Changelog

Source: NEWS.md

LEMMA 2.1.1

Minor improvements and fixes

• Minor additional outputs
• Added skip.second.dose.fraction

LEMMA 2.1

New Features

• Added outputs for outcomes among vaccinated and unvaccinated
• Added parameters for relative transmission among age 0-11, relative probability of previously infected to be vaccinated

Minor improvements and fixes

• Improved modelling of vaccinated and unvaccinated compartments to better match vaccine efficacy inputs

LEMMA 2.0.4

Minor improvements and fixes

• When adding automatic interventions, do not consider dates of future interventions

LEMMA 2.0.3

Minor improvements and fixes

• Update documentation

LEMMA 2.0.2

Minor improvements and fixes

• Update ProjectScenario to quickly run new scenarios if interventions/vaccines/variants only change after last observed data

LEMMA 2.0.1

Minor improvements and fixes

• New Excel input file format

LEMMA 2.0.0

New Features

• Accounts for vaccines, including dose-specific efficacy for blocking transmission and hospitalizations/deaths
• Accounts for age targeting in vaccine rollout
• Allows for variants, including the possibility of increased transmission, increased hospitalization/death, decreased vaccine efficacy, decreased duration of vaccine and/or natural immunity
• Fits to seroprevalence estimates, hospital admissions, cases (in addition to hospital census, ICU census, deaths)
• Runs quickly (~20 seconds - old LEMMA was taking over 12 hours)
• In order to run in reasonable time, we removed the calculation of credibility intervals by default and now only compute a point estimate. [in progress - bringing back credibility intervals as an option]

Minor improvements and fixes

• Made len_inter an estimated parameter again

LEMMA 0.6.0.9000

New Features

• Added an error term to the projections so that future projections reflected the degree to which past projections differed from past actuals. This should increase the width of the short-term credibility intervals so that around 95% of the actuals lie within the 95% interval.
• Make len_inter and frac_PUI fixed instead of estimated parameters (very minor impact on projections but increases speed)

LEMMA 0.5.0.9007

Minor improvements and fixes

• Rt plot shows credibility interval

LEMMA 0.5.0.9001

New Features

• Moved credibility interval calculation to Stan based on the Santa Cruz County COVID-19 Model (https://github.com/jpmattern/seir-covid19). Many thanks to Jann Paul Mattern and Mikala Caton!

LEMMA 0.4.0.9000

New Features

• Added fitting to ICU, deaths and cumulative hospital admissions

LEMMA 0.3.0.9005

Minor improvements and fixes

• CredibilityIntervalFromExcel now supports up to 9 interventions (see FAQ for details)

LEMMA 0.3.0.9004

New Features

• “Best Guess” was sometimes misinterpreted so we changed “Best Guess” to “User’s Prior Projection”. User’s Prior Projection is only displayed if niter < 100.

• PDF now includes short-term (dates of observed data) and long-term (until Projection End Date) plots

• plot.observed.data.long.term, plot.observed.data.short.term added to internal.args (Internal sheet). These logicals control plotting the observed data bounds on the long-term and short-term plots.

• lower.bound.label, upper.bound.label added to internal.args (Internal sheet). For example, in San Francisco these are “Confirmed COVID19” and “Confirmed COVID19 + 30%PUI”.

Minor improvements and fixes

• Case Studies was updated to include plots