Changes in version 4.3-0 (2015-02-15)
* contrast.rms: added 3rd and 4th list of predictor settings to allow for double-difference (interaction) contrasts
* predictrms: don't call vcov if no covariates present (e.g. cph strata only)
* print.summary.rms, latex.summary.rms: print more significant digits for effect-related columns
* robcov, bootcov: added new object clusterInfo in the fit object
* all fitting functions: print method prints clusterInfo
* residuals.lrm: negated Li-Shepherd residuals to make them correct
* residuals.orm: put in namespace and added examples from Qi Liu
* plot.calibrate: added par.corrected so user can specify graphics parameters for plotting overfitting-corrected estimates
* robcov: dropped unused levels from cluster so that clusterInfo is correct
* plot.Predict: added example in help file for how to set lattice graphics parameters
* datadist: quit rounding quantiles to integers if raw data were integer
* predictrms, Predict: fixed bug with ref.zero=TRUE and with handling Cox models; added new test code in tests/cph3.r
* cph, dxy.cens: fixed bug - Dxy was negative of what it should have been for cph. Thanks: Irantzu Barrio
* ggplot.Predict: new function for ggplot2 graphics for Predict objects
* contrast.rms: added ... for print method (e.g., to allow digits=4)
* survplot: raredd fixed bug with 1 observation per group - see http://stackoverflow.com/questions/24459078/error-message-when-ploting-subjects-at-risk-with-survplot
* latex.rms: changed notation for indicator variables from {} to [] a la Knuth
* latex.anova.rms: stopped putting d.f. and Partial SS in math mode
* npsurv: neatened help file
* residuals.orm: fixed bug for score residuals. This fixed robcov.
* orm-residuals.r: new test code
* vcov.orm: handled case where fit was run through robcov
* print: for LaTeX fixed prStats to translate clustering variable to LaTeX
* vcov.orm: handled case where fit was run through bootcov
* bootcov: for orm stored intercepts attribute in var
* tests: new test for orm bootcov
* contrast, vcov.orm: made to work if fit run through robcov, bootcov
* print.anova.rms: fixed bug with subscripts,names,dots
Changes in version 4.2-1 (2014-09-18)
* plot.summary.rms: allowed a vector for lwd, and passed lwd to confbar. Thanks: Michael Friendly
* gendata: Starting in R 3.1.0, as.data.frame.labelled or as.data.frame.list quit working when length vary; workaround
* predictrms, ols: handle offset in formula. Thanks: Max Gordon
* pentrace: neatened code, added new argument noaddzero if user wants to prevent unpenalized model from being tried; add new test script in tests
* bplot: fixed bug whereby xlabrot was ignored. Thanks: Sven Krackow ; new test for bplot in tests directory
* plot.Predict: fixed bug in which 2nd argument to perim was not correct
* validate.ols: Shane McIntosh fixed the passing of the tolerance argument to predab.resample
* predictrms: computed offset earlier so always defined no matter the value of type
* plot.Predict: added scaletrans argument, fixed use of subscripts in pan
* lrm, lrm.fit: added scale argument
* orm, orm.fit: added scale argument
* vcov.orm: accounted for scale when extracting covariance matrix
* npsurv: was not passing type argument
* npsurv: start storing all classes created by survfit.formula
* logLik.Gls: added. Makes AIC(Gls object) work.
* NAMESPACE: several changes
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
* 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 )
* 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
* Fixed bug in survdiffplot where conf.int was always overridden by value from survfit. Thanks: Kamil Fijorek
* 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 )
* 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 )
* 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
* 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 ); 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
* 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 )
* Changed default adjust.subtitle in bplot to depend on ref.zero, thanks to David Winsemius
* 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 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)