fix(reproduction): change med_adherence (not redundant medication_adh…

…erence, which was not impacting the model in any way, hence med adherence scenarios weren't being implemented)
pythonhealthdatascience · Oct 18, 2024 · 08f9b9c · 08f9b9c
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diff --git a/reproduction/scripts/Case_Detection_Results.Rmd b/reproduction/scripts/Case_Detection_Results.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=3
 medication_utility=0.0367
-medication_adherence=0.7
+med_adherence=0.7
 smoking_adherence=0.7
 
 other_years_btw_case_detection=5 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`

diff --git a/reproduction/scripts/Case_Detection_Results_5yrs.Rmd b/reproduction/scripts/Case_Detection_Results_5yrs.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=5
 medication_utility=0.0367
-medication_adherence=0.7
+med_adherence=0.7
 smoking_adherence=0.7
 
 other_years_btw_case_detection=3 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`

diff --git a/reproduction/scripts/Sensitivity_Analysis/Sen1_No_Smoking_Cessation3yrs.Rmd b/reproduction/scripts/Sensitivity_Analysis/Sen1_No_Smoking_Cessation3yrs.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=3
 medication_utility=0.0367
-medication_adherence=0.7
+med_adherence=0.7
 smoking_adherence=0
 
 other_years_btw_case_detection=5 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`

diff --git a/reproduction/scripts/Sensitivity_Analysis/Sen1_No_Smoking_Cessation5yrs.Rmd b/reproduction/scripts/Sensitivity_Analysis/Sen1_No_Smoking_Cessation5yrs.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=5
 medication_utility=0.0367
-medication_adherence=0.7
+med_adherence=0.7
 smoking_adherence=0
 
 other_years_btw_case_detection=3 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`

diff --git a/reproduction/scripts/Sensitivity_Analysis/Sen2_50_Med_Adherence3yrs.Rmd b/reproduction/scripts/Sensitivity_Analysis/Sen2_50_Med_Adherence3yrs.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=3
 medication_utility=0.0367
-medication_adherence=0.5
+med_adherence=0.5
 smoking_adherence=0.7
 
 other_years_btw_case_detection=5 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`
@@ -113,7 +113,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -201,7 +201,7 @@ yrs_btw_CD = other_years_btw_case_detection
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -292,7 +292,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -383,7 +383,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -474,7 +474,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -618,7 +618,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=1 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -707,7 +707,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=1 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -834,7 +834,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -922,7 +922,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1013,7 +1013,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1104,7 +1104,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1195,7 +1195,7 @@ yrs_btw_CD = 3 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 

diff --git a/reproduction/scripts/Sensitivity_Analysis/Sen2_50_Med_Adherence5yrs.Rmd b/reproduction/scripts/Sensitivity_Analysis/Sen2_50_Med_Adherence5yrs.Rmd
@@ -74,15 +74,15 @@ input <- init_input()
 
 years_btw_case_detection=5
 medication_utility=0.0367
-medication_adherence=0.5
+med_adherence=0.5
 smoking_adherence=0.7
 
 other_years_btw_case_detection=3 # other time interval
 ```
 
 **Global inputs:**
 
-  - Medication adherence is `r medication_adherence`
+  - Medication adherence is `r med_adherence`
   - Smoking adherence is `r smoking_adherence`
   - Cost discounting: `r input$values$global_parameters$discount_cost`
   - QALY discounting: `r input$values$global_parameters$discount_qaly`
@@ -112,7 +112,7 @@ yrs_btw_CD = other_years_btw_case_detection
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -200,7 +200,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -291,7 +291,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -382,7 +382,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -473,7 +473,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -617,7 +617,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=1 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -706,7 +706,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 40 # change inputs here
 min_pack_years = 0 # change inputs here
 num_symptoms=1 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -833,7 +833,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -921,7 +921,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1012,7 +1012,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1103,7 +1103,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367 
@@ -1194,7 +1194,7 @@ yrs_btw_CD = 5 # change inputs here
 min_age = 50 # change inputs here
 min_pack_years = 0.001 # change inputs here
 num_symptoms=0 # change inputs here
-med_adherence=0.7
+med_adherence=0.5
 smoking_adherence=0.7
 time_horizon=20
 medication_utility=0.0367