r-cran-rms 3.3-3-1 / usr / lib / R / site-library / rms / NEWS

Changes in version 3.3-3 (2011-12-06)
   * robcov: used vcov to get var-cov matrix
   * vcov.Glm: gave precedence to $var object in fit
   * Added residuals.Glm to force call to residuals.glm, and make robcov fail as type="score" is not implemented for glm
   * Fixed bootcov for Glm to sense NA in coefficients and skip that iteration
   * Fixed digit -> digits error in latex.rms
   * Fixed f$coef error in pentrace; thanks christopher.hane@optum.com
   * Added new feature for Predict() to plot bootstrap nonparametric confidence limits if fit was run through bootcov with coef.reps=TRUE
   * Added ylim argument to plot.residuals.lrm

Changes in version 3.3-2 (2011-11-09)
   * calibrate.default: add var-cov matrix to ols objects
   * print.lrtest: discarded two formula attributes before printing
   * Added digits, size, and after arguments for latex methods for model fits, made before argument work with inline=TRUE, changed \needspace to \Needspace in latex.validate and prModFit
   * latex: fixed to consider digits for main effects
   * plot.xmean.ordinaly: added new argument cex.points
   * print.lrm: improved printing of -2 LL overall penalty
   * plot.calibrate.default: invisibly return prediction errors
   * plot.Predict: added cex.axis argument to pass to x scales; added subdata
   * print.pentrace: neatened up output
   * added title as an argument to all high-level function print methods
   * prModFit: fixed bug where Score chi2 was not translated to LaTeX
   * prModFit: changed to use LaTeX longtable style for coefficients etc.
   * prModFit: added arguments long and needspace
   * prModFit: suppressed title if title=""
   * rmsMisc: added nobs.rms and added nobs to object returned by logLik.rms
   * Added new argument cex.points to plot.xmean.ordinaly
   * Changed example in anova.rms to use reorder instead of reorder.factor

Changes in version 3.3-1 (2011-06-01)
   * Added new example for anova.rms for making dot plots of partial R^2 of predictors
   * Defined logLik.ols (calls logLik.lm)
   * Fixed and cleaned up logLik.rms, AIC.rms
   * Fixed residuals.psm to allow other type= values used by residuals.survreg
   * Fixed Predict and survplot.rms to allow for case where no covariates present
   * Fixed bug in val.prob where Eavg wasn't being defined if pl=FALSE (thanks: Ben Haller)
   * Fixed bug in Predict so that it could get a list or vector from predictrms
   * Fixed latex.rms to not treat * as a wild card in various contexts (may be interaction)
   * Fixed predictrms to temporarily get std.err if conf.int requested even it std.err not; omitted std.err in returned object if not wanted
   * Enhanced plot.Predict to allow plots for different predictors to be combined, after running rbind.Predict (varypred argument)
   * Also enhanced to allow groups= and cond= when varying the predictors
   * Corrected bug where sometimes would try to plot confidence limits when conf.int=FALSE was given to Predict
   * Added india, indnl arguments to anova.rms to suppress printing individual tests of interaction/nonlinearity
   * Changed anova.rms so that if all non-summary terms have (Factor+Higher Order Factor) in their labels, this part of the labels is suppressed (useful with india and indnl)

Changes in version 3.3-0 (2011-02-28)
   * In survplot.rms, fixed bug (curves were undefined if conf='bands' and labelc was FALSE)
   * In survfit.cph, fixed bug by which n wasn't always defined
   * In cph, put survival::: on exact fit call
   * Quit ignoring zlim argument in bplot; added xlabrot argument
   * Added caption argument for latex.anova.rms
   * Changed predab to not print summaries of variables selected if bw=TRUE
   * Changed predab to pass force argument to fastbw
   * fastbw: implemented force argument
   * Added force argument to validate.lrm, validate.bj, calibrate.default, calibrate.cph, calibrate.psm, validate.bj, validate.cph, validate.ols
   * print.validate: added B argument to limit how many resamples are printed summarizing variables selected if BW=TRUE
   * print.calibrate, print.calibrate.default: added B argument
   * Added latex method for results produced by validate functions
   * Fixed survest.cph to convert summary.survfit std.err to log S(t) scale
   * Fixed val.surv by pulling surv object from survest result
   * Clarified in predict.lrm help file that doesn't always use the first intercept
   * lrm.fit, lrm: linear predictor stored in fit object now uses first intercept and not middle one (NOT DOWNWARD COMPATIBLE but makes predict work when using stored linear.predictors)
   * Fixed argument consistency with validate methods   

Changes in version 3.2-0 (2011-02-14)
   * Changed to be compatible with survival 2.36-3 which is now required
   * Added logLik.rms and AIC.rms functions to be compatible with standard R
   * Fixed oos.loglik.Glm
   * Fixed bootcov related to nfit='Glm'
   * Fixed (probably) old bug in latexrms with strat predictors

Changes in version 3.1-0 (2010-09-12)
   * Fixed gIndex to not use scale for labeling unless character
   * Changed default na.action in Gls to na.omit and added a note in the help file that na.delete does not work with Gls
   * Added terms component to Gls fit object (latex was not working)
   * Added examples in robcov help file testing sandwich covariance estimator
   * Added reference related to the effects package under help file for plot.Predict
   * Added more examples and simulations to gIndex
   * Fixed ancient bug in lrm.fit Fortran code to handle case where initial estimates are nearly perfect (was trying to step halve); thanks: Dan Hogan
   * Changed survdiffplot to use gray(.85) for bands instead of gray(.95)
   * Fixed formatting problem in print.psm
   * Added prStats and reVector functions to rmsMisc.s
   * Changed formatting of all print.* functions for model fits to use new prStats function
   * Added latex=TRUE option to all model fit print methods; requires LaTeX package needspace
   * Re-wrote printing routines to make use of more general model
   * Removed long and scale options from cph printing-related routines
   * Prepare for version 2.36-1 of survival package by adding censor=FALSE argument to survfit.coxph
   * Added type="ccterms" to various predict methods
   * Made type="ccterms" the default for partial g-indexes in gIndex, i.e., combine all indirectly related (through interactions) terms
   * Added Spiegelhalter calibration test to val.prob
   * Added a check in cph to trigger an error if strata() is used in formula
   * Fixed drawing of polygon for shaded confidence bands for survplot.survfit (thanks to Patrick Breheny <patrick.breheny@uky.edu>)
   * Changed default adjust.subtitle in bplot to depend on ref.zero, thanks to David Winsemius <dwinsemius@comcast.net>
   * Used a namespace and simplified referenced to a few survival package functions that survival actually exports

Changes in version 3.0-0 (2010-05-16)
   * Made Gls not store data label() in residuals object, instead storing a label of 'Residuals'
   * Fixed handling of na.action and check for presence of offsets in Glm
   * Added type="cterms" to predict methods; computes combined terms for main effects + any interaction terms involving that main effect; in preparation for new geffects function
   * Added GiniMd and gIndex functions
   * Change lrm (lrm.fit) to use the middle intercept in computing Brier score
   * Added 3 g-indexes to lrm fits
   * Added 1 g-index to ols, Rq, Glm, Gls fits
   * Added 2 g-indexes to cph, psm fits
   * Added g to validate.ols, .lrm, .cph, .psm, but not to validate.bj
   * Added print.validate to set default digits to 4
   * Changed validate.lrm to compute 3 indexes even on ordinal response data

Changes in version 2.2-0 (2010-02-23)
   * Added levels.only option to survplot.* to remove variablename= from curve labels
   * Added digits argument to calibrate.default
   * Added new ref in val.prob help page
   * Corrected location of dataset in residuals.lrm help page (thanks frederic.holzwarth@bgc-jena.mpg.de)
   * Fixed latex.rms to latex-escape percent signs inside value labels
   * Added scat1d.opts to plot.Predict
   * Changed method of specifying variables to vary by not requiring an equals sign and a dot after the variable name, for Predict, summary, nomogram, gendata, survplot.rms
   * Added factors argument to Predict to handle the above for survplot
   * Made gendata a non-generic function, changed the order of its arguments, removed editor options, relying on R de function always
   * Thanks to Kevin Thorpe <kevin.thorpe@utoronto.ca> to make latex.summary.rms and latex.anova.rms respect the table.env argument
   * Fixed bug in calibrate.default related to digits argument
   * Re-wrote bplot to use lattice graphics (e.g., levelplot contourplot wireframe), allowing for multiple panels for 3-d plots
   * Changed all Rd files to use {arg1,arg2,...} instead of having empty {}

Changes in version 2.1-0 (2009-09-30)
   * Made Predict not return invisibly if predictors not specified
   * New option nlines for plot.Predict for getting line plots with 2 categorical predictors
   * Added rename option to rbind.Predict to handle case where predictor name has changed between models
   * Added ties=mean to approx( ) calls that did not have ties= specified
   * Added nlevels argument to bplot to pass to contour
   * Added par argument to iLegend - list to pass to par().
   * Redirected ... argument to iLegend to image( ).
   * Fixed groupkm - was printing warning messages wrongly
   * Added new semiparametric survival prediction calibration curve method in val.surv for external validation; this is the first implementation of smooth calibration curves for survival probability validation with right-censored data
   * Fixed calibrate confidence limits from groupkm
   * Added smooth calibration curve using hare (polspline package) for calibrate.cph and calibrate.psm
   * Added display of predicted risks for cph and psm models even for the stratified KM method (old default)