Description Usage Arguments Details Value
This function generates new posterior samples from a ‘FluHMM’ object, or runs more iterations to increase the length of the existing ones.
1 2 3 |
x |
An object of class ‘FluHMM’, from which to generate posterior samples. |
iter |
Number of iterations to run |
thin |
Thinning interval between consequtive iterations to keep. |
Rhat |
Gelman-Rubin diagnostic cutoff value to determine convergence. |
enlarge |
If |
After reaching initial convergence (i.e. convergence for the sigma[1] parameter, which
is the standard deviation of the pre- and post-epidemic phases), update
should be run
to generate a fresh posterior sample, for as many iterations as required based on the desired
level of precision.
Afterwards, convergence should be checked by examining the converged
and gelman
elements of the FluHMM object. If the chains have not converged, update
should be run
again (or alternatively autoUpdate
). However, parameters beta[2] and beta[3]
(the slopes of the epidemic growth and epidemic decline phases) are naturally slow-mixing and
thus convergence may take longer to achieve. If all other parameters have converged (i.e. the
Gelman-Rubin statistic is below 1.1) but beta[2] and beta[3] have not, it is recommended to
*extend* the sample by running update
with option enlarge=TRUE
.
None. The function mutates its argument ‘x’ directly.
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