tableone introduction

I followed the “Introduction to tableone” notes by Kazuki Yoshida (see: https://cran.r-project.org/web/packages/tableone/vignettes/introduction.html)

Load tableone package

library(tableone)
library(distill)

Load survival package for Mayo Clinic’s PBC data

library(survival)
data(pbc)

Single group summary

Simplest use case

CreateTableOne(data = pbc)

                      
                       Overall          
  n                        418          
  id (mean (SD))        209.50 (120.81) 
  time (mean (SD))     1917.78 (1104.67)
  status (mean (SD))      0.83 (0.96)   
  trt (mean (SD))         1.49 (0.50)   
  age (mean (SD))        50.74 (10.45)  
  sex = f (%)              374 (89.5)   
  ascites (mean (SD))     0.08 (0.27)   
  hepato (mean (SD))      0.51 (0.50)   
  spiders (mean (SD))     0.29 (0.45)   
  edema (mean (SD))       0.10 (0.25)   
  bili (mean (SD))        3.22 (4.41)   
  chol (mean (SD))      369.51 (231.94) 
  albumin (mean (SD))     3.50 (0.42)   
  copper (mean (SD))     97.65 (85.61)  
  alk.phos (mean (SD)) 1982.66 (2140.39)
  ast (mean (SD))       122.56 (56.70)  
  trig (mean (SD))      124.70 (65.15)  
  platelet (mean (SD))  257.02 (98.33)  
  protime (mean (SD))    10.73 (1.02)   
  stage (mean (SD))       3.02 (0.88)   

Categorical variable conversion

Get variable names

dput(names(pbc))

c("id", "time", "status", "trt", "age", "sex", "ascites", "hepato", 
"spiders", "edema", "bili", "chol", "albumin", "copper", "alk.phos", 
"ast", "trig", "platelet", "protime", "stage")

Vector of variables to summarise

myVars <- c("time", "status", "trt", "age", "sex", "ascites", "hepato", "spiders", "edema", "bili", "chol", "albumin", "copper", "alk.phos", "ast", "trig", "platelet", "protime", "stage")

Vector of categorical variables that need transformation

catVars <- c("status", "trt", "ascites", "hepato", "spiders", "edema", "stage")

Create a TableOne object

tab2 <- CreateTableOne(vars = myVars, data = pbc, factorVars = catVars)

Showing all levels for categorical variables

print(tab2, showAllLevels = TRUE, formatOptions = list(big.mark = ","))

                      
                       level Overall            
  n                               418           
  time (mean (SD))           1,917.78 (1,104.67)
  status (%)           0          232 (55.5)    
                       1           25 ( 6.0)    
                       2          161 (38.5)    
  trt (%)              1          158 (50.6)    
                       2          154 (49.4)    
  age (mean (SD))               50.74 (10.45)   
  sex (%)              m           44 (10.5)    
                       f          374 (89.5)    
  ascites (%)          0          288 (92.3)    
                       1           24 ( 7.7)    
  hepato (%)           0          152 (48.7)    
                       1          160 (51.3)    
  spiders (%)          0          222 (71.2)    
                       1           90 (28.8)    
  edema (%)            0          354 (84.7)    
                       0.5         44 (10.5)    
                       1           20 ( 4.8)    
  bili (mean (SD))               3.22 (4.41)    
  chol (mean (SD))             369.51 (231.94)  
  albumin (mean (SD))            3.50 (0.42)    
  copper (mean (SD))            97.65 (85.61)   
  alk.phos (mean (SD))       1,982.66 (2,140.39)
  ast (mean (SD))              122.56 (56.70)   
  trig (mean (SD))             124.70 (65.15)   
  platelet (mean (SD))         257.02 (98.33)   
  protime (mean (SD))           10.73 (1.02)    
  stage (%)            1           21 ( 5.1)    
                       2           92 (22.3)    
                       3          155 (37.6)    
                       4          144 (35.0)    

Detailed information including missingness

summary(tab2)

     ### Summary of continuous variables ###

strata: Overall
           n miss p.miss mean    sd median   p25  p75   min   max
time     418    0    0.0 1918 1e+03   1730 1e+03 2614  41.0  4795
age      418    0    0.0   51 1e+01     51 4e+01   58  26.3    78
bili     418    0    0.0    3 4e+00      1 8e-01    3   0.3    28
chol     418  134   32.1  370 2e+02    310 2e+02  400 120.0  1775
albumin  418    0    0.0    3 4e-01      4 3e+00    4   2.0     5
copper   418  108   25.8   98 9e+01     73 4e+01  123   4.0   588
alk.phos 418  106   25.4 1983 2e+03   1259 9e+02 1980 289.0 13862
ast      418  106   25.4  123 6e+01    115 8e+01  152  26.4   457
trig     418  136   32.5  125 7e+01    108 8e+01  151  33.0   598
platelet 418   11    2.6  257 1e+02    251 2e+02  318  62.0   721
protime  418    2    0.5   11 1e+00     11 1e+01   11   9.0    18
          skew kurt
time      0.47 -0.5
age       0.09 -0.6
bili      2.72  8.1
chol      3.41 14.3
albumin  -0.47  0.6
copper    2.30  7.6
alk.phos  2.99  9.7
ast       1.45  4.3
trig      2.52 11.8
platelet  0.63  0.9
protime   2.22 10.0

=======================================================================================

     ### Summary of categorical variables ### 

strata: Overall
     var   n miss p.miss level freq percent cum.percent
  status 418    0    0.0     0  232    55.5        55.5
                             1   25     6.0        61.5
                             2  161    38.5       100.0
                                                       
     trt 418  106   25.4     1  158    50.6        50.6
                             2  154    49.4       100.0
                                                       
     sex 418    0    0.0     m   44    10.5        10.5
                             f  374    89.5       100.0
                                                       
 ascites 418  106   25.4     0  288    92.3        92.3
                             1   24     7.7       100.0
                                                       
  hepato 418  106   25.4     0  152    48.7        48.7
                             1  160    51.3       100.0
                                                       
 spiders 418  106   25.4     0  222    71.2        71.2
                             1   90    28.8       100.0
                                                       
   edema 418    0    0.0     0  354    84.7        84.7
                           0.5   44    10.5        95.2
                             1   20     4.8       100.0
                                                       
   stage 418    6    1.4     1   21     5.1         5.1
                             2   92    22.3        27.4
                             3  155    37.6        65.0
                             4  144    35.0       100.0
                                                       

Summarising nonnormal variables

biomarkers <- c("bili", "chol", "copper", "alk.phos", "trig", "protime")
print(tab2, nonnormal = biomarkers, formatOptions = list(big.mark = ","))

                         
                          Overall                    
  n                            418                   
  time (mean (SD))        1,917.78 (1,104.67)        
  status (%)                                         
     0                         232 (55.5)            
     1                          25 ( 6.0)            
     2                         161 (38.5)            
  trt = 2 (%)                  154 (49.4)            
  age (mean (SD))            50.74 (10.45)           
  sex = f (%)                  374 (89.5)            
  ascites = 1 (%)               24 ( 7.7)            
  hepato = 1 (%)               160 (51.3)            
  spiders = 1 (%)               90 (28.8)            
  edema (%)                                          
     0                         354 (84.7)            
     0.5                        44 (10.5)            
     1                          20 ( 4.8)            
  bili (median [IQR])         1.40 [0.80, 3.40]      
  chol (median [IQR])       309.50 [249.50, 400.00]  
  albumin (mean (SD))         3.50 (0.42)            
  copper (median [IQR])      73.00 [41.25, 123.00]   
  alk.phos (median [IQR]) 1,259.00 [871.50, 1,980.00]
  ast (mean (SD))           122.56 (56.70)           
  trig (median [IQR])       108.00 [84.25, 151.00]   
  platelet (mean (SD))      257.02 (98.33)           
  protime (median [IQR])     10.60 [10.00, 11.10]    
  stage (%)                                          
     1                          21 ( 5.1)            
     2                          92 (22.3)            
     3                         155 (37.6)            
     4                         144 (35.0)            

Multiple group summary

tab3 <- CreateTableOne(vars = myVars, strata = "trt", data = pbc, factorVars = catVars)
print(tab3, nonnormal = biomarkers, formatOptions = list(big.mark = ","))

                         Stratified by trt
                          1                          
  n                            158                   
  time (mean (SD))        2,015.62 (1,094.12)        
  status (%)                                         
     0                          83 (52.5)            
     1                          10 ( 6.3)            
     2                          65 (41.1)            
  trt = 2 (%)                    0 ( 0.0)            
  age (mean (SD))            51.42 (11.01)           
  sex = f (%)                  137 (86.7)            
  ascites = 1 (%)               14 ( 8.9)            
  hepato = 1 (%)                73 (46.2)            
  spiders = 1 (%)               45 (28.5)            
  edema (%)                                          
     0                         132 (83.5)            
     0.5                        16 (10.1)            
     1                          10 ( 6.3)            
  bili (median [IQR])         1.40 [0.80, 3.20]      
  chol (median [IQR])       315.50 [247.75, 417.00]  
  albumin (mean (SD))         3.52 (0.44)            
  copper (median [IQR])      73.00 [40.00, 121.00]   
  alk.phos (median [IQR]) 1,214.50 [840.75, 2,028.00]
  ast (mean (SD))           120.21 (54.52)           
  trig (median [IQR])       106.00 [84.50, 146.00]   
  platelet (mean (SD))      258.75 (100.32)          
  protime (median [IQR])     10.60 [10.03, 11.00]    
  stage (%)                                          
     1                          12 ( 7.6)            
     2                          35 (22.2)            
     3                          56 (35.4)            
     4                          55 (34.8)            
                         Stratified by trt
                          2                           p      test   
  n                            154                                  
  time (mean (SD))        1,996.86 (1,155.93)          0.883        
  status (%)                                           0.894        
     0                          85 ( 55.2)                          
     1                           9 (  5.8)                          
     2                          60 ( 39.0)                          
  trt = 2 (%)                  154 (100.0)            <0.001        
  age (mean (SD))            48.58 (9.96)              0.018        
  sex = f (%)                  139 ( 90.3)             0.421        
  ascites = 1 (%)               10 (  6.5)             0.567        
  hepato = 1 (%)                87 ( 56.5)             0.088        
  spiders = 1 (%)               45 ( 29.2)             0.985        
  edema (%)                                            0.877        
     0                         131 ( 85.1)                          
     0.5                        13 (  8.4)                          
     1                          10 (  6.5)                          
  bili (median [IQR])         1.30 [0.72, 3.60]        0.842 nonnorm
  chol (median [IQR])       303.50 [254.25, 377.00]    0.544 nonnorm
  albumin (mean (SD))         3.52 (0.40)              0.874        
  copper (median [IQR])      73.00 [43.00, 139.00]     0.717 nonnorm
  alk.phos (median [IQR]) 1,283.00 [922.50, 1,949.75]  0.812 nonnorm
  ast (mean (SD))           124.97 (58.93)             0.460        
  trig (median [IQR])       113.00 [84.50, 155.00]     0.370 nonnorm
  platelet (mean (SD))      265.20 (90.73)             0.555        
  protime (median [IQR])     10.60 [10.00, 11.40]      0.588 nonnorm
  stage (%)                                            0.201        
     1                           4 (  2.6)                          
     2                          32 ( 20.8)                          
     3                          64 ( 41.6)                          
     4                          54 ( 35.1)                          

Testing

print(tab3, nonnormal = biomarkers, exact = "stage", smd = TRUE)

                         Stratified by trt
                          1                        
  n                           158                  
  time (mean (SD))        2015.62 (1094.12)        
  status (%)                                       
     0                         83 (52.5)           
     1                         10 ( 6.3)           
     2                         65 (41.1)           
  trt = 2 (%)                   0 ( 0.0)           
  age (mean (SD))           51.42 (11.01)          
  sex = f (%)                 137 (86.7)           
  ascites = 1 (%)              14 ( 8.9)           
  hepato = 1 (%)               73 (46.2)           
  spiders = 1 (%)              45 (28.5)           
  edema (%)                                        
     0                        132 (83.5)           
     0.5                       16 (10.1)           
     1                         10 ( 6.3)           
  bili (median [IQR])        1.40 [0.80, 3.20]     
  chol (median [IQR])      315.50 [247.75, 417.00] 
  albumin (mean (SD))        3.52 (0.44)           
  copper (median [IQR])     73.00 [40.00, 121.00]  
  alk.phos (median [IQR]) 1214.50 [840.75, 2028.00]
  ast (mean (SD))          120.21 (54.52)          
  trig (median [IQR])      106.00 [84.50, 146.00]  
  platelet (mean (SD))     258.75 (100.32)         
  protime (median [IQR])    10.60 [10.03, 11.00]   
  stage (%)                                        
     1                         12 ( 7.6)           
     2                         35 (22.2)           
     3                         56 (35.4)           
     4                         55 (34.8)           
                         Stratified by trt
                          2                         p      test   
  n                           154                                 
  time (mean (SD))        1996.86 (1155.93)          0.883        
  status (%)                                         0.894        
     0                         85 ( 55.2)                         
     1                          9 (  5.8)                         
     2                         60 ( 39.0)                         
  trt = 2 (%)                 154 (100.0)           <0.001        
  age (mean (SD))           48.58 (9.96)             0.018        
  sex = f (%)                 139 ( 90.3)            0.421        
  ascites = 1 (%)              10 (  6.5)            0.567        
  hepato = 1 (%)               87 ( 56.5)            0.088        
  spiders = 1 (%)              45 ( 29.2)            0.985        
  edema (%)                                          0.877        
     0                        131 ( 85.1)                         
     0.5                       13 (  8.4)                         
     1                         10 (  6.5)                         
  bili (median [IQR])        1.30 [0.72, 3.60]       0.842 nonnorm
  chol (median [IQR])      303.50 [254.25, 377.00]   0.544 nonnorm
  albumin (mean (SD))        3.52 (0.40)             0.874        
  copper (median [IQR])     73.00 [43.00, 139.00]    0.717 nonnorm
  alk.phos (median [IQR]) 1283.00 [922.50, 1949.75]  0.812 nonnorm
  ast (mean (SD))          124.97 (58.93)            0.460        
  trig (median [IQR])      113.00 [84.50, 155.00]    0.370 nonnorm
  platelet (mean (SD))     265.20 (90.73)            0.555        
  protime (median [IQR])    10.60 [10.00, 11.40]     0.588 nonnorm
  stage (%)                                          0.205 exact  
     1                          4 (  2.6)                         
     2                         32 ( 20.8)                         
     3                         64 ( 41.6)                         
     4                         54 ( 35.1)                         
                         Stratified by trt
                          SMD   
  n                             
  time (mean (SD))         0.017
  status (%)               0.054
     0                          
     1                          
     2                          
  trt = 2 (%)                NaN
  age (mean (SD))          0.270
  sex = f (%)              0.111
  ascites = 1 (%)          0.089
  hepato = 1 (%)           0.207
  spiders = 1 (%)          0.016
  edema (%)                0.058
     0                          
     0.5                        
     1                          
  bili (median [IQR])      0.171
  chol (median [IQR])      0.038
  albumin (mean (SD))      0.018
  copper (median [IQR])   <0.001
  alk.phos (median [IQR])  0.037
  ast (mean (SD))          0.084
  trig (median [IQR])      0.017
  platelet (mean (SD))     0.067
  protime (median [IQR])   0.146
  stage (%)                0.246
     1                          
     2                          
     3                          
     4                          

Miscellaneous

Categorical or continuous variables-only

Categorical part only

tab3$CatTable

                 Stratified by trt
                  1           2            p      test
  n               158         154                     
  status (%)                                0.894     
     0             83 (52.5)   85 ( 55.2)             
     1             10 ( 6.3)    9 (  5.8)             
     2             65 (41.1)   60 ( 39.0)             
  trt = 2 (%)       0 ( 0.0)  154 (100.0)  <0.001     
  sex = f (%)     137 (86.7)  139 ( 90.3)   0.421     
  ascites = 1 (%)  14 ( 8.9)   10 (  6.5)   0.567     
  hepato = 1 (%)   73 (46.2)   87 ( 56.5)   0.088     
  spiders = 1 (%)  45 (28.5)   45 ( 29.2)   0.985     
  edema (%)                                 0.877     
     0            132 (83.5)  131 ( 85.1)             
     0.5           16 (10.1)   13 (  8.4)             
     1             10 ( 6.3)   10 (  6.5)             
  stage (%)                                 0.201     
     1             12 ( 7.6)    4 (  2.6)             
     2             35 (22.2)   32 ( 20.8)             
     3             56 (35.4)   64 ( 41.6)             
     4             55 (34.8)   54 ( 35.1)             

Continuous part only

print(tab3$ContTable, nonnormal = biomarkers)

                         Stratified by trt
                          1                        
  n                       158                      
  time (mean (SD))        2015.62 (1094.12)        
  age (mean (SD))           51.42 (11.01)          
  bili (median [IQR])        1.40 [0.80, 3.20]     
  chol (median [IQR])      315.50 [247.75, 417.00] 
  albumin (mean (SD))        3.52 (0.44)           
  copper (median [IQR])     73.00 [40.00, 121.00]  
  alk.phos (median [IQR]) 1214.50 [840.75, 2028.00]
  ast (mean (SD))          120.21 (54.52)          
  trig (median [IQR])      106.00 [84.50, 146.00]  
  platelet (mean (SD))     258.75 (100.32)         
  protime (median [IQR])    10.60 [10.03, 11.00]   
                         Stratified by trt
                          2                         p      test   
  n                       154                                     
  time (mean (SD))        1996.86 (1155.93)          0.883        
  age (mean (SD))           48.58 (9.96)             0.018        
  bili (median [IQR])        1.30 [0.72, 3.60]       0.842 nonnorm
  chol (median [IQR])      303.50 [254.25, 377.00]   0.544 nonnorm
  albumin (mean (SD))        3.52 (0.40)             0.874        
  copper (median [IQR])     73.00 [43.00, 139.00]    0.717 nonnorm
  alk.phos (median [IQR]) 1283.00 [922.50, 1949.75]  0.812 nonnorm
  ast (mean (SD))          124.97 (58.93)            0.460        
  trig (median [IQR])      113.00 [84.50, 155.00]    0.370 nonnorm
  platelet (mean (SD))     265.20 (90.73)            0.555        
  protime (median [IQR])    10.60 [10.00, 11.40]     0.588 nonnorm