gtsummary (development version)

Updated tbl_regression() to be compatible with models created with the {parsnip} and {workflows} packages (#890, #647)
Added the modify_table_styling(text_format = "indent2") option to double indent a row. (#864)
Messaging update when inline_text.gtsummary() suspects a variable has been repeated in the gtsummary table. (#855)
Bug fix in add_p.tbl_summary() for columns that are all NA. These variables no longer error; rather, a message is printed indicating the p-value is not possible to calculate. (#889)
Updated tbl_svysummary() to be compatible with {srvyr} package (#886)
Updated default header when using tbl_uvregression(x=) to "**Outcome**" (#867)
The tbl_summary(by=) variable is now added to include= by default (#871)
Variables are converted to numeric before being passed to wilcox.test() in add_p(). This avoids an error when a date difference is passed. (#880)
Bug fix for {Hmisc} labeled data with tbl_summary() (#876)
Updates to the default formatting functions in the add_glance_*() functions. P-values are now styled with style_pvalue() and No. Obs. and degrees of freedom with style_number() (#870)

gtsummary 1.4.0

New Functions

Added new function add_glance_table() as a companion to add_glance_source_note(). Function adds model statistics, such as R-squared, to the bottom of the model summary table.
Added new function add_significance_stars() adding star indicators to significant estimates and an explanatory footnote.
Added new function tbl_strata(). The function aids prepares gtsummary tables stratified by one or more variables (#679)
Adding coefficient plot() methods for tbl_regression() and tbl_uvregression(). Function creates a forest plot of model coefficients via GGally::ggcoef_plot().
New function modify_fmt_fun() has been introduced to help update the functions that format numeric columns and rows in .x$table_body.
New function introduced, modify_table_styling(), to update printing instructions of tables. This function replaces modify_table_header(), which is now soft deprecated.
Added function add_vif() to include variance inflation factors in tbl_regression() output. (#717)
Added a generic function inline_text.gtsummary() that can report results from any gtsummary table. (#398)

New Functionality

Print infrastructure has been updated to allow for both row and column specification when formatting data or table styling. The x$table_header object has been replaced with a more general x$table_styling. Review the updated vignette "gtsummary_definition.Rmd" for details. The x$table_body is no longer grouped after tbl_stack(); rather, the grouping variable is specified in gt::gt(groupname_col=)
tbl_summary() now accepts any class as input. Previously only non-date base classes were accepted. For non-base R classes, the summary type must be specified using tbl_summary(type=). The default summary statistic for dates/times is the minimum and maximum. (#488)
The add_stat() function may now return multiple columns of new statistics. Some arguments have been deprecated in the update. (#746)
tbl_uvregression() now accepts both data frames and survey design objects as input. (#742)
If the default tidy_fun = broom::tidy fails, parameters::model_parameters() attempts to tidy the model, if {parameters} is installed. (#854)
Added a custom tidier for mgcv::gam() models (tidy_gam()) and a method function (tbl_regression.gam()) that uses the new tidier by default. (#745)
Added default support for brmsfit model in tbl_regression() with new method function. (#751)
Functions modify_footnote() and modify_spanning_header() now include the text_interpret= argument indicating whether to use gt::md() or gt::html() to format text. Default is gt::md().
Added/updated functions add_n() and add_nevent() to work with tbl_regression and tbl_uvregression objects. Each function now has an argument to place Ns on the label or level rows. (#744)
Added The Quarterly Journal of Economics to theme_gtsummary_journal(). This journal theme will be updated again after the gt package updates cols_merge() with a rows argument and allows for line breaks within cell.
Korean and Icelandic language translations added for theme_gtsummary_language().
Ability to merge two or more columns with modify_table_styling(cols_merge_pattern=) argument.
Added theme element "pkgwide-fun:pre_conversion". The function specified here will be executed on the gtsummary object before it is printed or converted with the as_gt(), as_flex_table(), etc functions. (#773)
The modify_table_body(fun=) argument has been generalized to accept formula shortcut notation.
Added exploratory data analysis theme that shows more details by default, theme_gtsummary_eda().

Other Updates

Updated tbl_merge() and tbl_stack() to capture the first source note and caption in the merged/stacked tables. Previously, any captions and source notes were lost.
Added messaging when table caption requested via modify_caption() for a gt table when using a version of gt that does not support captions.
Updates to the table gallery vignette reflecting changes in the package. (#775)
Improved error messaging when there is a problem constructing one of the univariate regression models in tbl_uvregression().
Added variable-specific formatting to add_difference(estimate_fun=) allowing a single table to show, for example, mean and rate differences that are formatted/rounded differently.
Improved handling and messaging to users when columns with "haven_labelled" class are passed to gtsummary functions. (#805)
Improved handling of ordered factors as the by= variable (#569, #540)
Removed {usethis} package dependency and replaced with {cli}. (#768)
Added the survey-adapted t-test to theme_gtsummary_mean_sd() for continuous variables in add_p.tbl_svysummary() (#758)
Allowing for tidyverse shortcut notation in tbl_survfit(estimate_fun=) specification, e.g. tbl_survfit(estimate_fun= ~style_sigfig(.x * 100)) (#761)
The JAMA journal theme has been updated to merge the coefficient and confidence interval columns.
Updated other inline_text() functions to wrap inline_text.gtsummary()

Bug Fixes

The label= argument for unstratified models was being ignored in tbl_survfit() (#842)
Preserve ordering for factor variables in tbl_survfit(). (#764)
Bug fix for spanning headers with kableExtra output. The spanning header was misplaced when the header text was sandwiched between two blank spanning headers.
Bug fix when displaying an unobserved level of a factor variable dichotomously in tbl_summary(). (#780)
Bug fix in add_p() where test name footnote was not being translated with theme_gtsummary_language().

Breaking Changes

tbl_survival() has moved from questioning to deprecated. This function maintains the old x$table_header format (instead of the more flexible x$table_styling). The "level_label" column was renamed to "groupname_col" and the x$table_body is no longer grouped with group_by(level_label)
The back-end implementation of add_stat_label(location = "row") has been updated. The function now merges columns "label" and "stat_label" instead of modifying the "label" column directly. This could be a breaking change if users had manually updated results, for example, from a tbl_regression() table to merge with tbl_summary() using tbl_merge()
The function add_stat_label() no longer auto-switches location = "column" requests to "row" in the presence of "continuous2" variables.

gtsummary 1.3.7

No changes. Resubmitting to resolve CRAN quirk.

gtsummary 1.3.6

New Functions

Added function add_difference(), which adds difference between groups, confidence interval and p-value. (#617)
Added function modify_caption() that includes table captions. For gt output, requires gt version > 0.2.2 (#701)
Added function modify_table_body() allowing users to more easily make changes to gtsummary tables
Added function remove_row_type() for removing header, reference, or missing rows from a gtsummary tables. (#678)
Added selecting function all_stat_cols() that selects columns from tbl_summary/tbl_svysummary object with summary statistics (i.e. "stat_0", "stat_1", "stat_2", etc.).
New selecting function was added all_tests() to make it easier to select variables based on the test used to calculate the p-value, e.g. add_p(test = c(age, marker) ~ "t.test", test.args = all_tests("t.test") ~ list(var.equal = TRUE))
Added functions modify_column_hide() and modify_column_unhide() to hide and unhide columns in .$table_body. Simple wrappers for modify_table_header().

New Functionality

Previously, the tbl_summary(digits=) only accepted integer values specifying the number of decimal places to round a statistic. The argument now accepts both integers or functions, e.g. digits = age ~ style_sigfig. (#708)
The add_stat() function now supports tbl_svysummary() objects in addition to tbl_summary() (#688)
The add_stat() function can now place statistics on the label row, or the level rows for categorical variables. (#714)
inline_text.tbl_survfit() updated to allow users to select p-value (and other) columns. (#589)

Other Updates

modify_header() has been updated so users may more easily access internal data while defining headers and so that it no longer adds its call to the gtsummary .$call_list (#719)
The default value for include= argument for the add_global_p.tbl_regression() and add_global_p.tbl_uvregression() methods have been made the same with include = everything(), and the help files for these methods have been brought together in a single file. (#721)
Introducing new package dependency {broom.helpers}
- The tidying and preparation of tbl_regression() tables are now being performed by {broom.helpers} (#636, #607)
- All select helper functions and the utility functions that make them possible, have been cleaned up and migrated to {broom.helpers}. (#648, #680)
- Importing .generic_selector(), .select_to_varnames(), and .formula_list_to_named_list() from {broom.helpers}: this is a function that makes it easy to create selecting functions like all_continuous(). The internals allow for it to be used in {broom.helpers} and {gtsummary} seamlessly. (#680)
- Theme element has been added for controlling the other tidy_plus_plus() arguments. (#692)
- Variables that do not follow standard naming conventions are now parsed correctly and presented in the regression tables.
The tbl_regression() function is now an S3 method. The new interface allows for special handling of different model types using S3 methods: tbl_regression.default(), tbl_regression.lmer(), tbl_regression.glmer(), tbl_regression.survreg()
tbl_regression(add_estimate_to_reference_rows=) argument has been added. Also added to tbl_uvregression(). (#692)
Theme element for tbl_regression(add_estimate_to_reference_rows=) has been added. (#677)
Removed "Statistics presented:" and "Statistical tests performed:" prefixes from the tbl_summary() %>% add_p() footnotes.
The codebase powering add_p() and related methods has been refactored for better performance, organization, and customizability. (#622)
- For clarity, a help file listing each test available within gtsummary and the pseudo code for calculating the p-value has been added (see ?tests)
- Each add_p() method now has the test.args= argument. Use this argument to pass additional arguments to the statistical method, e.g. add_p(test = c(age, marker) ~ "t.test", test.args = c(age, marker) ~ list(var.equal = TRUE))
- Additional tests have been added: paired t-test, signed rank test, and more. See ?tests for full list.
- More robust unit testing implemented for all add_p() methods.
Added messaging to tbl_stack() to inform users that the attributes from the first table passed take precedent over the others'. (#699)
In the modfiy_*() functions, if users did not select any columns, they encountered an error. Now, if no columns are selected, instructions are printed for how to correctly select columns in a gtsummary table. Moreover, if no columns are selected, the gtsummary object is now returned unaltered. (#699)
The add_glance_source_note() function has been generalized so users may pass any glance function. Previously, broom::glance() was being used with no option to change it. (#699)
The ... arguments have been added to as_gt(). These dots are subsequently passed to gt::gt(...). (#701)
Multiple imputation models created with {mice}, and multinomial regression models created with {nnet} are now supported in tbl_regression() (#645)
Updates to add_global_p.tbl_regression() allowing for variable names with spaces and special characters (#682)
Added digits= argument to style_percent() (#690)
Users may now choose which tbl_regression() columns to report with a theme element. they can choose among the "estimate", "std.error", "statistic", "ci", "conf.low", "conf.high" and "p.value" (#637)
Allow users to include the reference value in tbl_regression() via a theme element
Users may change the symbol with a reference row symbol with a theme element. (#628)

Bug Fixes

Bug fix when a default statistic is set using themes for "continuous2" variables that has length larger than one
Bug fix when missing/non-missing percentages requested in add_n.tbl_summary()

Breaking Changes

The default test for 2-by-2 tables with expected cell counts has been updated from the chi-squared test with continuity correction to the original chi-squared test for add_p.tbl_summary() (#721)
Experimental function add_p.tbl_survfit(test.args=) in addition to accepting the formula list notation, also accepted a single string naming a test that was interpreted as everything() ~ "test_name". The single string is no longer accepted, and users must use the formula notation.
Removed theme element N_fun that was previously marked as questioning and likely to be removed from the package.

gtsummary 1.3.5

New Functionality

New summary type continuous2 allows adding labelled statistic rows to tables in tbl_summary() and tbl_svysummary(). You can report several lines of statistics with this type. (#620)
- The all_continuous() function now selects summary types continuous and continuous2 by default.
- Added all_continuous2() function for selecting summary type continuous2 exclusively.
- Added theme_gtsummary_continuous2() to make continuous2 the default summary type for all continuous variables.
New function add_glance_source_note() adds the statistics returned in broom::glance() as a source note on a tbl_regression() (#434)
Exporting the modify_table_header() function, which is an advanced-use function used to make modifications to the .$table_header object to update printing instructions for the gtsummary object.
Added two custom tidiers for use in tbl_regression() and tbl_uvregression(). (#635)
- tidy_standardize() returns standardized coefficients using the {effectsize} package
- tidy_bootstrap() gives bootstrapped parameter estimates, calculated using the {parameters} package

Bug Fixes

Bug fix where estimate_fun= and pvalue_fun= were not being passed to tbl_regression() in tbl_uvregression()
There was an environments bug when evaluating the LHS of the formula inputs. In some complex situations, a stored character vector of column names could not properly evaluate (#604)
Fixed style_ratio() bug where there were rounding errors near one (#651)
Fixed style_sigfig() bug where there were rounding errors near thresholds (#638)
Adding the footnote from the stat columns describing the statistics presented to the overall column (#643)

Other Updates

Refresh of vignettes to use recently released functions (#649)
Moved the nevent column to after the N column when add_nevent() is called on a tbl_regression() object (#439)
gtsummary themes updates
- Add theme_gtsummary_mean_sd() theme to report mean and SD by default and use t-tests and ANOVA in add_p() (#654)
- Added first draft of the NEJM theme
- Added the mid-point decimal separator for the Lancet theme

gtsummary 1.3.4

Added a copy of tidyselect's where() function to allow users to use predicate select helpers (#632)
Fixed tbl_cross() bug where function defaulted to 'column' when margin = NULL. Now it defaults to display no margins when NULL. (#624)
Changed default of tbl_survfit() missing argument from '\U2014' (em dash) to NULL (CRAN issue). Em dash is still displayed by default in tables but it is set later in function.

gtsummary 1.3.3

New Functions

The {flextable} has graduated from Experimental status! Introducing as_flex_table(), which replaces as_flextable(). The updated function includes improvements to the default aesthetics of the tables, and improved consistency for spanning header rows.
Added tbl_svysummary() function to summarize complex and weighted survey designs. tbl_svysummary is now its own class that works with add_n(), add_p(), add_q(), add_stat_label(), add_overall(), inline_text(), tbl_merge() and tbl_stack() (#460).
The family of tbl_survfit() functions has been greatly expanded!
- tbl_survfit.survfit(), tbl_survfit.list(), and tbl_survfit.data.frame() have been added that accept a single survfit object, list of survfit objects, or a data frame for more flexible creation of univariate survival tables.
- add_p.tbl_survfit(), add_n.tbl_survfit(), add_nevent.tbl_survfit() have been added to include additional information in tbl_survfit() tables.
Adding as_hux_table() after the huxtable 5.0.0 release.
Added show_header_names() function to assist when updating table headers, footnotes, and spanning headers. The function prints the current underlying column names along with their labels easing the process of identifying the column names needed to make updates. (#539)
Added a language theme, theme_gtsummary_language() for translating tables into Spanish, French, Portuguese, German, Chinese (Traditional and Simplified), Hindi, Marathi, Gujarati, Japanese and Swedish (#511)
Added style_number() function which allows for granular control of how numbers are formatted throughout the package. The style_percent(), style_pvalue(), style_sigfig(), and style_ratio() functions have been updated to use style_number() in the background. The implication is that users can now control how every number in a gtsummary table appears. For example, formatting can be updated to use the comma as the decimal mark and also specify the big mark using the gtsummary themes. (#458)

User-facing Updates

Added support for competing risk cumulative incidence estimates to tbl_survfit() (#64, #448)
Updated API for set_gtsummary_theme(). Users no longer need call set_gtsummary_theme(theme_gtsummary_journal()); rather, they call theme_gtsummary_journal(). Each built-in theme now has an argument set_theme = TRUE. When FALSE, the theme function will invisibly return the named list the theme elements, and the theme will not be set. (#522)
Users can now specify how many decimal places to round statistics for categorical variables in tbl_summary(), e.g. 45 / 100 (45.0%). (#458)
Added the 'The Lancet' theme to theme_gtsummary_journal()
Updated the handling for arguments that accept functions to allow users to pass anonymous functions using the tidyverse shortcut notation, e.g. ~style_pvalue(.x, digits = 2).
The header for the tbl_stack(group_header=) column is now integrated into a typical gtsummary framework, meaning that all standard functions can be executed on it, e.g. modify_header() for non-gt output.
Added type= argument to add_global_p(), and added include= and keep= arguments to add_global_p.tbl_uvregression() (#554)

Internal Updates

Updated add_n() internals to be more efficient without recalculating statistics previously saved in tbl_summary()
{survival} package moved from Imports to Suggests
The add_overall() function is now a method function, and add_overall.tbl_summary and add_overall.tbl_svysummary added (#460).
Updated the variable labels for age and marker in the trial dataset.
Removed large *.gif files out of the package to reduce build size (#485)

Bug Fixes

Fixed bug where source note was not made smaller font size with compact theme when table was printed with {flextable} (#584)
Bug fix for tbl_summary() when a data frame contained an ordered factor column (#567)
Bug fix when only categorical summary statistics were requested for continuous variables in tbl_summary() and tbl_svysummary() (#528)
Bug fix when named list of {gtsummary} objects is passed to tbl_merge(x=) (#541)
Bug fix when for tbl_uvregression() when adjustment variables were included in formula = "{y} ~ {x} + age". The adjustment variables were being printed in the resulting table. (#555)

Breaking Changes

All lifecycle::deprecate_warn() have been upgraded to lifecycle::deprecate_stop() for <= v1.2.0 (released Aug 2019)
Removing as_flextable() and replacing with as_flex_table() due to a name conflict with flextable::as_flextable (#462)

gtsummary 1.3.2

Now returning all columns from broom::tidy() in .$table_body() (#516)
tbl_stack() now accepts a named list of gtsummary tables when using the group_header= argument (#524)
add_p.tbl_summary() bug fix for Wilcoxon rank-sum p-value calculation introduced in the last release (#525)
Delaying the release of as_huxtable() until the next {huxtable} release.

gtsummary 1.3.1

New Functions

Introducing themes in {gtsummary}. Use the function set_gtsummary_theme() to set new themes, and review the themes vignette for details on setting and creating personalized themes. (#424)
New functions modify_footnote() and modify_spanning_header() give users control over table footnotes and spanning headers. (#464)
Introducing as_huxtable()! The function converts gtsummary objects to {huxtable} objects. {huxtable} supports indentation, footnotes, and spanning headers with Word, HTML, and PDF output. (#469)
New function add_stat()! Add a new column of any statistic to a tbl_summary() table (#495)

User-facing Updates

The following columns in tbl_summary() are now available to print for both continuous and categorical variables: total number of observations {N_obs}, number of missing observations {N_miss}, number of non-missing observations {N_nomiss}, proportion of missing observations {p_miss}, proportion of non-missing observations {p_nomiss}. (#473)
Improved appearance of default as_flextable() output (#499)
Added tbl_cross(margin=) argument to control which margins are shown in the output table. (#444)
The missing values are now included in the calculation of p-values in tbl_cross().
Messaging about statistical methods used has been added for add_global_p(), add_q(), and combine_terms(). (#471)
Added include= argument to tbl_summary(). The preferred syntax for p-values with correlated data is now tbl_summary(..., include = -group_var) %>% add_p(group = group_var). The group variable is now no longer removed from the table summary. (#477)
add_stat_label() function updated with location= and label= arguments to change the location of the statistic labels and to modify the text of the labels. location = "row" is now the default. (#467)
tbl_stack() function added the group_header= argument that groups the stacked tables and adds a horizontal header row between them. (#468)
Updated handling for interaction terms in tbl_regression(). Interaction terms may now be specified in the show_single_row= and label= arguments. (#451, #452)

Internal Updates

Improved error messaging when invalid statistics are requested in tbl_summary(statistic=) (#502)
All columns in as_tibble() are now styled and converted to character. Previously, styling was applied to most columns, but there were a few that relied on default printing for the type of underlying data. This was ok to rely on this default behavior for as_kable(), but with the introduction of as_flextable() we needed to style and format each column to character. Potential to break some code in edge cases. (#493)
Handling of passed custom p-value functions in add_p.tbl_summary() has been improved with more careful handling of the environments from which the functions were passed. Other related updates were also made:
- Users may pass their custom p-value function as a quoted string or bare.
- The basic functions for calculating p-values, such as t.test() can now be passed directly e.g. test = age ~ t.test. We now perform a check match check for functions passed. If it is passed, we replace it with our internal version that returns the p-value and assigns the test name.
- If a user passes a custom function, and it's not the proper form (i.e. a named list return object) AND the function returns a single numeric value, we assume that is the p-value and it's added to the gtsummary table.
Updated the gtsummary core script, utils-gtsummary_core.R, to refer to all non-base R functions with the pkg:: prefix, so other packages that copy the file don't need to import the same functions as {gtsummary} in the NAMESPACE. Now they just need to depend on the same packages. (#454)

Bug Fixes

Bug fix for inline_text.tbl_summary() when categorical variable contained levels with empty strings. There is still an issue if a user tries to select the empty string, however.
Fixed bug where some variables in tbl_cross() defaulted to dichotomous instead of showing as categorical (#506)
Bug fix when using a tbl_summary(by=) with missing observations in by= followed by add_overall()
Bug fix where values ">0.9" were incorrectly made bold using bold_p(). (#489)
Bug fix for as_flextable(). (#482)
- Added a formatting function to all numeric columns to force conversion to character.
- Spanning headers were being printed in alphabetical order! Update to preserve the ordering.

gtsummary 1.3.0

New Functions

Introducing tbl_cross(), add_p.tbl_cross(), and inline_text.tbl_cross()! Easily construct cross tabulations of two variables.
Introducing tbl_survfit() and inline_text.tbl_survfit()! These will eventually replace tbl_survival(), which will no longer be encouraged. The new functions follow the structural guidelines of a {gtsummary} object and can be merged and stacked with any other {gtsummary} object (#280)
Introducing as_flextable()! The function converts gtsummary objects to {flextable} objects. {flextable} is a great option when using R markdown with Microsoft Word output. {flextable} supports indentation, footnotes, and spanning headers with Word, HTML, and PDF output.
Introducing as_kable_extra()! The function converts gtsummary objects to {kableExtra} objects. {kableExtra} supports indentation, footnotes, and spanning headers with HTML and PDF output. (#394)

User-facing Updates

Updated default print engine for {gtsummary} objects. {gt} is the default printer for the R console and R markdown documents with HTML output. PDF, RTF, and Word output default to using {kable} with a note referring users to a new vignette explaining why {gt} was not used. (#395, #396)
Updated add_p() custom p-value description to NOT require double escape characters for quotation marks (#361)
Created structure and enumerated list of unit tests each vetted model must pass, and added the tests (#383)

Internal Updates

Each gtsummary object has an associated .$table_header. The code needed to print a table with either gt or kable was previously a mix of information stored in the table_header, and code manually added to the gt_calls or kable_calls object. Now, all the information needed to print a table is stored in table_header. This has the advantage that any updates to the printing will now require an update to table_header only, and we no longer need to update the tibble, kable and gt calls. (#412, #414)
The {gt} package is now released on CRAN, and we've updated to depend on the CRAN version instead of the version on GitHub. This also resulted in significant updates throughout the documentation and code. For example, we no longer provide instructions for installing {gt}, or include internal checks if {gt} is installed. (#420)
Several functions have been made general, and may now be applied to any {gtsummary}-like object. Functions updated are add_q(), bold_p(), sort_p(), tbl_merge(), tbl_stack(), bold_labels(), bold_levels(), italicize_labels(), and italicize_levels(). (#434, #429, #373)
In tbl_regression() we previously printed the estimate, confidence interval, and p-value for all models. But some models don't have associated methods for calculating the p-value or the confidence intervals. In this update, we now print the p-value if tidy() returns a "p.value" column. Similarly, the confidence interval is printed if tidy() returns "conf.low" and "conf.high" columns. (#391, #404)

Bug Fixes

Bug fix when data frame passed to tbl_summary() with a single column (#389)
In tbl_summary() passing an ordered factor in the by= argument no longer causes as error. (#453)

gtsummary 1.2.6

Bug fix for random effects regression model where coefficients were not exponentiated when requested. Using broom.mixed::tidy() rather than broom::tidy() resolved issue.

gtsummary 1.2.5

Documentation

Updated documentation and README to improve readability, added more cross-linking across pages, added search terms to help users find our package, and added gif demonstrations (#340)
README images now build differently for website vs GitHub markdown to accommodate different output formats

Breaking changes

Removed deprecated fmt*_() and cols_label_summary() functions (#365)
Functions tbl_summary_() and add_p_() have been deprecated because the by= and group= arguments now accept strings (#250)

Syntax

Package-wide update allowing arguments that accept variable names to accept bare/symbol inputs, character inputs, stored character inputs, and tidyselect helpers. When passing a single variable, the vars() function wrapper is no longer required. (#250)

tbl_summary(trial, label = age ~ "NEW LABEL"))
tbl_summary(trial, label = "age" ~ "NEW LABEL"))
tbl_summary(trial, label = c("age", "trt") ~ "NEW LABEL"))
tbl_summary(trial, label = c(age, trt) ~ "NEW LABEL"))
tbl_summary(trial, label = vars(age, trt) ~ "NEW LABEL"))
tbl_summary(trial, label = vars(everything(), -age, -trt) ~ "NEW LABEL"))

age_column = "age"
tbl_summary(trial, label = age_column ~ "NEW LABEL"))
tbl_summary(trial, label = vars(age_column) ~ "NEW LABEL")

purrr::map(c("trt", "grade"), ~tbl_summary(trial, by = .x))

Updated tbl_uvregression() to allow flexible tidyselect inputs and improved error messaging for arguments x and y (#249)
After the input updates in #250, the exclude= argument appearing in add_p(), tbl_regression(), tbl_uvregression(), as_gt(), as_kable(), and as_tibble() was redundant. The exclude= argument is now deprecated. Use include= instead, with tidyselect syntax. (#331)
Functions all_categorical(), all_dichotomous(), and all_continuous() may now be used in tbl_summary() argument type= (#256)

User-facing improvements

New pattern= argument in inline_text.tbl_summary(). Previously, we could only grab the entire cell from a tbl_summary() with inline_text(), and now we can get any single statistic reported (#254)
Improved messaging for users who use knitr::kable() to print gtsummary tables, and users who have not yet installed the {gt} package (#347)
New function combine_terms() allows users to combine multiple independent variables in a regression model into a single line after tbl_regression(). The single line does not report regression coefficients, rather a single p-value from the anova() function. (#310)
In the regression modeling functions tbl_regression() and tbl_uvregression(), the users are presented an informative error message when the tidier fails (e.g. broom::tidy()) alerting them to the location of the error so they may address the issue (#337, #338)
For each release of gtsummary, we now can make reference to the version of gt our release coincides with. The commit SHA for gt is now saved in an object called gt_sha, and the version of gt can be installed with remotes::install_github("rstudio/gt", ref = gt_sha) (#329)
Created "style" family of functions
Improved error messaging in tidyselect_to_list() (#300)

Other features and fixes

Updated class detection to use inherits(), and added secondary class of "gtsummary" to all objects. This allows users to create their own cobbled/custom gtsummary objects while utilizing the gtsummary print functions (#249)
tbl_summary() will now summarize columns of class difftime (#343)
Infrastructure update to the way styling/formatting functions are returned. Styling functions are now returned as a column in the .$table_header tibble. The update simplifies handling of these styling functions in tbl_merge() and tbl_stack(). (#298, #299)
Bug fix for tbl_summary() when variables were all NA (#344)
The data summary function add_p() now uses probabilities rather than counts to calculate expected cell counts to avoid an error when working with large data sets. (#341)
Cubic spline terms are now accurately matched to a variable name/term (#312)
Bug fix when non-standard evaluation arguments were passed in method.args= argument of tbl_uvregression() (#322)
Updates after the gt package deprecated gt::cells_data() in favor of gt::cells_body(). Check added to as_gt() ensuring a version of gt with gt::cells_body() in its NAMESPACE
Lowered minimum required version of R to v3.4 (#356)
Removed {broom.mixed} dependency as the {broom} package contained all necessary tidiers (#354)

gtsummary 1.2.4

Bug fix in as_kable() where column header did not match statistics presented when certain levels of the by= variable are entirely missing in tbl_summary() (#304)
Updated the trial example data set "trt" variable to be "Drug A" and "Drug B" instead of "Placebo" and "Drug"
Improved messaging to users when an error or warning occurs while calculating a p-value in add_p(). Also, p-values are no longer omitted from output when a warning is encountered during their calculation (#283)
Added tidy_fun= argument to tbl_regression() and tbl_uvregression() allowing users to pass tidiers that are not in the {broom} and {broom.mixed} packages (#247)

gtsummary 1.2.3

tbl_uvregression() now accepts an x= argument to build univariate regression models where the covariate x remains the same while models are built the with remaining variables as the outcome (#294)
Internal updates to the way {gt} is installed during CRAN checks.
Bug fix when stacking tbl_summary objects with calculated p-values.

gtsummary 1.2.2

New Features

tbl_summary objects may be stacked and merged with tbl_stack() and tbl_merge() (#230, #255)
The add_n() function now reports additional statistics: total N, non-missing N, missing N, and their percentages. The missing = argument has been deprecated in favor of the statistic = argument. (#237)
Users may now pass a list of formulas, named lists, or a combination of both (#251)
Users can add an option to their script to append any {gt} calls when a {gtsummary} object is printed: gtsummary.as_gt.addl_cmds
Added include = and exclude = arguments to tbl_uvregression() (#240)
Added standard evaluation variants, tbl_summary_() and add_p_() (#223)
Added as_tibble() function that converts any {gtsummary} table to a tibble (#245)
New show_single_row argument in tbl_regression() and tbl_uvregression() allows any binary variable to be printed on a single row. Previous argument show_yesno is now deprecated. (#220)

Documentation

Added a gallery of tables possible by merging, stacking, and modifying {gtsummary} arguments (#258)
Added a vignette documenting each global option that can be set in {gtsummary} (#289)
Added {lifecycle} badges to mark deprecated and experimental functions (#225)

Other Updates

The by = column in tbl_summary() now has missing variables dropped rather than halting with error (#279)
Bug fix in vars() selection where only first variable listed was being selected (#259)
Bug fix where logical variable labels printed as NA in tbl_regression() (#248)
tbl_merge() now interprets tab_spanner = text with gt::md() (#253)
No longer checking outcome variable name for consistency in tbl_regression()---only checking independent variable names (#287)
Improved error messaging for add_global_p() (#243)
Removed gt::cols_merge() function ahead of the {gt} package PR 355 that changes the cols_merge() API (#222)
Updated API for using custom functions to calculate p-values in add_p(). User now may reference a custom function by its name. (#226)
Removed legacy support for tidyr version less than 1.0.0 (#235)

gtsummary 1.2.1

Vignettes no longer install the {gt} package (required for CRAN check) (#217)
Added ability to name custom add_p() tests (#213)

gtsummary 1.2.0

Users can pass variable names in backticks (#212)
The group = argument in tbl_summary() has been moved to add_p() (#208)
Users can now write custom functions to calculate p-values in add_p() (#194)
In tbl_summary() the by = argument accepts a bare variable name instead of the variable name passed as a string (#193)
Added support for column, row, and cell percentages in tbl_summary() (#181)
Users can now set default p-value formatting functions, regression coefficient formatting functions, default level for confidence intervals, and formatting functions in tbl_survival() (#120)
The {gt} package is no longer a required dependency. If {gt} is not installed, tables will be printed with knitr::kable(). The as_kable() function was added to the package as well. (#180)
The function as_gt() now has include = and exclude = arguments
Updated some function names to be the same as they were in the first version

    bold_p()            <-  tab_style_bold_p()  
    bold_labels()       <-  tab_style_bold_labels()  
    bold_levels()       <-  tab_style_bold_levels()  
    italicize_labels()  <-  tab_style_italicize_labels()  
    italicize_levels()  <-  tab_style_italicize_levels()

Passing named lists in tbl_summary() is now defunct.
tbl_stack() fix for tbl_uvregression objects (#175)
Option to exclude some variables from testing when using add_p() (#164)
Updates after {gt} package renamed cells_style() to cell_text() (#78)

gtsummary 1.1.1

Modified tbl_merge() to accommodate tbl_stack() object (#167)
Bug fix with incorrect column order in tbl_summary() with 10+ levels of by variable (#166)

gtsummary 1.1.0

Added {tidyselect} and {gtsummary} variable select functions (#146)
Added tbl_stack() function (#152)
Bug fix for dichotomous yes/no variables in tbl_summary (#158)
Changed add_comparison() and add_global() to add_p() and add_global_p() (#143)
Added sort_p() function (#105)
Allow unobserved values to serve as the level for dichotomous variables (#149)
Bug fix in add_nevent() when formula was passed to glm() as a string (#148)
Added returned call_list to some functions without it previously (#137)
Corrected name of call list in returned tbl_regression() results (#128)
tbl_survival(): bug fix when upper bound of CI was not able to be estimated (#134)
tbl_survival(): the groupname column name has been changed to label_level (#133)

gtsummary 1.0.0

First release since major re-factoring. The {gt} package is now used as the print engine to create all tables. Some function names have been modified to be more in line with other {gt} function calls, and additional functions have been added. The API for some functions has also been updated. Review documentation and vignettes for details.

Updated Function Names

    tbl_summary()       <-  fmt_table1()  
    tbl_regression()    <-  fmt_regression()  
    tbl_uvregression()  <-  fmt_uni_regression()  
    style_pvalue()      <-  fmt_pvalue()  
    style_percent       <-  fmt_percent()  
    style_ratio         <-  fmt_beta()

New Functions

    tbl_survival()          as_gt()  
    tbl_merge()             style_sigfig()  
    add_nevent()            gtsummary_logo()

gtsummary 0.1.0

First version of package available here.

Files

NEWS.md

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History

NEWS.md

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gtsummary (development version)

gtsummary 1.4.0

New Functions

New Functionality

Other Updates

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gtsummary 1.3.7

gtsummary 1.3.6

New Functions

New Functionality

Other Updates

Bug Fixes

Breaking Changes

gtsummary 1.3.5

New Functionality

Bug Fixes

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gtsummary 1.3.4

gtsummary 1.3.3

New Functions

User-facing Updates

Internal Updates

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Breaking Changes

gtsummary 1.3.2

gtsummary 1.3.1

New Functions

User-facing Updates

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gtsummary 1.3.0

New Functions

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gtsummary 1.2.6

gtsummary 1.2.5

Documentation

Breaking changes

Syntax

User-facing improvements

Other features and fixes

gtsummary 1.2.4

gtsummary 1.2.3

gtsummary 1.2.2

New Features

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gtsummary 1.2.1

gtsummary 1.2.0

gtsummary 1.1.1

gtsummary 1.1.0

gtsummary 1.0.0

Updated Function Names

New Functions

gtsummary 0.1.0