README.md

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coverage DOI:10.32614/RJ-2021-053

gtsummary

The {gtsummary} package provides an elegant and flexible way to create publication-ready analytical and summary tables using the R programming language. The {gtsummary} package summarizes data sets, regression models, and more, using sensible defaults with highly customizable capabilities.

By leveraging {broom}, {gt}, and {labelled} packages, {gtsummary} creates beautifully formatted, ready-to-share summary and result tables in a single line of R code!

Check out the examples below, review the vignettes for a detailed exploration of the output options, and view the gallery for various customization examples.

Installation

The {gtsummary} package was written as a companion to the {gt} package from RStudio. You can install {gtsummary} with the following code.

install.packages("gtsummary")

Install the development version of {gtsummary} with:

remotes::install_github("ddsjoberg/gtsummary")

Examples

Summary Table

Use tbl_summary() to summarize a data frame.

animated

Example basic table:

library(gtsummary)
# make dataset with a few variables to summarize
trial2 <- trial %>% select(age, grade, response, trt)

# summarize the data with our package
table1 <- tbl_summary(trial2)

There are many customization options to add information (like comparing groups) and format results (like bold labels) in your table. See the tbl_summary() tutorial for many more options, or below for one example.

table2 <- 
  tbl_summary(
    trial2,
    by = trt, # split table by group
    missing = "no" # don't list missing data separately
  ) %>%
  add_n() %>% # add column with total number of non-missing observations
  add_p() %>% # test for a difference between groups
  modify_header(label = "**Variable**") %>% # update the column header
  bold_labels() 

Regression Models

Use tbl_regression() to easily and beautifully display regression model results in a table. See the tutorial for customization options.

mod1 <- glm(response ~ trt + age + grade, trial, family = binomial)

t1 <- tbl_regression(mod1, exponentiate = TRUE)

Side-by-side Regression Models

You can also present side-by-side regression model results using tbl_merge()

library(survival)

# build survival model table
t2 <-
  coxph(Surv(ttdeath, death) ~ trt + grade + age, trial) %>%
  tbl_regression(exponentiate = TRUE)

# merge tables 
tbl_merge_ex1 <-
  tbl_merge(
    tbls = list(t1, t2),
    tab_spanner = c("**Tumor Response**", "**Time to Death**")
  )

Review even more output options in the table gallery.

gtsummary + R Markdown

The {gtsummary} package was written to be a companion to the {gt} package from RStudio. But not all output types are supported by the {gt} package. Therefore, we have made it possible to print {gtsummary} tables with various engines.

Review the gtsummary + R Markdown vignette for details.

Save Individual Tables

{gtsummary} tables can also be saved directly to file as an image, RTF, LaTeX, and Word file.

tbl %>%
  as_gt() %>%
  gt::gtsave(filename = ".") # use extensions .html .tex .ltx .rtf

For a Word file, use

tbl %>%
  as_flex_table() %>%
  flextable::save_as_docx()

Additional Resources

Cite gtsummary

> citation("gtsummary")

To cite gtsummary in publications use:

  Sjoberg DD, Whiting K, Curry M, Lavery JA, Larmarange J. Reproducible summary tables with the gtsummary package.
  The R Journal 2021;13:570–80. https://doi.org/10.32614/RJ-2021-053.

A BibTeX entry for LaTeX users is

  @Article{gtsummary,
    author = {Daniel D. Sjoberg and Karissa Whiting and Michael Curry and Jessica A. Lavery and Joseph Larmarange},
    title = {Reproducible Summary Tables with the gtsummary Package},
    journal = {{The R Journal}},
    year = {2021},
    url = {https://doi.org/10.32614/RJ-2021-053},
    doi = {10.32614/RJ-2021-053},
    volume = {13},
    issue = {1},
    pages = {570-580},
  }

Contributing

Big thank you to @jeffreybears for the hex sticker!

Please note that the {gtsummary} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. Thank you to all contributors! @ablack3, @ABorakati, @aghaynes, @ahinton-mmc, @aito123, @akarsteve, @akefley, @albertostefanelli, @alexis-catherine, @amygimma, @anaavu, @andrader, @angelgar, @arbet003, @arnmayer, @aspina7, @asshah4, @awcm0n, @barthelmes, @BeauMeche, @benediktclaus, @berg-michael, @bhattmaulik, @brachem-christian, @bwiernik, @bx259, @calebasaraba, @CarolineXGao, @Chris-M-P, @chrisleitzinger, @cjprobst, @clmawhorter, @CodieMonster, @coeus-analytics, @coreysparks, @ctlamb, @davidgohel, @davidkane9, @dax44, @dchiu911, @ddsjoberg, @DeFilippis, @denis-or, @dieuv0, @discoleo, @djbirke, @dmenne, @eamoncaddigan, @ElfatihHasabo, @emilyvertosick, @ercbk, @erikvona, @eweisbrod, @feizhadj, @fh-jsnider, @ge-generation, @gjones1219, @gorkang, @GuiMarthe, @hass91, @HichemLa, @hughjonesd, @iaingallagher, @ilyamusabirov, @IndrajeetPatil, @IsadoraBM, @j-tamad, @jalavery, @jeanmanguy, @jemus42, @jenifav, @jennybc, @JeremyPasco, @JesseRop, @jflynn264, @jjallaire, @jmbarajas, @JoanneF1229, @joelgautschi, @jojosgithub, @JonGretar, @jthomasmock, @juseer, @jwilliman, @karissawhiting, @kmdono02, @kwakuduahc1, @lamhine, @larmarange, @leejasme, @loukesio, @lspeetluk, @ltin1214, @lucavd, @LuiNov, @maia-sh, @Marsus1972, @matthieu-faron, @mbac, @mdidish, @MelissaAssel, @michaelcurry1123, @mljaniczek, @moleps, @motocci, @mvuorre, @MyKo101, @oranwutang, @palantre, @Pascal-Schmidt, @pedersebastian, @philsf, @polc1410, @postgres-newbie, @proshano, @raphidoc, @rich-iannone, @RiversPharmD, @rmgpanw, @roman2023, @ryzhu75, @sachijay, @saifelayan, @sammo3182, @sbalci, @shannonpileggi, @shengchaohou, @ShixiangWang, @simonpcouch, @slb2240, @slobaugh, @spiralparagon, @StaffanBetner, @Stephonomon, @storopoli, @szimmer, @tamytsujimoto, @TarJae, @themichjam, @THIB20, @tibirkrajc, @tjmeyers, @tldrcharlene, @tormodb, @toshifumikuroda, @UAB-BST-680, @uakimix, @uriahf, @Valja64, @vvm02, @xkcococo, @yonicd, @yoursdearboy, @zabore, @zachariae, @zaddyzad, @zeyunlu, @zhengnow, @zlkrvsm, and @zongell-star



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gtsummary documentation built on June 22, 2022, 9:07 a.m.