Descriptive Statistics, Transition Plots, and More

Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories, flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.


Tools for making:

  • the descriptive "Table 1" used in medical articles
  • transition plot for showing changes between categories
  • flow charts based on the grid package
  • a method for variable selection based on the SVD
  • Bézier lines with arrows complementing the ones in the 'grid' package, and more.

News

NEWS for the Gmisc package

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 connectGrob options for arrows
  • Added default options for connectGrob, 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 rowname 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

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

Reference manual

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install.packages("Gmisc")

1.6.4 by Max Gordon, 18 hours ago


http://gforge.se


Report a bug at https://github.com/gforge/Gmisc/issues


Browse source code at https://github.com/cran/Gmisc


Authors: Max Gordon <[email protected]>


Documentation:   PDF Manual  


GPL (>= 3) license


Imports grid, grDevices, graphics, lattice, Hmisc, forestplot, abind, methods, knitr, magrittr, rmarkdown, XML, utils, stats, checkmate

Depends on Rcpp, htmlTable

Suggests testthat, datasets, stringr

Linking to Rcpp


Depended on by Greg.


See at CRAN