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Survival Time Analysis

Source: R/survival_time.R
survival_time.Rd

[Stable]

Summarize median survival time and CIs, percentiles of survival times, survival time range of censored/event patients.

Usage

s_surv_time(df, .var, is_event, control = control_surv_time())

a_surv_time(df, .var, is_event, control = control_surv_time())

surv_time(
  lyt,
  vars,
  na_str = NA_character_,
  nested = TRUE,
  ...,
  var_labels = "Time to Event",
  table_names = vars,
  .stats = c("median", "median_ci", "quantiles", "range_censor", "range_event"),
  .formats = NULL,
  .labels = NULL,
  .indent_mods = c(median = 0L, median_ci = 1L, quantiles = 0L, range_censor = 0L,
    range_event = 0L, range = 0L)
)

Arguments

df

(data.frame)
data set containing all analysis variables.

.var

(string)
single variable name that is passed by rtables when requested by a statistics function.

is_event

(logical)
TRUE if event, FALSE if time to event is censored.

control

(list)
parameters for comparison details, specified by using the helper function control_surv_time(). Some possible parameter options are:

  • conf_level (proportion)
    confidence level of the interval for survival time.

  • conf_type (string)
    confidence interval type. Options are "plain" (default), "log", or "log-log", see more in survival::survfit(). Note option "none" is not supported.

  • quantiles (numeric)
    vector of length two to specify the quantiles of survival time.

lyt

(layout)
input layout where analyses will be added to.

vars

(character)
variable names for the primary analysis variable to be iterated over.

na_str

(string)
string used to replace all NA or empty values in the output.

nested

(flag)
whether this layout instruction should be applied within the existing layout structure if possible (TRUE, the default) or as a new top-level element (FALSE). Ignored if it would nest a split. underneath analyses, which is not allowed.

...

additional arguments for the lower level functions.

var_labels

(character)
character for label.

table_names

(character)
this can be customized in case that the same vars are analyzed multiple times, to avoid warnings from rtables.

.stats

(character)
statistics to select for the table.

.formats

(named character or list)
formats for the statistics. See Details in analyze_vars for more information on the "auto" setting.

.labels

(named character)
labels for the statistics (without indent).

.indent_mods

(named vector of integer)
indent modifiers for the labels. Each element of the vector should be a name-value pair with name corresponding to a statistic specified in .stats and value the indentation for that statistic's row label.

Value

  • s_surv_time() returns the statistics:

    • median: Median survival time.

    • median_ci: Confidence interval for median time.

    • quantiles: Survival time for two specified quantiles.

    • range_censor: Survival time range for censored observations.

    • range_event: Survival time range for observations with events.

    • range: Survival time range for all observations.

  • surv_time() returns a layout object suitable for passing to further layouting functions, or to rtables::build_table(). Adding this function to an rtable layout will add formatted rows containing the statistics from s_surv_time() to the table layout.

Functions

  • s_surv_time(): Statistics function which analyzes survival times.

  • a_surv_time(): Formatted analysis function which is used as afun in surv_time().

  • surv_time(): Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper for rtables::analyze().

Examples

library(dplyr)

adtte_f <- tern_ex_adtte %>%
  filter(PARAMCD == "OS") %>%
  mutate(
    AVAL = day2month(AVAL),
    is_event = CNSR == 0
  )
df <- adtte_f %>% filter(ARMCD == "ARM A")

basic_table() %>%
  split_cols_by(var = "ARMCD") %>%
  add_colcounts() %>%
  surv_time(
    vars = "AVAL",
    var_labels = "Survival Time (Months)",
    is_event = "is_event",
    control = control_surv_time(conf_level = 0.9, conf_type = "log-log")
  ) %>%
  build_table(df = adtte_f)
#>                             ARM A          ARM B          ARM C    
#>                             (N=69)         (N=73)         (N=58)   
#> ———————————————————————————————————————————————————————————————————
#> Survival Time (Months)                                             
#>   Median                     32.0           23.9           20.8    
#>     90% CI               (22.6, 46.5)   (18.3, 29.2)   (12.9, 25.9)
#>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1  
#>   Range (censored)       0.8 to 63.5    6.2 to 78.9    3.4 to 52.4 
#>   Range (event)          0.3 to 155.5   0.1 to 154.1   0.6 to 80.7