NEWS.md

rtables 0.6.10.9004

Miscellaneous

• Split docx document generation to the new package rtables.officer.

New Features

• Experimental pagination is now possible in tt_as_flextable() and export_as_docx().
• Added handling of widths in tt_as_flextable(). Now it is possible to change column widths for .docx exports.

Bug Fixes

• Fixed bug that was keeping indentation space characters in top left information when making a flextable from a TableTree object.

rtables 0.6.10

New Features

• Added top left information handling (now bold and bottom aligned).
• Added section_properties_default() function to define standard portrait properties for tables.
• Added default theme for .html outputs.
• Added parameter bold_titles to tt_to_flextable() to bold titles.
• Now users can add more than one theme to tt_to_flextable(), and/or extend themes.

Enhancements

• Modified reorder_split_levels() to cover more edge cases and be more stringent in the allowed inputs.
• Removed table tree tt input from theme_docx_default() and added code to handle row classes and number of columns internally.
• Reworked padding and spacing in default theme theme_docx_default().
• Added parameter bold_titles to tt_to_flextable() to bold titles.

Bug Fixes

• Fixed "\n" newline issues in as_html by relying onto output devices for newline handling. Added expand_newlines = FALSE default to allow previous behavior.
• keep_split_levels() throws now an error if the user requests to keep levels that are not present in data.
• Fixed issue with removal of horizontal lines in tt_as_flextable() header when title was added.
• Fixed multiple counts in header issue when exporting to flextable.
• Fixed issue with empty cells "" having larger imposed margins than filled cell. They are transformed into " " before rendering.
• Fixed issue with borders appearing in theme_docx_default() when only one line of column names is present, but top left information is on multiple lines.

Miscellaneous

• Added option to change sep = "\t" and set other parameters via ... parameter propagation in export_as_tsv.
• Added developer's guide vignette. New materials are focused on printing methods, specifically matrix_form and toString.
• Grouped split functions documentation into one page with precise descriptions of each function and relative examples.
• Moved simple_analysis into utils file.
• Added examples to theme_docx_default() showing how to extend the default theme.
• Added the possibility to remove internal borders from label rows in theme_html_default().
• Split export functions into separate source files. Similarly for test files.

rtables 0.6.9

Miscellaneous

• Update col_counts vignette wording, as CRAN macOS check failed. Raised the issue with the R-core team already.

rtables 0.6.8

New Features

• Add support for truetype fonts based on formatters version >= 0.5.8. Nearly all functions related to pagination or export now accept fontspec argument and pass it around accordingly, by @gmbecker.
• Core splitting machinery can now be overridden in column space via make_split_fun provided that core_split associates the generated facets with subsetting expressions. Subsetting expressions remain unnecessary for splits in row space. By @gmbecker.
• ValueWrapper objects now carry around subsetting expressions for use during tabulation, by @gmbecker.
• make_split_res, add_to_split_result now accept a list of subsetting expressions which will be attached to the values, by @gmbecker.
• New value_expr internal getter and setter methods, by @gmbecker.
• All tables are now guaranteed to have fully path-traversable column structures (all facets in column space uniquely reachable via pathing) @gmbecker.
• Display of higher order (non-leaf) column counts is now supported (#135) @gmbecker.
• Column count visibility and format can be set independently for each block of sibling facets (#752) @gmbecker.
• split_cols_by* functions now accept show_colcounts and colcount_format arguments.
• New (column-) path based colcount_visible getter and setter for changing column count visibility in an already built table @gmbecker.
• New (column-) path based facet_colcount getter and setter column count value at arbitrary point in column structure of built table @gmbecker.
• New facet_colcounts_visible setter to conveniently set the column count visibility of a set of sibling facets in column space
• New rm_all_colcounts convenience function for turning off visibility all column counts throughout the column structure @gmbecker.

Bug Fixes

• Fixed bug in as_html preventing indentation from being applied in Viewer output.
• col_counts<- and col_total<- methods now explicitly convert value to integer, by @gmbecker.
• col_gap is now respected in nlines row methods, and thus by make_row_df, by @gmbecker.

Miscellaneous

• Added lifecycle badge files for deprecated documentation.
• Deprecated the gap and check_headers arguments to rbindl_rtables using lifecycle.

rtables 0.6.7

New Features

• Added top_level_section_div for basic_table to set section dividers for top level rows.
• Added keep_label_rows to as_result_df to have these lines visible.
• sort_at_path now gives informative error messages when the given path does not exist.

Bug Fixes

• Fixed rlistings decoration (e.g. titles and footers) expansion when there are new lines. Moved relevant handling from rtables' matrix_form function to formatters' dedicated mform_handle_newlines function.
• Fixed issue with rtables_root not being removed when using as_result_df.
• Fixed edge case bug in as_result_df where rows of the table have only "root" as path index.
• Fixed sort_at_path pathing to ignore leading "root" element (regardless of actual root element name) to match current tt_at_path behavior.
• Fixed section_div for analysis of multiple variables (AnalyzeMultiVars).
• Fixed mismatch between indentation declared in row info (mf_rinfo(mf)) and actual selected indentation from matrix_form(mf, indent_rownames = FALSE).
• Fixed bug in as_html preventing indentation from being applied in Viewer output.
• col_counts<- and col_total<- methods now explicitly convert value to integer, by @gmbecker.
• col_gap is now respected in nlines row methods, and thus by make_row_df, by @gmbecker.
• Updated as_html to accommodate \n characters.

Miscellaneous

• Removed deprecated functions add_analyzed_var and trim_zero_rows.

rtables 0.6.6

New Features

• Removed ref_group reordering in column splits so not to change the order.
• Added bold argument to as_html to bold specified elements, and header_sep_line argument to print a horizontal line under the table header in rendered HTML output.
• Duplicate referential footnotes are consolidated when tables are rendered.
• Section divisors can be set for analysis rows.
• Added setter and getter for section dividers (section_div and section_div<-). They also accept split section structure assignment.
• Added header_section_div setters and getters for layout and table objects along with related basic_table parameter.
• Added na_str argument to analyze_colvars to set custom string to print in place of missing values.
• Added flat data.frame outputs for as_result_df() via flag parameters as_viewer, as_strings, and expand_colnames.
• Migrated export_as_pdf function to formatters.

Bug Fixes

• Fixed a bug that was failing when wrapping and section dividers were used at the same time.
• Fixed a bug in as_result_df causing misalignment of column names.
• Fixed a bug that was not allowing path indexing as row_paths() was giving a different path due to it being made of named values.
• Fixed a bug in as_result_df when called on tables with less than 3 rows.

Miscellaneous

• Applied styler and resolved package lint. Changed default indentation from 4 spaces to 2.
• Added Developer Guide with Debugging, Split Machinery, and Tabulation sections.
• Whitespace is not trimmed when rendering tables with as_html.
• Started deprecation cycle for col_fnotes_here to be replaced with col_footnotes.
• Exported section_div methods now have a dedicated documentation page that is visible to users.
• When tables are exported as txt, they preserve the horizontal separator of the table.
• Added imports on stringi and checkmate as they are fundamental packages for string handling and argument checking.
• Updated introduction vignette and split it into two. Section on introspecting tables is now located in a separate vignette.

rtables 0.6.5

New Features

• Added support for white spaces in all labels and text by redesigning of wrapping functions in formatters.
• Added support for new line characters across rtables (titles, column names, row names, footers, and na_str).
• Modified top left information vertical alignment to stay at the bottom of the header.

Bug Fixes

• Fixed a bug causing Viewer and as_html to fail when new line characters were added.

Miscellaneous

• Added slide decks for advanced training as internal files.

rtables 0.6.4

New Features

• Added support for .docx exports with export_as_docx().
• Expanded support for flextable customization with theme function specific for word documents (theme_docx_default()).

Bug Fixes

• Fixed bug causing all-NA rows to be included in every .df_row split.

Miscellaneous

• Specified minimal version of package dependencies.

rtables 0.6.3

New Features

• Analysis functions (cfun/afun) can use new parameters to extend analysis calculations: .alt_df_row and .alt_df give access to alt_counts_df across columns, while .all_col_exprs and .all_col_counts contains global information about all columns.
• Binding objects via rbind will retain titles/footer information if identical in all objects or only present in the first object being bound.

Enhancements

• Analysis functions (cfun/afun) have more information about current column split; .spl_context has access to cur_col_id, cur_col_expr, cur_col_split, and cur_col_split_val.
• Added vignette on exploratory analysis with qtable.
• Extracted qtable_layout from qtable.

Bug Fixes

• Page-by splits which generate zero facets (and thus tables which would have zero pages when rendered) now throw an informative error at table build time.
• Removed superfluous warning which arose for custom split functions when reference group is is set (#707 (comment)).
• Fixed qtable labeling via row_labels (#698).
• Error catching and test coverage for cases where alt_counts_df presents different splits from df.

Miscellaneous

• Cleaned up spelling in documentation (#685)
• Custom appearance vignette updated with decimal alignment support.
• Alignment checks have been moved into formatters: formatters::check_aligns superseded internal function chk_rtables_align and formatters::list_valid_aligns superseded rtables_aligns.

rtables 0.6.2

• Fixed major regressions for page_by machinery caused by migration to formatters 0.5.1 pagination framework.
• Fixed page_by labels become missing when only one level exist in the split_rows_by.
• Fixed a bug when dropping var levels but not lblvar levels.
• Added checks to catch bad labels (with {}) and throw informative error.
• Added qtable function to create a table with a single top-level structure in both row and column dimensions involving faceting by 0 or more variables in each.
• Added as_result_df function to flatten a table into a dataframe.
• Added sanitize_table_struct, validate_table_struct, find_degen_struct to support degenerative table rendering.

rtables 0.6.1

• Improved resilience of pagination machinery (paginate_table) by generalizing parameters' defaults (cpp, lpp, and font_size).
• Moved export_as_txt to formatters. Added to reexports.
• Migrated export_as_rtf to formatters. Not re-exported.
• add r2rtf to Suggests
• pagination logic has been migrated completely (excepting page_by splits) to formatters and is now invoked from there. paginate_table remains as a convenience function.
• Removed warning in str method when called upon table objects.
• Provide str method for VTableTree objects with a default max.level of 3, as the infinite default from base is not useful or informative.
• default font_size value is now 8 across pagination and export machinery
• margins argument in pagination and export machinery now (correctly) interpreted as inches. This change is inherited from formatters
• lpp and cpp now default to NA_integer_, which is interpreted as inferring their value from the physical page size specified.
• Horizontal pagination now occurs by default due to the above (because there is a default page type - "letter". Pagination can still be turned off in either direction by setting l/cpp to NULL explicitly.
• Referential footnotes now have both a symbol and an index. Messages associated with symbols will only appear once per page in the footer materials regardless of number of elements referenced in the page with that symbol. Matches and inherits from changes in formatters
• Started deprecation cycle for trim_zero_rows.
• Fixed bug occurring when extracting cell_values after sorting.
• Removed deprecated function vpaginate_table.
• Added examples and details for sort_at_path.
• Added split_label to function split_rows_by_multivar and extra_args to function split_cols_by_multivar.
• Added split_rows_by_multivar documentation.

rtables 0.6.0

• added make_split_fun function for creation of custom split functions
• basic_table now accepts colcount_format
• 2d formats are now allowed for column counts provided one element is a percent, which will be automatically set to 100%
• spl_context now includes root row in row-split contexts.
• Added vignette on format precedence
• Added vignette on split functions
• Added custom appearance vignette
• Significant overhaul of sorting vignette
• extended and clarified documentation
• export_as_pdf now correctly takes margins into account when calculating lpp and cpp from page size.
• exporters now pass down non-default colwidths values correctly
• nlines TableRow method (used for both rows and column label extent in pagination) now correctly handles column spanning
• pagination with verbose = TRUE now includes original and adjusted lines-per page information
• cont_n_allcols and cont_n_onecol score functions now throw errors when they are applied to subtables that have no content table, instead of the previously returned NA
• sort_at_path now emits an informative error message when score functions fail.
• paginate_table now accepts colwidths and paginates assuming column label and cell values are wrapped to those widths.
• make_row_df now accepts colwidths and calculates row extents assuming cell values are wrapped to those widths
• nlines TableRow method now uses provided colwidths to assume cell-value wrapping
• export_to_txt now automatically paginates when any form of page dimension is provided (previously the default was unconditionally not paginating).
• Versioned dependency on formatters increased to >=0.4.0

rtables 0.5.3

• [<- now treats character i and j values as paths, the same as [ always has.
• [<- CellValue method now preserves CellValue attributes (e.g., format)
• More detailed subsetting and modification vignette
• nlines methods now accept both colwidths and max_width
• max_width is now used during pagination to determine lines taken up by referential footnotes
• make_col_df now accepts colwidths argument, and can be called directly on InstantiatedColumnInfo objects
• versioned dependency on formatters increase to >0.3.3.12
• word wrapping title/footer materials no longer fails in the presence of "" values.
• versioned dependency on formatters increase to >0.3.3.11
• paginate_table now accepts tf_wrap and max_width and respects title/footer word wrapping when present
• export functions now accepts tf_wrap and max_width and use them in both pagination (when turned on) and toString when used (pdf, txt exporters).
• versioned dependency on formatters increased to >0.3.3.10
• export_as_pdf now accepts standard page/font size parameters
• original parameters (width, height, fontsize are soft deprecated (no warning) and will be fully deprecated and then removed in the future.
• toString method for VTableTree now accepts tf_wrap and max_width
• export_as_txt and export_as_pdf now accept cpp, as well as tf_wrap and max_width and default to tf_wrap being on and max_width = cpp when cpp is non-NULL.
• basic_table now accepts inset argument for declaring table inset
• Table and Layout object classes now have a table_inset slot, with accessor functions.
• matrix_form method for VTableTree sets table_inset value
• Increase versioned dependency on formatters to >0.3.3.5 for table_inset support
• Use exact=TRUE in all calls to attr within access functions
• Increase versioned dependency on formatters to >0.3.3.4
• layouting instructions now accept na_str argument, which specifies na string with the same inheritance rules as formats
• (pre-data) Split and (post tabulation) Table/row S4 classes now carry around na_str information
• Increase versioned dependency on formatters to >= 0.3.3.3 for support of na_strs with NA_character_ values
• paginate_table now takes page dimension and font information and uses formatters::page_lcpp to calculate lpp and cpp automatically when those are provided.
• Increase versioned dependency on formatters to >= 0.3.3.2 for page_lcpp

rtables 0.5.2

• paginate_table now accepts cpp and will perform vertical pagination when it is non-null
• vpaginate_table is now deprecated
• Increased versioned dependency on formatters to >=0.3.2.4

rtables 0.5.1.5

• Support for section dividers (section_div argument in split_rows_by* function)
• Updated versioned dependency on formatters to >=0.3.2.3
• Equivalent split functions with different enclosing environments (e.g., 2 identical calls to add_combo_levels #340) no longer block rbinding
• Fixed various documentation bugs where description section was being added to header.

rtables 0.5.1.4

• empty level check for splitting variables reinstated.

rtables 0.5.1.3

• Throw informative error messages when custom analysis, content or split functions fail (#329)

rtables 0.5.1.2

• empty level check for splitting variables temporarily removed. It is very likely to be reinstated in a future release.

rtables 0.5.1.1

• col_counts getter and setter now accept path argument.
• empty levels of a splitting variable now result in an informative error message (character and factor cases).
• fixed bug in handling of column extra arguments that was preventing cbinding tables from working correctly ([#324]](#324))

rtables 0.5.1

• empty factor levels are now not dropped for column splits when ref_group is set (#323)
• linesep argument to toString and related functions renamed to hsep
• Increase versioned dependency on formatters to >=0.3.0
• Default "line separator" between header and body now falls back to "-" non-UTF charset locales.
• New hsep argument to build_table which sets the horizontal separator for the constructed table (and subtables thereof)
• New horizontal_sep and horizontal_sep<- accessors for constructed tables, the latter of which is mandatorily recursive.
• split_rows_by(var, child_labels="hidden") no longer removes the structural subtable corresponding to levels of var (#314)

rtables 0.5.0

• formatable dependency renamed to formatters for suitability of release to CRAN
• Update versioned dependency of formatters (previously formatable) to >=0.2.0

rtables 0.4.1.0004

• Fix bug when function format combined with NULL cfun caused error (#307)
• Fix bug in path_enriched_df (which powers tsv export), related to (#308)

rtables 0.4.1.0002

• added table_shell to display shell of table with formats

rtables 0.4.1.0001

• added linesep argument to toString to specify a character to create the line separator. Previously we used the en dash as the line separator character, now we changed the default to the em dash reducing the gap between the dash line elements.

rtables 0.4.0

• Initializing layouts with NULL is now deprecated
• insert_rrow is deprecated in favor of new insert_row_at_path and label_at_path<- functions
• split and analysis/content functions can now depend on values of splits they are nested inside by accepting and using the new .spl_context optional argument
• new trim_levels_to_map split function for dictating exact combinations of values which should appear across splits
• value_formats function now exported which returns/displays the effective formats of all cells in a table
• compare_rtables is now much faster for tables with many cells
• compare_rtables now accepts structure argument which adds comparison of structure (by way of row- and column-path positions)
• new tt_to_flextable coercion function
• new export_as_pdf exporter function
• value_at and cell_values functions now have methods for TableRow objects making them usable in sorting/pruning functions

rtables 0.3.8.9001

• new trim_levels_to_map split function based on [@wwojciech](https://github.com/wwojciech)'s work in #203
• support for column referential footnotes
• support for adding footnotes to existing table via fnotes_at_path<- function
• trim_levels_in_group now trims empty levels of outer (split) variable by default
• value_at and cell_values now work for tablerow objects
• Fixed as_html bug in multivar split columns case
• Fixed pagination off-by-one error

rtables 0.3.8.9000

rtables 0.3.8

• Add experimental support for newlines in column names, row labels, and cell values (not supported in top-left annotations)
• as_html refactored to support newlines while respecting table structure
• self_extent column of df returned by make_row_df now reflects extent in lines, thus will return larger values if the row-label or any cell values contain newlines.
• Fix bug where tables output using as_html (or viewed in Viewer) were missing the table class attribute (#194)
• inserting a DataRow with incorrect number of columns is now an error (#199)
• Referential footer machinery now works in colspan case.
• Fix extraneous footnote attribute bug (#198)
• Fix max -Inf warning when content rows appear at positions whose children have 0 visible rows (#200)
• Resync NEWS.md file
• Introduce titles and footnotes
• Support automatic population of top-left
• Introduce referential footnote support for cells and row labels
• Added vars_in_layout to list (explicitly named only) variables used in a layout
• Fix column label ordering bug when value label variable is a factor (#173)

rtables 0.3.7

Synchronize release with GitHub commit sha.

rtables 0.3.6

Documentation revisions as requested by CRAN. No change to package code.

rtables 0.3.5

Documentation-text only changes to introduction vignette to pass CRAN's URL checks. All package, example, test, and vignette code fully identical to that in tagged GitHub release 0.3.4

rtables 0.3.4

Minor changes to the 0.3.3 version in order to submit rtables to CRAN.

rtables 0.3.3

This version completely refactors the rtables package. We do provide a backwards compatibility layer with the rtable, rcell, rrow, rheader, and rtabulate family of functions. However the table data structure and main tabulation framework have changed. We provide extensive documentation in the manuals help(package = "rtables") and vignettes vignette(package = "rtables") of the package.

The changes to rtables have been undertaken to better meet the requirements of creating and analyzing & reporting tables in the context of clinical trials.

rtables 0.3.2.17.9046

• make_afun now force()s all customization arguments immediately, which prevents problems when called within loop/lapply constructs.

rtables 0.3.2.17.9045

• Tabulation machinery no longer removes NAs mandatorily in some cases, including multivar column splits
• analyze_colvars's inclNAs argument now respected.

rtables 0.3.2.17.9044

• Fix indent modifier propagation during tabulation
• Fix indent calculation in make_pagdf
• Add significant testing to ensure make_pagdf indent calculation remains correct

rtables 0.3.2.17.9043

• Rework how reference columns are handled so analyses which use .in_ref_col and .ref_group work correctly when custom splitting is used (including the provided combination-levels mechanism)

rtables 0.3.2.17.9042

• Fix naming/pathing for columns in multivar case (split itself now has default name "multivars")
• Fix labeling bug when same variable appears multiple times in MultiVarSplit with different associated levels

rtables 0.3.2.17.9041

• Allow single variable to be used within split_cols_by_multivar
• Various removal of defunct

rtables 0.3.2.17.9040

• Fix regression caused by 0.3.2.17.9039 where column split values were displayed by name rather than label.

rtables 0.3.2.17.9039

• Fix bug in display of column information when column structure is not symmetric, as with recursive cbinds.

rtables 0.3.2.17.9036

• Fixed bug in row subsetting when table has only content rows.
• Basic compare_rtables function now works as in previous versions, no awareness of row or column structure.

rtables 0.3.2.17.9036

• summarize_row_groups can now accept a list of functions for the cfun argument as analyze_colvars does.

rtables 0.3.2.17.9035

• Fix bug unearthed by change in 0.3.2.17.9034 where cell formats not retained during column subsetting

rtables 0.3.2.17.9034

• Fix internal value_formats accessor so it operates on CellValues rather than the raw contained values (thus always returning NULL)
• rrow constructor no longer interprets cell formats a row format when they are the same across all cells. Fixes bug in "correct way" code discussed in #112

rtables 0.3.2.17.9033

• Interpret .formats in in_rows as cell formats rather than row formats.

rtables 0.3.2.17.9031

• cbind_rtables can now take more than 2 tables.

rtables 0.3.2.17.9029

• Fix issue underlying spurious length-mismatch warning in some cases when using analyze_colvars

rtables 0.3.2.17.9028

• analyze_colvars now takes and adheres to inclNAs argument

rtables 0.3.2.17.9027

• issues with no news:

rtables 0.1.7

• added format xx.xx (xx.xx - xx.xx) and x.xxxx | (<0.0001)

rtables 0.1.6

• Minor changes.

rtables 0.1.5

• Changed testing approach to fit internal pipelines.

rtables 0.1.4

• Replaced dots to underscore in class checking functions.

rtables 0.1.3

• col_by in rtabulate now accepts matrices:

  • col_by_to_matrix, col_by_to_factor, by_factor_to_matrix.
  • by_add_total, by_all, by_combine, by_quartile, by_compare_subset, by_hierarchical, by_drop_empty_cols.

• New utility functions to deal with variable labels:

  • label, var_labels<-, var_labels, var_labels_remove, var_relabel, with_label.

• Other new functions:

  • cbing_rtables.
  • empty_rtables, is_empty_rtable, is_non_empty_rtable, is_rtable.
  • header_indent, header_indent<-, header_row.names, header_row.names<-.
  • insert_rrow.

rtables 0.1.2

• rbind.rtable now supports binding rtables with rows, e.g. rbind(tbl1, rrow(), tbl2) or rbind(tbl1, rrow("row name"), tbl2).
• rbindl_rtables supports NULL objects in the list (except for the first element).
• Add indent function.
• header_add_N deals gracefully with NULL objects.

rtables 0.1.1

• rtablulate family of functions do not support the row_*_data_args arguments anymore. Instead, the col_wise_args argument is introduced.
• Functions order_rrows, sort_rrows, order_rtables, and sort_rtables are introduced.
• Prevent rtables from being unlisted with unlist.rtables.

rtables 0.1.0.6

• Viewer now also accepts objects of class shiny.tag (defined in package htmltools).
• as.html accepts class.table, class.tr, class.th, and class.td as an argument.

rtables 0.1.0.5

• Added sprintf_format for formatting rcells (thanks to Doug Kelkhoff for the suggestion).
• Added "(N=xx)" and ">999.9" format labels.
• rtabulate has now an argument col_N and the function col_N().

rtables 0.1.0

• Version 0.1.0 is a major re-design with lots of internal refactoring and the following API changes:
  • Redesign: rtable has now header argument instead of col.names. A header can be created with rheader and is a collection of rrows. If header is set to c("A", "B") then rtable will create the rheader with a single rrow and by setting row.name to NULL.
  • header and header<- function added.
  • Renamed get_rcell_formats to list_rcell_format_labels.
  • If rcell format is NULL then the cell content will be converted to a string with paste(as.character(x), collapse = ', ').
  • Accessor [i,] works now to subset a table.
  • rbind method for rtables.
  • row.names<-.rtable method.
  • rtabulate added for creating tables.
  • indented_row.names function added.

rtables 0.0.1

• Initial public release