Updated summarize.py: extra sheet in summary sheet with select columns

RTIInternational · May 21, 2024 · e113128 · e113128
1 parent 88cce1f
commit e113128
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diff --git a/crcsim/experiment/parameters.json b/crcsim/experiment/parameters.json
@@ -23,7 +23,7 @@
   "proportion_survive_clin3": 0,
   "proportion_survive_clin4": 0,
 
-  "cost_polypectomy": 170,
+  "cost_polypectomy": 650,
   "cost_polyp_pathology": 65,
 
   "cost_treatment_stage1_initial": 34258,
@@ -71,31 +71,31 @@
   "tests": {
     "FIT": {
       "proportion": 1.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 1,
       "specificity": 0.97,
       "sensitivity_polyp1": 0.07,
       "sensitivity_polyp2": 0.07,
       "sensitivity_polyp3": 0.22,
       "sensitivity_cancer": 0.74,
-      "cost": 22,
+      "cost": 27,
       "proportion_perforation": 0,
       "cost_perforation": 0,
       "compliance_rate_given_prev_compliant":     [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 ],
       "compliance_rate_given_not_prev_compliant": [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ]
     },
     "Colonoscopy": {
       "proportion": 0.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 10,
       "specificity": 0.86,
       "sensitivity_polyp1": 0.75,
       "sensitivity_polyp2": 0.85,
       "sensitivity_polyp3": 0.95,
       "sensitivity_cancer": 0.95,
-      "cost": 700,
+      "cost": 1608,
       "proportion_perforation": 0.001,
       "cost_perforation": 6487,
       "compliance_rate_given_prev_compliant":     [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0 ],
@@ -107,9 +107,9 @@
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 0.00002,
 
-  "cost_discount_age": 50,
+  "cost_discount_age": 45,
   "cost_discount_rate": 0.03,
-  "lifespan_discount_age": 50,
+  "lifespan_discount_age": 45,
   "lifespan_discount_rate": 0.03,
 
   "death_rate_black_female_ages":  [        0,        1,        2,        3,        4,        5,        6,        7,        8,        9,       10,       11,       12,       13,       14,       15,       16,       17,       18,       19,       20,       21,       22,       23,       24,       25,       26,       27,       28,       29,       30,       31,       32,       33,       34,       35,       36,       37,       38,       39,       40,       41,       42,       43,       44,       45,       46,       47,       48,       49,       50,       51,       52,       53,       54,       55,       56,       57,       58,       59,       60,       61,       62,       63,       64,       65,       66,       67,       68,       69,       70,       71,       72,       73,       74,       75,       76,       77,       78,       79,       80,       81,       82,       83,       84,       85,       86,       87,       88,       89,       90,       91,       92,       93,       94,       95,       96,       97,       98,       99,      100 ],

diff --git a/crcsim/experiment/prepare.py b/crcsim/experiment/prepare.py
@@ -6,7 +6,7 @@
 import fire
 
 SEED: int = 49865106
-NUM_ITERATIONS: int = 10
+NUM_ITERATIONS: int = 100
 
 
 class Scenario:
@@ -92,12 +92,12 @@ def create_scenarios() -> List:
     initial_compliance = {
         "fqhc1": (0.522, 0.593),
         "fqhc2": (0.154, 0.421),
-        # "fqhc3": (0.519, 0.615),
-        # "fqhc4": (0.278, 0.374),
-        # "fqhc5": (0.383, 0.572),
-        # "fqhc6": (0.211, 0.392),
-        # "fqhc7": (0.257, 0.354),
-        # "fqhc8": (0.190, 0.390),
+        "fqhc3": (0.519, 0.615),
+        "fqhc4": (0.278, 0.374),
+        "fqhc5": (0.383, 0.572),
+        "fqhc6": (0.211, 0.392),
+        "fqhc7": (0.257, 0.354),
+        "fqhc8": (0.190, 0.390),
     }
 
     scenarios = []

diff --git a/crcsim/experiment/scenarios/fqhc1_baseline/params.json b/crcsim/experiment/scenarios/fqhc1_baseline/params.json
@@ -19,7 +19,7 @@
   "proportion_survive_clin2": 0,
   "proportion_survive_clin3": 0,
   "proportion_survive_clin4": 0,
-  "cost_polypectomy": 170,
+  "cost_polypectomy": 650,
   "cost_polyp_pathology": 65,
   "cost_treatment_stage1_initial": 34258,
   "cost_treatment_stage1_ongoing": 2685,
@@ -94,15 +94,15 @@
   "tests": {
     "FIT": {
       "proportion": 1.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 1,
       "specificity": 0.97,
       "sensitivity_polyp1": 0.07,
       "sensitivity_polyp2": 0.07,
       "sensitivity_polyp3": 0.22,
       "sensitivity_cancer": 0.74,
-      "cost": 22,
+      "cost": 27,
       "proportion_perforation": 0,
       "cost_perforation": 0,
       "compliance_rate_given_prev_compliant": [
@@ -184,15 +184,15 @@
     },
     "Colonoscopy": {
       "proportion": 0.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 10,
       "specificity": 0.86,
       "sensitivity_polyp1": 0.75,
       "sensitivity_polyp2": 0.85,
       "sensitivity_polyp3": 0.95,
       "sensitivity_cancer": 0.95,
-      "cost": 700,
+      "cost": 1608,
       "proportion_perforation": 0.001,
       "cost_perforation": 6487,
       "compliance_rate_given_prev_compliant": [
@@ -280,9 +280,9 @@
   "diagnostic_test": "Colonoscopy",
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 2e-05,
-  "cost_discount_age": 50,
+  "cost_discount_age": 45,
   "cost_discount_rate": 0.03,
-  "lifespan_discount_age": 50,
+  "lifespan_discount_age": 45,
   "lifespan_discount_rate": 0.03,
   "death_rate_black_female_ages": [
     0,

diff --git a/crcsim/experiment/scenarios/fqhc1_implementation/params.json b/crcsim/experiment/scenarios/fqhc1_implementation/params.json
@@ -19,7 +19,7 @@
   "proportion_survive_clin2": 0,
   "proportion_survive_clin3": 0,
   "proportion_survive_clin4": 0,
-  "cost_polypectomy": 170,
+  "cost_polypectomy": 650,
   "cost_polyp_pathology": 65,
   "cost_treatment_stage1_initial": 34258,
   "cost_treatment_stage1_ongoing": 2685,
@@ -94,15 +94,15 @@
   "tests": {
     "FIT": {
       "proportion": 1.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 1,
       "specificity": 0.97,
       "sensitivity_polyp1": 0.07,
       "sensitivity_polyp2": 0.07,
       "sensitivity_polyp3": 0.22,
       "sensitivity_cancer": 0.74,
-      "cost": 22,
+      "cost": 27,
       "proportion_perforation": 0,
       "cost_perforation": 0,
       "compliance_rate_given_prev_compliant": [
@@ -184,15 +184,15 @@
     },
     "Colonoscopy": {
       "proportion": 0.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 10,
       "specificity": 0.86,
       "sensitivity_polyp1": 0.75,
       "sensitivity_polyp2": 0.85,
       "sensitivity_polyp3": 0.95,
       "sensitivity_cancer": 0.95,
-      "cost": 700,
+      "cost": 1608,
       "proportion_perforation": 0.001,
       "cost_perforation": 6487,
       "compliance_rate_given_prev_compliant": [
@@ -280,9 +280,9 @@
   "diagnostic_test": "Colonoscopy",
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 2e-05,
-  "cost_discount_age": 50,
+  "cost_discount_age": 45,
   "cost_discount_rate": 0.03,
-  "lifespan_discount_age": 50,
+  "lifespan_discount_age": 45,
   "lifespan_discount_rate": 0.03,
   "death_rate_black_female_ages": [
     0,

diff --git a/crcsim/experiment/scenarios/fqhc2_baseline/params.json b/crcsim/experiment/scenarios/fqhc2_baseline/params.json
@@ -19,7 +19,7 @@
   "proportion_survive_clin2": 0,
   "proportion_survive_clin3": 0,
   "proportion_survive_clin4": 0,
-  "cost_polypectomy": 170,
+  "cost_polypectomy": 650,
   "cost_polyp_pathology": 65,
   "cost_treatment_stage1_initial": 34258,
   "cost_treatment_stage1_ongoing": 2685,
@@ -94,15 +94,15 @@
   "tests": {
     "FIT": {
       "proportion": 1.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 1,
       "specificity": 0.97,
       "sensitivity_polyp1": 0.07,
       "sensitivity_polyp2": 0.07,
       "sensitivity_polyp3": 0.22,
       "sensitivity_cancer": 0.74,
-      "cost": 22,
+      "cost": 27,
       "proportion_perforation": 0,
       "cost_perforation": 0,
       "compliance_rate_given_prev_compliant": [
@@ -184,15 +184,15 @@
     },
     "Colonoscopy": {
       "proportion": 0.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 10,
       "specificity": 0.86,
       "sensitivity_polyp1": 0.75,
       "sensitivity_polyp2": 0.85,
       "sensitivity_polyp3": 0.95,
       "sensitivity_cancer": 0.95,
-      "cost": 700,
+      "cost": 1608,
       "proportion_perforation": 0.001,
       "cost_perforation": 6487,
       "compliance_rate_given_prev_compliant": [
@@ -280,9 +280,9 @@
   "diagnostic_test": "Colonoscopy",
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 2e-05,
-  "cost_discount_age": 50,
+  "cost_discount_age": 45,
   "cost_discount_rate": 0.03,
-  "lifespan_discount_age": 50,
+  "lifespan_discount_age": 45,
   "lifespan_discount_rate": 0.03,
   "death_rate_black_female_ages": [
     0,

diff --git a/crcsim/experiment/scenarios/fqhc2_implementation/params.json b/crcsim/experiment/scenarios/fqhc2_implementation/params.json
@@ -19,7 +19,7 @@
   "proportion_survive_clin2": 0,
   "proportion_survive_clin3": 0,
   "proportion_survive_clin4": 0,
-  "cost_polypectomy": 170,
+  "cost_polypectomy": 650,
   "cost_polyp_pathology": 65,
   "cost_treatment_stage1_initial": 34258,
   "cost_treatment_stage1_ongoing": 2685,
@@ -94,15 +94,15 @@
   "tests": {
     "FIT": {
       "proportion": 1.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 1,
       "specificity": 0.97,
       "sensitivity_polyp1": 0.07,
       "sensitivity_polyp2": 0.07,
       "sensitivity_polyp3": 0.22,
       "sensitivity_cancer": 0.74,
-      "cost": 22,
+      "cost": 27,
       "proportion_perforation": 0,
       "cost_perforation": 0,
       "compliance_rate_given_prev_compliant": [
@@ -184,15 +184,15 @@
     },
     "Colonoscopy": {
       "proportion": 0.0,
-      "routine_start": 50,
+      "routine_start": 45,
       "routine_end": 75,
       "routine_freq": 10,
       "specificity": 0.86,
       "sensitivity_polyp1": 0.75,
       "sensitivity_polyp2": 0.85,
       "sensitivity_polyp3": 0.95,
       "sensitivity_cancer": 0.95,
-      "cost": 700,
+      "cost": 1608,
       "proportion_perforation": 0.001,
       "cost_perforation": 6487,
       "compliance_rate_given_prev_compliant": [
@@ -280,9 +280,9 @@
   "diagnostic_test": "Colonoscopy",
   "surveillance_test": "Colonoscopy",
   "polypectomy_proportion_lethal": 2e-05,
-  "cost_discount_age": 50,
+  "cost_discount_age": 45,
   "cost_discount_rate": 0.03,
-  "lifespan_discount_age": 50,
+  "lifespan_discount_age": 45,
   "lifespan_discount_rate": 0.03,
   "death_rate_black_female_ages": [
     0,