NEWS

NEWS for the Gmisc package

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 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