Plot Cumulative Risk Trajectories Over Time

Draw cumulative-risk trajectories over time for natural-course and intervention scenarios from a tvcQGcomp run object or a pre-summarized trajectory table. This is the primary plotting function for cumulative incidence.

Usage

plot_cumulative_risk_trajectory(
  x,
  include_natural = TRUE,
  natural_label = "Natural Course",
  include_average = FALSE,
  average_scenarios = paste0("Q", 0:3),
  average_label = "Average (Q0-Q3)",
  average_col = "black",
  scenario_col = "scenario",
  time_col = "TimeInn",
  risk_col = "mean_risk",
  percent = TRUE,
  scenario_order = NULL,
  scenario_labels = NULL,
  cols = NULL,
  include_points = TRUE,
  pch = 16,
  lwd = 2,
  xlab = "Follow-up time",
  ylab = if (percent) "Cumulative Risk (pct)" else "Cumulative Risk",
  main = "Cumulative risk over time",
  legend_pos = "topleft",
  ...
)

Arguments

x

A tvcQGcomp run object or a data.frame/data.table containing summarized risk trajectories.

include_natural

Logical; when x is a run object, include the natural-course curve if available.

natural_label

Label to use for the natural-course curve in the legend.

include_average

Logical; add a line for the average of average_scenarios at each follow-up time.

average_scenarios

Character vector of scenario names to average. Defaults to Q0 through Q3.

average_label

Legend label for the averaged trajectory.

average_col

Color for the averaged trajectory when cols is not supplied.

scenario_col

Name of the scenario column.

time_col

Name of the follow-up time column.

risk_col

Name of the cumulative risk column to plot.

percent

Logical; if TRUE, plot risk on the percent scale.

scenario_order

Optional character vector giving the desired plotting order of scenarios.

scenario_labels

Optional replacement labels for scenarios. May be a character vector named by scenario or an unnamed vector with one label per scenario.

cols

Optional vector of plotting colors. May be named by scenario.

include_points

Logical; whether to add points at each time value.

pch

Point character used when include_points = TRUE.

lwd

Line width.

xlab

X-axis label.

ylab

Y-axis label.

main

Plot title.

legend_pos

Legend position passed to legend.

...

Additional arguments passed to plot.

Value

The plotting helper returns the plotted data invisibly.

Examples

if (FALSE) { # \dontrun{
res <- tvcQGComp_survival(NO2_dt, cfg, mc_size = 100, seed = 1234)
plot_cumulative_risk_trajectory(res)
plot_cumulative_risk_trajectory(res, include_natural = FALSE, include_average = TRUE)
} # }