tableone palmerpenguins

Using the TableOne instructions from (https://cran.r-project.org/web/packages/tableone/vignettes/introduction.html) on the palmerpenguins package.

Bonnie Butler true
2021-03-07

Load packages

library(tableone)
library(tidyverse)
library(palmerpenguins)

Read datasets

data(penguins)

Single group summary

Simplest use case

CreateTableOne(data = penguins)

                               
                                Overall         
  n                                 344         
  species (%)                                   
     Adelie                         152 (44.2)  
     Chinstrap                       68 (19.8)  
     Gentoo                         124 (36.0)  
  island (%)                                    
     Biscoe                         168 (48.8)  
     Dream                          124 (36.0)  
     Torgersen                       52 (15.1)  
  bill_length_mm (mean (SD))      43.92 (5.46)  
  bill_depth_mm (mean (SD))       17.15 (1.97)  
  flipper_length_mm (mean (SD))  200.92 (14.06) 
  body_mass_g (mean (SD))       4201.75 (801.95)
  sex = male (%)                    168 (50.5)  
  year (mean (SD))              2008.03 (0.82)

Categorical variable conversion

Get variable names

dput(names(penguins))

c("species", "island", "bill_length_mm", "bill_depth_mm", "flipper_length_mm", 
"body_mass_g", "sex", "year")

Vector of variables to summarise

myVars <- c("species", "island", "bill_length_mm", "bill_depth_mm", "flipper_length_mm", "body_mass_g", "sex", "year")

Vector of categorical variables that need transformation

catVars <- c("species", "island", "sex", "year")

Create a TableOne object

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

Showing all levels for categorical variables

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

                               
                                level     Overall          
  n                                            344         
  species (%)                   Adelie         152 (44.2)  
                                Chinstrap       68 (19.8)  
                                Gentoo         124 (36.0)  
  island (%)                    Biscoe         168 (48.8)  
                                Dream          124 (36.0)  
                                Torgersen       52 (15.1)  
  bill_length_mm (mean (SD))                 43.92 (5.46)  
  bill_depth_mm (mean (SD))                  17.15 (1.97)  
  flipper_length_mm (mean (SD))             200.92 (14.06) 
  body_mass_g (mean (SD))                 4,201.75 (801.95)
  sex (%)                       female         165 (49.5)  
                                male           168 (50.5)  
  year (%)                      2007           110 (32.0)  
                                2008           114 (33.1)  
                                2009           120 (34.9)

Detailed information including missingness

summary(tab2)


     ### Summary of continuous variables ###

strata: Overall
                    n miss p.miss mean  sd median  p25  p75  min  max
bill_length_mm    344    2    0.6   44   5     44   39   48   32   60
bill_depth_mm     344    2    0.6   17   2     17   16   19   13   22
flipper_length_mm 344    2    0.6  201  14    197  190  213  172  231
body_mass_g       344    2    0.6 4202 802   4050 3550 4750 2700 6300
                   skew kurt
bill_length_mm     0.05 -0.9
bill_depth_mm     -0.14 -0.9
flipper_length_mm  0.35 -1.0
body_mass_g        0.47 -0.7

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

     ### Summary of categorical variables ### 

strata: Overall
     var   n miss p.miss     level freq percent cum.percent
 species 344    0    0.0    Adelie  152    44.2        44.2
                         Chinstrap   68    19.8        64.0
                            Gentoo  124    36.0       100.0
                                                           
  island 344    0    0.0    Biscoe  168    48.8        48.8
                             Dream  124    36.0        84.9
                         Torgersen   52    15.1       100.0
                                                           
     sex 344   11    3.2    female  165    49.5        49.5
                              male  168    50.5       100.0
                                                           
    year 344    0    0.0      2007  110    32.0        32.0
                              2008  114    33.1        65.1
                              2009  120    34.9       100.0

Multiple group summary

tab3 <- CreateTableOne(vars = myVars, strata = "species", data = penguins, factorVars = catVars)
print(tab3, formatOptions = list(big.mark = ","))

                               Stratified by species
                                Adelie            Chinstrap        
  n                                  152                68         
  species (%)                                                      
     Adelie                          152 (100.0)         0 (  0.0) 
     Chinstrap                         0 (  0.0)        68 (100.0) 
     Gentoo                            0 (  0.0)         0 (  0.0) 
  island (%)                                                       
     Biscoe                           44 ( 28.9)         0 (  0.0) 
     Dream                            56 ( 36.8)        68 (100.0) 
     Torgersen                        52 ( 34.2)         0 (  0.0) 
  bill_length_mm (mean (SD))       38.79 (2.66)      48.83 (3.34)  
  bill_depth_mm (mean (SD))        18.35 (1.22)      18.42 (1.14)  
  flipper_length_mm (mean (SD))   189.95 (6.54)     195.82 (7.13)  
  body_mass_g (mean (SD))       3,700.66 (458.57) 3,733.09 (384.34)
  sex = male (%)                      73 ( 50.0)        34 ( 50.0) 
  year (%)                                                         
     2007                             50 ( 32.9)        26 ( 38.2) 
     2008                             50 ( 32.9)        18 ( 26.5) 
     2009                             52 ( 34.2)        24 ( 35.3) 
                               Stratified by species
                                Gentoo            p      test
  n                                  124                     
  species (%)                                     <0.001     
     Adelie                            0 (  0.0)             
     Chinstrap                         0 (  0.0)             
     Gentoo                          124 (100.0)             
  island (%)                                      <0.001     
     Biscoe                          124 (100.0)             
     Dream                             0 (  0.0)             
     Torgersen                         0 (  0.0)             
  bill_length_mm (mean (SD))       47.50 (3.08)   <0.001     
  bill_depth_mm (mean (SD))        14.98 (0.98)   <0.001     
  flipper_length_mm (mean (SD))   217.19 (6.48)   <0.001     
  body_mass_g (mean (SD))       5,076.02 (504.12) <0.001     
  sex = male (%)                      61 ( 51.3)   0.976     
  year (%)                                         0.522     
     2007                             34 ( 27.4)             
     2008                             46 ( 37.1)             
     2009                             44 ( 35.5)

Testing

print(tab3, exact = "year", smd = TRUE)

                               Stratified by species
                                Adelie           Chinstrap       
  n                                 152               68         
  species (%)                                                    
     Adelie                         152 (100.0)        0 (  0.0) 
     Chinstrap                        0 (  0.0)       68 (100.0) 
     Gentoo                           0 (  0.0)        0 (  0.0) 
  island (%)                                                     
     Biscoe                          44 ( 28.9)        0 (  0.0) 
     Dream                           56 ( 36.8)       68 (100.0) 
     Torgersen                       52 ( 34.2)        0 (  0.0) 
  bill_length_mm (mean (SD))      38.79 (2.66)     48.83 (3.34)  
  bill_depth_mm (mean (SD))       18.35 (1.22)     18.42 (1.14)  
  flipper_length_mm (mean (SD))  189.95 (6.54)    195.82 (7.13)  
  body_mass_g (mean (SD))       3700.66 (458.57) 3733.09 (384.34)
  sex = male (%)                     73 ( 50.0)       34 ( 50.0) 
  year (%)                                                       
     2007                            50 ( 32.9)       26 ( 38.2) 
     2008                            50 ( 32.9)       18 ( 26.5) 
     2009                            52 ( 34.2)       24 ( 35.3) 
                               Stratified by species
                                Gentoo           p      test  SMD   
  n                                 124                             
  species (%)                                    <0.001          NaN
     Adelie                           0 (  0.0)                     
     Chinstrap                        0 (  0.0)                     
     Gentoo                         124 (100.0)                     
  island (%)                                     <0.001          NaN
     Biscoe                         124 (100.0)                     
     Dream                            0 (  0.0)                     
     Torgersen                        0 (  0.0)                     
  bill_length_mm (mean (SD))      47.50 (3.08)   <0.001        2.255
  bill_depth_mm (mean (SD))       14.98 (0.98)   <0.001        2.116
  flipper_length_mm (mean (SD))  217.19 (6.48)   <0.001        2.725
  body_mass_g (mean (SD))       5076.02 (504.12) <0.001        1.976
  sex = male (%)                     61 ( 51.3)   0.976        0.017
  year (%)                                        0.522 exact  0.181
     2007                            34 ( 27.4)                     
     2008                            46 ( 37.1)                     
     2009                            44 ( 35.5)

Miscellaneous

Categorical or continuous variables-only

Categorical part only

tab3$CatTable

                Stratified by species
                 Adelie       Chinstrap   Gentoo       p      test
  n              152          68          124                     
  species (%)                                          <0.001     
     Adelie      152 (100.0)   0 (  0.0)    0 (  0.0)             
     Chinstrap     0 (  0.0)  68 (100.0)    0 (  0.0)             
     Gentoo        0 (  0.0)   0 (  0.0)  124 (100.0)             
  island (%)                                           <0.001     
     Biscoe       44 ( 28.9)   0 (  0.0)  124 (100.0)             
     Dream        56 ( 36.8)  68 (100.0)    0 (  0.0)             
     Torgersen    52 ( 34.2)   0 (  0.0)    0 (  0.0)             
  sex = male (%)  73 ( 50.0)  34 ( 50.0)   61 ( 51.3)   0.976     
  year (%)                                              0.522     
     2007         50 ( 32.9)  26 ( 38.2)   34 ( 27.4)             
     2008         50 ( 32.9)  18 ( 26.5)   46 ( 37.1)             
     2009         52 ( 34.2)  24 ( 35.3)   44 ( 35.5)

Continuous part only

print(tab3$ContTable)

                               Stratified by species
                                Adelie           Chinstrap       
  n                             152              68              
  bill_length_mm (mean (SD))      38.79 (2.66)     48.83 (3.34)  
  bill_depth_mm (mean (SD))       18.35 (1.22)     18.42 (1.14)  
  flipper_length_mm (mean (SD))  189.95 (6.54)    195.82 (7.13)  
  body_mass_g (mean (SD))       3700.66 (458.57) 3733.09 (384.34)
                               Stratified by species
                                Gentoo           p      test
  n                             124                         
  bill_length_mm (mean (SD))      47.50 (3.08)   <0.001     
  bill_depth_mm (mean (SD))       14.98 (0.98)   <0.001     
  flipper_length_mm (mean (SD))  217.19 (6.48)   <0.001     
  body_mass_g (mean (SD))       5076.02 (504.12) <0.001