Tabulate Adverse Events

The function tabulates adverse events. One AE per ID will be counted in the resulting table. If a by= variable is passed and a patient experienced more than one of the same AE, the AE associated with the highest by= level will be included. For example, if a patient has two of the same AE and by = grade, the AE with the highest grade will be included. Similarly, if tabulations within system organ class are requested, the AE within SOC associated with the highest grade will be tabulated.

Usage

tbl_ae(
  data,
  id,
  ae,
  soc = NULL,
  by = NULL,
  strata = NULL,
  id_df = NULL,
  statistic = "{n} ({p})",
  by_values = NULL,
  digits = NULL,
  sort = NULL,
  zero_symbol = "\U2014",
  missing_location = c("first", "last", "hide")
)

Arguments

data

Data frame

id

Variable name of the patient ID

ae

Variable name of the adverse event column

soc

Variable name of the system organ class column

by

Variable to split results by, e.g. report AEs by grade

strata

Variable to stratify results by, e.g. report AEs summaries by treatment group

id_df

Optional data frame of complete id values and strata to achieve correct base n for the situation in which not all subjects experience adverse events. See df_patient_characteristics for an example id_df that pairs with df_adverse_events.

statistic

String indicating the statistics that will be reported. The default is "{n} ({p})"

by_values

Optional vector of complete by values, listed in desired order, to achieve correct table structure for the situation in which an adverse event of a certain grade is not observed for a given soc

digits

Specifies the number of decimal places to round the summary statistics. By default integers are shown to zero decimal places, and percentages are formatted with style_percent(). If you would like to modify either of these, pass a vector of integers indicating the number of decimal places to round the statistics. For example, if the statistic being calculated is "{n} ({p}%)" and you want the percent rounded to 2 decimal places use digits = c(0, 2). User may also pass a styling function: digits = style_sigfig

sort

Controls order of AEs and SOCs in output table. The default is NULL, where AEs and SOCs are sorted alphanumerically (and factors sorted according to their factor level). Use sort = "ae" to sort AEs in decreasing frequency order, sort = "soc" to sort SOCs in decreasing order, and sort = c("ae", "soc") to sort both. AEs are sorted within SOC.

zero_symbol

String used to represent cells with zero counts. Default is the em-dash ("\U2014"). Using zero_symbol = NULL will print the zero count statistics, e.g. "0 (0)"

missing_location

location where the column summarizing values with missing levels by= will be located in the final table. Must be one of c("first", "last", "hide). Default is "first"

Value

a 'tbl_ae' object

Example Output

Example 1

Example 2

Examples

# \donttest{
# Example 1 -----------------------------------------------------------------
tbl_ae_ex1 <-
  df_adverse_events %>%
  tbl_ae(
    id = patient_id,
    ae = adverse_event,
    soc = system_organ_class,
    by = grade,
    strata = trt
  ) %>%
  modify_header(all_ae_cols() ~ "**Grade {by}**")

# Example 2 -----------------------------------------------------------------
tbl_ae_ex2 <-
  df_adverse_events %>%
  tbl_ae(
    id = patient_id,
    ae = adverse_event,
    by = grade
  ) %>%
  modify_header(all_ae_cols() ~ "**Grade {by}**")
# }