fanplot_prediction: Display prediction as a fan plot

In jbracher/hhh4addon: Extensions to endemic-epidemic timeseries modeling from package surveillance

Display prediction as a fan plot

Description

Plots a fanplot to display quantiles of (negative binomial approximations) of the week-wise predictive distributions

Usage

fanplot_prediction(
  pred,
  unit = 1,
  probs = 1:99/100,
  interpolate_probs = TRUE,
  add_observed = TRUE,
  add_pred_means = TRUE,
  fan.col = colorRampPalette(c("darkgreen", "gray90")),
  pt.col = "red",
  pt.cex = 0.6,
  l.col = "black",
  mean_col = "black",
  mean_lty = "dashed",
  ln = NULL,
  rlab = NULL,
  add = FALSE,
  add_legend = FALSE,
  width_legend = 0.1 * (max(pred$timepoints) - min(pred$timepoints))/pred$freq,
  probs_legend = c(1, 25, 50, 75, 99)/100,
  ylim = NULL,
  xlab = "t",
  ylab = "No. infected",
  return_matrix = FALSE,
  ...
)

Arguments

pred	the prediction as returned by longterm_prediction_hhh4 (and potentially aggregated using aggregate_prediction)
unit	numeric denoting the unit to display
probs	vector of probabilities: which quantiles shall be displayed in the fan plot?
interpolate_probs	logical: smooth curves by simple interpolation of quantiles
add_observed	logical: shall observed values be added?
fan.col, ln, rlab	graphical parameters passed on to fanplot::fan
pt.col, pt.cex, l.col	graphical parameters for display of observed values
add	logical: add to existing plot?
add_legend	logical: shall a color key legend be added?
width_legend	width of box for color key legend in user coordinates
probs_legend	vecor of probabilities to display in the legend
ylim	limit for the y-axis, passed to plot()
xlab, ylab	axis labels
return_matrix	logical: return matrix passed to fanplot::fan; useful to make more sophisticated plots.
...	other arguments passed on to plot()

Value

Only if return_matrix set to TRUE: the matrix passed to fanplot::fan

Examples

data("salmonella.agona")
# convert old "disProg" to new "sts" data class:
salmonella <- disProg2sts(salmonella.agona)
control_salmonella <- list(end = list(f = addSeason2formula(~ 1), lag = 1),
                           ar = list(f = addSeason2formula(~ 1), lag = 1),
                           family = "NegBinM", subset = 6:250)
fit_salmonella <- hhh4_lag(salmonella, control_salmonella) # fit model
# obtain prediction:
pred_mom <- predictive_moments(fit_salmonella, t_condition = 250, lgt = 52)
# plot the prediction only:
fanplot_prediction(pred_mom, add_legend = TRUE)
# or plot it along with the fit:
plot(fit_salmonella)
fanplot_prediction(pred_mom, add = TRUE) # add fan plot

jbracher/hhh4addon documentation built on Feb. 16, 2024, 1:45 a.m.