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better example table for README on github
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kaz-yos committed Feb 15, 2014
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Expand Up @@ -9,61 +9,50 @@ This package creates "Table 1", i.e., description of baseline patient characteri
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

```
## Make categorical variables factors
> varsToFactor <- c("status","trt","ascites","hepato","spiders","edema","stage")
> pbc[varsToFactor] <- lapply(pbc[varsToFactor], factor)
## Create a variable list. Use dput(names(pbc))
> vars <- c("time","status","age","sex","ascites","hepato",
+ "spiders","edema","bili","chol","albumin",
+ "copper","alk.phos","ast","trig","platelet",
+ "protime","stage")
## Create Table 1 stratified by trt (omit strata argument for overall table)
> tableOne <- CreateTableOne(vars = vars, strata = "trt", data = pbc)
## Just typing the object name will invoke the print.TableOne method
## Tests are by oneway.test/t.test for continuous, chisq.test for categorical
> tableOne
Stratified by trt
1 2 p test
n 158 154
time (mean (sd)) 2015.62 (1094.12) 1996.86 (1155.93) 0.883
status (%) 0.894
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 = 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)
bili (mean (sd)) 2.87 (3.63) 3.65 (5.28) 0.131
chol (mean (sd)) 365.01 (209.54) 373.88 (252.48) 0.748
albumin (mean (sd)) 3.52 (0.44) 3.52 (0.40) 0.874
copper (mean (sd)) 97.64 (90.59) 97.65 (80.49) 0.999
alk.phos (mean (sd)) 2021.30 (2183.44) 1943.01 (2101.69) 0.747
ast (mean (sd)) 120.21 (54.52) 124.97 (58.93) 0.460
trig (mean (sd)) 124.14 (71.54) 125.25 (58.52) 0.886
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 (%) 0.201
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)
> print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"), exact = c("status","stage"))
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 = 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)
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
-------------------------------------------------------------------------------

Installing tableone
--------------------
The tableone package for R is still in development, and is not available from the CRAN, yet. You can install it using one of the following ways.

The archive file for point releases are available from the following URL:
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