NEWS.md
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 of create_bst_project(). Members of the H.O.T. Team will see an option for the HOT template when create_bst_project() is run.
use_hot_file(), use_hot_gitignore(), use_hot_readme(), use_hot_setup(), use_hot_analysis(), and use_hot_report() have been deprecated in favor of the ‘bst’ alternatives.use_bst_setup(), use_bst_analysis(), and use_bst_report() have been added to the package.followup_time().Deprecated reinstall_prior_pkgs() in favor of updater::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.
"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() and add_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.
theme_gtsummary_msk("hot") theme.
logistic_reg_adj_diff(). (#20)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 using set_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() and egfr_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.
cite_r().Added new function add_sparkline()–a wrapper for gtExtras::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 of gtsummary::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(), and bstfun::gtsummary_butcher() in lieu of gtsummary::tbl_split(), gtsummary::separate_p_footnote(), and gtsummary::tbl_butcher().
Removed {tidyselect} dependency.
Added new function as_forest_plot() that converts a gtsummary table into a forest plot using forestplot::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 within bstfun::theme_gtsummary_msk(), matching the system login name to the name in bstfun::theme_gtsummary_msk()
Adding new function use_bst_rstudio_prefs()
Added new functions tbl_likert() and add_n.tbl_likert() for summarizing likert-scale data. (#53)
Updated the references file in the {bstfun} project template.
Exporting get_data_date() function used in here_data()
Bug fix in path_data() where getOption("path_data") was not correctly being imported. The arguments of path_data() have been re-arranged.
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.
Added new function create_bst_project(), a wrapper for starter::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(), and use_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 of gtsummary::add_difference().
Added hpcc_get_arg() and hpcc_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 to theme_gtsummary_msk()
style_tbl_compact() that makes the compact styling available in gtsummary::theme_gtsummary_compact() to any {gt}, {flextable}, {huxtable}, or knitr::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 to here::here() which returns your project directory, here_data() returns the path to your current data folder based on the date in data_date.txt.