Survival time analysis — survival

The analyze function surv_time() creates a layout element to analyze survival time by calculating survival time median, median confidence interval, quantiles, and range (for all, censored, or event patients). The primary analysis variable vars is the time variable and the secondary analysis variable is_event indicates whether or not an event has occurred.

Usage

surv_time(
  lyt,
  vars,
  is_event,
  control = control_surv_time(),
  ref_fn_censor = TRUE,
  na_str = default_na_str(),
  nested = TRUE,
  ...,
  var_labels = "Time to Event",
  show_labels = "visible",
  table_names = vars,
  .stats = c("median", "median_ci", "quantiles", "range"),
  .formats = NULL,
  .labels = NULL,
  .indent_mods = c(median_ci = 1L)
)

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

a_surv_time(
  df,
  labelstr = "",
  .var = NULL,
  .df_row = NULL,
  is_event,
  control = control_surv_time(),
  ref_fn_censor = TRUE,
  .stats = NULL,
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL,
  na_str = default_na_str()
)

Arguments

lyt

(PreDataTableLayouts)
layout that analyses will be added to.

vars

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

is_event

(flag)
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.

ref_fn_censor

(flag)
whether referential footnotes indicating censored observations should be printed when the range statistic is included.

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)
variable labels.

show_labels

(string)
label visibility: one of "default", "visible" and "hidden".

table_names

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

.stats

(character)
statistics to select for the table.

Options are: 'median', 'median_ci', 'median_ci_3d', 'quantiles', 'quantiles_lower', 'quantiles_upper', 'range_censor', 'range_event', 'range'

.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 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.

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.

labelstr

(string)
label of the level of the parent split currently being summarized (must be present as second argument in Content Row Functions). See rtables::summarize_row_groups() for more information.

.df_row

(data.frame)
data frame across all of the columns for the given row split.

Value

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.

s_surv_time() returns the statistics:
- median: Median survival time.
- median_ci: Confidence interval for median time.
- median_ci_3d: Median with confidence interval for median time.
- quantiles: Survival time for two specified quantiles.
- quantiles_lower: quantile with confidence interval for the first specified quantile.
- quantiles_upper: quantile with confidence interval for the second specified quantile.
- range_censor: Survival time range for censored observations.
- range_event: Survival time range for observations with events.
- range: Survival time range for all observations.

a_surv_time() returns the corresponding list with formatted rtables::CellValue().

Functions

surv_time(): Layout-creating function which can take statistics function arguments and additional format arguments. This function is a wrapper for rtables::analyze().
s_surv_time(): Statistics function which analyzes survival times.
a_surv_time(): Formatted analysis function which is used as afun in surv_time().

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                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7 

a_surv_time(
  df,
  .df_row = df,
  .var = "AVAL",
  is_event = "is_event"
)
#> RowsVerticalSection (in_rows) object print method:
#> ----------------------------
#>           row_name     formatted_cell indent_mod        row_label
#> 1           Median               32.0          0           Median
#> 2           95% CI       (22.5, 49.3)          0           95% CI
#> 3  Median (95% CI) 32.0 (22.5 - 49.3)          0  Median (95% CI)
#> 4  25% and 75%-ile         17.4, 65.3          0  25% and 75%-ile
#> 5 25%-ile (95% CI) 17.4 (10.1 - 22.5)          0 25%-ile (95% CI)
#> 6 75%-ile (95% CI) 65.3 (49.3 - 87.2)          0 75%-ile (95% CI)
#> 7 Range (censored)        0.8 to 63.5          0 Range (censored)
#> 8    Range (event)       0.3 to 155.5          0    Range (event)
#> 9            Range       0.3 to 155.5          0            Range