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Changelog

Source: NEWS.md

clinify 0.4.0

CRAN release: 2026-08-01

  • clin_column_headers() gained a merge argument to control the automatic merging of identical, adjacent header cells. Use merge = "spanners" to keep the bottom row of the header out of it, merge = FALSE to turn merging off entirely, or a vector of header row numbers for finer control. This lets a header row that legitimately repeats a label across adjacent columns keep those cells separate (#95)
  • clin_column_headers() can now be called with only the merge argument and no header text, which adjusts the merging of headers already in place - including headers built from column labels (#95)
  • Added clin_spanner_rule() to draw the rule that conventionally sits under a spanner label, across only the columns that spanner covers. The columns come from the header on the table, so the space over a stub or a trailing p-value column is left un-ruled and the rule follows the spanners as the layout changes instead of being given as column numbers that have to be kept in step with it. The rule is drawn after the default styling function, so it holds when an organisation’s clinify_table_default() clears the borders it started from, and border takes an officer::fp_border() for a dashed or hairline pen, or FALSE to keep a house style from underlining the spanners at all (#105)
  • Added clin_header_pad() to set the vertical space around the column headers: above and below each header row, and rule_to_body between the rule under the header and the first body row. The pieces are named for where the space sits because a cell’s bottom border is drawn below its bottom padding, so padding under the header moves the rule toward the body rather than opening space beneath it - the space under the rule has to come from the body side. above and below apply to every header row, so a spanned header keeps the space between its levels, and rule_to_body is applied to the first row of every page (#97)
  • clin_header_pad() can now space header rows differently, either by taking a value per row (above = c(18, 34)) or by aiming a call at particular rows (rows = 1). Because the spacing is applied as the table renders, after anything the caller did, a call covering every row overwrote a per-row flextable::padding() set beforehand - so a house wide header buffer could not sit alongside the handful of tables needing a different gap on one row (#113)
  • Added clin_row_height() to set the row pitch of a table’s body, titles, and footnotes. Regulatory outputs are specified to an exact pitch, and rendered row height is what decides how much fits on a page; {flextable} leaves rows at a nominal quarter inch with a rule of “auto”. Pitches are given in points by default, and the rule defaults to "atleast" so a cell whose text wraps grows past the pitch instead of being clipped (#97)
  • clin_row_height() gained header and header_leading, completing the vertical pitch controls asked for in #97. header bounds the column header rows the way body bounds the body rows, and header_leading closes the gap between the lines within a header cell, which is what a wrapped arm label sitting looser than a reference output actually needs. Leading is a multiple of single spacing rather than a length, since that is how flextable and Word express it (#117)
  • Title and footnote row pitch is now reachable from the ls = argument of clin_add_titles() and clin_add_footnotes(). Previously the only way to set it was to hand build a flextable and pass it as ft = (#97)
  • Group label and caption rows, which clinify inserts as it renders, take the body pitch (#97)
  • Added clin_table_align() to set how a table sits across the page. It is applied after the default styling function, so it holds even when an organisation’s own clinify_table_default() rebuilds the table properties (#98)
  • clintable() gained a coerce_character argument which coerces every column to character before the flextable is built, so pre-formatted values render exactly as supplied. {flextable} formats a double column as a whole, so a clinical summary column holding a count in one row and a statistic in another renders the count against its neighbours - c(86, 75.2) puts “86.0” in the table. This replaces the lapply(x, as.character) line that otherwise has to be written ahead of every table. Column label attributes survive the coercion, so use_labels still finds them. Defaults to FALSE. NA is deliberately left as NA rather than replaced with "", which still renders as a blank cell but does not act as padding in a page_by, group_by or caption_by column - see ?clintable (#104)
  • clin_add_titles(), clin_add_footnotes() and clin_add_footnote_page() now accept a data frame for ls, holding every line for a table in one place with type, text1, text2 and align columns. Each function takes the rows that belong to it and leaves a surface with no rows alone, so one object feeds all three. Reading the spec in is left to the caller, so it can come from a spreadsheet, a CSV, or anywhere else (#7)
  • The same three functions gained a tokens argument that fills in {NAME} placeholders, so a program path or run date can reach text that was written somewhere else. {PAGE} and {NUMPAGES} are left alone for clin_replace_pagenums() (#7)
  • clin_add_titles(), clin_add_footnotes(), clin_add_footnote_page() and new_title_footnote() gained an align argument to place each line, so a single left aligned title no longer needs its text passed twice (#98)
  • Whatever a table itself is configured with is now applied after the default styling function rather than before it, so a per table setting beats an organisation’s house style, which beats the {flextable} default. Previously a house clinify_table_default() that set a row height silently overrode an explicit one (#97, #98)
  • Fixed the default styling functions discarding a table’s other properties when they fixed its layout. flextable::set_table_properties() rebuilds the whole property list, so a table’s alignment on the page, its width, its Word accessibility fields and its opts_word/opts_html settings were all quietly reset at render time (#98)
  • Fixed a second call to clin_row_height(), clin_header_pad() or clin_spanner_rule() replacing the first instead of refining it. Arguments the later call does not name now keep whatever the earlier one set, so a house wide setting and a per table exception can both be stated without restating the rest. Previously the earlier values reverted to their defaults with no error or warning (#119)
  • Fixed the spacing clinify starts a column header with being lost as soon as the headers were set. Setting them rebuilds the header part, which dropped the padding applied at construction, so a table with custom headers or || column labels sat on flextable’s own default while a plain one kept clinify’s. It is applied as a starting point, so a later flextable::padding() or clin_header_pad() still wins (#101)
  • Fixed clintable() erroring on data carrying haven value labels. attr() partial matches, so a labels attribute of value labels - which haven::read_xpt() attaches to coded variables - was answering a request for label and being read as header text (#107)
  • Fixed use_labels = FALSE not actually leaving column labels alone. flextable reads labels of its own accord and was never told not to, so the raw label string went into the header, || delimiter and all. This also gives a way past the flextable side of #107, since labels can now be turned off (#107)
  • Fixed merged cells being left in an invalid state when a table is paginated column wise with clin_alt_pages(). Merges are now recalculated for every row of the header, for the table body, and for merges running vertically, where previously only the top header row was corrected. Symptoms included header text disappearing from later pages, cells claiming to span more columns than the page has, and write_clindoc() failing with “missing value where TRUE/FALSE needed” when a page ended in a split spanner
  • Fixed a single column table losing all but the top level of a multi level column header
  • Fixed pagination discarding a table’s configuration when it dropped the page_by, group_by or caption_by columns
  • A title or footnote line with no elements now gives a clear error instead of failing inside data.frame()
  • The clinify_table_default() in defaults_template.R no longer merges header cells horizontally, which would have overridden the merge argument of clin_column_headers() at render time (#95)
  • The clinify_table_default() in defaults_template.R and in vignette("defaults") no longer rebuild the table properties either. Organisations that copied the template will want to pick up the change (#98)
  • The merge argument of clin_column_headers() now documents what merging a header row of repeated labels actually looks like: the run renders as one label centred over all of it, so the repeats are no longer there to read. The docs described the mechanism but not the symptom, which made it easy to lose a bottom row of per column labels without noticing that anything had gone (#120)
  • Because merge is now a parameter of clin_column_headers(), a column named merge can no longer be given a header through .... Use column labels for that column instead. This is a breaking change. (#95)

clinify 0.3.1

CRAN release: 2026-06-02

  • Updated for compatibility with {officer} (>= 0.7.0); the minimum required {officer} version is now 0.7.2
  • Group label styling now retains the configured font size
  • Fixed style application when column vectors were simplified incorrectly
  • Fixed slicing when a table is subset to a single column
  • Fixed handling of spanning header gaps when a spanner is split across pages
  • Made internal table-slicing tests robust to platform-dependent font-metric estimates (resolves an R CMD check error on r-devel-linux-x86_64-fedora-gcc)

clinify 0.3.0

CRAN release: 2025-07-07

  • Incorporate performance improvements from {officer} package updates
  • Fix issue with clin_col_widths() where numeric precision issues could cause unexpected errors
  • Group labels can be formatted and by default moved above header line (#79)
  • Added make_grouped_pagenums() helper function
  • Added function to create clindoc() objects specifically, and multiple tables can be passed to clindoc() (#63, #80)
  • Titles and footnotes now only split into two parts to avoid line wrapping (#69). This is a breaking change.
  • Added clin_group_pad() function (#72)
  • Updated group tracking in clin_group_by(), clin_auto_page() and clin_group_pad() to find groups by changed values or by populated values.
  • clin_auto_page() now has an option to drop the page_by variable. Does not drop variable by default. This is a breaking change.
  • Renamed write_clintable() to write_clindoc(). This is a breaking change.
  • New vignette on Document Objects and Saving

clinify 0.2.0

  • Added in body captions (#26 and #28)
  • Dedicated footnote pages #29
  • Fixed column header bugs #61
  • Allow return as rdocx object #63
  • Automatic page numbers #4
  • Added clin_auto_page() function for auto pagination using word’s keep_with_next (#16)
  • Several new vignettes

clinify 0.1.2

CRAN release: 2025-03-13

CRAN review comments, including: - Updated description file for reference links - Updated help documentation dontrun{} examples avoid unnecessary use of dontrun{} - Updated help example to not write file to local directory, and ensured all tests and vignettes write to files in tempdir()

clinify 0.1.1

CRAN review comment updates in DESCRIPTION file

clinify 0.1.0

Initial CRAN submission