# Major Update to rms package: 5.0-0

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*Written by Frank E Harrell Jr (first published here)*

A major new version of the rms package is now on CRAN. The most

user-visible changes are:

– interactive plotly graphic methods for model fits. The best example of

this is survplot for npsurv (Kaplan-Meier) estimates where the number of

risk pop up as you hover over the curves, and you can click to bring up

confidence bands for differences in survival curves

– html methods for model fit summaries especially when using Rmarkdown html

notebooks

– instead of running print(fit, latex=TRUE) use

options(prType=’latex’)

print(fit)

Or: options(prType=’html’)

A complete list of changes is below. See

http://biostat.mc.vanderbilt.

of new features.

Changes in version 5.0-0 (2016-10-31)

* plot.summary.rms: implemented plotly interactive plots if

options(grType=’plotly’) in effect

* plot.anova.rms: implemented plotly interactive plots if

options(grType=’plotly’) in effect; remove psmall argument; changed margin

default to chisq and P

* ggplot.Predict: implemented plotly interactive plots if

options(grType=’plotly’) in effect

* print(fit, md=TRUE), prModFit, prStats: added latex/html methods using

htmlTable package and MathJax for latex math

* html.anova.rms, html.validate, html.summary.rms: new functions for use

with html and MathJax/knitr/RStudio

* latex methods for model fits: added md=TRUE argument to produce

MathJax-compatible latex and html code for fitted models when using R

Markdown

* html: new methods for model fit objects for use with R Markdown

* formatNP: fixed error when digits=NA

* latex.anova.rms: fixed error in not rounding enough columns doe to using

all.is.numeric intead of is.numeric

* catg: corrected bug that disallowed explicit catg() in formulas

* ggplot.Predict: added height and width for plotly

* survplot: respected xlim with diffbands. Thanks: Toni G

* reVector: changed to reListclean and stored model stats components as

lists so can handle mixture of numeric and character, e.g., name of

clustering variable

* survplotp.npsurv: new function for interactive survival curve graphs

using plotly

* anova, summary, latex, print for model fits: use options(grType=’html’)

or ‘latex’ to set output type, output htmltools::HTML marked html so that

chunk header doesn’t need results=’asis’

* latex methods – set file default to ”

* GiniMd: moved to Hmisc package

* plot.nomogram: fixed bug where abbreviations were being ignored. Thanks:

Zongheng Zhang

* nomogram: improved examples in help file

* survplot.npsurv: fixed n.risk when competing risks

* survest.cph, survfit.cph, others: fixed large problems due to

incompatibility with survival 2.39-5 for survival predictions; changed

object Strata to strata in cph to be compatible with survival package

* new test survest.r to more comprehensively check survfit.cph and

survest.cph

* ggplot.Predict: quit ignoring xlim; suppress confidence bands if two

group bariables because ggplot2 geom_ribbon doesn’t support multiple

aesthetics

* predictrms: set contrasts for ordered factors to contr.treatment instead

of contr.poly

* val.prob: changed line of identity to use wide grayscale line instead of

dashed line

——————————

Frank E Harrell Jr Professor and Chairman School of Medicine

Department of *Biostatistics* *Vanderbilt University*