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Plot cumulative incidence of mortality and exposure states

Source: R/plot_survival_mort.R
plot_surv_mort.Rd

Estimates cumulative incidence curves for mortality before and after exposure using competing risks and multistate survival models. The function constructs follow-up time variables, models exposure as a time-dependent event, and produces a publication-ready cumulative incidence plot.

Usage

plot_surv_mort(
  dpop,
  censoring_date,
  lines = c("Death after exposure", "Death without exposure", "Overall mortality",
    "Ever exposed", "Total mortality among exposed")
)

Arguments

dpop

Data frame containing the study population and follow-up information.

censoring_date

Date. Administrative censoring date for follow-up.

lines

Character vector specifying which curves to include in the plot. Default options are:

  • `"Death after exposure"`

  • `"Death without exposure"`

  • `"Overall mortality"`

  • `"Ever exposed"`

  • `"Total mortality among exposed"`

Value

A list containing:

  • `data` Data frame used for plotting cumulative incidence curves.

  • `plot` A `ggplot2` object containing the cumulative incidence plot.

Details

Follow-up starts at `resp.DATE` and ends at the earliest of: death, migration, or the administrative censoring date.

Exposure is treated as a time-dependent event using `survival::tmerge`. The function estimates:

* Competing risk models for exposure and death before exposure * Multistate models for death after exposure

When events occur at identical time points (e.g., exposure and death on the same day), small time offsets are introduced to avoid numerical issues in survival estimation.

The resulting curves represent cumulative incidence for:

* Death without exposure * Death after exposure * Overall mortality * Exposure incidence

Required variables in `dpop`

| Variable | Description | |——–|————-| | `ID` | Unique individual identifier | | `resp.DATE` | Start of follow-up (index/response date) | | `exp.DATE` | Exposure date | | `DATE_DEATH` | Date of death | | `DATE_MIGRATION` | Date of emigration or loss to follow-up |

Examples

if (FALSE) { # \dontrun{
res <- plot_surv_mort(
  dpop = population_data,
  censoring_date = as.Date("2023-12-31")
)

# Show plot
res$plot

# Access plotting data
head(res$data)
} # }