An R package to create "Table 1", description of baseline characteristics
This package creates "Table 1", i.e., description of baseline patient characteristics, which is essential every medical research. This package provides functions to create such summaries for continuous and categorical variables, optionally with subgroup comparisons. The package was inspired by and based on descriptive statistics functions in Deducer, a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for command-line users.
The tableone package creates tables like the one below. In this table, continuous and categorical variables are ordered in an arbitrary order. The p-valeus are from exact tests for pre-specified variables. For nonnormal variables, it shows median and IQR instead of mean and SD, and test is via nonparametric tests.
See also the demonstration here: http://rpubs.com/kaz_yos/tableone-demo-e
> tableOne <- CreateTableOne(vars = vars, strata = "trt", data = pbc)
> print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+ exact = c("status","stage"), cramVars = "sex")
Stratified by trt
1 2 p test
n 158 154
time (mean (sd)) 2015.62 (1094.12) 1996.86 (1155.93) 0.883
status (%) 0.884 exact
0 83 (52.5) 85 (55.2)
1 10 ( 6.3) 9 ( 5.8)
2 65 (41.1) 60 (39.0)
age (mean (sd)) 51.42 (11.01) 48.58 (9.96) 0.018
sex = m/f (%) 21/137 (13.3/86.7) 15/139 (9.7/90.3) 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)
bili (median [IQR]) 1.40 [0.80, 3.20] 1.30 [0.72, 3.60] 0.842 nonnorm
chol (median [IQR]) 315.50 [247.75, 417.00] 303.50 [254.25, 377.00] 0.544 nonnorm
albumin (mean (sd)) 3.52 (0.44) 3.52 (0.40) 0.874
copper (median [IQR]) 73.00 [40.00, 121.00] 73.00 [43.00, 139.00] 0.717 nonnorm
alk.phos (median [IQR]) 1214.50 [840.75, 2028.00] 1283.00 [922.50, 1949.75] 0.812 nonnorm
ast (mean (sd)) 120.21 (54.52) 124.97 (58.93) 0.460
trig (median [IQR]) 106.00 [84.50, 146.00] 113.00 [84.50, 155.00] 0.370 nonnorm
platelet (mean (sd)) 258.75 (100.32) 265.20 (90.73) 0.555
protime (mean (sd)) 10.65 (0.85) 10.80 (1.14) 0.197
stage (%) 0.205 exact
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)
This is the release version of the tableone package either to be released on CRAN or is already on CRAN. The installation can be done by the usual package installation via CRAN.
If you prefer to follow the latest development, please see the developmetal repo:
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