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Calculate descriptive summary statistics for a numeric variable

calc_desc.Rd

calc_desc() summarises a numeric variable (target) by another (treat) and reports summary statistics in clinical trial reporting format. The following statistics are calculated for target, per group, i.e. by variable treat levels:

  • n: number of observations

  • Mean (SD): mean and standard deviation of target

  • Median: median of target

  • Min, Max: minimum and maximum of target

  • Missing: number of missing target values

Usage

calc_desc(
  dt,
  target,
  target_name = target,
  treat,
  indent = nbsp(n = 4L),
  pct_dec = 1
)

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.

target_name

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

treat

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

indent

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

pct_dec

Decimal places for reported figures.

Value

A list containing a data.table formatted as follows:

  • First column is named stats and contains the target variable name indicated in target in the first row. Subsequent rows contain the summarised statistics labels.

  • Other columns are for the levels of the grouping variable (treat).

  • All columns are of character type.

This table is structured for easy integration with Shiny output widgets.

Examples

# Calculate summary statistics for the age of the subjects in each region.
calc_stats(dt = adsl, "AGE", treat = "REGION1")[[1]]
#>                                stats     Africa       Asia    Eurasia
#>                               <char>     <char>     <char>     <char>
#> 1:                               AGE                                 
#> 2:         &nbsp;&nbsp;&nbsp;&nbsp;n         26        268         19
#> 3: &nbsp;&nbsp;&nbsp;&nbsp;Mean (SD) 32.3 (7.7) 34.6 (6.9) 35.9 (8.3)
#> 4:    &nbsp;&nbsp;&nbsp;&nbsp;Median         31         34         36
#> 5:  &nbsp;&nbsp;&nbsp;&nbsp;Min, Max 20.0, 50.0 21.0, 58.0 25.0, 58.0
#> 6:   &nbsp;&nbsp;&nbsp;&nbsp;Missing          0          0          0
#>         Europe North America South America
#>         <char>        <char>        <char>
#> 1:                                        
#> 2:           9            48            30
#> 3: 38.4 (16.1)    36.2 (6.8)    36.1 (8.1)
#> 4:          30            35          35.5
#> 5:  26.0, 69.0    24.0, 57.0    24.0, 64.0
#> 6:           0             0             0

# Calculate summary statistics for biomarker 1 in each of the three arms
# (`ARM`).
calc_stats(dt = adsl, "BMRKR1", treat = "ARM")[[1]]
#>                                stats A: Drug X B: Placebo C: Combination
#>                               <char>    <char>     <char>         <char>
#> 1:                            BMRKR1                                    
#> 2:         &nbsp;&nbsp;&nbsp;&nbsp;n       134        134            132
#> 3: &nbsp;&nbsp;&nbsp;&nbsp;Mean (SD) 6.0 (3.6)  5.7 (3.3)      5.6 (3.5)
#> 4:    &nbsp;&nbsp;&nbsp;&nbsp;Median       5.4        4.8            4.6
#> 5:  &nbsp;&nbsp;&nbsp;&nbsp;Min, Max 0.4, 17.7  0.6, 14.2      0.2, 21.4
#> 6:   &nbsp;&nbsp;&nbsp;&nbsp;Missing         0          0              0