Skip to contents

Create a complete and expanded data frame for tabulating adverse events

Source: R/complete_ae_data.R
dot-complete_ae_data.Rd

Returns a data frame that has an observation for each patient in the study, with combinations for each ID, SOC, and AE. The returned data frame includes new logical columns "..ae.." and "..soc.." indicating whether that row should be included when tabulating the AE table. When multiple AEs of the same type are observed, the AE with the largest by= value is the observation to be used in the tabulation.

Usage

.complete_ae_data(
  data,
  id,
  ae,
  soc = NULL,
  by = NULL,
  strata = NULL,
  id_df = NULL,
  by_values = NULL,
  missing_text = "Unknown",
  missing_location = "first"
)

Arguments

data

Data frame

id

String variable name of the patient ID

ae

String variable name of the adverse event column

soc

Optional string variable name of the system organ class column

by

Optional string variable to split results by, e.g. report AEs by grade or attribution

strata

Optional string 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

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

missing_text

String that will be shown for missing levels of by=, Default is "Unknown"

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 tibble

Examples

df_adverse_events %>%
  .complete_ae_data(
    id = "patient_id",
    ae = "adverse_event",
    soc = "system_organ_class",
    by = "grade",
    strata = "trt"
  )
#> # A tibble: 126 × 7
#>    id    strata soc                                  ae     by    ..soc.. ..ae..
#>    <chr> <chr>  <fct>                                <chr>  <fct> <lgl>   <lgl> 
#>  1 ID 1  Drug B Blood and lymphatic system disorders Anaem… 4     FALSE   TRUE  
#>  2 ID 1  Drug B Blood and lymphatic system disorders Incre… 4     FALSE   FALSE 
#>  3 ID 1  Drug B Blood and lymphatic system disorders Incre… 5     TRUE    TRUE  
#>  4 ID 1  Drug B Blood and lymphatic system disorders Iron … NOT … FALSE   TRUE  
#>  5 ID 1  Drug B Blood and lymphatic system disorders Throm… 1     FALSE   FALSE 
#>  6 ID 1  Drug B Blood and lymphatic system disorders Throm… 3     FALSE   TRUE  
#>  7 ID 1  Drug B Gastrointestinal disorders           Diffi… NOT … FALSE   TRUE  
#>  8 ID 1  Drug B Gastrointestinal disorders           Intes… 1     FALSE   FALSE 
#>  9 ID 1  Drug B Gastrointestinal disorders           Intes… 2     FALSE   TRUE  
#> 10 ID 1  Drug B Gastrointestinal disorders           Myoch… 3     FALSE   FALSE 
#> # ℹ 116 more rows