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age_struct_seir_ode()
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Age-structured SEIR ODE model of vaccination with 2 doses and delay to protection |
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calc_ve_w_waning()
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Calculate amount of vaccine waning |
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choose_contact_matrix()
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Determine contact matrix based on thresholds of cases or IC admissions |
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convert_contact_matrices()
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Convert contact matrices to transmission matrices |
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convert_vac_schedule()
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convert cumulative vaccination schedule to non-cumulative ---------------------------------- |
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forward_sim_func_wrap()
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Wrapper function to perform forward simulations |
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get_foi()
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Calculate force of infection |
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get_transmission_matrix()
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Convert contact matrix to transmission matrix |
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likelihood_func()
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Likelihood function for fitting SEIR model to daily case data |
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model_run_wrapper()
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Function wrapper to run model for multiple time windows with set of
transmission rates |
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my_rmultinom()
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Postprocess output from age-structured SEIR ODE model of vaccination
with 2 doses and delay to protection |
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postprocess_age_struct_model_output()
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Postprocess output from age-structured SEIR ODE model of vaccination
with 2 doses and delay to protection |
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seir_ode()
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SEIR ODE model of vaccination with 2 doses and delay to protection |
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seir_ode_2()
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SEIR ODE model of vaccination with 2 doses and delay to protection |
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stochastic_age_struct_seir_ode()
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Stochastic Age-structured SEIR ODE model of vaccination with 2 doses and delay to protection |
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summarise_results()
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Summarise output from SEIR model for plotting |
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vac-a-mole-package
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A short title line describing what the package does |
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wide_to_long()
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Convert data from wide to long |
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wrangle_results()
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Post-process raw results from model run |