Skip to contents

Plot the route-decomposed effective reproductive number over time

Source: R/plot_Reff.R
plot_Reff.Rd

Renders the per-location R_eff(t) produced by calc_Reff or add_reproductive_numbers. When the input carries the route components (estimand "R_hum" and "R_env") and routes = TRUE, the environmental reproductive number is drawn as a filled area from zero and the human-to-human contribution is stacked on top of it, so the upper edge is the total \(R_{eff} = R_{env} + R_{hum}\) (purple line) and the height of the orange band is how much human transmission adds. A dashed reference line marks \(R_{eff} = 1\). Without route rows (older artifacts) the total alone is drawn.

Usage

plot_Reff(
  reff,
  show_iqr = FALSE,
  smooth_days = 14L,
  title = NULL,
  ncol = NULL,
  base_size = 12,
  routes = TRUE
)

Arguments

reff

A reproductive_numbers data.frame with columns location, date, central, optionally estimand and the quantile columns. Leading rows with a non-finite total are dropped per location.

show_iqr

Logical. Also draw the inner 50% (q25-q75) total-R band. Default FALSE.

smooth_days

Integer. Centered rolling-mean window (days) for the displayed series; 1 plots the raw daily values. Default 14.

title

Character or NULL for the default title.

ncol

Integer facet columns for multi-location input (NULL: min(3, n_locations)).

base_size

Numeric base font size for theme_mosaic.

routes

Logical. Stack R_env and R_hum under the total when present. Default TRUE.

Value

A ggplot object (not printed or saved).

Details

Headline series. On the re-simulation path central is the MEDOID trajectory's R_t (a coherent member, preserving peak timing and height); on the direct path it is the renewal on weighted-median incidence. The daily series is noisy, so each component is shown as a centered smooth_days rolling mean, taken over the days on which the total is defined (a silent route counts as 0 there, as in calc_Reff()) so the smoothed stack still sums to the smoothed total, with the raw daily total as a faint background line.

Faint band. When populated, the q2.5-q97.5 total-R band is the per-calendar-date range across members. Member peaks are phase-misaligned, so it does not show the epidemic's peak R_t; the per-member peak statistic (attr peak_Rt) is annotated instead.

See also

calc_Reff, add_reproductive_numbers.

Examples

if (FALSE) { # \dontrun{
tr  <- readRDS("2_calibration/trajectories_ensemble.rds")
# The medoid config carries the calibrated kernel and decay rates; the base
# 1_inputs/config.json holds prior centres (see add_reproductive_numbers()).
cfg <- jsonlite::fromJSON("2_calibration/best_model/config_medoid.json")
print(plot_Reff(calc_Reff(tr, cfg)))
} # }