Changes in version 0.7.0 - The drjacoby package can now be used to fit mcmc for deterministic model - drjacoby_mcmc function analogous to pmcmc for fitting models - convert_log_likelihood_func_for_drjacoby helps convert log likelihood functions, e.g. calc_loglikelihood into suitable likelihood functions that can be correctly passed as log_likelihood to drjacoby_mcmc. - convert_log_prior_func_for_drjacoby does the same for priors - The above changes are because drjacoby requires initial parameters and ranges to be passed as a data.frame internally, which means dates are internally handled as numerics, e.g. "2020-01-01" is 18262. Consequently, the sampled parameters from drjacoby_mcmc will have start_date values as numerics. See sample_drjacoby function for how these are handled correctly to align with converted log likelihood function draws. Changes in version 0.6.11 - parse_durations bug fix. Handles dur_E, dur_IMild and dur_ICase correctly now Changes in version 0.6.10 - sample_pmcmc bug fix dor negative posterior checks incorrectly. Changes in version 0.6.9 - atol and rtol can be passed to pmcmc fitting as named arguments in pars_obs to be used in run_deterministic_comparison - pmcmc can now be used to fit to PCR prevalence data (deterministic model only) by passing pcr_df and pcr_det as named list elements of pars_obs Changes in version 0.6.8 - run_deterministic_comparison patches for sero fitting and argument checks Changes in version 0.6.7 - 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 Changes in version 0.6.6 - projections can be used now for nimue models Changes in version 0.6.5 - pmcmc now accepts dates of change for vaccine efficacy for nimue Changes in version 0.6.4 - pmcmc changes to adapt for nimue class models and vaccines Changes in version 0.6.3 - beta_est accepts nimue models Changes in version 0.6.2 - Typo in dur_not_get_mv_survive Changes in version 0.6.1 - pmcmc(..., scaling_factor) allows scaling factors to be passed to pmcmc - Correction to deterministic_model model class Changes in version 0.6.0 - Waning added to squire Changes in version 0.5.8 - Updated to use odin 1.1.0 - odin_is_discrete new unexported function Changes in version 0.5.7 - Github actions included for automatic release tagging Changes in version 0.5.6 - pmcmc(..., gibbs_sampling = TRUE) implements Gibbs sampler Changes in version 0.5.5 - population$n are all integer class Changes in version 0.5.4 - beta_est accepts apothecary models - Updated json odin files that weren't compiled correctly Changes in version 0.5.3 - default_durations contains all durations - default_durations and default_probs now exported for ease - run_deterministic_SEIR_model has odin pars exported now Changes in version 0.5.2 - Parameters vignette updated to include new parameters - run_deterministic_comparison bug fix for when transmission is eliminated Changes in version 0.5.1 - projections bug fixed for setting time varying durations - Taiwan healthcare capacity added - default_durations updated for incorrect hospital durations Changes in version 0.5.0 0.5.0 Major - Parameter Updates. See parameters vignette for update. - triggering function for doing projections with model state triggered R0 changes - Time-varying durations of ICU and hospital stay 0.5.0 Minor - projections allows for different args to be passed to each replicate - projections allows for additional user model args to be passed Changes in version 0.4.34 - pmcmc argument treated_deaths_only will use deaths from treatment in likelihood Changes in version 0.4.33 - format_output accepts deaths_treatment and deaths_no_treatment Changes in version 0.4.32 - intervention_dates_for_odin fills dates earlier than date_R0_change Changes in version 0.4.31 - Correction to random walk parameters to more accurately continue the walk Changes in version 0.4.30 - evaluate_Rt_pmcmc takes Rt_rw_n for random walk esque shifts Changes in version 0.4.29 - format_output backwards compatible for incidence Changes in version 0.4.28 - calibrate patched as dt argument was not being passed through - format_output corrected for hospital/ICU incidence Changes in version 0.4.27 - evaluate_Rt_pmcmc patch for non specified Rt_shift in 3 parameter version Changes in version 0.4.26 - pmcmc more flexible for varying which parameters are fitted. - evaluate_Rt_pmcmc altered for increased flexibility Changes in version 0.4.25 - format_output now returns hospital_incidence and ICU_incidence - evaluate_Rt_pmcmc patch for Meff_switch_date earlier than date_R0_change[1] Changes in version 0.4.24 - Meff_pl can be scaled or not in relation to Meff Changes in version 0.4.23 - pmcmc no longer takes Rt_func as hard coded given Meff_pl complexity Changes in version 0.4.22 - Johnstone Change approach implemented for pmcmc RM Changes in version 0.4.21 - evaluate_Rt patch for roll of Meff Changes in version 0.4.20 - evaluate_Rt allows for date_Meff_change to be later/earlier than date_R0_change ends Changes in version 0.4.19 - Large overhaul to make projections and plotting work with deterministic models Changes in version 0.4.18 - calc_loglikelihood fix for reduced date vectors Changes in version 0.4.17 - pars_init for pmcmc can be provided as a list for where each chain starts Changes in version 0.4.16 - pmcmc method for 4 parameter estimation. Changes in version 0.4.15 - projections now matches by column names when including projection outputs - Patch to t0_variables for new Rt_func approach Changes in version 0.4.14 - replace chained binomials with mutivariate hypergeometric sampling in stochastic model - stochastic model to output number newly requiring ICU beds at each timepoint Changes in version 0.4.13 - calibrate now takes an Rt_func argument for specifying Rt calculation Changes in version 0.4.12 - Explicit Meff inclusion in R0_date_particle_filter and projections fix Changes in version 0.4.11 - patching projections when projecting further than original calibrate run Changes in version 0.4.10 - calibrate new argument for R0_prior Changes in version 0.4.9 - calibrate now allows intervetnion dates to be before epidemic start date Changes in version 0.4.8 - calibrate argument reporting_fraction implemented now in likelihood Changes in version 0.4.7 - calibrate can do 3D grid scans investigating Meff - plot.squire_scan will collapse n-dimensional scans using show argument Changes in version 0.4.6 - Patch for particle_filter_data when only 1 row of data is provided Changes in version 0.4.5 - Add functionality for running the deterministic model in javascript Changes in version 0.4.4 - Patch for calibrate to ensure correct dt values provided Changes in version 0.4.3 - calibrate can now take squire:::deterministic_model() as model type. - Output of above does not work with plotting or projections yet. Changes in version 0.4.2 - Patch for plot.scan_results where log likelihood was being plotted for both Changes in version 0.4.1 - Patch for passing in user defined population and matrices Changes in version 0.4.0 - calibrate now uses particle filter. See README for examples (#12) - Dates are to be provided for timings of interventions before today (#44, #17) - Custom populations, contact matrices and bed capacity allowed (#73, #80, #28, #16) - Increased modularity for new models (#62, #61, #49) - Returns lieklihood of different baseline R0s and start dates (#14) - get_mixing_matrix takes iso3c (#84) - Number of plotting enhancement (#72, #69) - Parameter references vignette and website update (#13, #1, #5, #78) Changes in version 0.3.0 - projection function for doing scenario projections Changes in version 0.2.3 - format_output and calibrate orderly plotting functioanlity in Changes in version 0.2.2 - calibrate now allows different seeding events (#50) and undereporting (#11) - New plotting functions for plot.squire_calibration - iso3c country codes in (#52) Changes in version 0.2.1 - extract_all_outputs and extract_specific_output (#37) Changes in version 0.2.0 - New minor version for iterative PR development cycle from now Changes in version 0.1.0 - initial version of the model