Merge pull request #198 from pph-collective/develop

Fix timeline scaling; add settings

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 <[email protected]>", "Mary McGrath <[email protected]>"]

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:

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

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

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

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