summarize_change.md
In tern: Create Common TLGs Used in Clinical Trials

s_change_from_baseline handles empty data (complete missing for a visit)

Code
  res
Output
  $n
  n 
  0

  $sum
  sum 
   NA

  $mean
  mean 
    NA

  $sd
  sd 
  NA

  $se
  se 
  NA

  $mean_sd
  mean   sd 
    NA   NA

  $mean_se
  mean   se 
    NA   NA

  $mean_ci
  mean_ci_lwr mean_ci_upr 
           NA          NA 
  attr(,"label")
  [1] "Mean 95% CI"

  $mean_sei
  mean_sei_lwr mean_sei_upr 
            NA           NA 
  attr(,"label")
  [1] "Mean -/+ 1xSE"

  $mean_sdi
  mean_sdi_lwr mean_sdi_upr 
            NA           NA 
  attr(,"label")
  [1] "Mean -/+ 1xSD"

  $mean_ci_3d
         mean mean_ci_lwr mean_ci_upr 
           NA          NA          NA 
  attr(,"label")
  [1] "Mean (95% CI)"

  $mean_pval
  p_value 
       NA 
  attr(,"label")
  [1] "Mean p-value (H0: mean = 0)"

  $median
  median 
      NA

  $mad
  mad 
   NA

  $median_ci
  median_ci_lwr median_ci_upr 
             NA            NA 
  attr(,"conf_level")
  [1] NA
  attr(,"label")
  [1] "Median 95% CI"

  $median_ci_3d
         median median_ci_lwr median_ci_upr 
             NA            NA            NA 
  attr(,"label")
  [1] "Median (95% CI)"

  $quantiles
  quantile_0.25 quantile_0.75 
             NA            NA 
  attr(,"label")
  [1] "25% and 75%-ile"

  $iqr
  iqr 
   NA

  $range
  min max 
   NA  NA

  $min
  min 
   NA

  $max
  max 
   NA

  $median_range
  median    min    max 
      NA     NA     NA 
  attr(,"label")
  [1] "Median (Min - Max)"

  $cv
  cv 
  NA

  $geom_mean
  geom_mean 
         NA

  $geom_sd
  geom_sd 
       NA

  $geom_mean_sd
  geom_mean   geom_sd 
         NA        NA

  $geom_mean_ci
  mean_ci_lwr mean_ci_upr 
           NA          NA 
  attr(,"label")
  [1] "Geometric Mean 95% CI"

  $geom_cv
  geom_cv 
       NA

  $geom_mean_ci_3d
    geom_mean mean_ci_lwr mean_ci_upr 
           NA          NA          NA 
  attr(,"label")
  [1] "Geometric Mean (95% CI)"

s_change_from_baseline handles NA in baseline values

Code
  res
Output
  $n
  n 
  3

  $sum
  sum 
    9

  $mean
  mean 
     3

  $sd
  sd 
   3

  $se
        se 
  1.732051

  $mean_sd
  mean   sd 
     3    3

  $mean_se
      mean       se 
  3.000000 1.732051

  $mean_ci
  mean_ci_lwr mean_ci_upr 
    -4.452413   10.452413 
  attr(,"label")
  [1] "Mean 95% CI"

  $mean_sei
  mean_sei_lwr mean_sei_upr 
      1.267949     4.732051 
  attr(,"label")
  [1] "Mean -/+ 1xSE"

  $mean_sdi
  mean_sdi_lwr mean_sdi_upr 
             0            6 
  attr(,"label")
  [1] "Mean -/+ 1xSD"

  $mean_ci_3d
         mean mean_ci_lwr mean_ci_upr 
     3.000000   -4.452413   10.452413 
  attr(,"label")
  [1] "Mean (95% CI)"

  $mean_pval
    p_value 
  0.2254033 
  attr(,"label")
  [1] "Mean p-value (H0: mean = 0)"

  $median
  median 
       3

  $mad
  mad 
    0

  $median_ci
  median_ci_lwr median_ci_upr 
             NA            NA 
  attr(,"conf_level")
  [1] NA
  attr(,"label")
  [1] "Median 95% CI"

  $median_ci_3d
         median median_ci_lwr median_ci_upr 
              3            NA            NA 
  attr(,"label")
  [1] "Median (95% CI)"

  $quantiles
  quantile_0.25 quantile_0.75 
              0             6 
  attr(,"label")
  [1] "25% and 75%-ile"

  $iqr
  iqr 
    6

  $range
  min max 
    0   6

  $min
  min 
    0

  $max
  max 
    6

  $median_range
  median    min    max 
       3      0      6 
  attr(,"label")
  [1] "Median (Min - Max)"

  $cv
   cv 
  100

  $geom_mean
  geom_mean 
         NA

  $geom_sd
  geom_sd 
       NA

  $geom_mean_sd
  geom_mean   geom_sd 
         NA        NA

  $geom_mean_ci
  mean_ci_lwr mean_ci_upr 
           NA          NA 
  attr(,"label")
  [1] "Geometric Mean 95% CI"

  $geom_cv
  geom_cv 
       NA

  $geom_mean_ci_3d
    geom_mean mean_ci_lwr mean_ci_upr 
           NA          NA          NA 
  attr(,"label")
  [1] "Geometric Mean (95% CI)"

s_change_from_baseline handles baseline substitution

Code
  res
Output
  $`FALSE`
  $`FALSE`$n
  n 
  2

  $`FALSE`$sum
  sum 
    3

  $`FALSE`$mean
  mean 
   1.5

  $`FALSE`$sd
         sd 
  0.7071068

  $`FALSE`$se
   se 
  0.5

  $`FALSE`$mean_sd
       mean        sd 
  1.5000000 0.7071068

  $`FALSE`$mean_se
  mean   se 
   1.5  0.5

  $`FALSE`$mean_ci
  mean_ci_lwr mean_ci_upr 
    -4.853102    7.853102 
  attr(,"label")
  [1] "Mean 95% CI"

  $`FALSE`$mean_sei
  mean_sei_lwr mean_sei_upr 
             1            2 
  attr(,"label")
  [1] "Mean -/+ 1xSE"

  $`FALSE`$mean_sdi
  mean_sdi_lwr mean_sdi_upr 
     0.7928932    2.2071068 
  attr(,"label")
  [1] "Mean -/+ 1xSD"

  $`FALSE`$mean_ci_3d
         mean mean_ci_lwr mean_ci_upr 
     1.500000   -4.853102    7.853102 
  attr(,"label")
  [1] "Mean (95% CI)"

  $`FALSE`$mean_pval
    p_value 
  0.2048328 
  attr(,"label")
  [1] "Mean p-value (H0: mean = 0)"

  $`FALSE`$median
  median 
     1.5

  $`FALSE`$mad
  mad 
    0

  $`FALSE`$median_ci
  median_ci_lwr median_ci_upr 
             NA            NA 
  attr(,"conf_level")
  [1] NA
  attr(,"label")
  [1] "Median 95% CI"

  $`FALSE`$median_ci_3d
         median median_ci_lwr median_ci_upr 
            1.5            NA            NA 
  attr(,"label")
  [1] "Median (95% CI)"

  $`FALSE`$quantiles
  quantile_0.25 quantile_0.75 
              1             2 
  attr(,"label")
  [1] "25% and 75%-ile"

  $`FALSE`$iqr
  iqr 
    1

  $`FALSE`$range
  min max 
    1   2

  $`FALSE`$min
  min 
    1

  $`FALSE`$max
  max 
    2

  $`FALSE`$median_range
  median    min    max 
     1.5    1.0    2.0 
  attr(,"label")
  [1] "Median (Min - Max)"

  $`FALSE`$cv
        cv 
  47.14045

  $`FALSE`$geom_mean
  geom_mean 
   1.414214

  $`FALSE`$geom_sd
   geom_sd 
  1.632527

  $`FALSE`$geom_mean_sd
  geom_mean   geom_sd 
   1.414214  1.632527

  $`FALSE`$geom_mean_ci
   mean_ci_lwr  mean_ci_upr 
    0.01729978 115.60839614 
  attr(,"label")
  [1] "Geometric Mean 95% CI"

  $`FALSE`$geom_cv
   geom_cv 
  52.10922

  $`FALSE`$geom_mean_ci_3d
     geom_mean  mean_ci_lwr  mean_ci_upr 
    1.41421356   0.01729978 115.60839614 
  attr(,"label")
  [1] "Geometric Mean (95% CI)"


  $`TRUE`
  $`TRUE`$n
  n 
  2

  $`TRUE`$sum
  sum 
    5

  $`TRUE`$mean
  mean 
   2.5

  $`TRUE`$sd
       sd 
  2.12132

  $`TRUE`$se
   se 
  1.5

  $`TRUE`$mean_sd
     mean      sd 
  2.50000 2.12132

  $`TRUE`$mean_se
  mean   se 
   2.5  1.5

  $`TRUE`$mean_ci
  mean_ci_lwr mean_ci_upr 
    -16.55931    21.55931 
  attr(,"label")
  [1] "Mean 95% CI"

  $`TRUE`$mean_sei
  mean_sei_lwr mean_sei_upr 
             1            4 
  attr(,"label")
  [1] "Mean -/+ 1xSE"

  $`TRUE`$mean_sdi
  mean_sdi_lwr mean_sdi_upr 
     0.3786797    4.6213203 
  attr(,"label")
  [1] "Mean -/+ 1xSD"

  $`TRUE`$mean_ci_3d
         mean mean_ci_lwr mean_ci_upr 
      2.50000   -16.55931    21.55931 
  attr(,"label")
  [1] "Mean (95% CI)"

  $`TRUE`$mean_pval
    p_value 
  0.3440417 
  attr(,"label")
  [1] "Mean p-value (H0: mean = 0)"

  $`TRUE`$median
  median 
     2.5

  $`TRUE`$mad
  mad 
    0

  $`TRUE`$median_ci
  median_ci_lwr median_ci_upr 
             NA            NA 
  attr(,"conf_level")
  [1] NA
  attr(,"label")
  [1] "Median 95% CI"

  $`TRUE`$median_ci_3d
         median median_ci_lwr median_ci_upr 
            2.5            NA            NA 
  attr(,"label")
  [1] "Median (95% CI)"

  $`TRUE`$quantiles
  quantile_0.25 quantile_0.75 
              1             4 
  attr(,"label")
  [1] "25% and 75%-ile"

  $`TRUE`$iqr
  iqr 
    3

  $`TRUE`$range
  min max 
    1   4

  $`TRUE`$min
  min 
    1

  $`TRUE`$max
  max 
    4

  $`TRUE`$median_range
  median    min    max 
     2.5    1.0    4.0 
  attr(,"label")
  [1] "Median (Min - Max)"

  $`TRUE`$cv
        cv 
  84.85281

  $`TRUE`$geom_mean
  geom_mean 
          2

  $`TRUE`$geom_sd
   geom_sd 
  2.665144

  $`TRUE`$geom_mean_sd
  geom_mean   geom_sd 
   2.000000  2.665144

  $`TRUE`$geom_mean_ci
   mean_ci_lwr  mean_ci_upr 
  2.992824e-04 1.336530e+04 
  attr(,"label")
  [1] "Geometric Mean 95% CI"

  $`TRUE`$geom_cv
   geom_cv 
  127.0458

  $`TRUE`$geom_mean_ci_3d
     geom_mean  mean_ci_lwr  mean_ci_upr 
  2.000000e+00 2.992824e-04 1.336530e+04 
  attr(,"label")
  [1] "Geometric Mean (95% CI)"

summarize_change works as expected

Code
  res
Output
                   all obs   
  ———————————————————————————
  V1                         
    n                 3      
    Mean (SD)    6.00 (3.00) 
    Median          6.00     
    Min - Max    3.00 - 9.00 
  V2                         
    n                 3      
    Mean (SD)   -1.00 (0.00) 
    Median          -1.00    
    Min - Max   -1.00 - -1.00
  V3                         
    n                 3      
    Mean (SD)   -2.00 (0.00) 
    Median          -2.00    
    Min - Max   -2.00 - -2.00

summarize_change works with custom statistical functions

Code
  res
Output
              all obs
  ———————————————————
  V1                 
    n            3   
    my_stat    1.00  
  V2                 
    n            3   
    my_stat    0.83  
  V3                 
    n            3   
    my_stat    0.67