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The LBT01 table provides an overview of the Lab values and its change from baseline of each respective arm over the course of the trial.

Usage

lbt01_main(
  adam_db,
  dataset = "adlb",
  arm_var = "ACTARM",
  lbl_overall = NULL,
  row_split_var = NULL,
  summaryvars = c("AVAL", "CHG"),
  visitvar = "AVISIT",
  precision = list(default = 2L),
  page_var = "PARAMCD",
  .stats = c("n", "mean_sd", "median", "range"),
  skip = list(CHG = "BASELINE"),
  ...
)

lbt01_pre(adam_db, dataset = "adlb", ...)

lbt01

Format

An object of class chevron_t of length 1.

Arguments

adam_db

(list of data.frames) object containing the ADaM datasets

dataset

(string) the name of a table in the adam_db object.

arm_var

(string) variable used for column splitting

lbl_overall

(string) label used for overall column, if set to NULL the overall column is omitted

row_split_var

(character) additional row split variables.

summaryvars

(character) variables to be analyzed. The label attribute of the corresponding column in table of adam_db is used as label.

visitvar

(string) typically one of "AVISIT" or user-defined visit incorporating "ATPT".

precision

(named list of integer) where names are values found in the PARAMCD column and the values indicate the number of digits in statistics. If default is set, and parameter precision not specified, the value for default will be used.

page_var

(string) variable name prior to which the row split is by page.

.stats

(character) statistics names, see tern::analyze_vars().

skip

Named (list) of visit values that need to be inhibited.

...

additional arguments like .indent_mods, .labels.

Value

the main function returns an rtables object.

the preprocessing function returns a list of data.frame.

Details

  • The Analysis Value column, displays the number of patients, the mean, standard deviation, median and range of the analysis value for each visit.

  • The Change from Baseline column, displays the number of patient and the mean, standard deviation, median and range of changes relative to the baseline.

  • Remove zero-count rows unless overridden with prune_0 = FALSE.

  • Split columns by arm, typically ACTARM.

  • Does not include a total column by default.

  • Sorted based on factor level; first by PARAM labels in alphabetic order then by chronological time point given by AVISIT. Re-level to customize order

Functions

  • lbt01_main(): Main TLG function

  • lbt01_pre(): Preprocessing

Note

  • adam_db object must contain table named as dataset with the columns specified in summaryvars.

Examples

run(lbt01, syn_data)
#>                                                      A: Drug X                          B: Placebo                        C: Combination          
#>                                                              Change from                        Change from                         Change from   
#>                                          Value at Visit       Baseline       Value at Visit       Baseline      Value at Visit        Baseline    
#>   Analysis Visit                             (N=15)            (N=15)            (N=15)            (N=15)           (N=15)             (N=15)     
#>   ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Alanine Aminotransferase Measurement                                                                                                            
#>     BASELINE                                                                                                                                      
#>       n                                        15                                  15                                 15                          
#>       Mean (SD)                          18.655 (12.455)                     16.835 (11.080)                    22.385 (9.452)                    
#>       Median                                 16.040                              17.453                             25.250                        
#>       Min - Max                           2.43 - 44.06                        1.48 - 31.99                       0.57 - 37.23                     
#>     WEEK 1 DAY 8                                                                                                                                  
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                          16.308 (10.850)   -2.348 (17.558)   22.055 (7.537)    5.220 (16.359)   19.574 (9.876)    -2.811 (10.902) 
#>       Median                                 14.664            -5.369            22.476            7.252            19.425             -0.995     
#>       Min - Max                           0.10 - 36.30     -30.18 - 22.66     9.72 - 33.81     -16.82 - 32.33    1.03 - 36.28      -19.61 - 18.45 
#>     WEEK 2 DAY 15                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                          16.646 (10.528)   -2.010 (15.773)   20.758 (9.578)    3.923 (14.084)   10.911 (7.721)    -11.474 (11.002)
#>       Median                                 15.470            -6.427            18.499            6.248             9.850             -8.657     
#>       Min - Max                           0.40 - 35.29     -29.99 - 32.86     1.56 - 42.84     -24.92 - 29.85    0.35 - 25.01      -27.38 - 2.52  
#>     WEEK 3 DAY 22                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                          17.488 (10.679)   -1.167 (15.759)   20.055 (8.086)    3.219 (16.285)   18.413 (9.513)     -3.973 (9.966) 
#>       Median                                 14.224             1.355            21.852            5.345            19.529             -7.194     
#>       Min - Max                           1.78 - 33.19     -40.09 - 18.58     3.46 - 34.44     -23.02 - 31.38    3.02 - 32.34      -18.70 - 17.30 
#>     WEEK 4 DAY 29                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                          16.793 (9.101)    -1.863 (15.499)   17.560 (9.857)    0.725 (13.170)   18.397 (11.618)   -3.989 (13.150) 
#>       Median                                 12.816             3.098            17.687            -3.104           18.532             -1.684     
#>       Min - Max                           3.58 - 34.00     -32.93 - 18.92     1.90 - 34.08     -16.29 - 22.18    0.72 - 34.47      -30.33 - 17.38 
#>     WEEK 5 DAY 36                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                          17.879 (7.239)    -0.776 (15.471)   17.417 (7.065)    0.581 (14.309)   15.173 (8.410)    -7.213 (10.518) 
#>       Median                                 18.749             1.108            17.751            2.055            16.394             -8.121     
#>       Min - Max                           3.99 - 29.40     -40.08 - 17.24     5.10 - 30.90     -21.68 - 23.41    0.28 - 26.73      -27.12 - 15.83 
#>   C-Reactive Protein Measurement                                                                                                                  
#>     BASELINE                                                                                                                                      
#>       n                                        15                                  15                                 15                          
#>       Mean (SD)                           9.032 (0.650)                       9.164 (0.900)                      8.652 (0.769)                    
#>       Median                                  8.819                               9.472                              8.502                        
#>       Min - Max                            7.81 - 9.93                        7.38 - 10.60                       7.73 - 10.86                     
#>     WEEK 1 DAY 8                                                                                                                                  
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           9.050 (1.222)     0.018 (1.242)     8.690 (0.990)    -0.474 (1.418)    9.507 (1.279)     0.854 (1.080)  
#>       Median                                  8.960            -0.180             8.734            -0.074            9.830             1.107      
#>       Min - Max                           6.87 - 11.33      -1.83 - 2.81      6.84 - 10.14      -3.14 - 1.55     7.27 - 11.09       -1.14 - 2.05  
#>     WEEK 2 DAY 15                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           8.825 (0.990)    -0.207 (1.204)     9.371 (1.185)    0.207 (1.572)     8.890 (1.021)     0.238 (1.263)  
#>       Median                                  8.860            -0.567             9.073            0.293             8.994             0.462      
#>       Min - Max                           7.12 - 10.44      -2.12 - 2.05      8.06 - 12.73      -2.35 - 3.19     6.68 - 10.84       -2.50 - 2.89  
#>     WEEK 3 DAY 22                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           9.134 (0.897)     0.102 (1.179)     9.288 (1.033)    0.124 (1.135)     9.176 (0.919)     0.523 (1.209)  
#>       Median                                  9.318             0.090             9.413            -0.022            8.963             0.564      
#>       Min - Max                           7.38 - 11.00      -1.57 - 1.86      7.42 - 10.66      -1.41 - 3.27     7.72 - 11.20       -2.25 - 3.26  
#>     WEEK 4 DAY 29                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           8.728 (0.959)    -0.303 (1.226)     8.971 (0.704)    -0.194 (1.077)    8.662 (0.712)     0.010 (1.039)  
#>       Median                                  8.704            -0.046             8.879            -0.375            8.718             0.143      
#>       Min - Max                           6.70 - 10.81      -3.17 - 1.99      7.88 - 10.23      -1.59 - 1.54      7.21 - 9.60       -2.63 - 1.68  
#>     WEEK 5 DAY 36                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           8.545 (0.846)    -0.487 (1.060)     9.165 (1.182)    0.000 (0.929)     8.654 (0.790)     0.002 (1.102)  
#>       Median                                  8.601            -0.452             8.755            0.153             8.766             0.008      
#>       Min - Max                           7.10 - 10.03      -2.39 - 1.66      7.86 - 12.50      -1.58 - 1.90      7.37 - 9.92       -3.14 - 1.67  
#>   Immunoglobulin A Measurement                                                                                                                    
#>     BASELINE                                                                                                                                      
#>       n                                        15                                  15                                 15                          
#>       Mean (SD)                           2.923 (0.059)                       2.866 (0.083)                      2.887 (0.120)                    
#>       Median                                  2.911                               2.862                              2.896                        
#>       Min - Max                            2.80 - 3.01                         2.76 - 3.01                        2.65 - 3.14                     
#>     WEEK 1 DAY 8                                                                                                                                  
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           2.885 (0.060)    -0.038 (0.082)     2.938 (0.137)    0.073 (0.152)     2.925 (0.091)     0.038 (0.128)  
#>       Median                                  2.886            -0.010             2.972            0.109             2.931             0.021      
#>       Min - Max                            2.76 - 2.96      -0.18 - 0.06       2.69 - 3.16      -0.27 - 0.27      2.78 - 3.10       -0.12 - 0.28  
#>     WEEK 2 DAY 15                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           2.889 (0.141)    -0.034 (0.171)     2.928 (0.075)    0.063 (0.124)     2.913 (0.080)     0.026 (0.156)  
#>       Median                                  2.871            -0.024             2.936            0.084             2.910             0.067      
#>       Min - Max                            2.67 - 3.16      -0.34 - 0.27       2.79 - 3.03      -0.12 - 0.26      2.78 - 3.09       -0.28 - 0.26  
#>     WEEK 3 DAY 22                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           2.875 (0.105)    -0.048 (0.120)     2.919 (0.114)    0.053 (0.151)     2.889 (0.082)     0.002 (0.128)  
#>       Median                                  2.861            -0.046             2.938            0.045             2.899             0.020      
#>       Min - Max                            2.67 - 3.07      -0.25 - 0.16       2.73 - 3.18      -0.19 - 0.33      2.75 - 3.02       -0.24 - 0.14  
#>     WEEK 4 DAY 29                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           2.912 (0.134)    -0.010 (0.140)     2.886 (0.097)    0.020 (0.136)     2.869 (0.104)     -0.019 (0.141) 
#>       Median                                  2.942             0.023             2.924            -0.012            2.840             -0.055     
#>       Min - Max                            2.63 - 3.16      -0.39 - 0.19       2.58 - 2.96      -0.28 - 0.20      2.74 - 3.08       -0.31 - 0.22  
#>     WEEK 5 DAY 36                                                                                                                                 
#>       n                                        15                15                15                15               15                 15       
#>       Mean (SD)                           2.933 (0.089)     0.010 (0.136)     2.899 (0.094)    0.034 (0.131)     2.902 (0.091)     0.015 (0.168)  
#>       Median                                  2.938             0.031             2.936            0.059             2.921             0.026      
#>       Min - Max                            2.78 - 3.08      -0.23 - 0.26       2.68 - 3.04      -0.25 - 0.19      2.78 - 3.13       -0.27 - 0.32