Counting Patients and Events in Columns

Usage

s_count_patients_and_multiple_events(
  df,
  id,
  filters_list,
  empty_stats = character(),
  labelstr = "",
  custom_label = NULL
)

summarize_patients_events_in_cols(
  lyt,
  id = "USUBJID",
  filters_list = list(),
  ...,
  .stats = c("unique", "all", names(filters_list)),
  .labels = c(unique = "Patients (All)", all = "Events (All)",
    labels_or_names(filters_list)),
  col_split = TRUE
)

Arguments

df

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

id

(string)
subject variable name.

filters_list

(named list of character)
each element in this list describes one type of event describe by filters, in the same format as s_count_patients_with_event(). If it has a label, then this will be used for the column title.

empty_stats

(character)
optional names of the statistics that should be returned empty such that corresponding table cells will stay blank.

labelstr

(character)
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.

custom_label

(string or NULL)
if provided and labelstr is empty then this will be used as label.

lyt

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

...

additional arguments for the lower level functions.

.stats

(character)
statistics to select for the table.

.labels

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

col_split

(flag)
whether the columns should be split. Set to FALSE when the required column split has been done already earlier in the layout pipe.

Value

• s_count_patients_and_multiple_events() returns a list with the statistics:

  • unique: number of unique patients in df.

  • all: number of rows in df.

  • one element with the same name as in filters_list: number of rows in df, i.e. events, fulfilling the filter condition.

• summarize_patients_events_in_cols() 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 content rows containing the statistics from s_count_patients_and_multiple_events() to the table layout.

Functions

• s_count_patients_and_multiple_events(): Statistics function which counts numbers of patients and multiple events defined by filters. Used as analysis function afun in summarize_patients_events_in_cols().

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

Examples

# `s_count_patients_and_multiple_events()`
df <- data.frame(
  USUBJID = rep(c("id1", "id2", "id3", "id4"), c(2, 3, 1, 1)),
  ARM = c("A", "A", "B", "B", "B", "B", "A"),
  AESER = rep("Y", 7),
  AESDTH = c("Y", "Y", "N", "Y", "Y", "N", "N"),
  AEREL = c("Y", "Y", "N", "Y", "Y", "N", "Y"),
  AEDECOD = c("A", "A", "A", "B", "B", "C", "D"),
  AEBODSYS = rep(c("SOC1", "SOC2", "SOC3"), c(3, 3, 1))
)

# Internal function - s_count_patients_and_multiple_events
if (FALSE) {
s_count_patients_and_multiple_events(
  df = df,
  id = "USUBJID",
  filters_list = list(
    serious = c(AESER = "Y"),
    fatal = c(AESDTH = "Y")
  )
)
}

# `summarize_patients_events_in_cols()`
basic_table() %>%
  summarize_patients_events_in_cols(
    filters_list = list(
      related = formatters::with_label(c(AEREL = "Y"), "Events (Related)"),
      fatal = c(AESDTH = "Y"),
      fatal_related = c(AEREL = "Y", AESDTH = "Y")
    ),
    custom_label = "%s Total number of patients and events"
  ) %>%
  build_table(df)
#>                                          Patients (All)   Events (All)   Events (Related)   fatal   fatal_related
#> —————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#> %s Total number of patients and events         4               7                5             4           4