start_here.RmdtibbleOne?The goal of tibbleOne is to make it easy for analysts to include a Table 1 object in html, LaTeX, and word documents. Notably, this package has far fewer features than the outstanding TableOne package and many similar types of R packages for this task, but tibbleOne is handy for getting a readable Table 1 into a markdown document with minimal effort.
The primary function in tibbleOne is tibble_one(). It is a formula-based function with some flexibility. In the code block below, I’ll use tibble_one() to tabulate participant characteristics in the primary biliary cirrhosis dataset (adapted from the pbc data in the survival package).
First, I make a meta dataset that contains data about our data. Initially, I will indicate the labels and groups for variables. In addition to setting groups and labels for variables, I may also want to write some key details about a variable or two, and pass that information into my tables as a footnote. Last, some variable labels have abbreviations in them, and those need to be expanded on in the footnotes of the table.
library(tibbleOne)
library(kableExtra)
library(survival)
# set attributes and then build a meta data set
meta <- pbc_tbl1 %>%
# labels are used to represent column names in table 1
set_variable_labels(
status = "Status ALC",
trt = "Treatment group",
age = 'Age',
sex = 'Sex at birth',
ascites = 'Ascites',
bili = 'Bili levels',
edema = 'Edema',
albumin = 'Serum Alb'
) %>%
# units must be attached to continuous variables
set_variable_units(
age = 'years',
bili = 'mg/dl',
albumin = 'g/dl'
) %>%
# variables in the same group are clustered together table 1
set_variable_groups(
Outcomes = c('status'),
Exposures = c('ascites','bili','albumin','edema','stage')
) %>%
set_variable_notes(
age = "important note about age"
) %>%
set_variable_abbrs(
status = c(ALC = "at last contact"),
bili = c(Bili = "bilirubin"),
albumin = c(Alb = 'albumin')
) %>%
build_meta()
meta
#> $data
#> # A tibble: 9 x 8
#> variable label type unit group abbr note labels
#> <chr> <chr> <chr> <chr> <chr> <list> <list> <list>
#> 1 age Age numeric years None <chr [1~ <chr [1~ <chr [1~
#> 2 sex Sex at birth factor % None <chr [1~ <chr [1~ <chr [1~
#> 3 status Status ALC factor % Outcomes <chr [1~ <chr [1~ <chr [4~
#> 4 trt Treatment gro~ factor % None <chr [1~ <chr [1~ <chr [1~
#> 5 stage Stage factor % Exposur~ <chr [1~ <chr [1~ <chr [5~
#> 6 ascites Ascites factor % Exposur~ <chr [1~ <chr [1~ <chr [1~
#> 7 bili Bili levels numeric mg/dl Exposur~ <chr [1~ <chr [1~ <chr [1~
#> 8 edema Edema factor % Exposur~ <chr [1~ <chr [1~ <chr [4~
#> 9 albumin Serum Alb numeric g/dl Exposur~ <chr [1~ <chr [1~ <chr [1~
#>
#> $group_levels
#> [1] "None" "Outcomes" "Exposures"
#>
#> $var_levels
#> [1] "status" "ascites" "bili" "albumin" "edema" "stage"
#>
#> $add_perc_to_cats
#> [1] TRUE
#>
#> attr(,"class")
#> [1] "meta"meta datameta data allows tibbleOne objects to carry along information that pertains to variable labels, abbreviations, units, and footnotes. Initially, this type of information was stored as an attribute on a tibble, but attributes of tibble objects can be wiped away by some operations, so it seemed much safer to store the information remotely in a meta data object.
kable outputThe kable() function from the knitr package and the host of extra functions from the kableExtra package are meant to be combined with tibbleOne objects to create publishable tables. A user may pass their tibble_one() output into the convenience function, to_kable(), to produce a table such as the one below.
|
Overall (N = 418) |
D-penicillmain (N = 158) |
Placebo (N = 154) |
|
|---|---|---|---|
| Age, years† | 50.7 (10.4) | 51.4 (11.0) | 48.6 (9.96) |
| Female, % | 89.5 | 86.7 | 90.3 |
| Outcomes | |||
| Status ALC, % | |||
| Censored | 55.5 | 52.5 | 55.2 |
| Transplant | 5.98 | 6.33 | 5.84 |
| Dead | 38.5 | 41.1 | 39.0 |
| Exposures | |||
| Ascites, % | 7.69 | 8.86 | 6.49 |
| Bili levels, mg/dl | 1.40 [0.80-3.40] | 1.40 [0.80-3.20] | 1.30 [0.72-3.60] |
| Serum Alb, g/dl | 3.53 [3.24-3.77] | 3.56 [3.21-3.83] | 3.54 [3.34-3.78] |
| Edema, % | |||
| None | 84.7 | 83.5 | 85.1 |
| Untreated or successfully treated | 10.5 | 10.1 | 8.44 |
| Treatment resistant | 4.78 | 6.33 | 6.49 |
| Stage, % | |||
| One | 5.10 | 7.59 | 2.60 |
| Two | 22.3 | 22.2 | 20.8 |
| Three | 37.6 | 35.4 | 41.6 |
| Four | 35.0 | 34.8 | 35.1 |
| Alb = albumin, ALC = at last contact, Bili = bilirubin | |||
| * Table values for continuous variables are mean (standard deviation) or median [interquartile range]. Table values for categorical variables are percent. | |||
| † important note about age | |||
kable also provides LaTex tables when the markdown output is set as a pdf.
flextable outputThe flextable() package comprises functions that help construct tables in Microsoft word. tibbleOne provides a function to help users send their tibble_out() output into the framework of flextable package. The function is called to_word()
|
Treatment group |
||
Characteristic* |
Overall |
D-penicillmain |
Placebo |
Age, years† |
50.7 (10.4) |
51.4 (11.0) |
48.6 (9.96) |
Female, % |
89.5 |
86.7 |
90.3 |
Outcomes | |||
Status ALC, % |
|||
Censored |
55.5 |
52.5 |
55.2 |
Transplant |
5.98 |
6.33 |
5.84 |
Dead |
38.5 |
41.1 |
39.0 |
Exposures | |||
Ascites, % |
7.69 |
8.86 |
6.49 |
Bili levels, mg/dl |
1.40 [0.80-3.40] |
1.40 [0.80-3.20] |
1.30 [0.72-3.60] |
Serum Alb, g/dl |
3.53 [3.24-3.77] |
3.56 [3.21-3.83] |
3.54 [3.34-3.78] |
Edema, % |
|||
None |
84.7 |
83.5 |
85.1 |
Untreated or successfully treated |
10.5 |
10.1 |
8.44 |
Treatment resistant |
4.78 |
6.33 |
6.49 |
Stage, % |
|||
One |
5.10 |
7.59 |
2.60 |
Two |
22.3 |
22.2 |
20.8 |
Three |
37.6 |
35.4 |
41.6 |
Four |
35.0 |
34.8 |
35.1 |
*Table values for continuous variables are mean (standard deviation) or median [interquartile range]. Table values for categorical variables are percent. | |||
†important note about age | |||
Alb = albumin, ALC = at last contact, Bili = bilirubin | |||
The example above shows how tibbleOne can be used to direct your R output into any of three formats for writing articles (Word, html, and Tex). The code used to create tibbleOne tables
is formula based, allowing users to create stratified tables with one or two variables (e.g. sex*trt for two stratifying variables, trt or sex for one stratifying variable)
gives the user some options for handling continuous variables, such as specifying whether they would like to present mean/median and conduct parametric (t-tests/chi-square) or non-parametric tests (kruskal-wallis) for each variable.