<div><div><div><div data-width="55" data-show-faces="false" data-send="true" data-layout="box_count" data-height="62" data-href="https://www.r-bloggers.com/major-update-to-rms-package-5-0-0/"></div></div><div><a data-url="https://www.r-bloggers.com/major-update-to-rms-package-5-0-0/" data-counturl="https://www.r-bloggers.com/major-update-to-rms-package-5-0-0/" data-count="vertical" data-text="Major Update to rms package: 5.0-0" target="_blank" class="twitter-share-button" data-via="rbloggers" rel="nofollow" href="https://twitter.com/share"></a></div><div></div></div><div></div></div>
<p><em>Written by Frank E Harrell Jr (first published <a target="_blank" rel="nofollow" href="http://r.789695.n4.nabble.com/R-pkgs-Major-Update-to-rms-package-5-0-0-td4726209.html">here</a>)</em></p>
<p>A major new version of the rms package is now on CRAN.  The most<br>
user-visible changes are:</p>
<p>– interactive plotly graphic methods for model fits.  The best example of<br>
this is survplot for npsurv (Kaplan-Meier) estimates where the number of<br>
risk pop up as you hover over the curves, and you can click to bring up<br>
confidence bands for differences in survival curves</p>
<p>– html methods for model fit summaries especially when using Rmarkdown html<br>
notebooks</p>
<p>– instead of running print(fit, latex=TRUE) use<br>
options(prType=’latex’)<br>
print(fit)<br>
Or: options(prType=’html’)</p>
<p>A complete list of changes is below.  See<br>
<a target="_blank" rel="nofollow" href="http://biostat.mc.vanderbilt.edu/Rrms" data-saferedirecturl="https://www.google.com/url?hl=en&amp;q=http://biostat.mc.vanderbilt.edu/Rrms&amp;source=gmail&amp;ust=1478903316887000&amp;usg=AFQjCNFJQXjL2GNsN5zG23UXFi780M1UcQ">http://biostat.mc.vanderbilt.<wbr>edu/Rrms</a> for an html notebook showing examples<br>
of new features.</p>
<p>Changes in version 5.0-0 (2016-10-31)<br>
* plot.summary.rms: implemented plotly interactive plots if<br>
options(grType=’plotly’) in effect<br>
* plot.anova.rms: implemented plotly interactive plots if<br>
options(grType=’plotly’) in effect; remove psmall argument; changed margin<br>
default to chisq and P<br>
* ggplot.Predict: implemented plotly interactive plots if<br>
options(grType=’plotly’) in effect<br>
* print(fit, md=TRUE), prModFit, prStats: added latex/html methods using<br>
htmlTable package and MathJax for latex math<br>
* html.anova.rms, html.validate, html.summary.rms: new functions for use<br>
with html and MathJax/knitr/RStudio<br>
* latex methods for model fits: added md=TRUE argument to produce<br>
MathJax-compatible latex and html code for fitted models when using R<br>
Markdown<br>
* html: new methods for model fit objects for use with R Markdown<br>
* formatNP: fixed error when digits=NA<br>
* latex.anova.rms: fixed error in not rounding enough columns doe to using<br>
all.is.numeric intead of is.numeric<br>
* catg: corrected bug that disallowed explicit catg() in formulas<br>
* ggplot.Predict: added height and width for plotly<br>
* survplot: respected xlim with diffbands.  Thanks: Toni G<br>
* reVector: changed to reListclean and stored model stats components as<br>
lists so can handle mixture of numeric and character, e.g., name of<br>
clustering variable<br>
* survplotp.npsurv: new function for interactive survival curve graphs<br>
using plotly<br>
* anova, summary, latex, print for model fits: use options(grType=’html’)<br>
or ‘latex’ to set output type, output htmltools::HTML marked html so that<br>
chunk header doesn’t need results=’asis’<br>
* latex methods – set file default to ”<br>
* GiniMd: moved to Hmisc package<br>
* plot.nomogram: fixed bug where abbreviations were being ignored.  Thanks:<br>
Zongheng Zhang<br>
* nomogram: improved examples in help file<br>
* survplot.npsurv: fixed n.risk when competing risks<br>
* survest.cph, survfit.cph, others: fixed large problems due to<br>
incompatibility with survival 2.39-5 for survival predictions; changed<br>
object Strata to strata in cph to be compatible with survival package<br>
* new test survest.r to more comprehensively check survfit.cph and<br>
survest.cph<br>
* ggplot.Predict: quit ignoring xlim; suppress confidence bands if two<br>
group bariables because ggplot2 geom_ribbon doesn’t support multiple<br>
aesthetics<br>
* predictrms: set contrasts for ordered factors to contr.treatment instead<br>
of contr.poly<br>
* val.prob: changed line of identity to use wide grayscale line instead of<br>
dashed line</p>
<p>——————————<br>
Frank E Harrell Jr      Professor and Chairman      School of Medicine</p>
<p>Department of *Biostatistics*      *Vanderbilt University*</p>
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