r-cran-rms 4.2-0-2 / usr / lib / R / site-library / rms / NEWS

Changes in version 4.2-0 (2014-04-13)
   * Deprecated survfit.formula so would not overlap with function in survival
   * Added function npsurv, survplot.npsurv
   * REMOVED survfit.formula
   * Used new type argument to label.Surv for fitting functions
   * cph: added weights argument to residuals.coxph (Thanks: Thomas Lumley)
   * survfit.cph: fixed bug in using wrong type variable.  Thanks: Zhiyuan Sun
   * cph: added weighted=TRUE in call to residuals.coxph (Thanks: T Lumley)
   * orm.fit: improved ormfit to not try to deal with NaN in V, assuming that step-halving will happen

Changes in version 4.1-3 (2014-03-02)
   * num.intercepts: removed (is in Hmisc)
	 * survfit.formula, cph, psm: changed to use inputAttributes attribute of Surv objects (introduced earlier in survival package so that rms could drop its customized Surv function)
   * Exported survfit.formula
   * Changed survival fitting functions and residuals to use units.Surv

Changes in version 4.1-2 (2014-02-28)
   * psm: Fixed bug to allow computation of Dxy with left censoring
   * val.prob: Fixed recently introduced bug that made calibration intercept and slope always 0,1.  Thanks: Lars.Engerstrom@lio.se
   * plot.Predict: added between to leave space between panels
   * orm.fit: fixed error in kmid calculation when heavy ties at first level of y.  Thanks: Yuwei Zhu
   * setPb: changed default to now use tktcl to show progress bars for simulations
   * predictrms: fixed bug with type='terms'
   * val.surv: handle case where survival estimates=0 or 1 when using log-log transform

Changes in version 4.1-1 (2014-01-22)
   * Removed use of under.unix in anova.rms, latex.summary, plot.nomogram
   * Removed use of oldUnclass, oldClass, is.category
   * Fixed class of Rq object; had failed with bootcov.  Thanks: Max Gordon
   * survplot: preserved par()
   * Srv: removed, changed all uses to Surv() for new survival package that preserves attributes for Surv inputs
   * survplot.survfit, survdiffplot: added conf='diffbands'
   * predictrms: fixed num. intercepts calculation order
   * survplot, survdiffplot: used original standard error for survdiffplot, and fun
   * dyx.cens: allow left-censoring

Changes in version 4.1-0 (2013-12-05)
   * 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@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@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 random.  Thanks: Kirsen Van Hoorde <Kirsten.VanHoorde@esat.kuleuven.be>
   * Fixed bug in survdiffplot where conf.int was always overridden by value from survfit.  Thanks: Kamil Fijorek <kamilfijorek@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:::

Changes in version 4.0-0 (2013-07-10)
   * Cleaned up label logic in Surv, made it work with interval2 (thanks:Chris Andrews)
   * Fixed bug in val.prob - wrong denominator for Brier score if obs removed for logistic calibration
   * Fixed inconsistency in predictrms where predict() for Cox models used a design matrix that was centered on medians and modes rather than means (thanks: David van Klaveren <d.vanklaveren.1@erasmusmc.nl>)
   * Added mean absolute prediction error to Rq output
   * Made pr argument passed to predab.resample more encompassing
   * Fixed logLik method for ols
   * Made contrast.rms and summary.rms automatically compute bootstrap nonparametric confidence limits if fit was run through bootcov
   * Fixed bug in Predict where conf.type='simultaneous' was being ignored if bootstrap coefficients were present
   * For plot.Predict made default gray scale shaded confidence bands darker
   * For bootcov exposed eps argument to fitters and default to lower value
   * Fixed bug in plot.pentrace regarding effective.df plotting
   * Added setPb function for pop-up progress bars for simulations; turn off using options(showprogress=FALSE) or options(showprogress='console')
   * Added progress bars for predab.resample (for validate, calibrate) and bootcov
   * Added bootBCa function
   * Added seed to bootcov object
   * Added boot.type='bca' to Predict, contrast.rms, summary.rms
   * Improved summary.rms to use t critical values if df.residual defined
   * Added simultaneous contrasts to summary.rms
   * Fixed calculation of Brier score, g, gp in lrm.fit by handling special case of computing linear predictor when there are no predictors in the model
   * Fixed bug in prModFit preventing successful latex'ing of penalized lrms
   * Removed \synopsis from two Rd files
   * Added prmodsel argument to predab.resample
   * Correct Rd files to change Design to rms
   * Restricted NAMESPACE to functions expected to be called by users
   * Improved Fortran code to use better dimensions for array declarations
   * Added the basic bootstrap for confidence limits for bootBCa, contrast, Predict, summary
   * Fixed bug in latex.pphsm, neatened pphsm code
   * Neatened code in rms.s
   * Improved code for bootstrapping ranks of variables in anova.rms help file
   * Fixed bug in Function.rms - undefined Nam[[i]] if strat.  Thanks: douglaswilkins@yahoo.com
   * Made quantreg be loaded at end of search list in Rq so it doesn't override latex generic in Hmisc
   * Improved plot.summary.rms to use blue of varying transparency instead of polygons to show confidence intervals, and to use only three confidence levels by default: 0.9 0.95 0.99
   * Changed Surv to Srv; use of Surv in fitting functions will result in lack of time labels and assumption of Day as time unit; no longer override Surv in survival
   * Changed calculation of Dxy (and c-index) to use survival package survConcordance service function when analyzing (censored) survival time; very fast
   * Changed default dxy to TRUE in validate.cph, validate.psm
   * Dxy is now negated if correlating Cox model log relative hazard with survival time
   * Removed dxy argument from validate.bj as it always computed
   * Added Dxy to standard output of cph, psm
   * Added help file for Srv
   * Removed reference to ps.slide from survplot help page
   * Added the general ordinal regression fitting function orm (and orm.fit) which efficiently handles thousands of intercepts because of sparse matrix representation of the information matrix; implements 5 distribution families
   * Added associated functions print.orm, vcov.orm, predict.orm, Mean.orm, Quantile.orm, latex.orm, validate.orm
   * Changed predab.resample to allow number of intercepts from resample to resample
   * Fixed bug in Mean.cph (thanks: Komal Kapoor <komal.bitsgoa@gmail.com>)
   * Removed incl.non.slopes and non.slopes arguments from all predict methods
   * Changed all functions to expect predict(..., type='x') to not return intercept columns, and all fitting functions to not store column of ones if x=TRUE
   * Changed nomogram argument intercept to kint, used default as fit$interceptRef
   * Made bootcov behave in a special way for orm, to use linear interpolation to select a single intercept targeted at median Y
   * Revamped all of rms to never store intercepts in design matrices in fit objects and to add intercepts on demand inside predictrms
   * Added new function generator ExProb to compute exceedance probabilities from orm fits

Changes in version 3.6-3 (2013-01-11)
   * Added Li-Shepherd residuals in residuals.lrm.s, become new default (same as ordinary residuals for binary models)
   * Remove glm null fit usage as this is no longer in R

Changes in version 3.6-2 (2012-12-09)
   * bootcov, predab.resample: captured errors in all fits (to ignore bootstrap rep) using tryCatch.  Thanks: Max Gordoin <max@gforge.se>
   * predab.resample: made as.matrix(y) conditional to handle change in the survival package whereby the "type" attribute did not exist for a matrix
   * anova.rms: added new parameter vnames to allow use of variable labels instead of names in anova table; added vinfo attribute
   * residuals.lrm: removed intercept from partial residuals for binary models
   * moved comprehensive examples in rmsOverview to ~/rms/demo/all.R; greatly speeds up package checking but demo needs to be run separately for better checking, using demo(all, 'rms')
   * Fixed survfit.formula to not use .Global environment

Changes in version 3.6-1 (2012-11-05)
   * bootcov: set loglik to default to FALSE and added code to fill in missing intercepts in coef vector for prop. odds model when levels of Y not resampled; see coef.reps to default to TRUE
   * Predict: implemented fun='mean' to get proper penalty for estimating the mean function for proportional odds models
   * Added usebootcov argument to Predict to allow the user to force the use of bootstrap covariance matrix even when coef.reps=TRUE was in effect for bootcov

Changes in version 3.6-0 (2012-10-26)
   * Gls: Updated optimization calls - had become inconsistent with gls and failed if > 1 correlation parameter (thanks: Mark Seeto <markseeto@gmail.com>); removed opmeth argument
   * print.fastbw: added argument: estimates
   * survplot.survfit: handled fact that survival:::summary.survfit may not preserve order of strata levels.  Also fixed survit.cph and cph; Thanks: William.Fulp@moffitt.org
   * plot.Predict: added example showing how to rename variables in plot
   * print(fit object, latex=TRUE): added latex.naprint.delete, used new Hmisc latexDotchart function to make a dot chart of number of NAs due to each model variable if at least 4 variables have NAs
   * added trans argument to plot.anova.rms to allow transformed scales
   * Corrected cph to use model.offset(); thanks: Simon Thornley <s.thornley@auckland.ac.nz>
   * Changed latex.anova.rms to use REGRESSION instead of TOTAL label
   * Changed gendata, contrast.rms to allow expand=FALSE to prevent expand.grid from being called to generate all combinations of predictors
   * Added type= to plot.Predict to allow user to specify a different default line/point type (especially useful when x is categorical)
   * Corrected bug in offset in psm - made default offset the length of X
   * Corrected bug in calibrate.psm (fixed -> parms)
   * predab.resample, calibrate.cph, calibrate.default, calibrate.psm: stopped putting results from overall initial fit into .Global and instead had predab.resample put them in attribute keepinfo, obtained from measure() 

Changes in version 3.5-0 (2012-03-24)
   * contrast.rms: saved conf.type and conf.int in returned object, added to print method
   * Added debug= to predab.resample so user can see all the training and test sample subscripts
   * Added validate.Rq function
   * Fixed bug in Rq that caused 2 copies of fitted.values to be in fit object, which caused fit.mult.impute to double fitted.values
   * Added how to reorder predictors if using plot(Predict(fit))
   * Added new function perlcode written by Jeremy Stephens and Thomas Dupont; converts result of Function to Perl code
   * Fixed partial argument matches in many functions to pass new R checks
   * Changed matrx and DesignAssign to allow validate.Rq to consider null models; neatened code

Changes in version 3.4-0 (2012-01-17)
   * psm: fixed logcorrect logic (thanks: Rob Kushler)
   * Added suggested package multcomp (required for simultaneous CLs)
   * Implemented simultaneous confidence intervals in Predict, predictrms, contrast.rms, all specific model predict methods
   * Add multiplicity adjustment for individual confidence limits computed by contrast.rms, to preserve family-wise coverage using multcomp package
   * Improved rbind.Predict to preserve order of groups as presented, as levels of .set.
   * Added example for plot.Predict showing how to suppress predictions for certain intervals/groups from being plotted
   * Added example in plot.Predict help file for graphing multiple types of confidence bands simultaneously

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)