NEWS for the Gmisc package

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 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 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