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)