tableone (release repo)

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.

Examples

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)

Installation

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.