Incidence Rate

Usage

s_incidence_rate(
  df,
  .var,
  n_events,
  is_event,
  control = control_incidence_rate()
)

a_incidence_rate(
  df,
  .var,
  n_events,
  is_event,
  control = control_incidence_rate()
)

estimate_incidence_rate(
  lyt,
  vars,
  ...,
  show_labels = "hidden",
  table_names = vars,
  .stats = NULL,
  .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.

n_events

(integer)
number of events observed.

is_event

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

control

(list)
parameters for estimation details, specified by using the helper function control_incidence_rate(). Possible parameter options are:

• conf_level (proportion)
  confidence level for the estimated incidence rate.

• conf_type (string)
  normal (default), normal_log, exact, or byar for confidence interval type.

• time_unit_input (string)
  day, week, month, or year (default) indicating time unit for data input.

• time_unit_output (numeric)
  time unit for desired output (in person-years).

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.

show_labels

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

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. Defaults to 0, which corresponds to the unmodified default behavior. Can be negative.

person_years

(numeric)
total person-years at risk.

alpha

(numeric)
two-sided alpha-level for confidence interval.

Value

• s_incidence_rate() returns the following statistics:

  • person_years: Total person-years at risk.

  • n_events: Total number of events observed.

  • rate: Estimated incidence rate.

  • rate_ci: Confidence interval for the incidence rate.

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

• estimate_incidence_rate() 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_incidence_rate() to the table layout.

Functions

• s_incidence_rate(): Statistics function which estimates the incidence rate and the associated confidence interval.

• a_incidence_rate(): Formatted analysis function which is used as afun in estimate_incidence_rate().

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

See also

Examples

library(dplyr)

df <- data.frame(
  USUBJID = as.character(seq(6)),
  CNSR = c(0, 1, 1, 0, 0, 0),
  AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),
  ARM = factor(c("A", "A", "A", "B", "B", "B"))
) %>%
  mutate(is_event = CNSR == 0) %>%
  mutate(n_events = as.integer(is_event))

# Internal function - s_incidence_rate
if (FALSE) {
s_incidence_rate(
  df,
  .var = "AVAL",
  n_events = "n_events",
  control = control_incidence_rate(
    time_unit_input = "month",
    time_unit_output = 100
  )
)
}

# Internal function - a_incidence_rate
if (FALSE) {
a_incidence_rate(
  df,
  .var = "AVAL",
  n_events = "n_events",
  control = control_incidence_rate(time_unit_input = "month", time_unit_output = 100)
)
}

basic_table() %>%
  split_cols_by("ARM") %>%
  add_colcounts() %>%
  estimate_incidence_rate(
    vars = "AVAL",
    n_events = "n_events",
    control = control_incidence_rate(
      time_unit_input = "month",
      time_unit_output = 100
    )
  ) %>%
  build_table(df)
#>                                            A                 B       
#>                                          (N=3)             (N=3)     
#> —————————————————————————————————————————————————————————————————————
#> Total patient-years at risk               3.8               5.2      
#> Number of adverse events observed          1                 3       
#> AE rate per 100 patient-years            26.20             57.23     
#> 95% CI                              (-25.15, 77.55)   (-7.53, 122.00)