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Add risk tables to visR plots through an S3 method

Source: R/add_risktable.R
add_risktable.Rd

S3 method for adding risk tables to visR plots. The function has following workflow:

  • The risktables are calculated using get_risktable

  • The risktables are placed underneath visR plots using plot_grid

  • Both the initial visR plot as the individual risktables are stored as attribute component in the final object to allow post-modification of the individual plots if desired

Usage

add_risktable(gg, ...)

# S3 method for ggsurvfit
add_risktable(
  gg,
  times = NULL,
  statlist = "n.risk",
  label = NULL,
  group = "strata",
  collapse = FALSE,
  rowgutter = 0.16,
  ...
)

# S3 method for ggtidycuminc
add_risktable(
  gg,
  times = NULL,
  statlist = "n.risk",
  label = NULL,
  group = "strata",
  collapse = FALSE,
  rowgutter = 0.16,
  ...
)

Arguments

gg

visR plot of class ggsurvfit or ggtidycmprsk

...

other arguments passed on to the method add_risktable

times

Numeric vector indicating the times at which the risk set, censored subjects, events are calculated.

statlist

Character vector indicating which summary data to present. Current choices are "n.risk" "n.event" "n.censor", "cum.event", "cum.censor". Default is "n.risk".

label

Character vector with labels for the statlist. Default matches "n.risk" with "At risk", "n.event" with "Events", "n.censor" with "Censored", "cum.event" with "Cum. Event", and "cum.censor" with "Cum. Censor".

group

String indicating the grouping variable for the risk tables. Current options are:

  • "strata": groups the risk tables per stratum. The label specifies the label within each risk table. The strata levels are used for the titles of the risk tables. This is the default

  • "statlist": groups the risk tables per statlist. The label specifies the title for each risk table. The strata levels are used for labeling within each risk table.

Default is "strata".

collapse

Boolean, indicates whether to present the data overall. Default is FALSE.

rowgutter

A numeric relative value between 0 and 1 indicates the height used by the table versus the height used by the plot, as described in cowplot::plot_grid(rel_heights=). The default is 0.16.

Value

Object of class ggplot with added risk table.

See also

plot_grid

Examples


## Display 2 risk tables, 1 per statlist
adtte %>%
  visR::estimate_KM(strata = "TRTP") %>%
  visR::visr() %>%
  visR::add_risktable(
    label = c("Subjects at Risk", "Censored"),
    statlist = c("n.risk", "n.censor", "n.event"),
    group = "statlist"
  )


## Display overall risk table at selected times
adtte %>%
  visR::estimate_KM(strata = "TRTP") %>%
  visR::visr() %>%
  visR::add_risktable(
    label = c("Subjects at Risk", "Censored"),
    statlist = c("n.risk", "n.censor"),
    collapse = TRUE,
    times = c(0, 20, 40, 60)
  )


## Add risk set as specified times
adtte %>%
  visR::estimate_KM(strata = "TRTP") %>%
  visR::visr() %>%
  visR::add_risktable(times = c(0, 20, 40, 100, 111, 200))