[R-pkgs] Major updates to Hmisc and rms packages

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[R-pkgs] Major updates to Hmisc and rms packages

Frank Harrell
New versions of Hmisc and rms are available on CRAN.  Changes are listed
below.

The most significant change to Hmisc is the addition of the ffCompress
function that creates an optimal ff package object for large data frames
by computing the maximum number of bits used by each numeric or logical
variable in the data frame.  And the html.latex method now implements
conversion of latex code generated by Hmisc to html for dynamic
insertion in R Markdown documents (if you install the system package
TeX4ht).

The most significant changes to rms are the correct handling of offset
variables and updating the demos.
----------------------------------------------------------------------------------------------------------------------------

Hmisc Changes in version 3.17-0 (2015-09-20)
    * format.df (used by latex.default): added space after textless,
textgreater
      * label: changed default for units to value of plot
      * getRs: replaced where argument with guser, grepo, gdir, dir to
allow easy fetching of updated functions from Hmisc etc.
      * Separated sas.get source code from other .get functions and from
upData/cleanup.import by putting into 3 separate files.  Moved stata.get
into misc.get.s
      * upData: for Stat/Transfer exported R workspaces, change
variables into factors to incorporate value labels when present; added
subset argument and reporting of number of observations pre and post
subsetting
      * latex.default: added comma after botcap directive for ctable.  
Thanks: Paul Trowbridge
    * Hmisc-internal.Rd: removed  alias{[.terms}
      * latex.default: for longtable when no caption is given, subtract
one from table counter
      * latex.summaryM: quit ignoring insert.bottom if it is a character
string (thanks: JoAnn Alvarez)
      * minor.tick: revised version by Earl Belllinger that fixes
problem reported in https://github.com/harrelfe/Hmisc/issues/28
      * several functions: used new names when assigning temporary functions
      * NAMESPACE: add imports to base functions to avoid new R CMD
CHECK warnings
      * ffCompress: new function
      * knitrSet: changed fig.path default to '' instead of NULL to work
with knitr 1.11
      * html.latex: added argument rmarkdown
      * htmltools: added to suggests in DESCRIPTION
      * tests: new test script latex-html.Rmd for latex -> html under
Rmarkdown/knitr/Rstudio, new test for cut2
      * plsmo, panel.plsmo: added method='intervals', mobs, ifun arguments


rms Changes in version 4.4-0 (2015-09-28)
    * contrast.rms: made SE a vector not a matrix, added 4 list logic
for nvary, added new test from JoAnn Alvarez
      * plot.summary.rms: correct bug where pch was ignored.  Thanks:
Tamas Ferenci
      * prModFit: fix print(fit, latex=FALSE) when fit is result of
robcov, bootcov
      * NAMESPACE: added imports for base functions used to avoid
warnings with R CMD CHECK; new test rcs.r
      * prModFit: added rmarkdown argument.  All print.* methods can
pass this argument.
      * All print methods for fit objects: left result as prModFit
instead of invisible() so that rmarkdown will work
      * demo/all.R: updated for plot and ggplot methods, npsurv
      * cph, predictrms, rms, rms.trans, rmsMisc: changed Design
function to return new objects sformula (formula without cluster()) and
mmcolnames which provides a new way to get rid of strat() main effects
and interactions involving non-reference cells; handle offsets in cph
and predict() (not yet in Predict); new internal function
removeFormulaTerms that does character manipulation to remove terms like
cluster() or offset() or the dependent variable(s).  This gets around
the problem with [.terms messing up offset terms when you subset on
non-offset terms
      * Glm, ols: fixed offset
      * bj, Gls, lrm, orm, psm, Rq: change to new offset method and sformula
      * Predict: added offset=list(offsetvariable=value)
      * several: made temporary function names unique to avoid warnings
with R CMD CHECK
      * ggplot.Predict: changed facet_wrap_labeller to not mess with
class of returned object from ggplotGrob
      * Design: fixed column names for matrix predictors
      * Design, cph: handled special case where model is fit on a fit$x
matrix
      * dxy.cens: exported
      * cph: added debug argument
      * tests/cph4.r: new tests for various predictor types
      * rms: changed warning to error if an ordered factor appears in
the model and options(contrasts) is not set properly
      * rms transformation functions: made more robust by checking !
length instead of is.null


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

        Department of *Biostatistics* *Vanderbilt University*


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Frank Harrell
Department of Biostatistics, Vanderbilt University