Major Update to rms package: 5.0-0

[social4i size=”large” align=”float-right”] 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 for an html notebook showing examples 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 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* 41jcfsrnrdl-_sx351_bo1204203200_

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