The goal of the tibbleOne
package is to make it easy for analysts to
include a Table 1 object in both LaTeX and html markdown documents. I
made this package because I was unable to get the html tables I wanted
from the existing table one R packages. Notably, this package has far
fewer features than the outstanding TableOne package, but it can get a
readable Table 1 object into a markdown document with less effort.
You can install the latest version of tibbleOne from github with:
devtools::install_github('bcjaeger/tibbleOne')
For a more detailed example, see the ‘start here’ vignette. This example
shows basic elements of tibbleOne
.
library(knitr)
library(kableExtra)
library(tibbleOne)
library(tidyverse)
The first step should be setting labels for the variables that will be
in the table. This can be done using set_variable_labels
and then
building a meta
data set. You may also just pipe the labelled dataset
into tibble_one()
, but it is generally more useful to keep the meta
data object in case you need to use the labels for other tables in your
analysis.
meta <- pbc_tbl1 %>%
set_variable_labels(
status = "Status at last contact",
trt = "Treatment group",
age = 'Age',
sex = 'Sex at birth',
ascites = 'Ascites',
bili = 'Bilirubin levels',
edema = 'Edema',
albumin = 'Serum Albumin'
) %>%
build_meta(add_perc_to_cats = TRUE)
tbl_one <- tibble_one(
data = pbc_tbl1,
meta_data = meta,
formula = ~ . | trt,
include_pval = TRUE
)
Last step, we pass tbl_one
into the to_kable()
function, which
provides a couple of nice formatting procedures to make the data look
like the type of Table 1 that you may see in a published article.
cap <- 'Characteristics of patients with primary biliarry cirrhosis.'
tbl_one %>%
to_kable(caption = cap) %>%
kable_styling(
position = 'center',
bootstrap_options = c('striped')
)
Characteristics of patients with primary biliarry
cirrhosis.
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