Amy Heather
September 9, 2024
A little bit of thinking around sensitivity analysis. Total time used: 14h 35m (36.5%)
The remaining items in the scope that I’ve not yet attempted - Figure 4 and appendix 7 - are both based on the results of the sensitivity analyses. I haven’t identified any code in the GitHub repository to run this analysis. As such, I am assuming that the provided scripts were directly modified to run each of these scenarios.
The contents of each figure as presented below, along with my identified snippets of code that we would likely need to alter for the scenario.
Figure 4 has INMB from:
smoking_adherence=0.7) (input$values$smoking$smoking_cessation_adherence <- smoking_adherence)medication_adherence=0.7)medication_adherence=0.7)medication_utility=0.0367)medication_utility=0.0367)Whilst appendix 7 has INMB from:
discount_rate=0.015)discount_rate=0.015)It’s handy that I could fairly easily identify each of these variables in the script since the variable names aligned pretty well with the concepts.
Whilst there is a global variables section at the top of the script, they then seem to be provided each time at the start of each scenario in Case_Detection_Results.Rmd - but I think this is just because each scenario changes something slightly in the inputs, so they repeat them all each time.
I would prefer not to duplicate the .Rmd files 8 times, so I started a Sensitivity_Analysis.Rmd file. I what differed between all the scenarios (in reference case, time intervals, and in sensitivity analysis).
On reflection, I think the simplest solution to this, instead of trying to restructure all the models to run easily from one file, would be to write a script that duplicates the Rmd file but alters one part of it.
import sys
sys.path.append('../')
from timings import calculate_times
# Minutes used prior to today
used_to_date = 848
# Times from today
times = [
('16.08', '16.18'),
('16.23', '16.40')]
calculate_times(used_to_date, times)Time spent today: 27m, or 0h 27m
Total used to date: 875m, or 14h 35m
Time remaining: 1525m, or 25h 25m
Used 36.5% of 40 hours max