[R] [R-pkgs] Massive Update to Hmisc package

[Frank Harrell]

Hmisc 4.0-0 is now on CRAN.  The package has undergone a massive update.
The most user-visable changes are;

- support for Rmarkdown html notebooks

- advanced html tables using the htmlTable package and summaryM function;
can copy and paste into word processors

- support for plotly interactive graphics, e.g.
  options(grType='plotly')
  plot(describe(mydata))

- new function ggfreqScatter

- new object markupSpecs that drives LaTeX and html translations

- describe function computes new statistics and relabels Unique as Distinct

The full list of changes is below.  You can look at examples of html
notebook reports produced using the new Hmisc at
http://biostat.mc.vanderbilt.edu/Hmisc .  These include interactive plotly
graphics.

Changes in version 4.0-0 (2016-10-31)
   * summaryP: fixed exclude1 logic - was not excluding enough levels
(inconsistent use of variable names vs. labels)
* latexTranslate: any NAs in first argument changed to "" before conversion
* minor.tick: added arguments to pass through (thanks: vhorvath)
* tests/latexpng.r: test conversion of LaTeX table to png
* latexTabular: made it properly call latexTranslate separately for each
column, convert argument to matrix or data frame if a vector
* tests/latexTabular.r: new test
* latexDotchart: added call to latexTranslate to escape special characters
for LaTeX such as underscore and pound sign
* ggfreqScatter: new function
* grType: new non-exported service function to sense if plotly is in effect
* plot.describe: new function to make plotly graph for describe objects
* describe: changed output: 3 decimal places for Info, new format for
frequency table, separated logic for 10 extreme values from logic for
frequency table, significant changes to print.describe
* dotchartp: new version of dotchart3 for plotly charts
* summaryD: modified to use dotchartp if options(grType='plotly') is in
effect
* nFm: added argument html
* label.default, label.Surv, labelPlotmath: added html argument to
implement HTML markup in place of plotmath (for plotly)
* now imports htmlTable, viridis
* html.contents.data.frame: return invisibly if file=''
* htmlVerbatim: new function
* html.contents.data.frame: improved html
* html.data.frame: changed column headers from h4 to <strong>
* ggfreqScatter: added html argument
* knitrSet: was ignoring default figure h and w
* html.summaryM: new function using new version of latex.summaryM
* markupSpecs: new list object defining markup elements for latex and html,
used by summaryM
* show.html, print.html: removed; conflicted with htmltools/rmarkdown
* label: required exact match on attribute name "label" to not retrieve the
"labels" attribute (thanks: Ivan Puzek)
* htmlSN: new function to convert floating point to scientific format usint
html
* upData, cleanup.import: fix NA becoming new factor levels (thanks: Beau
Bruce)
* htmlTranslate: new function
* plotlySave: new function
* histSpikep: new function
* upData: new argument html
* plot.describe: added ggplot2 graphics, improved continuous display using
ggplotly
* labelPlotmath: cleaned up by using markupSpecs
* capitalize: fixed bug - did not cap. first letter if other letters after
it were upper case (thanks: dchiu911)
* html.summaryM: added brmsd argument to put mean, SD on separate line
* Save: changed default back to use gzip for speed
* knitrSet: used new knitr way to set aliases for option names
* latexTabular: made translate argument apply to body of table also;
implemented multi-line header
* html.data.frame: added several arguments
* describe: added html method
* html markupSpecs object: added bibliographic database utility functions
* bppltp: new service function for extended box plots for plotly
* plot.summaryM: new plotly method
* prType: new service function used to detect user settings for html, latex
for print methods
* html.contents.data.frame: removed file and append arguments and output an
html character vector instead
* prList: new function
* GiniMd: moved to Hmisc from rms
* describe: added GMD (Gini's mean difference) and relabeled unique to
distinct
* latex.summaryM: added Needspace{2.7in} before 2nd and later strata
* ggplot.summaryP: added point labels for use with plotly as hover text
* latex.summaryP: fixed bad linebreak at strata boundaries
* dotchartpl: new plotly dot chart function especially for summaryP
* plot.summaryP: new plotly method using dotchartpl when
options(grType='plotly')
* putHfig: new function to render graphics with captions in HTML reports
* pngNeedle: new function, like latexNeedle but useful with HTML reports
* html.data.frame: added width and caption arguments
* plotlyParm: list object with plotly helper functions
* summaryD, dotchartp: added symbol and col arguments
* upData: improved efficiency, added labelled class to variables without it
but having labels (e.g., data imported using haven package)
* gbayesMixPost: mixed error in posterior odds of the mixing parameter that
resulted in incorrect posterior probabilities when the variance of the
statistic was appreciable; added option to compute posterior mean




------------------------------
Frank E Harrell Jr      Professor and Chairman      School of Medicine

Department of *Biostatistics*      *Vanderbilt University*

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