diff --git a/pyproject.toml b/pyproject.toml index 51a1d98d..06633311 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "titan-model" -version = "2.6.1" +version = "2.7.0" description = "TITAN Agent Based Model" license = "GPL-3.0-only" authors = ["Sam Bessey ", "Mary McGrath "] diff --git a/titan/model.py b/titan/model.py index 164f7fb7..4041de49 100644 --- a/titan/model.py +++ b/titan/model.py @@ -320,9 +320,9 @@ def timeline_scaling(self): return None # gather all of the param objectss to be scaled - params_set = {self.params} + params_set = [self.params] for location in self.pop.geography.locations.values(): - params_set.add(location.params) + params_set.append(location.params) # iterate over each param and update the values if the time is right for params in params_set: diff --git a/titan/settings/mississippi/model.yml b/titan/settings/mississippi/model.yml index 599fbbda..dd17e032 100644 --- a/titan/settings/mississippi/model.yml +++ b/titan/settings/mississippi/model.yml @@ -91,13 +91,5 @@ hiv: aids: prob: 0.00207 -timeline_scaling: - timeline: - haart_viral_suppression_scale: - parameter: demographics|black|MSM|haart|adherence - start_time: -47 - stop_time: 100 - scalar: 0.1088 - calibration: test_frequency: 0.55 diff --git a/titan/settings/missouri/demographics.yml b/titan/settings/missouri/demographics.yml index 05a55af7..4e07afa2 100644 --- a/titan/settings/missouri/demographics.yml +++ b/titan/settings/missouri/demographics.yml @@ -16,7 +16,7 @@ demographics: discontinue: 0.125 adherence: 0.75 init: 0.070 - cap: 0.03 + cap: 0.003 drug_type: None: ppl: 1.0 @@ -45,7 +45,7 @@ demographics: prob: 0.112 discontinue: 0.034 death_rate: - base: 0.902 + base: 5.399 hiv: 3.0 aids: 17.5 haart_adherent: 1.0 @@ -76,7 +76,7 @@ demographics: discontinue: 0.125 adherence: 0.75 init: 0.050 - cap: 0.03 + cap: 0.003 drug_type: None: ppl: 1.0 @@ -105,7 +105,7 @@ demographics: prob: 0.103 discontinue: 0.029 death_rate: - base: 1.674 + base: 12.228 hiv: 3.0 aids: 17.5 haart_adherent: 1.0 diff --git a/titan/settings/rhode-island/demographics.yml b/titan/settings/rhode-island/demographics.yml new file mode 100644 index 00000000..a45460ce --- /dev/null +++ b/titan/settings/rhode-island/demographics.yml @@ -0,0 +1,121 @@ +demographics: + white: + ppl: 0.845 + sex_type: + MSM: + ppl: 1.0 + sex_role: + init: + versatile: 0.380 + insertive: 0.356 + receptive: 0.264 + safe_sex: + Sex: + prob: 0.234 + prep: + discontinue: 0.125 + adherence: 0.75 + init: 0.045 + cap: 0.003 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.062 + dx: + init: 0.881 + prob: 0.063 + aids: + init: 0.493 + haart: + init: 0.723 + enroll: + enroll_1: + start: 0 + stop: 2 + prob: 0.918 + enroll_2: + start: 2 + stop: 13 + prob: 0.004 + reinit: + prob: 0.03 + adherence: + init: 0.676 + prob: 0.112 + discontinue: 0.022 + death_rate: + base: 4.565 + hiv: 3.0 + aids: 17.5 + haart_adherent: 1.0 + num_partners: + Sex: + dist_type: negative_binomial + vars: + 1: + value: 5.0 + value_type: float + 2: + value: 0.40 + value_type: float + latino: + ppl: 0.155 + sex_type: + MSM: + ppl: 1.0 + sex_role: + init: + versatile: 0.418 + insertive: 0.333 + receptive: 0.249 + safe_sex: + Sex: + prob: 0.312 + prep: + discontinue: 0.125 + adherence: 0.75 + init: 0.045 + cap: 0.003 + drug_type: + None: + ppl: 1.0 + hiv: + init: 0.116 + dx: + init: 0.799 + prob: 0.063 + aids: + init: 0.446 + haart: + init: 0.681 + enroll: + enroll_1: + start: 0 + stop: 2 + prob: 0.911 + enroll_2: + start: 2 + stop: 13 + prob: 0.006 + reinit: + prob: 0.03 + adherence: + init: 0.608 + prob: 0.116 + discontinue: 0.021 + death_rate: + base: 2.259 + hiv: 3.0 + aids: 17.5 + haart_adherent: 1.0 + num_partners: + Sex: + dist_type: negative_binomial + vars: + 1: + value: 4.0 + value_type: float + 2: + value: 0.50 + value_type: float diff --git a/titan/settings/rhode-island/model.yml b/titan/settings/rhode-island/model.yml new file mode 100644 index 00000000..bdd0b405 --- /dev/null +++ b/titan/settings/rhode-island/model.yml @@ -0,0 +1,110 @@ +model: + num_pop: 14500 + time: + num_steps: 84 + steps_per_year: 12 + burn_steps: 48 + +features: + prep: true + haart: true + die_and_replace: true + assort_mix: true + +classes: + races: + white: + hispanic: false + latino: + hispanic: true + sex_types: + MSM: + cis_trans: cis + gender: M + sleeps_with: + - MSM + +assort_mix: + assort_white: + attribute: race + agent_value: white + partner_values: + white: 0.5 + latino: 0.5 + assort_latino: + attribute: race + agent_value: latino + partner_values: + white: 0.5 + latino: 0.5 + +partnership: + sex: + frequency: + Sex: + type: distribution + distribution: + dist_type: gamma + vars: + 1: + value: 2.0 + value_type: float + 2: + value: 0.6 + value_type: float + acquisition: + MSM: + versatile: 0.0046 # mean of insertive and receptive + insertive: 0.0017 + receptive: 0.0075 + haart_scaling: + MSM: + non_adherent: 0.165 + adherent: 0 + duration: + Sex: + white: + type: distribution + distribution: + dist_type: weibull_modified + vars: + 1: + value: 1.31 + value_type: float + 2: + value: 5.71 + value_type: float + mean: 5 + latino: + type: distribution + distribution: + dist_type: weibull_modified + vars: + 1: + value: 1.30 + value_type: float + 2: + value: 4.64 + value_type: float + mean: 4 + +prep: + cap_as_prob: true + efficacy: + adherent: 0.96 + non_adherent: 0.76 + target_model: + - Racial + +hiv: + acute: + infectivity: 10.5 + duration: 4 + aids: + prob: 0.004 + +haart: + use_reinit: true + aids_scale: + non_adherent: 0.200 + adherent: 0.05