Skip to contents

The VST01 table provides an overview of the Vital Sign values and its change from baseline of each respective arm over the course of the trial.

Usage

vst01_main(
  adam_db,
  dataset = "advs",
  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"),
  ...
)

vst01_pre(adam_db, dataset = "advs", ...)

vst01

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

  • vst01_main(): Main TLG function

  • vst01_pre(): Preprocessing

Note

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

Examples

library(dunlin)

proc_data <- log_filter(
  syn_data,
  PARAMCD %in% c("DIABP", "SYSBP"), "advs"
)
run(vst01, proc_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)     
#>   —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
#>   Diastolic Blood Pressure                                                                                                                 
#>     SCREENING                                                                                                                              
#>       n                             15                 0                 15                 0                  15                 0        
#>       Mean (SD)              94.385 (17.067)        NE (NE)       106.381 (20.586)       NE (NE)        106.468 (12.628)       NE (NE)     
#>       Median                      94.933              NE              111.133               NE              108.359               NE       
#>       Min - Max               55.71 - 122.00        NE - NE        60.21 - 131.91        NE - NE         83.29 - 127.17        NE - NE     
#>     BASELINE                                                                                                                               
#>       n                             15                                   15                                    15                          
#>       Mean (SD)              96.133 (22.458)                      108.111 (15.074)                      103.149 (19.752)                   
#>       Median                      93.328                              108.951                               102.849                        
#>       Min - Max               60.58 - 136.59                       83.44 - 131.62                        66.05 - 136.55                    
#>     WEEK 1 DAY 8                                                                                                                           
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              98.977 (21.359)    2.844 (28.106)    104.110 (16.172)   -4.001 (21.867)    100.826 (19.027)   -2.323 (25.018) 
#>       Median                      92.447            -4.066            107.703             3.227             103.058             -2.476     
#>       Min - Max               67.55 - 130.37    -32.82 - 47.68     70.91 - 132.89     -52.94 - 28.63     70.04 - 128.68     -55.15 - 41.81 
#>     WEEK 2 DAY 15                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              99.758 (14.477)    3.626 (21.189)    97.473 (17.296)    -10.638 (20.831)   94.272 (16.961)    -8.877 (27.229) 
#>       Median                     101.498             1.731             99.501             -9.727             96.789            -10.155     
#>       Min - Max               71.98 - 122.81    -39.50 - 47.57     53.80 - 125.81     -55.15 - 25.26     63.45 - 117.47     -73.10 - 46.54 
#>     WEEK 3 DAY 22                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              99.101 (26.109)    2.968 (34.327)    91.984 (16.925)    -16.127 (21.881)   94.586 (13.560)    -8.563 (21.713) 
#>       Median                     101.146            -0.271             91.244            -14.384             98.398            -16.075     
#>       Min - Max               47.68 - 162.22    -47.87 - 76.64     67.80 - 119.72     -53.06 - 22.52     73.50 - 115.43     -37.90 - 32.66 
#>     WEEK 4 DAY 29                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              103.400 (22.273)   7.267 (30.740)    96.467 (19.451)    -11.644 (25.922)   108.338 (18.417)    5.189 (21.881) 
#>       Median                      98.168             2.510             97.385            -16.793            107.555             7.966      
#>       Min - Max               63.09 - 148.25    -38.43 - 61.90     63.35 - 131.57     -57.11 - 48.13     68.78 - 132.52     -33.96 - 41.50 
#>     WEEK 5 DAY 36                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              93.222 (18.536)    -2.911 (28.873)   97.890 (20.701)    -10.221 (27.593)   95.317 (16.401)    -7.832 (19.827) 
#>       Median                      90.799            -3.385             99.049            -11.319             93.876             -4.665     
#>       Min - Max               63.55 - 139.11    -48.63 - 47.35     69.47 - 137.64     -54.38 - 37.85     71.91 - 138.54     -44.47 - 29.11 
#>   Systolic Blood Pressure                                                                                                                  
#>     SCREENING                                                                                                                              
#>       n                             15                 0                 15                 0                  15                 0        
#>       Mean (SD)              154.073 (33.511)       NE (NE)       157.840 (34.393)       NE (NE)        152.407 (22.311)       NE (NE)     
#>       Median                     156.169              NE              161.670               NE              149.556               NE       
#>       Min - Max               78.31 - 210.70        NE - NE        79.76 - 210.40        NE - NE        108.21 - 184.88        NE - NE     
#>     BASELINE                                                                                                                               
#>       n                             15                                   15                                    15                          
#>       Mean (SD)              145.925 (28.231)                     152.007 (28.664)                      154.173 (26.317)                   
#>       Median                     142.705                              157.698                               155.282                        
#>       Min - Max               85.21 - 195.68                       98.90 - 194.62                        86.65 - 192.68                    
#>     WEEK 1 DAY 8                                                                                                                           
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              156.509 (21.097)   10.584 (34.598)   147.480 (33.473)   -4.527 (48.895)    143.319 (30.759)   -10.854 (34.553)
#>       Median                     160.711             5.802            155.030             2.758             145.548             -5.636     
#>       Min - Max              126.84 - 185.53    -53.28 - 91.52     85.22 - 189.88     -77.34 - 90.98     90.37 - 191.58     -65.71 - 49.04 
#>     WEEK 2 DAY 15                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              144.202 (33.676)   -1.723 (27.067)   136.892 (30.178)   -15.115 (37.794)   148.622 (27.088)   -5.551 (44.670) 
#>       Median                     144.253             5.325            142.679            -14.083            147.102            -11.512     
#>       Min - Max               62.56 - 203.66    -53.89 - 44.16     70.34 - 174.27     -83.07 - 62.39    108.82 - 200.23    -69.54 - 113.59 
#>     WEEK 3 DAY 22                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              154.887 (35.374)   8.962 (38.455)    149.761 (28.944)   -2.247 (44.835)    150.460 (21.352)   -3.712 (37.984) 
#>       Median                     158.938            17.191            155.044             -1.796            156.505             -7.606     
#>       Min - Max              112.32 - 218.83    -47.28 - 96.18     84.42 - 192.92    -110.20 - 94.02     94.70 - 180.41     -74.91 - 72.74 
#>     WEEK 4 DAY 29                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              150.159 (32.249)   4.234 (32.965)    156.043 (22.863)    4.036 (42.494)    145.714 (22.980)   -8.458 (33.175) 
#>       Median                     145.506             3.754            149.094            -10.000            150.797            -14.432     
#>       Min - Max               69.37 - 210.43    -89.16 - 54.32    113.57 - 195.10     -71.44 - 77.75    106.91 - 188.09     -41.95 - 65.16 
#>     WEEK 5 DAY 36                                                                                                                          
#>       n                             15                15                 15                 15                 15                 15       
#>       Mean (SD)              155.964 (30.945)   10.039 (42.252)   156.387 (35.274)    4.380 (51.782)    143.592 (33.170)   -10.581 (44.799)
#>       Median                     158.142             1.448            164.552             7.060             148.501             -2.385     
#>       Min - Max              110.61 - 212.47    -53.91 - 90.45     63.28 - 198.79    -131.34 - 86.84     92.18 - 191.05     -78.77 - 64.35