NEWS.md

In metrumresearchgroup/pmtables: Tables for Pharmacometrics

pmtables 0.8.1

Bugs Fixed

• Fixed a bug in preview helpers (st_as_image() and st2report()) where a list was getting passed as .envir to glue::glue() rather than an environment; this was causing glue::glue() to fail after changes rolled out in glue version 1.8.0 (#346).

pmtables 0.8.0

• New functionality to include output file path information in the table annotation (#341).

pmtables 0.7.0

• New functionality to create table notes from glossary files (#326).
• read_glossary() reads from .tex or .yaml formatted files, returning a glossary object
• select_glossary() selects specific entries from a glossary object
• as_glossary() creates a glossary object on the fly or from a list
• glossary_notes() creates notes from a glossary object, a list, or the name of a glossary file
• st_notes_glo() creates and and attaches notes to a table in a pipeline
• stable_save_image() added to create an image from a table and save to a specific location; this builds on st_aspdf() and st_aspng(), adding convenient syntax and options (#333).
• The maxex argument to sig() can now be set through the pmtables.maxex option (#328).

Bugs Fixed

• Fixed a bug in pt_cat_long() when the by argument is used with no all data summary (#330).

pmtables 0.6.0

• st_caption() function added to associate a caption (including short caption and possibly a label) to any table; captions will appear in st2report() outputs; captions will always be written to file for stable_long outputs and can be optionally written to file for stable outputs (#313).

• yaml_as_df() will now retain row names in a column named by the new argument row_var (#317).

• st_align(), st_left(), st_right() and st_center() can now be called multiple times in a pipeline, supported by new update method for aligncol objects (#315).

• st_clone() function added to make a copy of stobject objects (#314).

• The id_col argument to pt_cont_long() and pt_cont_wide() is deprecated (#305).

Bugs Fixed

• Fixed bug where sumrows was not recognized as a valid field in stobject objects (#312).

pmtables 0.5.2

• pmtables has been updated to be compatible with stringr 1.5.0, which changed the classes of pattern modifiers (#302).

pmtables 0.5.1

• New function st_filter() to filter data item in a pipeline (#298).

• Add summarize_all and all_name_stacked arguments to pt_data_inventory() (#297).

Bugs Fixed

• Fixed bug where all_name was not getting used in pt_data_inventory() (#297).

• Fixed bug where detached table notes were getting rendered too close to the main table when building standalone pdf under certain TeX distributions (#286).

pmtables 0.5.0

• New functions st_as_image(), st2pdf(), and st2png() to render tables with TeX to either pdf or png format; image files may be kept on disk or read back for display while knitting; pdflatex system dependency for pdf images and latex + dvipng for png images; additional Suggested packages include magick and pdftools (#277, #278).

• sig() now returns character when integer type is passed (#272).

• st_new() is now generic with dispatch for data.frame and objects with class pmtable; most pipeline functions can now be used to customize tables coming from pt_cat_*, pt_cont_*, pt_demographics() and pt_data_inventory() (#274).

• New functions st_notes_detach(), st_notes_rm(), st_notes_app(), st_notes_str(), st_notes_sub() and st_notes_conf() to help working with table notes in a pipe context (#274).

• st_span() and st_span_split() accept align argument to push column spanner titles to the left, right or center (default); the argument eventually gets passed to colgroup() (#261).

• pt_cat_wide(), pt_cat_long() and pt_demographics() gain argument denom to alter the denominator when calculating percents for categorical data summaries (#268).

• pt_cat_wide() gains argument complete to display missing levels of by and panel (#268).

• Put stories in yaml format; add script to build validation docs from the yaml file (#269, #270).

pmtables 0.4.1

• colgroup() (and st_span()) gains an align argument to position the spanner title on left or right in addition to the center (default) #260, #261.

• rowpanel() (and st_panel()) gains jutargument to push non-panel table contents to the right relative to the panel header row so that contents under the panel header are indented #251, #253.

• Panel header rows are now modified so that the header row stays with the first non-header row for longtable output #252, #253.

• Consistent BQL / BLQ handling for column titles and table notes for pt_data_inventory() #254, #255.

pmtables 0.4.0

• Add cols_omit option to omit column header data (#213)

• Add pt_demographics function to generate a new table of both continuous and categorical data (#186, #249)

• Add title_side argument to colsplit() so that the title can be taken from left or right side of split (#231)

• Add hline argument to rowgroup() constructor to make the horizontal line above the panel data optional (#215)

• Refactor pt_data_inventory() to calculate percent BLQ using denominator that is the sum of the number of observations BLQ and non-BLQ / non-missing (#221, #222)

• st_asis() gains a method for pmtable objects (#236)

• List names are now escaped when passing a list of tables to st2report() and friends (#232)

• Add newline after printing table text using st_asis() (#224)

pmtables 0.3.3

• Fix bug where arguments could not be passed along to stable_long() when coercing pmtable output (#203)

• Fix bug where user-specified font size was not getting propagated to long table output with stable_long() (#204)

pmtables 0.3.2

• Fix cols renaming and utilization of table argument in pt_cont_wide; add tests for column renaming for cat / cont / long / wide #199
• Fix error message when duplicate panels are found #198

pmtables 0.3.1

• Add .list argument to st_rename() allowing user to pass rename information as a named list with format old name = new name #189
• Fix bug where drop_miss wasn't executing correctly #182
• stable_long() is now a generic function with methods for data.frame, stobject and pmtable #179
• Expand documentation for data summary functions
• st_span() was slightly refactored so that it would dispatch to st_span_split() when the split argument was passed #173
• Fixed a bug where span_split() was updating column names, but this was happening before other spans were calculated #172
• The categorical data summary functions now check for missing values (NA) and will replace them with the string "NA" and issue a warning #117

pmtables 0.3.0

• Add landscape mode when previewing tables with st2report(), st2article() or st2doc(); see landscape argument to st_wrap() #129
• Add lt_cap_short argument to stable_long() to set a short table title that will appear in list of tables #131
• Fix a bug in continuous data summary tables when no observations were found in a particular group; use na_fill argument to set placeholder #133
• Add ability to accumulate hline indices when set with st_hline() #134
• Fix a bug in cols_bold that prevented sanitizing text prior to styling as bold #141
• Add ability to introduce row breaks in spanner titles #143
• Add st2report() to quickly preview tables in a real-like report document, build directly with pdflatex #148
• Add st2article() to quickly preview tables in a latex article-like, built directly with pdflatex #148
• Add st_asis() function and asis argument to st_wrap(); pipe tables to st_asis() or use asis argument to render tables in line in an Rmd document; in addition to formatting output "as-is", latex dependencies are also invoked #149
• Expand yaml_as_df() functionality to accept table columns by position, rather than name #154
• Add stable() method for stobject #159
• Fix bug where column spanners were not getting displayed in longtable #165

pmtables 0.2.0

• Add by argument to pt_cont_long so that, when panel is also passed, the table is paneled by col and is "by" the panel variable #92
• Refactor pt_cat_long so that summary numbers are shown underneath column labels #102
• Refactor longtable row and column spacing so that they use row and col in tab_size() with the same behavior as tabular / stable() #105
• Add cols_extra feature, allowing extra column header information passed as a data frame (see tab_cols()) #102, #118
• Added documentation for data arguments to reinforce that pmtables doesn't filter or subset data prior to processing or summarizing #120
• Fix bug in stable_long() where stable_file wasn't getting saved
• Add n summary column to pt_cat_wide() #80
• Add functions that return table notes for continuous and discrete data summaries and data inventory tables #114
• Make pt_wrap() generic; add method for stable_long that doesn't wrap with table #121

pmtables 0.1.0

• Adding NEWS file
• Add duplicates_ok argument to rowpanel
• Error if duplicate panel names found and duplicates_ok is FALSE
• Refactor how panel groupings are determined - non-repeating values rather than unique
• Added debug_data argument to stable; this adds an environment to the output with some data that underlies the table; the environment can be accessed with get_debug_data()
• Added complete series of st_* functions that can be used in a pipeline to set arguments for stable(); see inst/demo-pipe.pdf
• st2doc will render multiple page document when a list of tables is passed in as text
• Changed stable argument from bold_cols to col_bold
• Column names are only rendered with bold font when requested using col_bold argument
• The prefixes for r_file and output_file are only settable with options r.file.label and output.file.label, respectively
• Dropped col_space, row_space and fontsize arguments to stable(); they should be set with a call to tab_size
• Add st_sizes() to set sizes argument to stable()
• Refactor stable() function in order to reduce cyclomatic complexity and shorten overall function length in response to brief review and comment by TS representative
• Make stable a generic function; methods for data.frame and pmtable
• All pmtables functions now accept panel argument as a rowgroup object
• Add as.panel() function for constructing rowgroup objects
• For pmtables functions: when panel is passed with an alternate name, the name is is used to set the prefix
• Fixed bug where column names were getting sanitized before rename happened #62
• Pick up option pmtables.dir to set output directory for stable_save()
• Pick up option mrg.script to set script name in st_files() and tab_notes()
• Refactored the way that table cols and units are assembled; column labels are split on ... to create multi-line column names
• Add header_row argument to tab_cols() to control the spacing between column labels and between labels and units
• Fix warning message when trying to align a column not in the data set
• Fix warning message when trying to add unit to column not in the data set
• Add several new package options; see ?pt_opts
• Add center argument to col_fixed; when ragged is no, the column can still be fixed and centered
• Dots (...) added to st_new() / st_data() to be collected by args
• Add st_units() pipeline function
• Add tex_bold() function to style data frame contents
• Add tex_it() function to style data frame contents
• Add st_edit()
• Refactor st_hline(); allow to add hline by regexp across whole data frame or targeted
• Refactored st_bold and st_it to target columns or whole data frame
• Add st_drop()
• Add data sets analysis1, pmt_pk, pmt_first, pmt_obs
• Change argument names for tab_cols: all col_xyz arguments are renamed to cols_xyz
• Add find_bq_col function to allow either BQL or BLQ as default value for bq_col argument to pt_data_inventory
• Add pattern and cols arguments to st_sumrow; this allows calculation of rows based on a regular expression
• Add df_grep_rows and df_grepl_rows functions for finding rows where a regular expression is matched
• Add pmtables.escape option to pass a character vector of items to be escaped
• Unit of escape is now individual positions in a vector rather than the whole vector itself
• No longer requiring or assuming that header_row (tab_size()) is a negative number; enter a negative number if you want to remove space between header rows; this should only be required when row space is increased

metrumresearchgroup/pmtables documentation built on Oct. 27, 2024, 5:16 p.m.