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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 

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. Run get_stats("surv_time") to see available statistics for this function.

.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.

    • 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

  • 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  25% and 75%-ile     17.4, 65.3          0  25% and 75%-ile
#> 4 Range (censored)    0.8 to 63.5          0 Range (censored)
#> 5    Range (event)   0.3 to 155.5          0    Range (event)
#> 6            Range   0.3 to 155.5          0            Range