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Summary Table

Source: R/summary-table.R
summary_table.Rd

summary_table() summarises clinical variables into a report table using data.table as backend.

Usage

summary_table(
  dt,
  target,
  treat,
  target_name = target,
  indent = nbsp(n = 4L),
  .total_dt = dt,
  pct_dec = 1,
  treat_order = NULL,
  skip_absent = TRUE,
  inc_missing = TRUE
)

Arguments

dt

A data.frame containing, at least, the variables indicated in target and treat.

target

Target variable passed as a string for which summary statistics are to be calculated.

treat

A string indicating the grouping variable, e.g. the variable specifying the treatment population.

target_name

Heading for the target variable as a string. Defaults to target.

indent

A string to be used as indentation of summary statistics labels. Defaults to four HTML non-breaking spaces ( ).

.total_dt

Separate table from dt from which to derive total counts per group.

pct_dec

Decimal places for reported figures.

treat_order

Customise the column order of the output table.

skip_absent

Whether to ignore variables passed in treat_order that are absent from dt. Default is TRUE; FALSE will throw an error in case there are missing variables.

inc_missing

If any of the target variables are numeric, then used as a toggle to determine whether or not "Missing" appears in the summary stats:

TRUE

(default) The Missing row is always displayed

NA

The Missing row is only displayed if any missing values are present

FALSE

The Missing row is never included in the table

Value

A data.table of summary statistics. The format depends on the type of the target variable:

  • If the target variable is categorical, i.e. type character, factor or logical then the output is that of calc_counts().

  • If the target variable is numeric, then the output is that of calc_desc().

See also

tern_summary_table()

Examples

dmg_vars <- c("AGE", "RACE", "ETHNIC")
dmg_var_lbls <- c("Age (yr)", "Race", "Ethnicity")

# Demographics table (DMT01)
summary_table(
  adsl,
  target = dmg_vars,
  treat = 'ARM',
  target_name = dmg_var_lbls
)
#>                                                                 stats
#>                                                                <char>
#>  1:                                                          Age (yr)
#>  2:                                         &nbsp;&nbsp;&nbsp;&nbsp;n
#>  3:                                 &nbsp;&nbsp;&nbsp;&nbsp;Mean (SD)
#>  4:                                    &nbsp;&nbsp;&nbsp;&nbsp;Median
#>  5:                                  &nbsp;&nbsp;&nbsp;&nbsp;Min, Max
#>  6:                                   &nbsp;&nbsp;&nbsp;&nbsp;Missing
#>  7:                                                              Race
#>  8:          &nbsp;&nbsp;&nbsp;&nbsp;AMERICAN INDIAN OR ALASKA NATIVE
#>  9:                                     &nbsp;&nbsp;&nbsp;&nbsp;ASIAN
#> 10:                 &nbsp;&nbsp;&nbsp;&nbsp;BLACK OR AFRICAN AMERICAN
#> 11:                                  &nbsp;&nbsp;&nbsp;&nbsp;MULTIPLE
#> 12: &nbsp;&nbsp;&nbsp;&nbsp;NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
#> 13:                                     &nbsp;&nbsp;&nbsp;&nbsp;OTHER
#> 14:                                   &nbsp;&nbsp;&nbsp;&nbsp;UNKNOWN
#> 15:                                     &nbsp;&nbsp;&nbsp;&nbsp;WHITE
#> 16:                                                         Ethnicity
#> 17:                        &nbsp;&nbsp;&nbsp;&nbsp;HISPANIC OR LATINO
#> 18:                    &nbsp;&nbsp;&nbsp;&nbsp;NOT HISPANIC OR LATINO
#> 19:                              &nbsp;&nbsp;&nbsp;&nbsp;NOT REPORTED
#> 20:                                   &nbsp;&nbsp;&nbsp;&nbsp;UNKNOWN
#>                                                                 stats
#>                                                                <char>
#>       A: Drug X  B: Placebo C: Combination
#>          <char>      <char>         <char>
#>  1:                                       
#>  2:         134         134            132
#>  3:  33.8 (6.6)  35.4 (7.9)     35.4 (7.7)
#>  4:          33          35             35
#>  5:  21.0, 50.0  21.0, 62.0     20.0, 69.0
#>  6:           0           0              0
#>  7:                                       
#>  8:    8 (6.0%)   11 (8.2%)       6 (4.5%)
#>  9:  68 (50.7%)  67 (50.0%)     73 (55.3%)
#> 10:  31 (23.1%)  28 (20.9%)     32 (24.2%)
#> 11:           0    1 (0.7%)              0
#> 12:           0    1 (0.7%)              0
#> 13:           0           0              0
#> 14:           0           0              0
#> 15:  27 (20.1%)  26 (19.4%)     21 (15.9%)
#> 16:                                       
#> 17:  15 (11.2%)  18 (13.4%)     15 (11.4%)
#> 18: 104 (77.6%) 103 (76.9%)    101 (76.5%)
#> 19:    6 (4.5%)   10 (7.5%)      11 (8.3%)
#> 20:    9 (6.7%)    3 (2.2%)       5 (3.8%)
#>       A: Drug X  B: Placebo C: Combination
#>          <char>      <char>         <char>

# Demographics table (DMT01) with continuous variable (e.g., BMRKR1)
summary_table(
  adsl,
  target = c(dmg_vars, "BMRKR1"),
  treat = 'ARM',
  target_name = c(dmg_var_lbls, "Biomarker 1")
)
#>                                                                 stats
#>                                                                <char>
#>  1:                                                          Age (yr)
#>  2:                                         &nbsp;&nbsp;&nbsp;&nbsp;n
#>  3:                                 &nbsp;&nbsp;&nbsp;&nbsp;Mean (SD)
#>  4:                                    &nbsp;&nbsp;&nbsp;&nbsp;Median
#>  5:                                  &nbsp;&nbsp;&nbsp;&nbsp;Min, Max
#>  6:                                   &nbsp;&nbsp;&nbsp;&nbsp;Missing
#>  7:                                                              Race
#>  8:          &nbsp;&nbsp;&nbsp;&nbsp;AMERICAN INDIAN OR ALASKA NATIVE
#>  9:                                     &nbsp;&nbsp;&nbsp;&nbsp;ASIAN
#> 10:                 &nbsp;&nbsp;&nbsp;&nbsp;BLACK OR AFRICAN AMERICAN
#> 11:                                  &nbsp;&nbsp;&nbsp;&nbsp;MULTIPLE
#> 12: &nbsp;&nbsp;&nbsp;&nbsp;NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
#> 13:                                     &nbsp;&nbsp;&nbsp;&nbsp;OTHER
#> 14:                                   &nbsp;&nbsp;&nbsp;&nbsp;UNKNOWN
#> 15:                                     &nbsp;&nbsp;&nbsp;&nbsp;WHITE
#> 16:                                                         Ethnicity
#> 17:                        &nbsp;&nbsp;&nbsp;&nbsp;HISPANIC OR LATINO
#> 18:                    &nbsp;&nbsp;&nbsp;&nbsp;NOT HISPANIC OR LATINO
#> 19:                              &nbsp;&nbsp;&nbsp;&nbsp;NOT REPORTED
#> 20:                                   &nbsp;&nbsp;&nbsp;&nbsp;UNKNOWN
#> 21:                                                       Biomarker 1
#> 22:                                         &nbsp;&nbsp;&nbsp;&nbsp;n
#> 23:                                 &nbsp;&nbsp;&nbsp;&nbsp;Mean (SD)
#> 24:                                    &nbsp;&nbsp;&nbsp;&nbsp;Median
#> 25:                                  &nbsp;&nbsp;&nbsp;&nbsp;Min, Max
#> 26:                                   &nbsp;&nbsp;&nbsp;&nbsp;Missing
#>                                                                 stats
#>                                                                <char>
#>       A: Drug X  B: Placebo C: Combination
#>          <char>      <char>         <char>
#>  1:                                       
#>  2:         134         134            132
#>  3:  33.8 (6.6)  35.4 (7.9)     35.4 (7.7)
#>  4:          33          35             35
#>  5:  21.0, 50.0  21.0, 62.0     20.0, 69.0
#>  6:           0           0              0
#>  7:                                       
#>  8:    8 (6.0%)   11 (8.2%)       6 (4.5%)
#>  9:  68 (50.7%)  67 (50.0%)     73 (55.3%)
#> 10:  31 (23.1%)  28 (20.9%)     32 (24.2%)
#> 11:           0    1 (0.7%)              0
#> 12:           0    1 (0.7%)              0
#> 13:           0           0              0
#> 14:           0           0              0
#> 15:  27 (20.1%)  26 (19.4%)     21 (15.9%)
#> 16:                                       
#> 17:  15 (11.2%)  18 (13.4%)     15 (11.4%)
#> 18: 104 (77.6%) 103 (76.9%)    101 (76.5%)
#> 19:    6 (4.5%)   10 (7.5%)      11 (8.3%)
#> 20:    9 (6.7%)    3 (2.2%)       5 (3.8%)
#> 21:                                       
#> 22:         134         134            132
#> 23:   6.0 (3.6)   5.7 (3.3)      5.6 (3.5)
#> 24:         5.4         4.8            4.6
#> 25:   0.4, 17.7   0.6, 14.2      0.2, 21.4
#> 26:           0           0              0
#>       A: Drug X  B: Placebo C: Combination
#>          <char>      <char>         <char>