run_IFRmodel_age: Run Aggregate Model

In mrc-ide/COVIDCurve: Inferring the Infection Fatality Ratio from COVID-19 Aggregated Death and Seroprevalence Data

Description

Run Aggregate Model

Usage

run_IFRmodel_age(
  IFRmodel,
  binomial_likelihood = TRUE,
  reparamIFR = TRUE,
  reparamInfxn = TRUE,
  reparamKnots = TRUE,
  thinning = 0,
  burnin = 1000,
  samples = 10000,
  rungs = 1,
  chains = 5,
  coupling_on = TRUE,
  GTI_pow = 1,
  beta_manual = NULL,
  cluster = NULL,
  pb_markdown = FALSE,
  silent = FALSE
)

Arguments

IFRmodel	R6 class; Internal model object for COVIDCurve
binomial_likelihood	logical; Whether the binomial or the logit likelihood should be used
reparamIFR	logical; Whether IFRs should be reparameterized or inferred separately
reparamInfxn	logical; Whether infection curve (i.e. the y-coordinates infection spline) should be reparameterized or inferred separately
reparamKnots	logical; Whether infection knots (i.e. the x-coordinates of the infection spline) should be reparameterized or inferred separately
thinning	integer; The regular sequence to count by to thin MCMC posterior chain (iterations are kept as: seq(from = thinning, to = (burnin+samples), by = thinning)).
burnin	the number of burn-in iterations.
samples	the number of sampling iterations.
rungs	the number of temperature rungs used in Metropolis coupling (see coupling_on).
chains	the number of independent replicates of the MCMC chain to run. If a cluster object is defined then these chains are run in parallel, otherwise they are run in serial.
coupling_on	whether to implement Metropolis-coupling over temperature rungs.
GTI_pow	values in the temperature ladder are raised to this power.
beta_manual	option to manually define temperature ladder. These values are raised to the power GTI_pow, hence you should use GTI_code = 1 to fix powers exactly. If NULL then an equal spacing of length rungs is used between 0 and 1.
cluster	option to pass in a cluster environment, allowing chains to be run in parallel (see package "parallel").
pb_markdown	whether to run progress bars in markdown mode, meaning they are only updated when they reach 100 being printed to markdown files.
silent	whether to suppress all console output.

Details

Wraps the Metropolic-Coupled MCMC Framework from Dr. Jacoby

mrc-ide/COVIDCurve documentation built on June 2, 2021, 7:37 a.m.