Setup data to support the specified column type

tlgsetup is useful for pre-processing total columns and columns composed of other columns. tlgsetup is called internally by generate_results() and can be run manually for custom tables.

Usage

tlgsetup(
  df,
  var,
  column_metadata_file = NULL,
  column_metadata = NULL,
  tbltype = NULL
)

Arguments

df

dataframe of records for analysis

var

character vector that identifies the numeric column/treatment variable

column_metadata_file

A file containing the column metadata. Read in with readxl::read_excel(). If a column_metadata dataframe is passed in too, this is ignored.

column_metadata

A dataframe containing the column metadata. This will be used in place of column_metadata_file.

tbltype

A value used to subset the column_metadata, both this and the file requirements are needed to bind the data to the table.

Value

dataframe with observations added to support the column type as well as the factor variable colnbr which is used as our new column summary variable. Regardless of if a coldef exists in data, the column will exist in the table.

Examples

df <-
  tibble::tribble(
  ~TRT01AN, ~USUBJID,
  0,        "A",
 54,       "B",
 81,       "C"
)

tlgsetup(df, "TRT01AN", column_metadata = column_metadata)
#> # A tibble: 16 × 4
#>    tbltype colnbr TRT01AN USUBJID
#>    <chr>   <fct>  <chr>   <chr>  
#>  1 type1   col1   0       A      
#>  2 type1   col2   54      B      
#>  3 type1   col3   81      C      
#>  4 type2   col4   0       A      
#>  5 type2   col5   54      B      
#>  6 type2   col6   81      C      
#>  7 type2   col7   54      B      
#>  8 type2   col7   81      C      
#>  9 type3   col8   0       A      
#> 10 type3   col9   54      B      
#> 11 type3   col10  81      C      
#> 12 type3   col11  54      B      
#> 13 type3   col11  81      C      
#> 14 type3   col12  0       A      
#> 15 type3   col12  54      B      
#> 16 type3   col12  81      C      

# Using a dataframe of column metadata
column_metadata <-
  tibble::tribble(
    ~tbltype, ~coldef, ~decode,                ~span1,
    "type1",  "0",     "Placebo",              "",
    "type1",  "54",    "Low Dose",             "Xanomeline",
    "type1",  "81",    "High Dose",            "Xanomeline",
    "type1",  "54+81", "Total Xanomeline",     ""
  )

tlgsetup(df, "TRT01AN", column_metadata = column_metadata)
#> # A tibble: 5 × 4
#>   tbltype colnbr TRT01AN USUBJID
#>   <chr>   <fct>  <chr>   <chr>  
#> 1 type1   col1   0       A      
#> 2 type1   col2   54      B      
#> 3 type1   col3   81      C      
#> 4 type1   col4   54      B      
#> 5 type1   col4   81      C