View source: R/mcmcestpars_function.R
This function computes the set up to run the TSIR model, i.e. reconstructes susecptibles and estimates beta and alpha using MCMC computations. Used the same way as estpars.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | mcmcestpars(
data,
xreg = "cumcases",
IP = 2,
regtype = "gaussian",
sigmamax = 3,
seasonality = "standard",
userYhat = numeric(),
update.iter = 10000,
n.iter = 30000,
n.chains = 3,
n.adapt = 1000,
burn.in = 100,
sbar = NULL,
alpha = NULL,
printon = F
)
|
data |
The data frame containing cases and interpolated births and populations. |
xreg |
The x-axis for the regression. Options are 'cumcases' and 'cumbirths'. Defaults to 'cumcases'. |
IP |
The infectious period in weeks. Defaults to 2 weeks. |
regtype |
The type of regression used in susceptible reconstruction. Options are 'gaussian', 'lm' (linear model), 'spline' (smooth.spline with 2.5 degrees freedom), 'lowess' (with f = 2/3, iter = 1), 'loess' (degree 1), and 'user' which is just a user inputed vector. Defaults to 'gaussian' and if that fails then defaults to loess. |
sigmamax |
The inverse kernal width for the gaussian regression. Default is 3. Smaller, stochastic outbreaks tend to need a lower sigma. |
seasonality |
The type of contact to use. Options are standard for 52/IP point contact or schoolterm for just a two point on off contact or none for a single contact parameter. Defaults to standard. |
userYhat |
The inputed regression vector if regtype='user'. Defaults to NULL. |
update.iter |
Number of MCMC iterations to use in the update aspect. Default is 10000. |
n.iter |
Number of MCMC iterations to use. Default is 30000. |
n.chains |
Number of MCMC chains to use. Default is 3. |
n.adapt |
Adaptive number for MCMC. Default is 1000. |
burn.in |
Burn in number. Default is 100. |
sbar |
The mean number of susceptibles. Defaults to NULL, i.e. the function estimates sbar. |
alpha |
The mixing parameter. Defaults to NULL, i.e. the function estimates alpha. |
printon |
Whether to show diagnostic prints or not, defaults to FALSE. |
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