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

Frank Harrell f.harrell at Vanderbilt.Edu
Thu Oct 1 00:48:58 CEST 2015

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

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 

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, 
      * 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 
      * 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 
      * 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 
      * 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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