[R] [R-pkgs] rms 4.1-0

[Frank Harrell]

The rms package has had several updates in version 4.1-0:

    * Fixed orm.fit to not create penalty matrix if not needed 
(penalties are not yet implemented anyway)
    * Added yscale argument to plot.Predict
    * Added Wald test simulation to orm help file
    * Added example in help file for plot.anova.rms of adding a line 
combining the effects of two predictors in dot chart
    * Fixed grid interpretation error in survplot.survfit
    * Changed plot.anova.rms to use dotchart3 instead of dotchart2
    * Fixed bug in summary.rms - was taking reciprocal of effect ratio 
with orm even if not loglog family (thanks: Yong Hao Pua 
<puayonghao at gmail.com>
    * Removed link to print.lm, summary.lm in ols.Rd
    * Added ntrans argument to plot.anova.rms
    * Fixed handling of intercepts in Rq, validate.Rq
    * Removed residuals.Glm, residuals.rms (also from Rd, NAMESPACE)
    * Removed other .rms methods and other remnants from fooling S+ 
dispatcher
    * Fixed bug in lm.pfit when penalty used (thanks: Yong Hao Pua 
<puayonghao at gmail.com>)
    * Fixed bug in calibrate.default for ols (thanks: Andy Bush)
    * Change print.contrast.rms to insert NA for SE if fun is not the 
identity function
    * Added margin argument to plot.anova.rms to print selected stats in 
right margin of dot chart
    * Added anova argument to plot.Predict to allow overall association 
test statistics to be added to panels
    * Fixed bug in val.prob in which the logistic model was re-fitted 
instead of fixing coefficients at 0,1.  This resulted in model 
statistics (including c-index) to always be favorable even when 
predictions were worse than change.  Thanks: Kirsen Van Hoorde 
<Kirsten.VanHoorde at esat.kuleuven.be>
    * Fixed bug in survdiffplot where conf.int was always overridden by 
value from survfit.  Thanks: Kamil Fijorek <kamilfijorek at gmail.com>
    * Fixed bug in grid= for survplot.* and survdiffplot.  Thanks: Kamil 
Fijorek
    * Fixed rms.s to account for possible offset in names(nmiss). 
Thanks: Larry Hunsicker
    * Fixed psm.s to not compute Dxy if simple right censoring is not in 
effect.  Thanks: I.M. Nolte
    * rcs: respect system option fractied, passed to rcspline.eval; can 
be used to get old behavior
    * Gls: as nlme 3.1-113 exports more functions, removed nlme:::

-- 
Frank E Harrell Jr Professor and Chairman      School of Medicine
                    Department of Biostatistics Vanderbilt University

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