version 5.1-3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Hmisc
-Version: 5.1-2
-Date: 2024-03-09
+Version: 5.1-3
+Date: 2024-05-18
 Title: Harrell Miscellaneous
 Authors@R: 
     c(person(given = "Frank E",
@@ -35,9 +35,9 @@ URL: https://hbiostat.org/R/Hmisc/
 Encoding: UTF-8
 RoxygenNote: 7.3.1
 NeedsCompilation: yes
-Packaged: 2024-03-11 15:06:48 UTC; harrelfe
+Packaged: 2024-05-18 13:26:32 UTC; harrelfe
 Author: Frank E Harrell Jr [aut, cre] (<https://orcid.org/0000-0002-8271-5493>),
   Charles Dupont [ctb] (contributed several functions and maintains latex
     functions)
 Repository: CRAN
-Date/Publication: 2024-03-11 20:50:03 UTC
+Date/Publication: 2024-05-28 07:10:02 UTC

MD5

@@ -1,7 +1,7 @@
 16f8ea43efba90112351c5ecb33021c4 *COPYING
-1bd8e536b9bdde9eb3f6830006f9244f *DESCRIPTION
-17b85872f3bfe9144b6a327a177eff59 *NAMESPACE
-7485373d9a366e228b5951ebd5fa2677 *NEWS
+77dbeb98ec3ce4c4f0f2afdd5144db1a *DESCRIPTION
+567cedef1920aa3944bac88ae5e528ff *NAMESPACE
+39f3a27fdffa3badf4b28934948e4064 *NEWS
 76f90acbe9bf8ad2eaaa6b8813eb7c82 *R/AFirst.lib.s
 8fdbfa3b900cbbb42d94898093ec7fa5 *R/Cs.s
 314b24f935cf8e2ee7a677ed26479b83 *R/GiniMd.s
@@ -91,7 +91,7 @@ f4cc097babcda3c1edcd60f516713ff2 *R/matxv.s
 4148365f1c827715d531c4e642846410 *R/minor.tick.s
 ce09d5ff43279995bd138ab5dd654bc9 *R/misc.get.s
 32a369e847b95005134970ac15b4ba73 *R/model.frame.default.s
-d42e0a0b549039b88d7d54fce7fcf1fa *R/movStats.r
+a249184df64b5f38d91e174971dc0765 *R/movStats.r
 fc71dbaeeb57983dcfa3ac0497ed837b *R/mtitle.s
 1b91897d110771682243816be35059e1 *R/multLines.s
 97ebbb81148d208a3a8103861390453f *R/nCoincident.r
@@ -113,21 +113,23 @@ a50c8048a7546e224ca402d362c084cd *R/pairUpDiff.r
 abee077f086dd6b61303a1fb0edc3960 *R/popower.s
 a9771408bed89b32b030653ea46a614f *R/princmp.r
 9a1119c7949407c39968645e921a87a6 *R/print.char.list.s
+5e6df449d8b6cd6f06693d7298d47150 *R/printL.r
 efe9a9a6c90594d1e7425cc46f2fc061 *R/pstamp.s
-153a75111ea227762a2e1b7d2a4f9afc *R/qcrypt.r
+21e5f0670676be1ba7b4b2ad135de5e7 *R/qcrypt.r
+f3c43a8d39f1458c92a8d2d7df290d9a *R/r2describe.r
 2679a3e28310299f523e0ffb440db739 *R/rcorr.cens.s
 b9759f7459856f6eeb85e4ee3832f7ad *R/rcorr.s
 4bbed0ec0b6f43b54b8aa32effb023f5 *R/rcorrp.cens.s
 62264d939e616b9d1dc7070096b679e5 *R/rcspline.eval.s
 49063eb427181ee3016444380b8009cf *R/rcspline.plot.s
 42daef400a52ac984cb164ed67d35632 *R/rcspline.restate.s
 1aa8a7124aa396e467f86a42f6651a53 *R/reShape.s
-e02e7a855771dc46eecf99d2e1fedd66 *R/redun.s
+11e4c341765e538b58c4eb746814f792 *R/redun.s
 02946450a1d09319cea2cef1c360336a *R/reformM.r
 41b180f15250bedd222f2c334d13eb1f *R/regexpEscape.s
 a747dcb6f49ebcd6f1e54180e64deaa9 *R/responseSummary.s
 3978f2ee3511549cb906af4618024a53 *R/rm.boot.s
-d2e6a4433b2c8b01ef8615d66428a874 *R/runParallel.r
+223b5153c60f6b5fc5755066399c1561 *R/runParallel.r
 a1763e6429f086dd1783694da9b85342 *R/samplesize.bin.s
 d587d8ed7aee1aa12994f088da565dd8 *R/sas.get.s
 b77bb6020828f4e18cb5a12720911587 *R/scat1d.s
@@ -140,7 +142,7 @@ bfd1c58a14b5451fad603d2a20af2d47 *R/showPsfrag.s
 525a4048d60605a8de57a4db1b684271 *R/solvet.s
 e2e1ee6a263cca9a9f1036cee25dfc69 *R/somers2.s
 06ee4823f5d18fa93e99635bdf21a349 *R/spearman.test.s
-488ef5513ff3aef8c6e8c316a3361d36 *R/spower.s
+ff69c2235a6faeb4021a3bdb0914bb41 *R/spower.s
 a041b2aeb6c6af8ee47770b504538849 *R/src.s
 a3ca370ec684fbeeb54d0e7f489a7377 *R/stat-plsmo.r
 b47544f6b133f394f2fda329de60f733 *R/strgraphwrap.s
@@ -159,7 +161,7 @@ fc25014d239f92e9d37936a723d9858e *R/summaryP.s
 eb87b4f621bfa787f568ceca584f9240 *R/tabulr.s
 10578b4a45211889232005d4a67d49f2 *R/testCharDateTime.r
 c1dba69a612fd6fb121adb946a77596e *R/tex.s
-e4536ff8f59f4fc31e1a62182792d9e2 *R/transace.s
+64c2f77a348cee28854c396ba29130a4 *R/transace.s
 93f895d99d674bc46b750b858c758686 *R/transcan.s
 847daf7fa4e67d6641c763a7873df93c *R/translate.s
 91c82b7b8e9ad8cff084bf7b2069d11b *R/units.s
@@ -350,7 +352,7 @@ c2c3d7fd7b6118a5480308fcacb57afa *man/makeNstr.Rd
 5c92f2660d2cd3da53775dddbf20ddf3 *man/meltData.Rd
 ad5ca5884567e50edeba874e3f6e0566 *man/mgp.axis.Rd
 9d0b72af8d419f9a78263abf388a339f *man/minor.tick.Rd
-ef012c8bd400cfd0c77c846f12ab22b1 *man/movStats.Rd
+a647f8b2ac09ca4ddef385a031282e12 *man/movStats.Rd
 7e82c634be90a9db0751e0b9ec78778a *man/mtitle.Rd
 a6c96e43927dc9a895b515d69b8a4346 *man/multLines.Rd
 7d0729fa837191e15480d69e4ed9b2a1 *man/nCoincident.Rd
@@ -375,22 +377,24 @@ ddba6cfbe8781522fad083b7bc2c8b92 *man/princmp.Rd
 52be83076b1f0442cb5ab5c15bb16a3f *man/print.char.list.Rd
 0a25e1c6f349789159b7239ae0f0f620 *man/print.char.matrix.Rd
 1104d753bf0c6c1922c62a5861fcefc0 *man/print.princmp.Rd
-057da98d466a023bda3991abbf880855 *man/prnz.Rd
+7bac2453cdb4b35e558e06e062d3697c *man/printL.Rd
+bf58b8e484991792002b5479808eea55 *man/prnz.Rd
 7cc6decd6cb488bf6ef52ea36a1a349f *man/prselect.Rd
 260137fa18118deb3cf8f5e8cd09801f *man/pstamp.Rd
-1340eec37d1fbe58aea0d343521c3138 *man/qcrypt.Rd
+df90d6541f8e0c8d1a5444fe2274ab57 *man/qcrypt.Rd
+c89285950ff40f6516cabb5521cc41f0 *man/r2describe.Rd
 6595b75b4809474bad712063e08bb0ff *man/rMultinom.Rd
 888b130ec7fd2abd84cd5475170a0814 *man/rcorr.Rd
-8e50a363db2787b941bcdb97b1baa7ba *man/rcorr.cens.Rd
-a32fc84fb8d9077fd571a31ed83e08c8 *man/rcorrp.cens.Rd
+f459db9aa8d263e3e37230490a0f3791 *man/rcorr.cens.Rd
+c91c9b895bf92991301998a7e6f12d5b *man/rcorrp.cens.Rd
 0e09013825fbf352d7b6492af66a2485 *man/rcspline.eval.Rd
 e11508b0ff32c5fb382f41829d2de213 *man/rcspline.plot.Rd
 6857f9694fede7b9cf3986f75e45428e *man/rcspline.restate.Rd
 fa12a16c134db85d6d6afd1f95a70cb2 *man/reShape.Rd
-510751c7450cd75becf41e7589bde573 *man/redun.Rd
+d0079ed71417d0f8de2b29fca654e963 *man/redun.Rd
 a379ec34cf93cb46195c4900c56b4b78 *man/rlegend.Rd
 c123888600428367841f57d2d26e9080 *man/rm.boot.Rd
-8809c7514d68f02c8810386d0a4bab86 *man/runParallel.Rd
+f7e532ece5295a38e93b64603db186c7 *man/runParallel.Rd
 fa34dd6513e9995c87890ff22c320f6c *man/runifChanged.Rd
 326928a75e512ba40912a48fc355934e *man/samplesize.bin.Rd
 89c4eefbaac065e35e5becf8f6e5319d *man/sasxport.get.Rd
@@ -405,11 +409,11 @@ db05fb7a0b4ab6f2e3296104ab70dca1 *man/score.binary.Rd
 c63b29fcce92356968e66f1c66cd9bcd *man/simplifyDims.Rd
 baf8dcee242a5c39c4e6cddfc11b71ad *man/smean.sd.Rd
 32aeaf16b41f0b5cc1f9552b0e8946ff *man/solvet.Rd
-bf3f45e963edf51b7d01878ec1b534c6 *man/somers2.Rd
+ba32fcedcee35f8db3674fcb7fd5182b *man/somers2.Rd
 7a28776c28e986b906cf041f07b4ad74 *man/soprobMarkovOrd.Rd
 40c56a903db1c8731d357d519c2a7e6d *man/soprobMarkovOrdm.Rd
 584eb5885df8361333458acfba0d8165 *man/spikecomp.Rd
-3c8807018f080566a3315b896b562f59 *man/spower.Rd
+9a8ed935151b63601f404fc7df637ae5 *man/spower.Rd
 bcf38fffb93e2739eebe0e21ca00e070 *man/spss.get.Rd
 d63d4d4bd78f7c6e545bc226dfd58481 *man/src.Rd
 0cb5588f043d047c80ae3b90f7b3e6f9 *man/stat_plsmo.Rd

NAMESPACE

@@ -1,4 +1,4 @@
-export("%nin%",.q,abs.error.pred,addggLayers,addMarginal,all.digits,all.is.numeric,approxExtrap,areg,areg.boot,aregImpute,aregTran,arrGrob,as.discrete,asNumericMatrix,ballocation,bezier,binconf,biVar,bootkm,bpower,bpower.sim,bpplot,bpplotM,bpplt,bppltp,bpx,bsamsize,bystats,bystats2,capitalize,catTestchisq,Cbind,ceil,character.table,chiSquare,ciapower,cleanup.import,clowess,cnvrt.coords,code.levels,colorFacet,combine.levels,combineLabels,completer,combplotp,confbar,consolidate,contents,conTestkw,cpower,Cs,csv.get,cumcategory,curveRep,curveSmooth,cut2,datadensity,dataDensityString,dataframeReduce,dataRep,ddmmmyy,deff,describe,discrete,dhistboxp,dotchart2,dotchart3,dotchartp,dotchartpl,Dotplot,drawPlot,dvi,dvigv,dvips,ebpcomp,ecdfpM,Ecdf,ecdfSteps,equalBins,errbar,escapeBS,escapeRegex,estSeqMarkovOrd,estSeqSim,event.chart,event.convert,event.history,expr.tree,extractlabs,fillin,fImport,find.matches,first.word,fit.mult.impute,format.df,format.pval,formatCats,formatCons,formatDateTime,formatdescribeSingle,formatSep,formatTestStats,ftupwr,ftuss,Function,gbayes,gbayes1PowerNP,gbayes2,gbayesMixPost,gbayesMixPowerNP,gbayesMixPredNoData,gbayesSeqSim,get2rowHeads,getabd,getHdata,getLatestSource,GetModelFrame,getRs,getZip,ggfreqScatter,ggplotlyr,GiniMd,Gompertz2,groupn,grType,hashCheck,hdquantile,hidingTOC,hist.data.frame,histbackback,histboxp,histboxpM,histSpike,histSpikeg,hlab,hlabs,hoeffd,html,htmlGreek,htmlSN,htmlSpecial,htmlSpecialType,htmltabv,htmlTranslate,htmlVerbatim,importConvertDateTime,improveProb,impute,impute.transcan,inmChoice,inmChoicelike,intMarkovOrd,inverseFunction,invertTabulated,is.discrete,is.imputed,is.mChoice,is.present,is.special.miss,james.stein,jitter2,keepHattrib,Key,Key2,km.quick,knitrSet,labcurve,label,Label,labelLatex,labelPlotmath,Lag,largest.empty,latestFile,latex,latexBuild,latexCheckOptions,latexDotchart,latexNeedle,latexSN,latexTabular,latexTherm,latexTranslate,latexVerbatim,list.tree,llist,lm.fit.qr.bare,Load,Lognorm2,logrank,lookupSASContents,lrcum,makeNames,makeNstr,makeSteps,mApply,markupSpecs,mask,match.mChoice,matchCases,matrix2dataFrame,matxv,mbarclPanel,mbarclpl,mChoice,mdb.get,Mean,medvPanel,medvpl,meltData,Merge,mgp.axis,mgp.axis.labels,mhgr,minor.tick,monotone,monthDays,movStats,mtitle,multEventChart,multLines,na.delete,na.detail.response,na.include,na.keep,na.pattern,na.retain,naclus,nafitted.delete,Names2names,naplot,napredict.delete,naprint.delete,naprint.keep,naresid.delete,naresid.keep,nCoincident,nFm,nmChoice,nobsY,nomiss,nstr,num.denom.setup,num.intercepts,numeric.string,numericScale,oPar,optionsCmds,ordGridFun,ordTestpo,outerText,pairUpDiff,panel.bpplot,panel.Dotplot,panel.Ecdf,panel.plsmo,panel.xYplot,parGrid,partition.matrix,partition.vector,pasteFit,pBlock,pc1,plotCorrM,plotCorrPrecision,plotp,plotlyM,plotlyParm,plotlySave,plotmathTranslate,plotMultSim,plotpsummaryM,plsmo,pngNeedle,pomodm,popower,posamsize,prepanel.Dotplot,prepanel.Ecdf,prepanel.xYplot,princmp,print.char.matrix,prList,prn,propsPO,propsTrans,prselect,prType,pstamp,putHcap,putHfig,putKey,putKeyEmpty,qcrypt,Quantile,Quantile2,R2Measures,rcorr,rcorr.cens,rcorrcens,rcorrp.cens,rcspline.eval,rcspline.plot,rcspline.restate,rcsplineFunction,read.xportDataload,readSAScsv,redun,reformM,reLabelled,rendHTML,replace.substring.wild,reShape,responseSummary,restoreHattrib,rlegend,rlegendg,rm.boot,rMultinom,roundN,roundPOSIXt,runifChanged,runParallel,samplesize.bin,sas.codes,sas.get,sas.get.macro,sasdsLabels,sasxport.get,Save,scat1d,score.binary,sedit,sepUnitsTrans,seqFreq,setParNro,setTrellis,show.col,show.pch,showPsfrag,simMarkovOrd,simplifyDims,simPOcuts,simRegOrd,sKey,smean.cl.boot,smean.cl.normal,smean.sd,smean.sdl,smearingEst,smedian.hilow,solvet,somers2,soprobMarkovOrd,soprobMarkovOrdm,spearman,spearman.test,spearman2,spikecomp,spower,spss.get,src,stat_plsmo,stata.get,StatPlsmo,stepfun.eval,stratify,strgraphwrap,string.bounding.box,string.break.line,stringDims,stripChart,subplot,substi,substi.source,substring.location,substring2,summarize,summaryD,summaryDp,summaryM,summaryP,summaryRc,summaryS,symbol.freq,sys,t.test.cluster,table_formatpct,table_freq,table_latexdefs,table_N,table_pc,table_trio,tabulr,termsDrop,testCharDateTime,testDateTime,tex,tobase64image,transace,transcan,translate,trap.rule,trellis.strip.blank,truncPOSIXt,uncbind,units,unPaste,upData,upFirst,valueLabel,valueName,valueTags,valueUnit,var.inner,varclus,vlab,Weibull2,whichClosek,whichClosePW,whichClosest,wtd.Ecdf,wtd.loess.noiter,wtd.mean,wtd.quantile,wtd.rank,wtd.table,wtd.var,xInch,xless,xy.group,xYplot,xySortNoDupNoNA,yearDays,yInch,ynbind,zoom,"[<-.discrete","consolidate<-","is.na<-.discrete","label<-","length<-.discrete","substring2<-","valueLabel<-","valueName<-","valueTags<-","valueUnit<-")
+export("%nin%",.q,abs.error.pred,addggLayers,addMarginal,all.digits,all.is.numeric,approxExtrap,areg,areg.boot,aregImpute,aregTran,arrGrob,as.discrete,asNumericMatrix,ballocation,bezier,binconf,biVar,bootkm,bpower,bpower.sim,bpplot,bpplotM,bpplt,bppltp,bpx,bsamsize,bystats,bystats2,capitalize,catTestchisq,Cbind,ceil,character.table,chiSquare,ciapower,cleanup.import,clowess,cnvrt.coords,code.levels,colorFacet,combine.levels,combineLabels,completer,combplotp,confbar,consolidate,contents,conTestkw,cpower,Cs,csv.get,cumcategory,curveRep,curveSmooth,cut2,datadensity,dataDensityString,dataframeReduce,dataRep,ddmmmyy,deff,describe,discrete,dhistboxp,dotchart2,dotchart3,dotchartp,dotchartpl,Dotplot,drawPlot,dvi,dvigv,dvips,ebpcomp,ecdfpM,Ecdf,ecdfSteps,equalBins,errbar,escapeBS,escapeRegex,estSeqMarkovOrd,estSeqSim,event.chart,event.convert,event.history,expr.tree,extractlabs,fillin,fImport,find.matches,first.word,fit.mult.impute,format.df,format.pval,formatCats,formatCons,formatDateTime,formatdescribeSingle,formatSep,formatTestStats,ftupwr,ftuss,Function,gbayes,gbayes1PowerNP,gbayes2,gbayesMixPost,gbayesMixPowerNP,gbayesMixPredNoData,gbayesSeqSim,get2rowHeads,getabd,getHdata,getLatestSource,GetModelFrame,getRs,getZip,ggfreqScatter,ggplotlyr,GiniMd,Gompertz2,groupn,grType,hashCheck,hdquantile,hidingTOC,hist.data.frame,histbackback,histboxp,histboxpM,histSpike,histSpikeg,hlab,hlabs,hoeffd,html,htmlGreek,htmlSN,htmlSpecial,htmlSpecialType,htmltabv,htmlTranslate,htmlVerbatim,importConvertDateTime,improveProb,impute,impute.transcan,inmChoice,inmChoicelike,intMarkovOrd,inverseFunction,invertTabulated,is.discrete,is.imputed,is.mChoice,is.present,is.special.miss,james.stein,jitter2,keepHattrib,Key,Key2,km.quick,knitrSet,labcurve,label,Label,labelLatex,labelPlotmath,Lag,largest.empty,latestFile,latex,latexBuild,latexCheckOptions,latexDotchart,latexNeedle,latexSN,latexTabular,latexTherm,latexTranslate,latexVerbatim,list.tree,llist,lm.fit.qr.bare,Load,Lognorm2,logrank,lookupSASContents,lrcum,makeNames,makeNstr,makeSteps,mApply,markupSpecs,mask,match.mChoice,matchCases,matrix2dataFrame,matxv,mbarclPanel,mbarclpl,mChoice,mdb.get,Mean,medvPanel,medvpl,meltData,Merge,mgp.axis,mgp.axis.labels,mhgr,minor.tick,monotone,monthDays,movStats,mtitle,multEventChart,multLines,na.delete,na.detail.response,na.include,na.keep,na.pattern,na.retain,naclus,nafitted.delete,Names2names,naplot,napredict.delete,naprint.delete,naprint.keep,naresid.delete,naresid.keep,nCoincident,nFm,nmChoice,nobsY,nomiss,nstr,num.denom.setup,num.intercepts,numeric.string,numericScale,oPar,optionsCmds,ordGridFun,ordTestpo,outerText,pairUpDiff,panel.bpplot,panel.Dotplot,panel.Ecdf,panel.plsmo,panel.xYplot,parGrid,partition.matrix,partition.vector,pasteFit,pBlock,pc1,plotCorrM,plotCorrPrecision,plotp,plotlyM,plotlyParm,plotlySave,plotmathTranslate,plotMultSim,plotpsummaryM,plsmo,pngNeedle,pomodm,popower,posamsize,prepanel.Dotplot,prepanel.Ecdf,prepanel.xYplot,princmp,printL,print.char.matrix,prList,prn,propsPO,propsTrans,prselect,prType,pstamp,putHcap,putHfig,putKey,putKeyEmpty,qcrypt,Quantile,Quantile2,r2describe,R2Measures,rcorr,rcorr.cens,rcorrcens,rcorrp.cens,rcspline.eval,rcspline.plot,rcspline.restate,rcsplineFunction,read.xportDataload,readSAScsv,redun,reformM,reLabelled,rendHTML,replace.substring.wild,reShape,responseSummary,restoreHattrib,rlegend,rlegendg,rm.boot,rMultinom,roundN,roundPOSIXt,runifChanged,runParallel,samplesize.bin,sas.codes,sas.get,sas.get.macro,sasdsLabels,sasxport.get,Save,scat1d,score.binary,sedit,sepUnitsTrans,seqFreq,setParNro,setTrellis,show.col,show.pch,showPsfrag,simMarkovOrd,simplifyDims,simPOcuts,simRegOrd,sKey,smean.cl.boot,smean.cl.normal,smean.sd,smean.sdl,smearingEst,smedian.hilow,solvet,somers2,soprobMarkovOrd,soprobMarkovOrdm,spearman,spearman.test,spearman2,spikecomp,spower,spss.get,src,stat_plsmo,stata.get,StatPlsmo,stepfun.eval,stratify,strgraphwrap,string.bounding.box,string.break.line,stringDims,stripChart,subplot,substi,substi.source,substring.location,substring2,summarize,summaryD,summaryDp,summaryM,summaryP,summaryRc,summaryS,symbol.freq,sys,t.test.cluster,table_formatpct,table_freq,table_latexdefs,table_N,table_pc,table_trio,tabulr,termsDrop,testCharDateTime,testDateTime,tex,tobase64image,transace,transcan,translate,trap.rule,trellis.strip.blank,truncPOSIXt,uncbind,units,unPaste,upData,upFirst,valueLabel,valueName,valueTags,valueUnit,var.inner,varclus,vlab,Weibull2,whichClosek,whichClosePW,whichClosest,wtd.Ecdf,wtd.loess.noiter,wtd.mean,wtd.quantile,wtd.rank,wtd.table,wtd.var,xInch,xless,xy.group,xYplot,xySortNoDupNoNA,yearDays,yInch,ynbind,zoom,"[<-.discrete","consolidate<-","is.na<-.discrete","label<-","length<-.discrete","substring2<-","valueLabel<-","valueName<-","valueTags<-","valueUnit<-")
 
 useDynLib(Hmisc, .registration=TRUE, .fixes="F_")
 

NEWS

@@ -1,3 +1,14 @@
+Changes in version 5.1-3 (2024-05-18)
+   * areg.boot: intercepted use of xlim when y is categorical; need to improve logic on xout=
+   * redun: stored scores matrix in returned object, suitable for r2describe
+   * r2describe: new function to list strongest predictors of each variable in a matrix, from all the other columns
+   * movStats: added lrm_args argument
+   * logrank (in spower.s): removed non-working non-executed code for stratified log rank, change hazard ratio estimate to Pike's estimator.  Previous hazard ratio calculation was incorrect.
+   * qcrypt: added service=NA to bypass keyring
+   * runParallel: changed progress directory explicitly to /tmp for Mac
+   * printL: new function
+   * redun: got around model.frame problem so that negated variables are omitted from analysis
+
 Changes in version 5.1-2 (2024-03-09)
    * dotchartpl: remove length(ugroup) criterion (unsure what this was doing and made lower and upper be not plotted)
    * dotchartpl: got around new bug in plotly when numeric vectors were given to axis ticktext; changed to character via format()

R/movStats.r

@@ -42,6 +42,7 @@
 ##' @param lrm set to TRUE to include logistic regression estimates w rcspline
 ##' @param orm set to TRUE to include ordinal logistic regression estimates w rcspline (mean + quantiles in `tau`)
 ##' @param hare set to TRUE to include hazard regression estimtes of incidence at `times`, using the `polspline` package
+##' @param lrm_args a `list` of optional arguments to pass to `lrm` when `lrm=TRUE`, e.g., `list(maxit=20)`
 ##' @param family link function for ordinal regression (see `rms::orm`)
 ##' @param k number of knots to use for ols and/or qreg rcspline
 ##' @param tau quantile numbers to estimate with quantile regression
@@ -62,7 +63,8 @@ movStats <- function(formula, stat=NULL, discrete=FALSE,
                      trans=function(x) x, itrans=function(x) x,
                      loess=FALSE,
                      ols=FALSE, qreg=FALSE, lrm=FALSE,
-                     orm=FALSE, hare=FALSE, family='logistic',
+                     orm=FALSE, hare=FALSE, 
+                     lrm_args=NULL, family='logistic',
                      k=5, tau=(1:3)/4, melt=FALSE,
                      data=environment(formula),
                      pr=c('none', 'kable', 'plain', 'margin')) {
@@ -297,7 +299,9 @@ movStats <- function(formula, stat=NULL, discrete=FALSE,
     }
 
     if(lrm) {
-      f <- rms::lrm(y ~ rms::rcs(x, .knots.), data=s)
+      f <- if(length(lrm_args))
+        do.call(rms::lrm, c(list(y ~ rms::rcs(x, .knots.), data=s), lrm_args)) else
+        rms::lrm(y ~ rms::rcs(x, .knots.), data=s)
       pc <- predict(f, dat, type='fitted')
       w[, 'LR Proportion' := pc]
     }