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`Design`

Package Change Log Version up to Here Used for S-Plus 2000

9Jun Fixed problem with units in Design() Enhanced Design.trans to respect units attribute Enhanced specs.Design to use units attribute 21Jun Fixed Design() to not treat an ordered factor variable as scored() unless all its levels are legal numerics 24Jun Changed .First.lib to use correct path if not in SHOME 30Jun Changed plot.Design to respect val.lev when x is not a factor 30Jul Fixed bug in Varcov.glm that caused improper confidence limits plotted with plot.Design, and other problems (found by Bill Cox) 3Aug Fixed line wrapping in Overview help file for Unix (Tim Hesterberg) 16Aug Fixed bug in digits and row names in latex.anova.Design 19Aug Made lrtest test for fit failures Changed datadensity.plot.Design issue warnings instead of stop when there is a variable name mismatch Fixed bug in Dialog.Design not passing where= to Dialog.data.frame 17Sep Added to fastbw the ability to compute R^2 for ols fits. For all fits, also now stores a matrix of coefficients for all models in the result ("Coefficients"). 18Sep Added val.surv function (see val.prob). Augmented survest.psm and .cph with what='parallel'. val.surv is used to check calibration of survival models in external datasets using Cox-Snell residuals and related methods

Version up to here used for SP2000 service release

28Oct Added to contrast the ability to specify only one list of predictor settings, to facilitate getting C.L. for averages of predictions when one predictor is varied Fixed bug in contrast for SP2000 where table() returns an object with a dim even if a vector 18Nov Fixed subtitle in plot.pentrace 19Nov Changed all class to oldClass, unclass to oldUnclass, defined these functions for pre-S+ 2000 users. Done for compatibility with S-Plus 5.x 20Nov Fixed problem in Hmisc [.factor to caused strat() information to be lost for cph. Problem appeared when data had NAs and model frame was run through na.delete. 27Nov Changed nomogram.Design to preserve certain character variables (lims, adj). Allows nomogram to work with asis variables that underneath are character strings/factors. 29Nov Took labcurve out of help/List 8Dec Fixed bug in fastbw introduced when R^2 was added, that surfaced when bootstrapping (Thanks to Rob Balshaw balshaw@synectics.bc.ca) 23Dec Changed wording in output of val.prob re: grouped proportions Fixed bug in predab.resample that surfaced from using calibrate.cph with bw=T: predab.resample was c()'ing original fit$terms to fit object from fitter for resample, system was finding terms from fitter (no Design info). Thanks to Fredrik Lundgren <fredrik.lundgren@norrkoping.mail.telia.com

Used for S-Plus 6.1

7May Fixed survest.cph to check for absence of estimates from summary.survfit caused by user requesting times where limited data for one or more strata 15May Removed na.keep na.delete na.detail.response from Design (in Hmisc) Version used for Design_1.0.zip 20May Changed print(data frame) to print(as.matrix) in print.contrast 22May For R, changed fastbw to not use .Fortran('avia') - kept getting segmentation fault Changed summary.Design to use fit$formula instead of fit$terms 24May Fixed bug in print.lrtest (Thanks Carl Moons) 27May Changed survreg.auxinfo to treat t=0 as special case for hazard for Weibull distribution Changed survest.psm to set lower=upper=1 at t=0 for what='survival' Added fail=FALSE to psm for .R.,.SV4. Created R 1.0-1 30May Fixed use of getOldDesign in latex.cph, specs Changed anova.Design to store formula(fit) instead of formula(fit$terms) - to work with R on old fit objects. Added formula.Design for R (=formula.default) to faciliate this. Changed predict.Design for R to pass to delete.response the result of terms(formula(fit)) rather than terms(fit$terms). Was resulting in invalid formula object. Write oldDesignFit2R (in Design.Misc.s) to convert old Design fit objects to work in R (especially when read by read.S). Fixes problem with old ols stats object not having Sigma. Changed to as.character(formula(fit))[2], sep='') from as.character(fit$formula)[2], sep='') in summary.Design 2Jun Changed print.nomogram.Design print as matrix for R (R would not let me put all blanks for row.names) 4Jun Changed psm and related functions to sense existence of survReg in S-Plus instead of relying on .SV4. (also bootcov, calibrate.psm, pentrace, pphsm, print.psm, survest.psm, validate.psm Fixed Design() to handle weights. Checked for psm. 5Jun Changed psm to use sum of weights in calc of R^2 instead of N if weights present 6Jun Added case weights to lrm for R 16Jun Changed R help files to use \dontrun instead of if(FALSE) 25Jun Fixed fitPar to look for 'ols' in fit$fitFunction in addition to 'class'; verified Dialog works for S+ 6.1 for Windows 16Jul Fixed bug in plot.Design when plotting all variables and an interaction term is in the middle; was relying on variable numbers rather than names in adj[[]]. Thanks:David Wiltsee <david.wiltsee@merrickbank.com> 21Jul plot.Design method='dotchart' - not format( ) character values; allows right-justification 30Jul Fixed bug in survplot.psm.residuals.censored - had misspelled lognormal so that x-variable not antilogged before passed to theoretical distribution Fixed left margin calculation in plot.summary.Design 31Jul Intercepted logic in predict.Design for type='terms' when center.terms=T to remove an intercept from first element of adjto if not in first column of X (fixes problem for lrm) Also fixed updating of missing(non.slopes). Fixed all fitting functions for R by temporarily overriding default drop=T for [.factor and by specifying drop.unused.levels to model.frame.default; R was giving invalid model frame (wrong levels at integer values) when levels changed inside model.frame.default execution Finished changing all T, F to TRUE, FALSE for R CMD CHECK 16Aug Fixed glmD for S-Plus by keeping fitFunction component and using only one class for SV4 26Aug Fixed bug in print.lrtest, to return nothing, to avoid infinite loop. Thanks: Xin Wang <xwang@virginia.edu> 2Oct Changed plot.anova.Design to use dotchart2 instead of dotchart, add plotmath usage for R 8Oct Added plotmath for plot.Design by calling labelPlotmath, added inclusion of units in plot labels Checked for existence of .Random.seed in predab.resample before printing it 3Nov For R changed survplot.survfit, survplot.Design to set par(xpd=NA) if n.risk and y.n.risk specified 15Nov Incorporated Bill Pikounis' <v_bill_pikounis@merck.com> improvements in bootcov that allow both cluster and group to be specified. 22Nov Fixed bug in lrm when NAs and offset were both present. Thanks: Stefano Calza <stefano.calza@unimi.it> 23Nov Did this also for psm, cph Fixed predict.Design to work with offset variables for R (and probably S-Plus). Added function addOffset4ModelFrame to add an offset variable to a data frame if it's not already there, default value = 0 (and warning, as user did not define offset) Fixed loop over resulting model frame to ignore offset var. 24Nov Improved bootcov to include a fitter for glm (for glmD fits) Thanks: Fredrik Lundgren <fredrik.lundgren@norrkoping.mail.telia.com> Fixed glmD to include assign, to make anova, summary, etc. work Improved plot.Design to use R plotmath for ylab=X * Beta Fixed bootcov for S-Plus, to address fact that glm.fit needs something as family= other than what glm stores in fit object. 26Nov Put glmD before glm in class or fitFunction, wrote print.glmD, summary.glmD. Moved glmD code to new glmD.s Augmented lrtest to get deviance and null.deviance instead of stats for glmD fits 1Dec Changed lrm to incorporate weights (like R) for SV4 (S+ 6.x) 2Dec Fixed class of glmD object for non-SV4 S-Plus. Fixed tlab in summary.Design from empty scale attr for glmD fits. Thanks: Fredrik Lundgren 6Dec Wrote oos.loglik for glmD to allow bootcov to do simultaneous CLs. Thanks: Fredrik Lundgren Wrote oos.loglik.Design dispatcher for SV4 Renamed predict.Design predictDesign, wrote predict.Design as dispatcher. predict.lrm etc. were not getting called in SV4 Added predict.bj, .ols, .cph, .psm, .glmD, make them call predictDesign Also changed gendata, nomogram.Design, plot.Design, summary.Design, survfit.cph.s to call predictDesign Changed all T and F in help files to TRUE and FALSE 7Dec Several fixes in validate.tree, especially for tree() fits Thanks: Constantinos Kallis <C.Kallis@warwick.ac.uk> Changed panel.Dotplot to make y as.numeric(y) up front 12Dec One more fix in validate.tree. Thanks: C Kallis 22Dec Changed name of all fi= arguments in latex methods to file= 27Dec Added README files on web server s/library/splus6 .zip files 31Dec Version 1.1-1 for Unix,Linux,Windows put on web site. CHECK FOR SYSTEMATIC R DIFFERENCE: missing(arg) is updated

First port to S-Plus 6 for Windows by Insightful since 6.0 appeared

3Apr Fixed bug in plot.Design allowing partial matching of Limvals$values names. Thanks: Leping Zhou <leping.zhou@wachovia.com> 7Apr Improved plot.Design: if 'time' is a predictor and time= was specified, put time= in dotlist. Use length rather than missing(time) to sense time specified. Set time=NULL if put in dotlist. 8Apr Fixed contrast.Design to define db=da if b omitted, to avoid later error message 9Apr Added if(.R.) { plot.new(); par(new=TRUE)} for plot.summary.Design 16Apr Added univarLR in Design.Misc: computes all univariable LR chi-square statistics from a Design multivariable additive fit Wrote glsD, Design's implementation of gls in nlme, with cluster bootstrapping. Debugged for R. 24Apr Changed survplot.survfit, survplot.Design to always issue par(xpd=NA) ro R 25Apr Fixed validate.cph to allow for null models (2 lines changed) Thanks: Hyung Kim <kimhyung@mednet.ucla.edu> In calibrate.cph used cph with only strat predictor if NULL model Changed groupkm to give NA result if stratum has only 1 obs (before used 0 obs) 4May Fixed bug in latex.anova.Design to properly typeset is.na P values as '' 6May Fixed datadist for ordered factors caused by bug in S-Plus 6 on Linux: sort(c(1,2,3,NA)) == 1:3 Put warning message in Design if ordered factor is used without scored() and options(contrasts)[2] is not 'contr.treatment'. Thanks: Leping Zhou <leping.zhou@wachovia.com>

VERSION PORTED TO S-Plus 6 on Windows BY INSIGHTFUL CORP

16May Changed axisf in nomogram.Design for R, as R wasn't really passing cex to axis. Used par(cex) for R. 10Jul Re-wrote text.anova.Design, removed restrictions, changed x y arguments to at= 20Jul Fixed nomogram.Design for R 1.8 (R-devel); can no longer do dataframe[1:n,] <- otherdataframe where otherdataframe his more than one row and dataframe has one row (to duplicate obs); changed to do this with a list and rep 28Jul Similar change for summary.Design Changed predab.resample to not print .Random.seed

VERSION USED FOR CRAN 2.0-0, Splus6, Splus2000

6Oct Fixed big bug in vif - removed solve( ). Thanks: John Fox <jfox@mcmaster.ca>,Rajarshi Guha <rxg218@psu.edu> 16Oct NOTE: Problem in predictDesign if ordered factor used but not used with scored( ). model.matrix(Terms or Terms.ns) returns wild values, reason unknown. Need to explicitly use scored. Thanks: Wilson Wang <xwang@arcturusag.com> 17Oct Changed non-standard keywords in help files for R to \concept{} 22Nov Fixed bug in summary.Design introduced in sep03- reordered where xadj duplicated Thanks: Emir Veledar <eveleda@emory.edu> 16Dec Removed formula.Design from Design.Misc.s Thanks: Kurt.Hornik@wu-wien.ac.at

- 5Jan
- Changed
`cph`

to work with namespaces in R by adding`getN`

function to invoke`getFromNamespace`

when needed

Removed logic in`Design()`

to deal with`cluster( )`

variables with`cph`

.`term.labels`

may be incorrect length due to its not including offsets in R. - 6Jan
- In
`predict.cph`

made`non.slopes`

default to`NULL`

(was no default). Same for`predictDesign`

. Thanks: Mike Kattan; Also for`incl.non.slopes`

- 12Jan
- For R fixed
`bj, cph, groupkm, survfit, val.prob`

to get`survfit.km`

from`survival`

namespace if needed - 19Jan
- Changed
`psm`

and`survreg.fit2`

in`validate.psm`

to get`survreg.fit`

from namespace for`survival`

if needed for R - 7Feb
- Changed
`Function.Design`

for SV4 to internally sense if Cox model and take intercept = - centering constant. Changed intercept logic to sense length rather than`missing( )`

. Thanks: Mike Kattan (KattanM@MSKCC.ORG) - 8Feb
- Fixed
`survfit.cph`

,`survfit.cph.null`

for S-Plus 6.2 and later, to include`weights`

argument to`agsurv2`

. Thanks: Krista Kilmer (kkilmer@insightful.com) - 3Mar
- Removed conversion of design matrix
`X`

in`ols`

to single precision for S-Plus. Thanks: Patrick Aboyoun (aboyoun@insightful.com) - 12Mar
- Fixed bug in
`addOffset4ModelFrame`

for`predictDesign`

- 15Mar
- Fixed
`survest.cph`

to not run result through`naresid`

if`newdata, x, linear.predictors`

not specified. Was messing up`validate.cph`

if original data had`NA`

. Replaced`glsD`

with modified version by Patrick Aboyoun aboyoun@insightful.com that makes`glsD`

work with S-Plus6 in addition to R - 18Mar
- Changed
`cox.zph`

to make it work with frailty models when object is from`coxph`

. Thanks: Patrick Aboyoun - 29Mar
- Added
`theta`

,`phi`

,`ticktype`

arguments to`plot.Design`

for R when`method='persp'`

. Thanks: osman.al.radi@utoronto.ca - 21Apr
- Put the project in
**CVS**at http://biostat.mc.vanderbilt.edu:/usr/local/cvs - 28Apr
- Removed
`ticktype`

and replaced it with the more general`perspArgs`

which can be a list of any extra arguments to pass to`persp`

for R or S-Plus

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Topic revision: r7 - 06 May 2004, ColeBeck

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