Merge pull request #150 from marshall-lab/fast-track-feats

Fast track feats
pph-collective · Jan 20, 2021 · e9350e1 · e9350e1
2 parents 4e80932 + 5f53044
commit e9350e1
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Showing 41 changed files with 791 additions and 331 deletions.
diff --git a/settings/atlanta/demographics.yml b/settings/atlanta/demographics.yml
@@ -11,11 +11,13 @@ demographics:
             versatile: 0.437
             insertive: 0.242
             receptive: 0.321
-        safe_sex: 0.688
+        safe_sex:
+          Sex: 
+            prob: 0.688
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.258
+          cap: 0.258
           init: 0.258
         drug_type:
             NonInj:
@@ -36,7 +38,7 @@ demographics:
                   init: 0.232
               haart: &black_haart
                 init: 0.625
-                prob: 0.35
+                cap: 0.35
                 adherence:
                   init: 0.885
                   prob: 0.885
@@ -56,10 +58,12 @@ demographics:
             versatile: 0.544
             insertive: 0.228
             receptive: 0.228
-        safe_sex: 0.528
+        safe_sex:
+          Sex:
+            prob: 0.528
         prep:
           adherence: 0.911
-          target: 0.415
+          cap: 0.415
           discontinue: 0.0
           init: 0.415
         drug_type:
@@ -78,7 +82,7 @@ demographics:
               aids: 34.4
             haart: &white_haart
               init: 0.585
-              prob: 0.20
+              cap: 0.20
               adherence:
                 init: 0.817
                 prob: 0.817

diff --git a/settings/atlanta/partnership.yml b/settings/atlanta/partnership.yml
@@ -1,20 +1,22 @@
 partnership:
   duration:
     Sex:
-      type: bins
-      bins:
-        1:
-          prob: 0.456
-          min: 1
-          max: 3
-        2:
-          prob: 0.756
-          min: 3
-          max: 12
-        3:
-          prob: 1.0
-          min: 13
-          max: 24
+      white: &partnership_duration
+        type: bins
+        bins:
+          1:
+            prob: 0.456
+            min: 1
+            max: 3
+          2:
+            prob: 0.756
+            min: 3
+            max: 12
+          3:
+            prob: 1.0
+            min: 13
+            max: 24
+      black: *partnership_duration
   sex:
     frequency:
       Sex:

diff --git a/settings/chicago/chicago_baseCase.yml b/settings/chicago/chicago_baseCase.yml
@@ -37,9 +37,6 @@ features:
 calibration:
   injection:
     act: 1.0
-  sex:
-    partner: 1.0
-    act: 1.0
   acquisition: 1.0
   test_frequency: 1.0
   mortality: 1.0
@@ -84,7 +81,7 @@ prep:
   type:
   - Oral
   - Inj
-  target: 0.088
+  cap: 0.088
   init: 0.088
   start_time: 0
   efficacy:
@@ -102,14 +99,10 @@ demographics:
         incar:
           init: 0.0
           prob: 0.0
-        safe_sex: 0.312
-        injection:
-          unsafe_prob: 0.27
-          num_acts: 5.0
         prep:
           discontinue: 0.0
           adherence: 0.568
-          target: 0.5
+          cap: 0.5
           init: 0.5
         high_risk:
           init: 0.0
@@ -144,34 +137,29 @@ demographics:
 partnership:
   duration:
     Social:
-      type: bins
-      bins:
-        1:
-          prob: 0.585
-          min: 1
-          max: 6
-        2:
-          prob: 0.701
-          min: 7
-          max: 12
-        3:
-          prob: 0.822
-          min: 13
-          max: 24
-        4:
-          prob: 0.8819999999999999
-          min: 25
-          max: 36
-        5:
-          prob: 1.0
-          min: 37
-          max: 48
-  sex:
-    acquisition:
-      MSM:
-        versatile: 0.00745
-        insertive: 0.0011
-        receptive: 0.0138
+      black:
+        type: bins
+        bins:
+          1:
+            prob: 0.585
+            min: 1
+            max: 6
+          2:
+            prob: 0.701
+            min: 7
+            max: 12
+          3:
+            prob: 0.822
+            min: 13
+            max: 24
+          4:
+            prob: 0.8819999999999999
+            min: 25
+            max: 36
+          5:
+            prob: 1.0
+            min: 37
+            max: 48
   pca:
     frequency:
       Social:

diff --git a/settings/mississippi/demographics.yml b/settings/mississippi/demographics.yml
@@ -9,7 +9,9 @@ demographics:
             versatile: 0.671
             insertive: 0.169
             receptive: 0.160
-        safe_sex: 0.214
+        safe_sex:
+          Sex:
+            prob: 0.214
         prep:
           discontinue: 0.034
           adherence: 0.860
@@ -25,7 +27,21 @@ demographics:
                 init: 0.46
             haart:
               init: 0.690
-              prob: 0.057
+              enroll:
+                enroll_0:
+                  prob: 0.609
+                  start: 0
+                  stop: 1
+                enroll_1:
+                  prob: 0.074
+                  start: 1
+                  stop: 12
+                enroll_2:
+                  prob: 0.0
+                  start: 12
+                  stop: 9999
+              reinit:
+                prob: 0.01
               adherence:
                 init: 0.500
                 prob: 0.500

diff --git a/settings/mississippi/model.yml b/settings/mississippi/model.yml
@@ -57,24 +57,25 @@ partnership:
         versatile: 0.0026625
   duration:
     Sex:
-      type: distribution
-      distribution:
-        dist_type: weibull_modified
-        vars:
-          1:
-            value: 0.586
-            value_type: float
-          2:
-            value: 11.532
-            value_type: float
-        mean: 16
+      black:
+        type: distribution
+        distribution:
+          dist_type: weibull_modified
+          vars:
+            1:
+              value: 0.586
+              value_type: float
+            2:
+              value: 11.532
+              value_type: float
+          mean: 16
 
 prep:
   type:
     - Oral
-  target: 0.049
+  cap: 0.049
   init: 0.25
-  target_as_prob: true
+  cap_as_prob: true
   efficacy:
     adherent: 0.96
     non_adherent: 0.83