NEWS for the Gmisc package

## 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 `boxGrob`s
- 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 `Transtion`-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 `boxGrob`Prop

## 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 (&nbsp;)
- `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`/`transitionPlot`s
- 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 `mergeList`s() 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`
