-
deprecate
list_labels()
function and warn -
deprecate
style_tab_compact()
function and warn -
deprecate
add_cuminc_risktable()
function and warn -
gtsummary HOT theme (
lst_theme_hot
) uses a line break in the header (rather than a comma) between the "by" group levels and the N count when there is a "by" variable. -
Updated code based on tidyselect v1.2.0 updates.
- Making another release for RSPM testing.
-
The primary biostatistics project template and the HOT template have been converted to Quarto. (#117)
-
Updated 'H.O.T.' gtsummary theme and now flextables are printed in Calibri font to match the rest of the document.
-
The
create_hot_project()
has been deprecated in favor ofcreate_bst_project()
. Members of the H.O.T. Team will see an option for the HOT template whencreate_bst_project()
is run.- Similarly, functions
use_hot_file()
,use_hot_gitignore()
,use_hot_readme()
,use_hot_setup()
,use_hot_analysis()
, anduse_hot_report()
have been deprecated in favor of the 'bst' alternatives. - New functions
use_bst_setup()
,use_bst_analysis()
, anduse_bst_report()
have been added to the package.
- Similarly, functions
- Added gtreg, emmeans, ggsurvfit, and tidycmprsk to the template references document. (#112)
- Update to to RStudio preferences function.
- Added ability to report the number of events and the total number of observations in
followup_time()
.
- Added ability to add a smooth line in
ggcalibrate()
.
-
Deprecated
reinstall_prior_pkgs()
in favor ofupdater::install_pkgs()
. -
Added
ggcalibration()
function. -
Update to
add_sparkline()
to handle updated API in {gtExtras}. (#101) -
Added
use_bst_rstudio_prefs(profile=)
argument allowing users to modify the standard biostatistics preferences.
- Update to the HOT project template.
- Updated project template
.gitignore
file.
- Removed
"as_flex_table-lgl:use_ftExtra"
gtsummary theme element from HOT template. There seems to be an issue with {ftExtra} when the package is knit (but works interactively).
-
Re-exporting the
here::here()
function. -
Re-exporting
gtsummary::tbl_split()
function, and no longer warning about the function's use from within {bstfun}.
-
Overhaul to
create_bst_project()
including updated interface and templates. -
Updated
auc_density()
to better handle cut points and 0 and 1 and improved output structure by adding sensitivity and specificity estimates to a tibble. -
Added new functions
add_n.tbl_likert()
andadd_continuous_stat().tbl_likert()
(#55) -
Updated templates associated with
create_bst_project()
including adding a SAS template (#84)
-
No longer depending on the development version of {gtsummary}.
-
Improved messaging in
reinstall_prior_pkgs()
.
-
Bug fix in
set_derived_variables()
moving ID variables to the front of the data frame. -
Added
add_variable_grouping()
function that can group variable summaries together under a single header. (#79) -
Adding new function
reinstall_prior_pkgs()
to assist in re-populating an R package library after a fresh install.
-
Updates the the
theme_gtsummary_msk("hot")
theme.- Default chi-square test without continuity correction removed since it is the current default for tbl_summary.
- Added the compact theme to the the HOT theme.
-
Added a method to calculate adjusted differences for binary endpoints using logistic regression
logistic_reg_adj_diff()
. (#20)
- No changes. Making release for RSPM.
-
Bug fix in HOT project template where the
reference.bib
file was being placed in the incorrect folder. -
Columns
"mrn"
,"id"
, or"patient_id"
will now be moved to the front of the data frame after labels have been applied usingset_derived_variables()
.
-
Fix to the H.O.T.
use_hot_file()
default template specification. -
Increased minimum R version and minimum version of {starter} package (after bug fix).
-
Updates to the templating files.
-
Updated custom template definitions to utilize parts from the default template, reducing the amount of code needed to create a custom template.
-
Added new function
bold_italicize_group_labels()
to bold and italicize group header labels in gtsummary tables. (#65)
-
Function
add_cuminc_risktables()
now allows for 3 groups. Makes colors consistent between labels and estimates. Removed "Number at risk" label and places a label ", n:" next to each strata name. -
Migrated the H.O.T. project templates from {hotfun} to {bstfun}.
-
Added new function
clean_mrn()
to clean and check consistency of MRN columns. -
Added new function
set_derived_variables()
that imports variable labels from an excel file and applies the labels to the data frame. -
Added new function
count_map()
to aid in checking variable derivations. -
Added new function
count_na()
to assess variable missing patterns. -
Added new function
get_mode()
to obtain the mode of a variable. -
Added new function
list_labels()
to obtain a named list of column names and their labels. -
Added new function
assign_timepoint()
to aid in selecting observations at various follow-up times, e.g. selecting the 6 and 12 month lab result from a long data set of all labs. -
Added new function
add_splines()
. -
Added new functions for calculating eGFR:
egfr_mdrd()
andegfr_ckdepi()
. -
Migrated H.O.T. project creation functions from the hotfun package.
-
Added two functions for calculating AUC based on the distribution of a variable.
-
Removed use of deprecated function in
tbl_likert()
. -
Added new function
followup_time()
that reports the amount of follow-up among censored patients. -
Added new function
list_labels()
to extract the variable labels from a data frame. -
Added new function
rm_logs()
to delete logs created from submitting jobs to the HPCC.
- Updated how references are added in
cite_r()
.
-
Added new function
add_sparkline()
--a wrapper forgtExtras::gt_sparkline()
that adds distributional figures in a new column of a 'tbl_summary' table. -
Updated default argument value:
as_forest_plot(xlog = x$inputs$exponentiate)
.
-
Deprecated
tbl_2way_summary()
in favor ofgtsummary::tbl_continous()
. -
Cleaning up functions that have been deprecated.
-
Removing old {gtsummary} "core" code that had been copied into the package.
-
Deprecated
bstfun::tbl_split()
,bstfun::gts_add_p_footnote()
, andbstfun::gtsummary_butcher()
in lieu ofgtsummary::tbl_split()
,gtsummary::separate_p_footnote()
, andgtsummary::tbl_butcher()
. -
Removed {tidyselect} dependency.
-
Added new function
as_forest_plot()
that converts a gtsummary table into a forest plot usingforestplot::forestplot()
. -
Added new function
add_cuminc_risktable()
to plot cumulative incidence estimates with both the at-risk table and the estimates printed below the table. -
Updated Rmd files in project template to use user's custom
gtsummary
theme if it exists withinbstfun::theme_gtsummary_msk()
, matching the system login name to thename
inbstfun::theme_gtsummary_msk()
-
Adding new function
use_bst_rstudio_prefs()
-
Added new functions
tbl_likert()
andadd_n.tbl_likert()
for summarizing likert-scale data. (#53)
-
Updated the references file in the {bstfun} project template.
-
Exporting
get_data_date()
function used inhere_data()
-
Bug fix in
path_data()
wheregetOption("path_data")
was not correctly being imported. The arguments ofpath_data()
have been re-arranged.
- Update to
here_data()
to import the data date properly when the date is not followed by a hard return. (#42)
-
Added function
cite_r()
to assist in citing R and R packages in R markdown reports. -
Updated default project template to include references in
report.Rmd
. -
Added function
use_varnames_as_labels()
to assign title case (or all CAP) labels from the column names of a data frame. -
Switched {starter} dependency from GitHub to CRAN.
-
Bug fix in
tbl_2way_summary()
. Now forcing the continuous variable to be summarized continuously. -
Added
path_data()
function.
- Updates to project templates.
-
Added new function
create_bst_project()
, a wrapper forstarter::create_project()
that drops a copy of the Biostatistics project template into a new or existing folder. The function defaults to the Biostatistics template, but any template may be passed. -
Added new functions
use_bst_file()
,use_bst_gitignore()
, anduse_bst_readme()
to drop files from the HOT template into the active project. -
Migrated the Biostatistics template from the biostatR package (behind a firewall) to the bstfun package.
-
Added function
gtsummary_butcher()
to reduce the size of a gtsummary table. After an object has been butchered, other gtsummary functions may not be able to execute on the object.
-
Added
here_data(path_to_data_date=)
argument to specify location of data date file. -
Adding
add_inline_forest_plot()
function to add forest plots to gtsummary tables. (#27)
-
Updated
gts_add_p_footnotes()
to maintain 'gtsummary' class, where previously the table was converted to gt or flextable. -
Added
tbl_2way_summary()
function. -
Deprecated
tbl_ancova()
in favor ofgtsummary::add_difference()
.
-
Added
hpcc_get_arg()
andhpcc_get_seq_number()
functions to aid working with the high performance computing cluster. (#19) -
Added
as_ggplot()
function to convert gt and gtsummary tables to ggplot -
Added
tbl_split()
function to actively split a gtsummary table to more easily show on multiple pages. -
Added
"leej"
theme totheme_gtsummary_msk()
- Added new function
style_tbl_compact()
that makes the compact styling available ingtsummary::theme_gtsummary_compact()
to any {gt}, {flextable}, {huxtable}, orknitr::kable()
table.
-
Added new function
gts_add_p_footnotes()
-
Added new themes to
theme_gtsummary_msk()
-
Added the
theme_gtsummary_msk()
function. This is a place for any member of the MSK community to add their person gtsummary theme. -
Added the
here_data()
function. Similar tohere::here()
which returns your project directory,here_data()
returns the path to your current data folder based on the date indata_date.txt
.
- First release