Creates table of medical history features — create_clinical_hist

Uses the IDDO-SDTM clinical and adverse events (SA) domain to create a single dataset with various historic clinical information summarised. Historic refers to events that occurred before the study start.

Usage

create_clinical_hist_table(
  dm_domain,
  sa_domain,
  timing_variables = c("SAHR", "SADY", "SASTDY", "VISITDY", "VISITNUM", "VISIT", "EPOCH",
    "SAEVLINT", "SAEVINTX"),
  values_funct = first
)

Arguments

dm_domain

A demographics/DM domain data frame.

sa_domain

A clinical and adverse events/SA domain data frame.

timing_variables

Character list. List of timing variables which are to be used to separate time points, this is hierarchical so the order is taken into account. Default is: SAHR, SADY, SASTDY, VISITDY, VISITNUM, VISIT, EPOCH, SAEVLINT, SAEVINTX.

(using default for example) Each row will be initially summarised based on the –HR (study hour) variable, if that is missing then the –DY (study day) variable is used, and so on. The output will be one row per participant, per time point, where the time point for each row is the first available variable listed in timing_variables.

values_funct

Function. The function which will determine which data row is used in the output, in the event there are multiple rows for the same subject with the same time points (as listed in timing_variables). Default is first(), i.e. if there is two rows from the same day and time, the first record will be taken, the second will be dropped. Choice of timing_variables will impact the number of rows affected.

Value

An analysis dataset, one row per person, per timepoint.

Examples

create_clinical_hist_table(DM_RPTESTB, SA_RPTESTB)
#> [1] "Number of rows where values_fn has been used to pick record in the SA domain: 0"
#> Joining with `by = join_by(STUDYID, USUBJID)`
#> # A tibble: 1 × 6
#>   STUDYID USUBJID     TIME  TIME_SOURCE FEVER_PRESP FEVER_OCCUR
#>   <chr>   <chr>       <chr> <chr>       <chr>       <chr>      
#> 1 RPTESTB RPTESTB_001 -18   STDY        N           Y          

# Change which timing_variables are used to summarise the data
create_clinical_hist_table(DM_RPTESTB, SA_RPTESTB,
                           timing_variables = c("VISITDY", "EPOCH"))
#> [1] "Number of rows where values_fn has been used to pick record in the SA domain: 0"
#> Joining with `by = join_by(STUDYID, USUBJID)`
#> # A tibble: 1 × 6
#>   STUDYID USUBJID     TIME  TIME_SOURCE FEVER_PRESP FEVER_OCCUR
#>   <chr>   <chr>       <chr> <chr>       <chr>       <chr>      
#> 1 RPTESTB RPTESTB_001 1     VISITDY     N           Y