NEWS.md
combine_rt
function, to use more flexibly for Rt and severity aggregationlancelot_parameters
now allows multiple boosterslancelot_parameters
functionlancelot_parameters
vaccine_eligibility
for computing lancelot
-compatible vaccine eligibility vectors based on a minimum age.vacc_skip_from
and vacc_skip_to
, for the purpose of allowing boosting before waningvaccine_schedule_from_data
function refactored to deal with flexible number of dosesp_NC
and phi_pillar2_cases
now must be age-specific for lancelot
model, including when fitting to aggregated Pillar 2 data.booster_groups
renamed to boosters_proportion
and now allows partial exclusion of age groups. For backward compatibility defaults have the same effect on the priority population.sircovid_models
and check_sircovid_model
to list and check sircovid models respectivelylancelot
model. Initially a clone of the carehomes
model with the added flexibility to fit to positivity or cases (pillar 2) by age. Respectively, p_NC
and phi_pillar2_cases
parameters can be generic or age-specific for fitting to aggregate or age stratified data.phi_pillar2_cases_weekend
, which is used instead of phi_pillar2_cases
on weekendscarehomes_forecast
via the random_sample
logical inputp_R
, the probability a non-fatal infection leads to post-infection immunity, otherwise the individual instantly becomes susceptible again post-infectionbeta_type
option to carehomes_parameters
, now allowing it to be "piecewise-linear"
or "piecewise-constant"
modify_severity
function to modify severity and transmission params of a VOC from VE assumptions1
for all age groupspopulation
and carehome_beds
to carehomes_parameters
to allow use for regions where these are not included in the packagelag_groups
and lag_days
parameters to vaccine_schedule_future
to manually add lags for given age groups to the vaccine schedulesircovid::inflate_state_strains
for adding empty strain compartments to a model state that was run without multiple strainscarehomes_check_severity
to check all severity probabilities lie in [0, 1] after transformation and all relative parameters are mirrored as expectedsircovid::inflate_state_strains
for adding empty strain compartments to a model state that was run without multiple strainscarehomes_parameters_progression
and carehomes_parameters_severity
.sircovid_parameters_beta
renamed to sircovid_parameters_piecewise_linear
and sircovid_parameters_beta_expand
renamed to sircovid_parameters_expand_step
carehomes_rt
function to have flexibility for multiple dimensions, given strains, age categories and vaccinations classes.carehomes_parameters
function instead of taking the default observation parameters.cross_immunity
to control the amount of immunity conferred by one strain that decreases the probability of immediately being exposed to the other strain (ignored in single strain model).model_super_infection
as model_super_infection = 0
is equivalent to cross_immunity = 1
(default)rel_susceptibility
, rel_p_sympt
, rel_p_hosp_if_sympt
and rel_infectivity
) can now take array values for varying across age groups, vaccination classes, and pathogen strains.model_super_infection
.T_sero_neg
or T_PCR_neg
compartments.strain_rel_severity
for varying the probabilities of p_G_D
, p_H_D
, p_W_D
and p_ICU_D
by strain.strain_rel_gamma_
for varying gamma_A
, gamma_P
, gamma_C_1
, and gamma_C_2
by strain.strain_seed_value
to stochastic strain_seed_rate
vectorstrain_seed_date
from vector of start and end seeding dates to a vector of dates corresponding to rates set by strain_seed_rate
sircovid::compile_gpu
which compiles sircovid to run on a GPU (#237)add_future_betas
and future_Rt
for constructing future transmission scenariosadd_trajectory_incidence
, drop_trajectory_incidence
and drop_trajectory_predicted
N_age
was split into n_age_groups
(both models) and n_groups
(carehomes)