|
aggregate()
|
aggregate model runs by vaccination group x vaccine strata |
|
compare()
|
Calculate the log likelihood of the data given the parameters
diagnoses and attendances lhoods are negative binomial
p_symp lhood is betabinomial |
|
compare_basic()
|
Calculate the log likelihood of the data given the parameters |
|
create_vax_map()
|
Create mapping for movement between strata due to vaccination |
|
create_waning_map()
|
Create mapping for movement between strata due to vaccine waning |
|
dbetabinom()
|
pdf of a betabinomial parametrised in terms of probability and
over-dispersion |
|
extract_flows()
|
extract flows used for run_grid |
|
gono_params()
|
Posterior parameters of gonorrhoea natural history |
|
gonovax_data()
|
Get gonovax data |
|
gonovax_year()
|
Convert a year into the number of years after 2009 |
|
gonovax_year_as_year()
|
Convert a gonovax year into calendar years |
|
initial_params()
|
Initial conditions for the model |
|
mcmc()
|
Run a mcmc sampler |
|
mcmc_combine()
|
Combine mcmc samples |
|
mcmc_thin() mcmc_sample()
|
Thin a mcmc chain |
|
model
|
Model of gonorrhoea with dual vaccines
This is an odin model. |
|
model_params()
|
Parameters for the dualvax model |
|
restart_params()
|
Create initial conditions to start the model from the end of a run |
|
run()
|
Run odin model of gonorrhoea with or without vaccination |
|
run_grid()
|
run model from equilibrium with single vaccine at the input
efficacy / duration grid locations for n parameter sets |
|
run_onevax_xvwr()
|
run model with single vaccine for input parameter sets, either from
initialisation or from equilibrium, those with waned vaccines are eligible
for revaccination (R), and return to the R stratum |
|
run_onevax_xvwv()
|
run model with single vaccine for input parameter sets, either from
initialisation or from equilibrium, those with waned vaccines are eligible
for revaccination, and return to the V compartment |
|
transform()
|
Transform fitted parameters into gonovax params |
|
transform_fixed()
|
Transform fitted parameters into non-time-varying gonovax params |
|
vax_params0()
|
create vaccination parameters for use in novax model (null) |
|
vax_params_xvwr()
|
create vaccination parameters for use in onevax_xvwr model |
|
vax_params_xvwv()
|
create vaccination parameters for use in onevax_xvwv model |