NEWS.md

NEWS for the Gmisc package

Changes for 3.4.0

• Added vertical_axis and horizontal_axis connector types for flowcharts. These opt-in connectors preserve the source box's x- or y-axis and project it onto the target boundary, giving true 90-degree vertical/horizontal arrows for shared wide or tall target boxes. Existing vertical and horizontal connector behavior is unchanged.
• Added phaseLabel() for flowchart box lists: a one-call-per-stage helper that adds a CONSORT-style phase label (e.g. Allocation, Follow-up, Analysis) centred between a stage's arms, sitting slightly above it and drawn on top. The label width adapts to the stage — spanning the central gap (plus a small corner overlap) for two arms, or the full stage width as a banner for three or more arms — and can be set explicitly via width. It correctly handles nested arm lists (arms that are themselves lists of boxes) by resolving their merged bounding box.
• Added on_top to insert() for flowchart box lists. A box inserted with insert(..., on_top = TRUE) is drawn on top of the other boxes and connections, regardless of its position in the list, and the marker is preserved through subsequent move()/align() operations. This is the lower-level overlay mechanism that phaseLabel() builds on.
• insert() now resolves grouped (list) neighbours via their merged bounding box, so a box can be inserted between grouped stages without error.
• Added a CONSORT phase-label example to the grid-based flowchart vignette showing phaseLabel() centred between randomisation arms.
• Updated flowchart examples to emphasize the flowchart() + pipe (|>) style API in inst/examples/connectGrob_example.R, inst/examples/spreadBox_ex.R, and inst/examples/alignBox_ex.R.
• Clarified spread/connect documentation to state that spread/align return updated objects (no in-place mutation) and that connectors should use the returned boxes.
• Improved interactive example ergonomics by pausing between graph pages in multi-plot examples.
• Added box_fn_args parameter to boxGrob() for passing extra arguments directly to the box drawing function. The default is now list(r = unit(5, "pt")), giving every box a fixed 5 pt corner radius (approximately equivalent to the widely-used 5 px CSS border-radius) regardless of box size — solving the issue where larger boxes had visibly rounder corners than smaller ones. Override per box or globally via options(boxGrobFnArgs = list(...)).
• Added equalizeHeights() for flowchart box lists, mirroring the existing equalizeWidths(). It sets selected boxes to a shared height (defaulting to the tallest among the selection) and supports the same subelement path syntax as equalizeWidths().
• Added exclude to spreadVertical()/spreadHorizontal() and the S3 spread() wrapper, allowing side branches to be left out of the main spread while preserving them in the flowchart list for later align(), move(), and connect() calls.
• Improved spread() span handling: explicit from/to spans now work naturally with margin as an inset inside that span (for example spread(axis = "x", from = 0, to = 0.7, margin = 0.05) spreads within the left 70% of the viewport with padding), and subelement spreads can use deferred position() endpoints such as from = position("log", "top", "y").
• Added references to alignVertical()/alignHorizontal() and the S3 align() wrapper. Supplying two references aligns the target to their midpoint on the selected axis, useful for centering side boxes between the main boxes before and after them.
• Clarified and tested moveBox()/move() justification semantics: for absolute moves, just = "right" makes x the right border, just = "left" makes x the left border, and the same edge-based interpretation applies vertically for top/bottom.
• Added one-to-many grouped side fan-out support to the S3 connect() API for connect("source", "group", type = "side"). The shared fan-out bus now honors side_route = "outside" and side_offset before branching to the destination boxes, which keeps side-branch arrows away from the source box edge.
• Added many-to-one grouped side fan-in to the S3 connect() API for connect(list("a", "b"), "target", type = "side"). The shared return bus now honors side/end_side and side_route/side_offset, routing to the requested outer side instead of letting each line independently pick the closest side of the target.
• Fixed one-to-one connect(..., type = "side") connectors so they honor side_route/side_offset. The vertical segment now steps out from the source box edge by the offset (matching the grouped fan-in/fan-out behavior); previously the offset was ignored and the line hugged the box edge. Use side_route = "edge" to keep the old edge-hugging route.
• Extended connector labels to grouped side fan-out connectors. label can now be used directly on a grouped type = "side" fan-out; the label is centered on the offset bus, drawn on the outgoing line, and uses a semi-transparent white background by default so the line remains visually legible.
• Added and expanded alternate flowchart shape examples using boxEllipseGrob(), boxDatabaseGrob(), boxDocumentGrob(), boxDocumentsGrob(), boxDiamondGrob(), and boxTapeGrob() together with spread()/align() positioning.
• Improved alternate shape helpers so non-rectangular shapes add appropriate text padding and expose visible bounds for connector anchoring. This keeps labels inside ellipse/database/document/tape shapes and lets connectors hit the visible shape edge instead of the surrounding viewport, and fan_in_top trunks now terminate exactly on the target's top edge.
• Added position() with relative moves.
• Added dotted arrows lines for flowcharts
• Added regex selector for box lists

Changes for 3.3.0

• Added equalizeWidths() for flowchart box lists, allowing selected boxes (including nested subelement paths and list-of-boxes targets) to share a common width while preserving center positions.
• Added txt_padding to boxGrob() and support for a global default via options(boxGrobTxtPadding = ...).
• Expanded the flowchart vignette with a grouped CONSORT-style example showing both global box text padding and width equalization across grouped levels.
• Added tests for the new behavior in tests/testthat/test-equalizeWidths.R and tests/testthat/test-boxGrob-padding-option.R.
• Updated package documentation pages generated from roxygen to include the new API and refreshed examples.

Changes for 3.2.0

• Added boxHeaderGrob() for creating flowchart boxes with centered header text and left-justified body text (e.g., bullet points). Fully compatible with all Gmisc flowchart helpers (coords(), distance(), connectGrob(), spreadVertical(), alignHorizontal(), etc.).
• Added deep-path support for subelement and reference in alignVertical, alignHorizontal, spreadVertical, spreadHorizontal, and moveBox, allowing nested paths (e.g. c("detail", 1)) and multiple targets (e.g. list(c(...), c(...))).
• Added helpers get_list_element_by_path() and set_list_element_by_path() to support nested selection and assignment.
• Updated examples (inst/examples/alignBox_ex.R, inst/examples/spreadBox_ex.R) and added tests (tests/testthat/test-align-deep-path.R, tests/testthat/test-spread-move-deep-path.R, tests/testthat/test-align-subelement-deep.R) covering deep-path selection and informative error messages.
• Fixed subelement resolution when a list of boxes is piped into alignHorizontal() or alignVertical() while providing a named reference argument; the piped list is now unwrapped so nested targets (e.g., c("step_1", "non-surgical")) are correctly found and aligned.
• Fixed many-to-one connectors (N, fan_in_center, fan_in_top) to handle container-like inputs by automatically targeting the first box within a group.

Changes for 3.1.0

• Added support for lists of boxes in prConvert2Coords, allowing for merged bounding box calculations in npc units.
• Extended moveBox to support moving lists of boxes (groups) as a single unit, with improved name preservation.
• Added subelement parameter to spreadVertical, spreadHorizontal, alignVertical, and alignHorizontal for targeting specific elements within a list of boxes.
• Added box label connector
• Improved connecting lines between boxes
• Added a .margin and a more flexble .to/.from management for the box spreading
• Improved connecting boxes

Changes for 3.0.4

• Update for new CRAN policy
• Improved cpp code for bezier arrows

Changes for 3.0.3

• Fixed bug in getSvdMostInfluential with bad names appearing in graph due to bad reference, thanks Felipe (see issue #66)

Changes for 3.0.1

• Fixed pathJoin for vector inputs
• Added difftime as numeric to getDescriptionStatsBy

Changes for 3.0.0

• BREAKING: The input parameters have changed for getDescriptionStatsBy and dropped old deprecated parameter conversion:
  • show_missing_digits -> show_missing.digits
  • show_missing -> useNA
  • sig.limit -> statistics.sig_lim
  • two_dec.limit -> statistics.two_dec_lim
• Fixed bug in getDescriptionStatsBy when providing a character input
• Made getDescriptionStatsBy S3 aware with tidyselect pattern for generating tables.
• The yamlDump can now take a character string and assume that is a json that needs conversion
• Added set_column_labels and set_column_units for using dplyr syntax for Hmisc::label and Hmisc::units operations.
• The units column in getDescrptionStatsBy can now have a custom name (also changed default name to "Units")
• Changed addBoxClr to addBoxStyle for Transition-class (minor breaking change)

Changes for 2.1.0

• getSvdMostInfluential now returns the data needed for plotting
• added fontsize dependent padding to boxGrob

Changes for 2.0.2

• Minor RCPP changes

Changes for 2.0.1

• Minor CRAN check fixes

Changes for 2.0.0

• BREAKING: The mergeList merges vectors into vectors instead of assuming that they should be bound as a matrix

Changes for 1.11.0

• Fix for adjustment in box justification, thanks Carl Suster
• Fix for incorrect boxPropGrob height calculation, bad handling of missing arguments and ignored gpar arguments (issue #46)
• Slightly changed color scheme for boxGrobs
• Added moveBox for moving boxGrob objects
• Added alignVertical and alignHorizontal for aligning boxGrob objects
• Added spreadVertival and spreadHorizontal for spreading boxGrob objects over the viewport
• Styling of htmlTable removed due to the 2.0 api change, nbow. the css.rgroup should be set using set htmlTable::setHtmlTableTheme or by passing the output through htmlTable::addHtmlTableStyle.
• The boxes now accept language input, thanks Carl Suster

Changes for 1.10.0

• Added yamlDump for quick object review
• Added pathJoin for joining paths without worrying about trailing '/'
• Added time2spanTxt for printing time span descriptor

Changes for 1.9.1

• Fixed new handling of data.frame stringsAsFactors in next R release

Changes for 1.9.0

• Added id as a parameter to the Transition-class
• Fixed bad no. of popViewport() not adequately leaving the transitionClass viewport tree
• Fixed bad viewport naming in Transition-class that was creating a conflict with multiple plots

Changes for 1.8.1

• Fixed cran requirement where class(x) != class(y) could be of length > 1

Changes for 1.8

• Added digits.nonzero for allowing values with extra digits where values are close to 0
• Changed sprintf to txtRound for many of the descriptors
• Fixed vignette names for CRAN
• Fixed bug in retrieve

Changes for 1.7

• Expressions are now allowed in boxGrob (Thanks Alan Haynes)
• Added lodash similar functions retrieve and has

Changes for 1.6.4

• Removed changed constant for STRICT_R_HEADERS compliance

Changes for 1.6.3

• Fixed minor issue related to new CPP error

Changes for 1.6.1

• Removed test for CRAN compliance
• Changed abs to fabs in bezierArrowFn's c++ code

Changes for 1.6

• Added skip_shadows to Transition-class

Changes for 1.4.3

• Fixes non-existing values in different by-groups (issue #24)

Changes for 1.4.2

• Added box functions between and coords
• Added more Transition options for arrows
• Added default options for Transition, boxGrob and boxGrobProp

Changes for 1.4.1

• Fixed merge with master external descGetMissing (Thanks Peter)

Changes for 1.4

• Added grid grobs for creating boxes and connecting these with lines
• Added checkmate for argument checking

Changes for 1.3.2

• Fixed bug when providing getDescriptionStatsBy with custom function
• Added ability add alternative column instead of the p-value column

Changes for 1.3.1

• Fixed use_unit issue #16
• Fixed bug in vignette
• Added R-version dependency

Changes for 1.3

• The Transition-class can now handle non-square matrix input
• The total column is now also passed through the txtInt function
• Fixed header_count bug in getDescriptionStatsBy - thanks rvlevitin (iss#13)

Changes for 1.2

• Fixed the naming of proportions in getDescriptionStatsBy
• If a variable has units set it can now be added into the row name in getDescriptionStatsBy
• Merged with the Grmd-package allowing direct access to the docx_document()
• Prepared for stricter requirements for R 3.3

Changes for 1.1

• Created the Transition class that can handle multiple transitions in contrast to transitionPlot
• The bezierArrowGradient has a simpler handling of the gradient proportion
• The bezier arrows have been rewritten with a > 20x speed increase
• The getDescriptionStatsBy function is now accompanied by mergeDesc that takes care of merging everything into one table
• Added ability to customize statistics for getDescriptionStatsBy
• transitionPlot: The color_bar_labels are now automatically extracted from the transition_flow input
• transitionPlot: Fixed bug so that the end viewport is the root
• transitionPlot: Fixed grid arrow bug
• transitionPlot: When using 3D matrices and two colors there should only be a colorbar when used with gradient arrows
• transitionPlot: If line width is smaller than the minimum width it is now set to 0

Changes for 1.0

• htmlTable and some of the formatters have now moved to the htmlTable package
• forestplot2 has now moved to the forestplot package
• added the mergeDesc in order to merge lists from getDescriptionStatsBy for
• All functions default to html = TRUE instead of FALSE
• show_missing is now useNA in order to match the table() call handling of missing
• Fixed a few bugs

Changes for 0.6.8

• Applied the DRY-documentation principle

Changes for 0.6.7

• Added an interactive() check before using the viewer
• Minor adjustments to the htmlTable handling of no-blank spaces ( )
• htmlTable now remember the ... argument and passes it on to the print.htmlTable() and cat()
• Added figCapNo and associated caption function for numbering figure captions
• Improved documentation

Changes for 0.6.6

• Improved the htmlTable viewer handling (thanks Adam Smith)

Changes for 0.6.5

• Changed the getDescriptionsBy example to work with the htmlTable() instead of the Hmisc::latex()
• Fixed getDescriptionsBy bug - the Total column failed when specified to be last - thanks Alexandre Vivot
• Added example for side-by side plotting for forestplot2
• As of 0.98.932 the knitr package isn't loaded, instead the metadata or device options indicates that it is knitting
• htmlTable bug: The function can now handle matrices without column names
• htmlTable bug: The function deletes and warns when n.rgroup/n.cgroup < 1

Changes for 0.6.4

• Bug fix for alt_col not respecting missing rgroup - added also a simple matrix output test
• Added visual tests for htmlTable and moved one of the examples there
• Added tableCSSclass option for htmlTable - thanks jphiplip

Changes for 0.6.3

• Changed versioning to a 3-digit system as suggested by Yihui Xie http://yihui.name/en/2013/06/r-package-versioning/
• Added alt_col for coloring the rows of the htmlTable rgroups - thanks raredd

Changes for 0.6.2.3

• Roxygen2 v 4.0.0 upgrade + other doc upgrades
• Percentages are now default without space between the number and the %-sign in order to better comply with English language standards

Changes for 0.6.2.2

• transitionPlot - fixed arrow size and empty boxes
• outputInt now defaults to the ',' formatting according to the English language. It also has no-breaking space if html option is set. It can also handle complex vector/matrix input.
• describeMean now allows for custom plus minus sign
• describe* now use the outputInt with the default english settings
• Minor fix for the print.htmlTable

Changes for 0.6.2.1

• bezierArrowSmplGradient changed name to just bezierArrowGradient
• Added visual tests and debugged the bezierArrowGradient/transitionPlots
• Externalized all internal functions of the transitionplot
• Added proportions for the transitionplot
• Managed thanks to Baptiste Auguié help on Stack Overflow I know now how to calculate the height of axisGrobs - useful both in the forestplot2 and the transitionPlot functions
• Fixed the adjustment of the xlabel, the lineheight argument, the viewports for the forestplot2 function
• Simplified the transitionPlot defaults
• Fixed a gradient bug in bezierArrowGradient

Changes for 0.6.2.0

• Added the viewer for htmlTable allowing for direct visualisation in RStudio of the tables. Outside RStudio the utils::browseURL is used.
• htmlTable added table spanner functionality, some man-page update, removed the default NULL arguments in favor of the missing() funciton, and a few minor bugfixes.

Changes for 0.6.1.1

• The bezierArrowSmpl now uses "mm" internally instead of the default "npc" - this improves the rendering as the "npc" is dependent on the axis. A few adjustments to arrow functions were also added.
• Bugfixes for the bezierArrowSmplGradient.
• Bugfixed missing data for getDescriptionStats and generated a test-file in order to check most combinations that they work
• Fixed the legend-bug for forestplot2 when using points

Changes for 0.6.1.0

• Added legend markers option for the forestplot2 function

Changes for 0.6.0.2

• Fixed ticks for forestplot2 - the prFpGetGraphTicksAndClips used the exp() for regular values.
• Cleaned up some of the code for the fpDrawXXXCI functions

Changes for 0.6.0.1

• Changed depends and imports for the package

Changes for 0.6.0.0

• For LibreOffice compatibility htmlTable now includes caption inside the table when compatibility='LibreOffice'
• Split the package to exclude regression functions, these are now in the Greg package
• Added title and label options to transitionPlot
• Added a size-autofit for the transitionPlot text

Changes for 0.5.8.2

• htmlTable caused too large colspans when cgroup was set

Changes for 0.5.8.1

• Bugfixes for printC&A and getDesc.
• Added a pvalueFormatter
• Fixed Intercept bug for get/printCrudeAndAdjusted - didn't include the intercept term

Changes for 0.5.8.0

• Added to forestplot2 ability create customly drawn confidence intervals/boxes
• Generated diamond, circle and point custom draw functions for forestplot2
• Added forestplot2 compatibility for the summary
• Minor bugfixes behind the scenes
• Fixed issue with getCrudeAndAdjustedModelData mixing up rows for rms objects

Changes for 0.5.7.11

• Added tfoot option to the htmlTable function
• Switched to the proper caption-align for htmlTable
• Added options for htmlTable() where you now can format the table counter text and change to Arabic numerals.
• Bug: changed just to align for printCrudeAndAdjustedModel()

Changes for 0.5.7.10

• Switched the order in the multi-line forestplot for the legend

Changes for 0.5.7.9

• Bugfix for getTics so that it can handle small spans < .5

Changes for 0.5.7.8

• Bugfix for forestplot2 with headers

Changes for 0.5.7.7

• Added title for forestplot2
• Fixed the margins for forestplot2

Changes for 0.5.7.6

• Added more legend border and fill options to the forestplot2
• Added the legend.title option in the forestplot2
• Fixed the auto-sizing of the area for the forestplot2
• Rows/elements with NA are now not included in the zero-line as they are considered to be headers

Changes for 0.5.7.5

• Added more legend options to the forestplot2
• Minor changes to simleRmsAnova

Changes for 0.5.7.4

• Added some debugging info for the getDescriptionStatsBy with more detailed errors when unit/total columns don't match

Changes for 0.5.7.4

• Externalized many of the forestplot2 functions and added the option of having a set line height
• Added new_page option for grid-based plots
• Updated the simpleRmsAnova function

Changes for 0.5.7.3

• Removed the plot.new() from transitionplot, this is in order to allow splitting plots, adding it to a viewport etc.

Changes for 0.5.7.2

• Added the lineheight option for forestplot2
• Fixed the R CMD Check --as-cran to run without any objections
• Updated dependencies

Changes for 0.5.7.1

• Fixed rownames in printCrudeAndAdjusted
• Changed printCrudeAndAdjusted to return a matrix subclass instead of immediately printing
• Ran through som Pkg-check and hopefully cleared out some bugs

Changes for 0.5.7.0

• getCrudeAndAdjusted is now an S3 method that has a default method and a method for rms objects. The rms relies on rms:::summaryrms and returns a matrix that is pruned and used for the situation.
• printCrudeAndAdjusted has externalized a lot of its functions and handling of the new rms getCrudeAndAdjusted output
• printCrudeAndAdjusted now ignores any interaction variables

Changes for 0.5.6.1

• forestplot2 fix so that it properly handles data.frames as arguments
• printCrudeAndAdjustedModel has a better handling of the groups argument
• Improved import to importFrom

Changes for 0.5.6.0

• The forestplot2 is updated - the widths are now relative to the window size, there is a margin option, and many of the inside functions have moved to helpers outside. Also fixed the alignment of the summary label to work better.
• Fixed a minor bug for cgroup without rowlabels
• Added default_ref for both getDescriptionStatsBy and describeProp function.
• The percentage sign in getDescriptionStatsBy, describProp and describeFactors is now optional.
• A minor bug fix for cgroup.just for the htmlTable function

Changes for 0.5.4.5

• Minor fix to rownames in htmlTable... again.
• Had to remove the "terms" option from the plotHR rms:::cph() alternative as it did caused an error ** The error seems to stem from predictrms() where the Adjto function deletes the adjto output in: ** adjto <- if (int.pres) ** model.matrix(Terms.ns, adjto)[, -1, drop = FALSE] ** I will have to look into it one day...

Changes for 0.5.4.4

• Fixed a rowname problem for htmlTable
• Changed the rowlabel.pos to be by default at the bottom, seems more natural with multi-layered tables.

Changes for 0.5.4.3

• Fixed a caption problem for htmlTable

Changes for 0.5.4.2

• bezierArrowSmpl needed a color for the arrow line as it turned black by default. The line was added to fix the anti-aliasing issue.
• Changed CSS-defaults for groups when using the function printCrudeAndAdjusted

Changes for 0.5.4.2

• Minor regular expression fix for printCrudeAndAdjusted for the addref. function
• Minor fix for cgroup.just as this was affected by the previous update
• Fixed the htmlTable cgroup.just issue
• The htmlTable is now rendering correct w3c-validated code

Changes for 0.5.4.1

• Minor improvement to the htmlTable function with align now accepting vectors
• Added multiline cgroup alternative

Changes for 0.5.4.0

• Added a robust alternative for rms ols regressions that now can use the sandwich package

Changes for 0.5.3.5

• Added mergeLists() function for merging multiple lists

Changes for 0.5.3.4

• New options for plotHR

Changes for 0.5.3.3

• Minor fixes to the bezier arrows
• Update for transitionPlot to avoid overlapping background arrows

Changes for 0.5.3.2

• Thank you Adam Van Iwaarden for fixing the htmlTable alignment and a few bugs!
• Bug fix for prGetModelVariables affecting model with functions as parameters
• Added poisson (link=log) to the getCrudeAndAdjusted function to ret exp() values

Changes for 0.5.3.1

• Added transitionPlot ability to indicate proportions in the rectangles

Changes for 0.5.3.0

• Added the bezier arrows to the transition plot
• Added a bridge option for the transition plot arrows
• Bugfix for the bezierSmplGradient

Changes for 0.5.2.0

• Added the bezier arrows.

Changes for 0.5.1.1

• Added lwd parameters to the transitionPlot lines
• Changed the transition matrix - the sums were not necessary as they easily can be calculated from the rowSums/colSums.

Changes for 0.5.1.0

• Added the transitionPlot

Changes for 0.5.0.2

• Bugfix for htmlTable - throws error if a one dimensional x is provided

Changes for 0.5.0.1

• Bugfix for plotHR - there were issues with getting the model data
• Added option for having specific digits in printCrudeAndAdjustedModel in the model and the descriptive part

Changes for 0.5.0.0

• Added the option of having descriptive data to the printCrudeAndAdjustedModel
• A completely new way to extract the model dataset

Changes for 0.4.9.1

• Change the option for printCrudeAndAdjustedModel from just html to output alternatives html, latex or raw
• Altered the name of the describe_ functions to follow the camelCase style, i.e. describe_mean is now describeMean

Changes for 0.4.9.0

• Added the getSvdMostInfluential function

Changes for 0.4.8.2

• The simpleRmsAnovaLatex now has a better handling of the low p-values
• Fixed a minor but with printCrudeAndAdjusted with the automated reference

Changes for 0.4.8.2

• Added the option of hadding a total column even in "vertical" mode
• Changed parameter names hrzl_prop.show_perc to total_col_show_perc
• Bugfix: The total column causes errors if the by contains missing values

Changes for 0.4.8.1

• Fixed a few bugs to the forestplot2