- Add function
read_epp_workset_options()to read ANC prevalence adjustment and EPP-ASM model option selections in EPP Curve Fitting page. - Update
read_epp_data()to read household survey ART coverage inputs.
- Add function
read_eppxml_results()to read projection outputs from EPP .xml file including ART coverage.
- Add type.convert(..., as.is = TRUE) to silence R 4.1 warning.
- Handle new data structure for household survey data introduced in EPP 2019.
- Update EPP .xml file parsers to use
xml2package instead ofXMLpackage. Improved logic and efficiency for parsers. - Search XML node trees rather than rely on node position. More robust and code now works to read data from concentrated epidemic structured EPP files
- Parse subpopulation characteristics and turnover from concentrated epidemic files.
- Read incidence data inputs.
- Only read ANC-RT data if used in EPP fit
IMIS offsets likelihood by maximum log-likelihood to avoid underflow.Rolled this back because it introduced a pernicious little bug in mixture weights when offset changes numerical underflow. Should be re-implemented more carefully later.- Added option to likelihood() to return log values.
- Updates to IMIS optimization step:
- Do random sample as well in each iteration
- Reduce numerical integration stepsize and try again if BFGS encounters non-finite difference error
- Use last value from center_all to initialise optimization if no positive samples remain
- Implement ANC routine testing (ANC-RT) likelihood in EPP 2017 (Spectrum 5.52)