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Convert a Kaplan-Meier Summary Table to a GraphPad Prism Survival Table

Source: R/km_summary_to_prism.R
km_summary_to_prism.Rd

Expands a summary-by-time table of event and censoring counts (as from `summary(survival::survfit(...))`) into Prism's survival data layout: one row per subject, an `X` column of times, and one column per group holding 1 for an event, 0 for censored, and `NA` for the other groups.

Usage

km_summary_to_prism(
  x,
  sheet = NULL,
  time_col = "time",
  strata_col = "strata",
  n_event_col = "n.event",
  n_censor_col = "n.censor",
  strata_levels = NULL,
  drop_time0 = TRUE,
  validate_totals = TRUE,
  out_xlsx = NULL,
  out_xlsx_paste = NULL
)

Arguments

x

A data frame, or a path to an `.xlsx`, `.xls`, `.csv`, or `.txt` file, with one row per time per group.

sheet

Sheet name or index when `x` is an Excel file.

time_col, strata_col, n_event_col, n_censor_col

Column names of the time, group, number of events, and number censored.

strata_levels

Optional group order for the output columns. Every group in the data must be listed.

drop_time0

Drop rows at time 0 (default `TRUE`).

validate_totals

If `TRUE` (default) and `x` has an `n.risk` column, warn when a group's `n.risk` at its earliest time differs from its total events plus censored.

out_xlsx

Optional path to write the table as Excel (requires `writexl`).

out_xlsx_paste

Optional path to write a copy with blanks instead of `NA`, convenient for pasting into Prism.

Value

A data frame with column `X` and one integer column per group, with a `"notes"` attribute describing the layout.

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  fit <- survival::survfit(survival::Surv(time, status) ~ sex, data = survival::lung)
  s <- summary(fit, censored = TRUE)
  km <- data.frame(time = s$time, strata = s$strata, n.risk = s$n.risk,
                   n.event = s$n.event, n.censor = s$n.censor)
  head(km_summary_to_prism(km))
}
#>    X sex=1 sex=2
#> 1  5    NA     1
#> 2 11     1    NA
#> 3 11     1    NA
#> 4 11     1    NA
#> 5 12     1    NA
#> 6 13     1    NA