NEWS

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squire 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.

squire 0.6.11

• parse_durations bug fix. Handles dur_E, dur_IMild and dur_ICase correctly now

squire 0.6.10

• sample_pmcmc bug fix dor negative posterior checks incorrectly.

squire 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

squire 0.6.8

• run_deterministic_comparison patches for sero fitting and argument checks

squire 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

squire 0.6.6

• projections can be used now for nimue models

squire 0.6.5

• pmcmc now accepts dates of change for vaccine efficacy for nimue

squire 0.6.4

• pmcmc changes to adapt for nimue class models and vaccines

squire 0.6.3

• beta_est accepts nimue models

squire 0.6.2

• Typo in dur_not_get_mv_survive

squire 0.6.1

• pmcmc(..., scaling_factor) allows scaling factors to be passed to pmcmc
• Correction to deterministic_model model class

squire 0.6.0

• Waning added to squire

squire 0.5.8

• Updated to use odin 1.1.0
• odin_is_discrete new unexported function

squire 0.5.7

• Github actions included for automatic release tagging

squire 0.5.6

• pmcmc(..., gibbs_sampling = TRUE) implements Gibbs sampler

squire 0.5.5

• population$n are all integer class

squire 0.5.4

• beta_est accepts apothecary models
• Updated json odin files that weren't compiled correctly

squire 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

squire 0.5.2

• Parameters vignette updated to include new parameters
• run_deterministic_comparison bug fix for when transmission is eliminated

squire 0.5.1

• projections bug fixed for setting time varying durations
• Taiwan healthcare capacity added
• default_durations updated for incorrect hospital durations

squire 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

squire 0.4.34

• pmcmc argument treated_deaths_only will use deaths from treatment in likelihood

squire 0.4.33

• format_output accepts deaths_treatment and deaths_no_treatment

squire 0.4.32

• intervention_dates_for_odin fills dates earlier than date_R0_change

squire 0.4.31

• Correction to random walk parameters to more accurately continue the walk

squire 0.4.30

• evaluate_Rt_pmcmc takes Rt_rw_n for random walk esque shifts

squire 0.4.29

• format_output backwards compatible for incidence

squire 0.4.28

• calibrate patched as dt argument was not being passed through
• format_output corrected for hospital/ICU incidence

squire 0.4.27

• evaluate_Rt_pmcmc patch for non specified Rt_shift in 3 parameter version

squire 0.4.26

• pmcmc more flexible for varying which parameters are fitted.
• evaluate_Rt_pmcmc altered for increased flexibility

squire 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]

squire 0.4.24

• Meff_pl can be scaled or not in relation to Meff

squire 0.4.23

• pmcmc no longer takes Rt_func as hard coded given Meff_pl complexity

squire 0.4.22

• Johnstone Change approach implemented for pmcmc RM

squire 0.4.21

• evaluate_Rt patch for roll of Meff

squire 0.4.20

• evaluate_Rt allows for date_Meff_change to be later/earlier than date_R0_change ends

squire 0.4.19

• Large overhaul to make projections and plotting work with deterministic models

squire 0.4.18

• calc_loglikelihood fix for reduced date vectors

squire 0.4.17

• pars_init for pmcmc can be provided as a list for where each chain starts

squire 0.4.16

• pmcmc method for 4 parameter estimation.

squire 0.4.15

• projections now matches by column names when including projection outputs
• Patch to t0_variables for new Rt_func approach

squire 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

squire 0.4.13

• calibrate now takes an Rt_func argument for specifying Rt calculation

squire 0.4.12

• Explicit Meff inclusion in R0_date_particle_filter and projections fix

squire 0.4.11

• patching projections when projecting further than original calibrate run

squire 0.4.10

• calibrate new argument for R0_prior

squire 0.4.9

• calibrate now allows intervetnion dates to be before epidemic start date

squire 0.4.8

• calibrate argument reporting_fraction implemented now in likelihood

squire 0.4.7

• calibrate can do 3D grid scans investigating Meff
• plot.squire_scan will collapse n-dimensional scans using show argument

squire 0.4.6

• Patch for particle_filter_data when only 1 row of data is provided

squire 0.4.5

• Add functionality for running the deterministic model in javascript

squire 0.4.4

• Patch for calibrate to ensure correct dt values provided

squire 0.4.3

• calibrate can now take squire:::deterministic_model() as model type.
• Output of above does not work with plotting or projections yet.

squire 0.4.2

• Patch for plot.scan_results where log likelihood was being plotted for both

squire 0.4.1

• Patch for passing in user defined population and matrices

squire 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)

squire 0.3.0

• projection function for doing scenario projections

squire 0.2.3

• format_output and calibrate orderly plotting functioanlity in

squire 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)

squire 0.2.1

• extract_all_outputs and extract_specific_output (#37)

squire 0.2.0

• New minor version for iterative PR development cycle from now

squire 0.1.0

• initial version of the model