-msm/model.yml @@ -2,8 +2,11 @@ model: num_pop: 171990 time: num_steps: 27 - burn_steps: 48 - + burn_steps: 47 +calibration: + haart: + coverage: 1.1 + test_frequency: 0.9 classes: races: white: @@ -28,12 +31,24 @@ classes: drug_types: - None locations: - high_test: - ppl: .190 - mid_test: - ppl: .634 - low_test: - ppl: .176 + high_test_b: + ppl: .046 + mid_test_b: + ppl: .091 + low_test_b: + ppl: .045 + high_test_w: + ppl: .115 + mid_test_w: + ppl: .336 + low_test_w: + ppl: .106 + high_test_l: + ppl: 0.086 + mid_test_l: + ppl: .146 + low_test_l: + ppl: .029 features: From 8c5abf34892baff4735a20026a2080d012829179 Mon Sep 17 00:00:00 2001 From: sbessey Date: Wed, 23 Jun 2021 09:01:40 -0400 Subject: [PATCH 2/3] build: bump version number --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 06633311..f3556816 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "titan-model" -version = "2.7.0" +version = "2.8.0" description = "TITAN Agent Based Model" license = "GPL-3.0-only" authors = ["Sam Bessey ", "Mary McGrath "] From 4e4abdf22647d47707a59967445a922f59bca437 Mon Sep 17 00:00:00 2001 From: sbessey Date: Wed, 23 Jun 2021 12:28:47 -0400 Subject: [PATCH 3/3] refactor: change version to patch; renamed ags to agents --- pyproject.toml | 2 +- titan/settings/nyc-msm/location.yml | 72 ++++++++++++++++++----------- 2 files changed, 45 insertions(+), 29 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f3556816..26a523dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "titan-model" -version = "2.8.0" +version = "2.7.1" description = "TITAN Agent Based Model" license = "GPL-3.0-only" authors = ["Sam Bessey ", "Mary McGrath "] diff --git a/titan/settings/nyc-msm/location.yml b/titan/settings/nyc-msm/location.yml index a6e91277..d72617d5 100644 --- a/titan/settings/nyc-msm/location.yml +++ b/titan/settings/nyc-msm/location.yml @@ -1,63 +1,80 @@ location: scaling: high_test_w: - demographics|white|ppl: &all_ags + demographics|white|ppl: &all_agents field: override override: 1.0 - demographics|black|ppl: &no_ags + demographics|black|ppl: &no_agents override: 0.0 field: override - demographics|latino|ppl: *no_ags + demographics|latino|ppl: *no_agents + demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &high_test_prob field: override override: 0.333 high_test_b: - demographics|black|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|latino|ppl: *no_ags + demographics|black|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|latino|ppl: *no_agents + demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob high_test_l: - demographics|latino|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|black|ppl: *no_ags + demographics|latino|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|black|ppl: *no_agents + demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *high_test_prob mid_test_w: - demographics|white|ppl: *all_ags - demographics|latino|ppl: *no_ags - demographics|black|ppl: *no_ags + demographics|white|ppl: *all_agents + demographics|latino|ppl: *no_agents + + demographics|black|ppl: *no_agents + demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: field: override override: 0.137 mid_test_b: - demographics|black|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|latino|ppl: *no_ags + demographics|black|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|latino|ppl: *no_agents + demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob field: override override: 0.167 mid_test_l: - demographics|latino|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|black|ppl: *no_ags + demographics|latino|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|black|ppl: *no_agents + low_test_w: - demographics|white|ppl: *all_ags - demographics|latino|ppl: *no_ags - demographics|black|ppl: *no_ags + demographics|white|ppl: *all_agents + demographics|latino|ppl: *no_agents + + demographics|black|ppl: *no_agents + demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: field: override override: 0.022 low_test_b: - demographics|black|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|latino|ppl: *no_ags + demographics|black|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|latino|ppl: *no_agents + demographics|black|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob field: override override: 0.042 low_test_l: - demographics|latino|ppl: *all_ags - demographics|white|ppl: *no_ags - demographics|black|ppl: *no_ags + demographics|latino|ppl: *all_agents + demographics|white|ppl: *no_agents + + demographics|black|ppl: *no_agents + demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *low_test_prob edges: @@ -65,4 +82,3 @@ location: location_1: high_test_l location_2: high_test_l distance: 0 - \ No newline at end of file