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* [[alternative HTML version deleted]]