Plot state series of a JAGS state-space model with two seasons

Plot state series of a JAGS state-space model with two seasons

Usage

plotJagsSsm2ss(
  fit,
  ssm_counts,
  linear = TRUE,
  plot_options = list(colors = NULL, pers_theme = NULL)
)

Arguments

fit

A JAGS state-space model fitted to CWAC data

ssm_counts

A data frame with the count data use to fit the state-space model

linear

If TRUE (default) abundance estimates and data are transformed back to its original scale.

plot_options

A list with two elements: colors - the colours of the points that will appear in the plot (two values), and pers_theme - A personalized ggplot theme.

Value

A list with two elements: i) plot: a plot with summer and winter fitted states, as well as the long-term trend, ii) data: the data used to create the individual plots. This is useful for extracting the data used by ggplot to render the plots (e.g. for exporting to the dashboard)

Examples

if (FALSE) {
counts <- barberspan
ssmcounts <- prepSsmData(counts, species = NULL)
fit <- fitCwacSsm(ssmcounts, mod_file = "mymodel.jags",
param = c("beta", "lambda", "sig.zeta",
"sig.w", "sig.eps", "sig.alpha", "sig.e", "mu_t", "mu_wt"))
plotSsm2ss(fit = fit, ssm_counts = ssmcounts)
}