Survival Time Analysis

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,
  ...,
  var_labels = "Time to Event",
  table_names = vars,
  .stats = c("median", "median_ci", "quantiles", "range_censor", "range_event"),
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

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.

...

additional arguments for the lower level functions.

var_labels

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.

.labels

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

.indent_mods

(named integer)
indent modifiers for the labels.

Value

The statistics are:

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.

Functions

• s_surv_time(): Statistics Function which analyzes survival times. range_censor and range_event.

• a_surv_time(): Formatted Analysis function which can be further customized by calling rtables::make_afun() on it. It is used as afun in rtables::analyze().

• surv_time(): Analyze Function which adds the survival times analysis to the input layout. Note that additional formatting arguments can be used here.

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")

# Internal function - s_surv_time
if (FALSE) {
s_surv_time(df, .var = "AVAL", is_event = "is_event")
}

# Internal function - a_surv_time
if (FALSE) {
a_surv_time(df, .var = "AVAL", is_event = "is_event")
}

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