pmcmc
can now be used to fit to serology data (deterministic model only) by passing sero_df
and sero_det
as names list elements of pars_obs
projections
can be used now for nimue
modelspmcmc
now accepts dates of change for vaccine efficacy for nimue
pmcmc
changes to adapt for nimue
class models and vaccinesbeta_est
accepts nimue
modelsdur_not_get_mv_survive
pmcmc(..., scaling_factor)
allows scaling factors to be passed to pmcmcdeterministic_model
model classodin_is_discrete
new unexported functionpmcmc(..., gibbs_sampling = TRUE)
implements Gibbs samplerpopulation$n
are all integer classbeta_est
accepts apothecary modelsdefault_durations
contains all durationsdefault_durations
and default_probs
now exported for easerun_deterministic_SEIR_model
has odin pars exported nowParameters
vignette updated to include new parametersrun_deterministic_comparison
bug fix for when transmission is eliminatedprojections
bug fixed for setting time varying durationsdefault_durations
updated for incorrect hospital durationstriggering
function for doing projections
with model state triggered R0 changesprojections
allows for different args to be passed to each replicateprojections
allows for additional user model args to be passedpmcmc
argument treated_deaths_only
will use deaths from treatment in likelihoodformat_output
accepts deaths_treatment
and deaths_no_treatment
intervention_dates_for_odin
fills dates earlier than date_R0_change
evaluate_Rt_pmcmc
takes Rt_rw_n
for random walk esque shiftsformat_output
backwards compatible for incidencecalibrate
patched as dt
argument was not being passed throughformat_output
corrected for hospital/ICU incidenceevaluate_Rt_pmcmc
patch for non specified Rt_shift
in 3 parameter versionpmcmc
more flexible for varying which parameters are fitted.evaluate_Rt_pmcmc
altered for increased flexibilityformat_output
now returns hospital_incidence
and ICU_incidence
evaluate_Rt_pmcmc
patch for Meff_switch_date
earlier than date_R0_change[1]
Meff_pl
can be scaled or not in relation to Meffpmcmc
no longer takes Rt_func as hard coded given Meff_pl complexityevaluate_Rt
patch for roll
of Meffevaluate_Rt
allows for date_Meff_change
to be later/earlier than date_R0_change
endsprojections
and plotting work with deterministic modelscalc_loglikelihood
fix for reduced date vectorspars_init
for pmcmc
can be provided as a list for where each chain startspmcmc
method for 4 parameter estimation.projections
now matches by column names when including projection outputst0_variables
for new Rt_func approachcalibrate
now takes an Rt_func
argument for specifying Rt calculationR0_date_particle_filter
and projections
fixprojections
when projecting further than original calibrate runcalibrate
new argument for R0_prior
calibrate
now allows intervetnion dates to be before epidemic start datecalibrate
argument reporting_fraction
implemented now in likelihoodcalibrate
can do 3D grid scans investigating Meffplot.squire_scan
will collapse n-dimensional scans using show
argumentparticle_filter_data
when only 1 row of data is providedcalibrate
to ensure correct dt values providedcalibrate
can now take squire:::deterministic_model()
as model type.plot.scan_results
where log likelihood was being plotted for bothcalibrate
now uses particle filter. See README for examples (#12)
get_mixing_matrix
takes iso3c (#84)projection
function for doing scenario projectionsformat_output
and calibrate orderly plotting functioanlity incalibrate
now allows different seeding events (#50) and undereporting (#11)plot.squire_calibration
extract_all_outputs
and extract_specific_output
(#37)