Merge pull request #1887 from ihmeuw/alzheimers/model-11-run-request

Alzheimer's: Model 11 run request and clarifications

Author: SylLutze

docs/source/models/concept_models/vivarium_alzheimers/concept_model.rst

@@ -367,8 +367,10 @@ scenario, and input draw.
       Note that the diagram states `Full treatment effect LONG` and `Full treatment effect SHORT` are both considered the same status (`Full treatment effect`),
       but are stratified by completion status.
   * - Months on treatment
-    - 
-    - Only needed for simulants who discontinue treatment as others are definitionally 0 or 9.
+    - Number of months on treatment (integer between 0 and 9, inclusive)
+    - Count the number of simulants in each (year, sex, age group,
+      months on treatment) stratum. This will be used for cost
+      estimates.
   * - Treatment status person-time
     - Status (`In treatment/ Waiting for treatment`, `Full treatment effect`, `Waning treatment effect`, `No treatment effect`).
       Also stratify by treatment completion (completed, discontinuated) from transition observer
@@ -673,6 +675,12 @@ scenario, and input draw.
         run, it just happened to be what was already on ``main``
     - Stratify disease state transitions and person-time by treatment
     - Default
+  * - 11.0
+    - Updates to treatment model
+    - Baseline, Alternative Scenario 2
+    - * Locations: USA, China, Brazil
+    - Stratify disease state transitions and person-time by treatment
+    - Add observer for months on treatment
 
 5.2 V & V Tracking
 ------------------------

docs/source/models/intervention_models/alzheimers/hypothetical_treatment.rst

@@ -168,8 +168,17 @@ is defined below.
     - Drawn uniformly from :math:`[0,1)`
     - Lower value means more likely to initiate testing. Independent from testing propensities.
   * - :math:`I`
-    - Time- and location-specific treatment initiation rate
-    - The percent of patients with a positive BBBM test who initiate treatment will vary over time – but will not vary by age, sex, or location. We will use a piecewise linear ramp-up with knots at the following (year, level) values: `(2022.0, 0), (2027.0, 0), (2035.5, 30), (2100.0, 80), (2101.0, 80)`.
+    - Time-varying treatment initiation rate
+    - The percent of patients with a positive BBBM test who initiate
+      treatment will vary over time – but will not vary by age, sex, or
+      location. We will use a piecewise linear ramp-up with knots at the
+      following (year, level) values: `(2022.0, 0), (2027.0, 0),
+      (2035.5, 30), (2100.0, 80), (2101.0, 80)`.
+
+      This captures the CSU client's specification that "30% of eligible patients
+      initiate by 2035, with a steady increase to 80% by 2100, for all
+      countries," and that treatment should first be available in 2027,
+      slowly ramping up to 30% in 2035.
     - 
   * - :math:`D_t`
     - Months to discontinuation
@@ -200,7 +209,8 @@ is defined below.
     - See :ref:`testing intervention <intervention_alzheimers_testing_diagnosis>`
   * - BBBM test received
     -
-    - Zero duration. Random draw
+    - Zero duration. Independent random draw to determine whether test
+      is positive or negative
   * - BBBM test positive
     -
     - Zero duration. :math:`\text{prop}_I < I`\: initiate. :math:`\text{prop}_I >=  I`\: don't initiate.
@@ -211,11 +221,14 @@ is defined below.
     - 
     - Fixed duration
   * - Receiving treatment
-    - Treatment period is instantaneous. See :ref:`alzheimers_intervention_treatment_assumptions` for info about treatment/discontinuation timing.
-    - Zero duration. Random draw
+    - Treatment effect is instantaneous. See :ref:`alzheimers_intervention_treatment_assumptions` for info about treatment/discontinuation timing.
+    - Zero duration. Independent random draw to determine whether
+      simulant completes or discontinues treatment.
   * - Months to discontinuation
-    - Period is instantaneous. See above notes for selection of months to discontinuation.
-    - Zero duration. Random draw.
+    - See :math:`D_t` in the `Data values and sources` table above for
+      instructions on assigning the number of months to discontinuation
+    - Zero duration. Independent random draw to determine how many
+      months of treatment simulant receives before discontinuation.
   * - Full treatment effect LONG
     - Treatment takes effect exactly 6 months after receiving a positive BBBM test (if :math:`\text{prop}_I < I`)
     - On transition to this state, :math:`R_h = R_d`. Set :math:`h_{adj} = R_h \cdot h_{MCI}`, slowing progression to MCI.
@@ -273,9 +286,16 @@ Assumptions and Limitations
 
 - Those who do not initiate treatment following their first positive BBBM test result, or those who discontinue, 
   will never take the intervention, so propensity can be assigned for simulant lifetime
-- Treatment occurs instantaneously (ie, the duration of the treatment period is zero), following a six-month waiting period from time of BBBM test. 
-  So, treatment takes effect exactly six months after BBBM testing. 
-  This interprets the following two Lilly specifications: "The treatment takes immediate full effect in the first 6-month time step" and 
-  "There is an average of 6 months between a positive BBBM test result and initiating treatment". We simplify 
-  average of 6 months to fixed 6 month duration for all simulants. 
-  Discontinuation occurs during this instantaneous treatment period.
+- Treatment occurs instantaneously (i.e., the duration of the "receiving
+  treatment" period is zero), following a six-month waiting period from
+  time of BBBM test. So, treatment takes effect exactly six months after
+  BBBM testing. This interprets the following two client specifications:
+  "The treatment takes immediate full effect in the first 6-month time
+  step" and "There is an average of 6 months between a positive BBBM
+  test result and initiating treatment". We simplify "average of 6
+  months" to a fixed 6 month duration for all simulants. Treatment
+  discontinuation only affects the duration of time the treatment will
+  last, not the immediate effect size, so it is consistent with the client's
+  assumptions to model discontinuation occurring instantaneously during
+  the transient "receiving treatment" and "months to discontinuation"
+  states as above.