SF_12_PCS

[ld-archer]

Opening this PR for all the work on the SF_12_PCS outcome and pathways leading to it.

At time of opening, the SF_12_PCS module has been created and added to the default.yaml config file. It is running smoothly, and changes have been made to include PCS in outcome visualisations (AGG_VAR is now set in the Makefile so we can use existing code to create plots for both MCS and PCS), and validations in the form of handovers and cross-validation (soon to be renamed/reworked). There is still a lot of work needing to be done, including developing the pathways from start to finish, and doing QALE/QALY calculations using both the MCS and PCS.

DONE:

• Renamed all previous instances of SF_12 to SF_12_MCS when referring to mental wellbeing
• Renamed all previous instances of SF_12p to SF_12_PCS when referring to physical wellbeing
• Created SF_12_PCS module and added to default.yaml and cross_validation.yaml
• Defined transition model for PCS in model_definitions.txt, and modified estimate_transitions.R to handle both MCS and PCS
• Included PCS in handovers and cross-validation notebooks
• Adapted outcome visualisation to allow for both MCS and PCS as outcomes to visualise

To Do:

• Pathways from start to finish
• QALE/QALY calculations when PCS pathways complete
• Further testing/validation?

Also probably part of this:

• Replace the current phealth proxy from using SF12 questions to instead use GHQ
• Create an mhealth proxy using GHQ