Description Usage Arguments Value See Also Examples
View source: R/runmcmccountry.R
Run MCMC estimation of a single time series using JAGS.
1 2 3 4 |
df |
A dataframe of x and y observations, and standard errors around ys |
nyears |
number of years of observations |
method |
The method of smoothing to implement (choices: ar, arma, splines, gp) |
order |
The order of splines penalization (either 1 or 2) |
I |
Knot spacing for splines |
matern.cov |
Whether or not to use Matern covariance function. Default is |
obs.err |
is TRUE if standard errors are observed |
measurement.err |
is TRUE if there is assumed to be measurement error |
nchains |
Number of MCMC chains |
nburnin |
Number of iterations to throw away as burn in. |
niter |
Number of total iterations. |
nthin |
Degree of thinning of MCMC chains |
model.file.path |
Text file which contains the model to be fitted. If |
A JAGS model object
1 2 3 4 5 6 7 8 9 10 11 | nyears <- 100
prop.sample <- 0.7
obs.err <- TRUE
sigma.y <- 0.5
seed <- 123
method <- 'splines'
params <- list(sigma.alpha = 1, order = 1)
df <- simulateFluctuations(nyears, prop.sample, method, params, obs.err, sigma.y)
df$se <- 1
mod <- runMCMCCountry(df = df, nyears = 100, method = "splines", order = 1,
nchains = 4, nburnin = 100, niter = 100+3000, nthin = 3)
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