Non vax infections mod screen #111
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-Set screening coverage at run time. Also designate vectors with screening ages and HIV groups across all algorithms used in scenario at run time. -Automatically set screening age mults vector based on screening ages
-Stratify screening algorithm parameters and outcomes for HPV and CIN1 -Begin outlining separate algorithm behavior for genotyping algorithm
- Add new screening algorithms - Add separate test sensitivity values for HPV/CIN1 and by HIV and treatment status - Define treatment retention parameters to calculate proportion returning for treatment (in some cases, weighted average between LEEP and ablative therapy)
-Update loadUp2 screening algorithm name outputs -Change screening parameter matrices to have rows for HIV disease states, standardizing matrix shape -Pre-define treatment efficacy and HPV persistence parameters and pre-calculate weighted HPV persistence accounting for different eligibility for LEEP across CIN stages. cinTreatHpvPersistHivNeg parameter now varies by CIN state
-Revise futureSim description of how to specify screening algorithm parameters at run time -Update loadUp2 screening algorithm name outputs -Update names for algorithm assignment -Adjust for new structure in which the same algorithm is used across HIV states, in algorithm assignment and in definition of numScreenAge and agesComb for looping through algorithm ages to pre-define indices
-Assign additional run time parameters to baseline screening algorithm and update numScreenAge and agesComb vectors for index assignment according to new algorithm structure where same algorithm is used across HIV states -Update loadUp2 screening algorithm name outputs
-Update CIN1-CC screening/treatment multipliers according to updated
parameter names/shapes (HPV, Sus/Imm unfinished)
-Change from screenAlgs{i} to screenAlgs and fix log for looping through
HIV state groups and ages according to new algorithm structure where
same aglorithm used across HIV states
Set the proportion who remain in the HPV+(no CIN) compartment after treatment to be equal to the proportion with HPV persistence before we subtract treatment failure. In other words, the proportion persons moving from HPV+(no CIN) to immune will be multiplid by (1-HPV persistence).
Adjust coverage by (0.7/0.9) to represent the proportion of cancers prevented by the bivalent/ 9v vaccines vs. (2/7), the proportion of oncogenic type infections prevented. Types 16/18 have increased progression compared to other types, and there is also cross-protection. Although the type distribution will change over time with vaccination, believe this is a better way to adjust coverage.
…Models/HHCoM into nonVaxInfections_modScreen
… into nonVaxInfections_modScreen
ART initiation does not occur in all ART-eligible age groups because we want to achieve the designated population-level ART coverage while maintaining a reasonable distribution of coverage by age. Young persons tend to initiate ART while discontinuation occurs in the mid to upper age groups. Therefore, in age groups where zero persons initiate ART, the proportions discontinuating ART into CD4+ compartments are calculated as 0/0, or NaN. I previously changed these to zero. This falsely led to persons discontinuing ART but not being placed into the appropriate HIV+ untreated compartments. To correct this, in age groups with no ART initiation, I set the proportion discontinuing by CD4 to the distribution of the next youngest age group with persons initiating ART. If a < youngest age of ART eligibility, or no ages initiate ART, this proportion is set equal to zero.
… into nonVaxInfections_modScreen Change back newScreen dimensions in vaxCEA_multSims_CIs.m
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Change structure of screening module and add new screening algorithms, accounting for backwards-compatibility.