Merge pull request #200 from pph-collective/develop

NYC update
pph-collective · Jun 23, 2021 · 378d785 · 378d785
2 parents 7aeabc7 + 00505bb
commit 378d785
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Showing 4 changed files with 109 additions and 65 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "titan-model"
-version = "2.7.0"
+version = "2.7.1"
 description = "TITAN Agent Based Model"
 license = "GPL-3.0-only"
 authors = ["Sam Bessey <[email protected]>", "Mary McGrath <[email protected]>"]

diff --git 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
@@ -1,55 +1,84 @@
 location:
   scaling:
-    high_test:
-      demographics|white|ppl:
+    high_test_w:
+      demographics|white|ppl: &all_agents
         field: override
-        override: 0.384
+        override: 1.0
+      demographics|black|ppl: &no_agents
+        override: 0.0
+        field: override
+      demographics|latino|ppl: *no_agents
+
       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_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
-      demographics|latino|ppl:
-        field: override
-        override: 0.338
+    high_test_l:
+      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:
-      demographics|white|ppl:
+    mid_test_w:
+      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: 0.587
-      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &mid_test_prob
+        override: 0.137
+    mid_test_b:
+      demographics|black|ppl: *all_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
-      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:
-        field: override
-        override: 0.226
-      demographics|latino|sex_type|MSM|drug_type|None|hiv|dx|prob: *mid_test_prob
+    mid_test_l:
+      demographics|latino|ppl: *all_agents
+      demographics|white|ppl: *no_agents
+
+      demographics|black|ppl: *no_agents
 
-    low_test:
-      demographics|white|ppl:
+    low_test_w:
+      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: 0.605
-      demographics|white|sex_type|MSM|drug_type|None|hiv|dx|prob: &low_test_prob
+        override: 0.022
+    low_test_b:
+      demographics|black|ppl: *all_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
-      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_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:
     edge_default:
-      location_1: high_test
-      location_2: high_test
-      distance: 0
+      location_1: high_test_l
+      location_2: high_test_l
+      distance: 0
diff --git 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: