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R package to create "Table 1", description of baseline characteristics
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README.md

tableone (developmental repo)

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An R package to create "Table 1", description of baseline characteristics

Creates "Table 1", i.e., description of baseline patient characteristics, which is essential in every medical research. Supports both continuous and categorical variables, as well as p-values and standardized mean differences. Weighted data are supported via the survey package.

tableone was inspired by 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.

tableone in action

screencast

The code being executed can be found in the introduction vignette.

A higher quality version is available at YouTube: https://www.youtube.com/watch?v=IZgDKmOC0Wg&feature=youtu.be

tableone code example

In this table, continuous and categorical variables can be placed in any 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 p-values are from nonparametric tests. Numerically coded categorical variables can be transformed on the fly with factorVars. SMD stands for standardized mean differences. For weighted data, first created a svydesign object, and use the svyCreateTableOne() function. Most other options remain the same.


> ## Load data
> library(survival); data(pbc)
> # drop ID from variable list
> vars <- names(pbc)[-1]
> ## Create Table 1 stratified by trt (can add more stratifying variables)
> tableOne <- CreateTableOne(vars = vars, strata = c("trt"), data = pbc,
+                             factorVars = c("status","edema","stage"))
> ## Specifying nonnormal variables will show the variables appropriately,
> ## and show nonparametric test p-values. Specify variables in the exact
> ## argument to obtain the exact test p-values.
> print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
+       exact = c("status","stage"), smd = TRUE)


                        Stratified by trt
                        1                         2                         p      test    SMD
n                           158                       154
time (mean (SD))        2015.62 (1094.12)         1996.86 (1155.93)          0.883          0.017
status (%)                                                                   0.884 exact    0.054
   0                         83 (52.5)                 85 (55.2)
   1                         10 ( 6.3)                  9 ( 5.8)
   2                         65 (41.1)                 60 (39.0)
trt (mean (SD))            1.00 (0.00)               2.00 (0.00)            <0.001          Inf
age (mean (SD))           51.42 (11.01)             48.58 (9.96)             0.018          0.270
sex = f (%)                 137 (86.7)                139 (90.3)             0.421          0.111
ascites (mean (SD))        0.09 (0.29)               0.06 (0.25)             0.434          0.089
hepato (mean (SD))         0.46 (0.50)               0.56 (0.50)             0.069          0.206
spiders (mean (SD))        0.28 (0.45)               0.29 (0.46)             0.886          0.016
edema (%)                                                                    0.877          0.058
   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  0.171
chol (median [IQR])      315.50 [247.75, 417.00]   303.50 [254.25, 377.00]   0.544 nonnorm  0.038
albumin (mean (SD))        3.52 (0.44)               3.52 (0.40)             0.874          0.018
copper (median [IQR])     73.00 [40.00, 121.00]     73.00 [43.00, 139.00]    0.717 nonnorm <0.001
alk.phos (median [IQR]) 1214.50 [840.75, 2028.00] 1283.00 [922.50, 1949.75]  0.812 nonnorm  0.037
ast (mean (SD))          120.21 (54.52)            124.97 (58.93)            0.460          0.084
trig (median [IQR])      106.00 [84.50, 146.00]    113.00 [84.50, 155.00]    0.370 nonnorm  0.017
platelet (mean (SD))     258.75 (100.32)           265.20 (90.73)            0.555          0.067
protime (mean (SD))       10.65 (0.85)              10.80 (1.14)             0.197          0.146
stage (%)                                                                    0.205 exact    0.246
   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 version of tableone package for R is developmetal, and may not be available from the CRAN. You can install it using one of the following way.

Direct installation from github

You first need to install the devtools package to do the following. You can choose from the latest stable version and the latest development version.


## Install devtools (if you do not have it already)
> install.packages("devtools")
## Install directly from github (develop branch)
> devtools::install_github(repo = "kaz-yos/tableone", ref = "develop")

Using devtools may requires some preparation, please see the following link for information.

http://www.rstudio.com/projects/devtools/

Similar or complementary projects

There are multiple similar or complementary projects of interest.

Contributors

I would like to thank all the contributors!

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