Commit upstream/4.7-2 - hmisc

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DESCRIPTION less more

0	0	Package: Hmisc
1		Version: 4.7-1
2		Date: 2022-08-13
	1	Version: 4.7-2
	2	Date: 2022-11-18
3	3	Title: Harrell Miscellaneous
4	4	Authors@R:
5	5	c(person(given = "Frank E",

17	17	Imports: methods, latticeExtra, cluster, rpart, nnet, foreign, gtable,
18	18	grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis,
19	19	htmltools, base64enc
20		Suggests: acepack, chron, rms, mice, tables, knitr, plotly (>= 4.5.6),
21		rlang, plyr, VGAM
	20	Suggests: acepack, chron, rms, mice, rstudioapi, tables, knitr, plotly
	21	(>= 4.5.6), rlang, plyr, VGAM
22	22	Description: Contains many functions useful for data
23	23	analysis, high-level graphics, utility operations, functions for
24	24	computing sample size and power, simulation, importing and annotating datasets,

31	31	Encoding: UTF-8
32	32	RoxygenNote: 7.1.2
33	33	NeedsCompilation: yes
34		Packaged: 2022-08-13 16:19:03 UTC; harrelfe
	34	Packaged: 2022-11-18 21:34:48 UTC; harrelfe
35	35	Author: Frank E Harrell Jr [aut, cre] (<https://orcid.org/0000-0002-8271-5493>),
36	36	Charles Dupont [ctb] (contributed several functions and maintains latex
37	37	functions)
38	38	Repository: CRAN
39		Date/Publication: 2022-08-15 08:30:07 UTC
	39	Date/Publication: 2022-11-18 23:10:06 UTC

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0	0	16f8ea43efba90112351c5ecb33021c4 *COPYING
1		4f4db629bb7f3c02c2d3e3eb1383ae93 *DESCRIPTION
2		69ecc0f3b7619c0c9c485f9e4090876b *NAMESPACE
3		29f47d500e691390810394ac086e08d6 *NEWS
	1	82b2ae379b6767250be8cb87fa3de2d1 *DESCRIPTION
	2	5992b9f2844076f7afd6b4e6bfd6f3d5 *NAMESPACE
	3	63e15b1afbf17d92df36ef95a76e7e19 *NEWS
4	4	76f90acbe9bf8ad2eaaa6b8813eb7c82 *R/AFirst.lib.s
5	5	8fdbfa3b900cbbb42d94898093ec7fa5 *R/Cs.s
6	6	85683865508739ff7a19b280e562ab67 *R/GiniMd.s
7	7	7d0b0014572f85d46fa6a3417707344c *R/Key.s
8		b4731cac9abe82106e4b535a77f688d2 *R/Merge.r
9		9c7f09bcf89619e07189e8f7552e7c4f *R/Misc.s
	8	10afe48276f47fe7b9cbeba8b151ee42 *R/Merge.r
	9	0091bb7f60a12a811825db0b06fb01ef *R/Misc.s
10	10	081320dfb53e3362cfb0918952b60cce *R/R2Measures.r
11	11	9043da0ab6b8288636bb399cdb0f89bf *R/abs.error.pred.s
12	12	bdf1cbb1952b1cdf53a296a6d29ecb08 *R/areg.s

30	30	97dc5dcc48cb719088b817833067352c *R/dataRep.s
31	31	ec8af558be91e1fa3415f1a99dd469b2 *R/dates.s
32	32	3f02d2486d14e095a96fe5ee10e483c7 *R/deff.s
33		c7e75ba0cf44a10c97633ab3a82e5beb *R/describe.s
	33	7c467c898b81b927a07e19bfbc50ffc5 *R/describe.s
34	34	6cb5b3a77860b605f102bb528e84a071 *R/discrete.s
35	35	510723f9ba799696bf0196fc231e2ca2 *R/dotchart3.s
36	36	14ad428dacb6bed7013fdef6c05d9239 *R/dotchartpl.s

63	63	8cf9e0a10997c59a5be3f19a39c73684 *R/james.stein.s
64	64	8015b8ce84b2cc4686fca6ebba40e916 *R/labcurve.s
65	65	bb1e0963d40b2a6df05f9277484c5ebb *R/label.s
66		838bc6afccec32608b1bc14fc05d27e6 *R/latex.s
	66	526e1c9a614e4914908b00f675466117 *R/latex.s
67	67	4e31dcfc293ca68d459764b5d32515f3 *R/latexCheckOptions.r
68	68	dda324419c115accb95440b58d422d43 *R/latexDotchart.s
69	69	b160964c8423acea603c95a04c791084 *R/latexTabular.s
70	70	67c8a6450a4ead25d7fe5a7944a40d12 *R/latexTherm.s
71	71	f15937a81b1e2a57a9707f5fbdd6c878 *R/list.tree.s
72	72	ce608a6c653ec8c6fe828448f9a78eb6 *R/mApply.s
73		2d052be3962a7b8042d0cef39231d48d *R/mChoice.s
	73	d62470527f34181cace3f8935e4e35ea *R/mChoice.s
74	74	e21c3cbb9b9c17b07223d4f805433395 *R/makeNstr.s
75	75	e5f0eef89d954522d56fb5399066a6d3 *R/mask.s
76	76	f4cc097babcda3c1edcd60f516713ff2 *R/matxv.s

140	140	eb87b4f621bfa787f568ceca584f9240 *R/tabulr.s
141	141	c1dba69a612fd6fb121adb946a77596e *R/tex.s
142	142	2b30ea0d0be2d1eca4d07d2bcd1cc2aa *R/transace.s
143		9eb090abfa2d4a84995078c72761f3eb *R/transcan.s
	143	d1bfd0b35c0217dfd3b3d9b96929142b *R/transcan.s
144	144	847daf7fa4e67d6641c763a7873df93c *R/translate.s
145	145	91c82b7b8e9ad8cff084bf7b2069d11b *R/units.s
146	146	9cc4a154ada63f71e4eb19c38453e445 *R/upData.s

238	238	71a62f91bcd26f7cbfa9a2755bed0830 *man/Save.Rd
239	239	79ed6280942247ec7b4580638c1cc885 *man/abs.error.pred.Rd
240	240	6ed0de6a1ac299e867fea5c42fd49024 *man/addMarginal.Rd
241		2db34295a22ca5a59d3557f50e4ac2e7 *man/all.is.numeric.Rd
	241	77a208cf321e5241f5e11e4dbb6d101e *man/all.is.numeric.Rd
242	242	89bde30f0578686f86512ffe08e7e4be *man/approxExtrap.Rd
243	243	03eed851f558773c200c8e2e09c9fff3 *man/areg.Rd
244	244	162611103783a62d004aa9af0666690a *man/aregImpute.Rd

282	282	ebdd21800ffc4beea994eaac7d5b4668 *man/gbayes.Rd
283	283	47920142f9583c30c3b4bbd60d9a3035 *man/gbayesSeqSim.Rd
284	284	bd9c601a3778a3bc502d85fa39dcb058 *man/getHdata.Rd
285		cf232c11fafdccc1efa3a6b67a3708c0 *man/getRs.Rd
	285	2e3625a44c067d7004d304ca7940e9f6 *man/getRs.Rd
286	286	c10b701ac0c5fbf3a3a3654378694a1c *man/getZip.Rd
287	287	ac60ee276185df5b27c0819a3e781bae *man/ggMisc.Rd
288	288	da13083c7f23c4a36a1b49ccfc1e87e3 *man/ggfreqScatter.Rd
289	289	988163ff858c2a7b23ed89d50e056403 *man/ggplotlyr.Rd
290	290	bd30d6597a6591b2d3b6202931502245 *man/hdquantile.Rd
291		9bde85cef5a8815e6a4adbc2163aa870 *man/hidingTOC.Rd
	291	3ad9255f40b316ad3c4349c842daad6a *man/hidingTOC.Rd
292	292	8256dd2a02e789ad86ec974fa90420cd *man/hist.data.frame.Rd
293	293	901875cc993a500f248fb22af00183d4 *man/histbackback.Rd
294	294	450305dcabbc06b9fb94f85d4dd4dbb0 *man/histboxp.Rd

299	299	396c791f149027eeafaa9515e93d3d27 *man/knitrSet.Rd
300	300	8fcd85e7402db30d54a27e1222355606 *man/labcurve.Rd
301	301	af738949158db99a2448cb48d3b310d3 *man/label.Rd
302		b4e0d1d0f22212f7e2c5b31f570196a4 *man/latex.Rd
	302	bebcb911d2f805ec0079cf0d7e4c02c7 *man/latex.Rd
303	303	9c1dfa5242426105b1ca4669b0977997 *man/latexCheckOptions.Rd
304	304	c4a248262270a156d9723212daba90ff *man/latexDotchart.Rd
305	305	32f49f9726f15c0cae64179b3df74f20 *man/latexTabular.Rd

307	307	e110de27ad37decbe96987691beb7555 *man/legendfunctions.Rd
308	308	3e0817d289b96a7d59847a1144f5fa59 *man/list.tree.Rd
309	309	a327d909648492c3e5b524888e27c35a *man/mApply.Rd
310		0d4948a3cd6757749816fbb2cdb6f96b *man/mChoice.Rd
	310	f66d70a00d4ac8c6e69a916c41a23871 *man/mChoice.Rd
311	311	c2c3d7fd7b6118a5480308fcacb57afa *man/makeNstr.Rd
312	312	1f4cb5e4cb669550dc4aca2745280286 *man/mdb.get.Rd
313	313	ad5ca5884567e50edeba874e3f6e0566 *man/mgp.axis.Rd

329	329	a3aed45d350c39121d61700f94e859cb *man/plotCorrPrecision.Rd
330	330	88d93c5117d432cbe4ba996c5c74d0d8 *man/plotlyM.Rd
331	331	81937c2b724d0ec42f817ebb88748e70 *man/plsmo.Rd
332		4af8df34929b776410ae3b007f01a15f *man/popower.Rd
	332	a05ef4564d6773ed63e6430f9d52eae7 *man/popower.Rd
333	333	52be83076b1f0442cb5ab5c15bb16a3f *man/print.char.list.Rd
334	334	0a25e1c6f349789159b7239ae0f0f620 *man/print.char.matrix.Rd
335	335	057da98d466a023bda3991abbf880855 *man/prnz.Rd

409	409	2d0aa4a90313d361f628383dd5fcf7fb *src/mChoice.c
410	410	703f73252fe6efaf8244b0713aaabe6b *src/maxempr.f
411	411	69d3a08b2cd911161ba22af68f97f611 *src/nstr.c
412		f698976ca9ef8a852edd2c37939b66a2 *src/ranksort.c
	412	5fd3cecbf580b3cb32f365f1f9036794 *src/ranksort.c
413	413	df53032c14b9c8a41bfe9529411c7729 *src/ratfor/cidxcn.r
414	414	ebb3e56a96c8678a2e3184d176af9926 *src/ratfor/cidxcp.r
415	415	4549893e527bae0e3140b29579c74720 *src/ratfor/hoeffd.r

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NAMESPACE less more

0		export("%nin%",.q,abs.error.pred,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,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,ecdfpM,Ecdf,equalBins,errbar,escapeBS,escapeRegex,estSeqMarkovOrd,estSeqSim,event.chart,event.convert,event.history,expr.tree,fillin,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,getHdata,getLatestSource,GetModelFrame,getRs,getZip,ggfreqScatter,ggplotlyr,GiniMd,Gompertz2,groupn,grType,hdquantile,hidingTOC,hist.data.frame,histbackback,histboxp,histboxpM,histSpike,histSpikeg,hoeffd,html,htmlGreek,htmlSN,htmlSpecial,htmlSpecialType,htmlTranslate,htmlVerbatim,importConvertDateTime,improveProb,impute,impute.transcan,inmChoice,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,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,Merge,mgp.axis,mgp.axis.labels,mhgr,minor.tick,monotone,monthDays,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,nFm,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,print.char.matrix,prList,prn,propsPO,propsTrans,prselect,prType,pstamp,putHcap,putHfig,putKey,putKeyEmpty,Quantile,Quantile2,R2Measures,rcorr,rcorr.cens,rcorrcens,rcorrp.cens,rcspline.eval,rcspline.plot,rcspline.restate,rcsplineFunction,read.xportDataload,readSAScsv,redun,reformM,reLabelled,replace.substring.wild,reShape,responseSummary,restoreHattrib,rlegend,rlegendg,rm.boot,rMultinom,roundN,roundPOSIXt,samplesize.bin,sas.codes,sas.get,sas.get.macro,sasdsLabels,sasxport.get,Save,scat1d,score.binary,sedit,sepUnitsTrans,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,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,testDateTime,tex,tobase64image,transace,transcan,translate,trap.rule,trellis.strip.blank,truncPOSIXt,uncbind,units,unPaste,upData,upFirst,valueLabel,valueName,valueTags,valueUnit,var.inner,varclus,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<-")
	0	export("%nin%",.q,abs.error.pred,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,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,ecdfpM,Ecdf,equalBins,errbar,escapeBS,escapeRegex,estSeqMarkovOrd,estSeqSim,event.chart,event.convert,event.history,expr.tree,fillin,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,getHdata,getLatestSource,GetModelFrame,getRs,getZip,ggfreqScatter,ggplotlyr,GiniMd,Gompertz2,groupn,grType,hdquantile,hidingTOC,hist.data.frame,histbackback,histboxp,histboxpM,histSpike,histSpikeg,hoeffd,html,htmlGreek,htmlSN,htmlSpecial,htmlSpecialType,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,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,Merge,mgp.axis,mgp.axis.labels,mhgr,minor.tick,monotone,monthDays,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,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,print.char.matrix,prList,prn,propsPO,propsTrans,prselect,prType,pstamp,putHcap,putHfig,putKey,putKeyEmpty,Quantile,Quantile2,R2Measures,rcorr,rcorr.cens,rcorrcens,rcorrp.cens,rcspline.eval,rcspline.plot,rcspline.restate,rcsplineFunction,read.xportDataload,readSAScsv,redun,reformM,reLabelled,replace.substring.wild,reShape,responseSummary,restoreHattrib,rlegend,rlegendg,rm.boot,rMultinom,roundN,roundPOSIXt,samplesize.bin,sas.codes,sas.get,sas.get.macro,sasdsLabels,sasxport.get,Save,scat1d,score.binary,sedit,sepUnitsTrans,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,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,testDateTime,tex,tobase64image,transace,transcan,translate,trap.rule,trellis.strip.blank,truncPOSIXt,uncbind,units,unPaste,upData,upFirst,valueLabel,valueName,valueTags,valueUnit,var.inner,varclus,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<-")
1	1
2	2	useDynLib(Hmisc, .registration=TRUE, .fixes="F_")
3	3

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NEWS less more

0		Changes in version 4.7-1 (2022-08-13}
	0	Changes in version 4.7-2 (2022-11-18)
	1	* grType: changed to use find.package() instead of the slow installed.packages() (thanks: Uwe Ligges)
	2	* latex.default: changed to by default omit the LaTeX comment; specify options(omitlatexcom=FALSE) to get original behavior
	3	* ggplot.transcan: corrected color/color assignments; thanks: David Norris
	4	* restoreHattrib: fixed to ignore attributes for variables that are not in obj
	5	* popower: fixed URL for Live Free or Dichotomize
	6	* getRs: improved to use rstudioapi to load the file into a script editor window
	7	* mChoice: added ignoreNA argument and made new default behavior ignoreNA=TRUE unlike the prior versions; made value (appearing with semicolons) null instead of 0 when no choice was selected, which makes option add.none finally work
	8	* mChoice: added condition argument to intersect all values instead of unioning them
	9	* mChoicelike: new function like inmChoice but allowing matching on pieces of labels and optionally ignoring the case
	10	* nmChoice: new function to compute the number of choices that were made per observation
	11	* describe: fixed length > 1 problem with check for timeDate class
	12	* Merge: better error message if unexpected variable from non-id-variable overlap
	13	* all.is.numeric: corrected to return TRUE is the only non-NA values after converting to numeric were originally NA, addedd what='nonnum' argument
	14
	15	Changes in version 4.7-1 (2022-08-13)
1	16	* plot.describe: added bvspace argument to control spacing between categorical variables
2	17	* getRs: changed default put argument to 'source', changed RStudio code
3	18	* html.contents.data.frame: changed long space to &emsp; to render in more browser

+2

-0

R/Merge.r less more

92	92	x <- M[[i]]
93	93	ni <- nm[i]
94	94	changed <- FALSE
	95	if(ni %nin% names(lab))
	96	stop(paste('Unexpected variable:', ni))
95	97	if(lab[ni] != '' && ! length(attr(x, 'label'))) {
96	98	label(x) <- lab[ni]
97	99	changed <- TRUE

+23

-16

R/Misc.s less more

236	236	res
237	237	}
238	238
239		all.is.numeric <- function(x, what=c('test','vector'),
	239	all.is.numeric <- function(x, what=c('test','vector','nonnum'),
240	240	extras=c('.','NA'))
241	241	{
242	242	what <- match.arg(what)
243	243	x <- sub('[[:space:]]+$', '', x)
244	244	x <- sub('^[[:space:]]+', '', x)
245		xs <- x[x %nin% c('',extras)]
246		if(! length(xs)) return(if(what == 'test') FALSE else x)
247		isnum <- suppressWarnings(!any(is.na(as.numeric(xs))))
248		if(what=='test')
249		isnum
250		else if(isnum)
251		as.numeric(x)
252		else x
	245	xs <- x[x %nin% c('', extras)]
	246	if(! length(xs) \|\| all(is.na(x)))
	247	return(switch(what, test = FALSE, vector=x, nonnum=x[0]))
	248	isnon <- suppressWarnings(! is.na(xs) & is.na(as.numeric(xs)))
	249	isnum <- ! any(isnon)
	250	# suppressWarnings below handles extras present in x
	251	switch(what,
	252	test = isnum,
	253	vector = if(isnum) suppressWarnings(as.numeric(x)) else x,
	254	nonnum = xs[isnon])
253	255	}
254	256
255	257	Lag <- function(x, shift=1)

1671	1673
1672	1674	if(localrepo) file.copy(paste(where, file, sel='/'), file)
1673	1675	else download.file.HTTPS(paste(where, file, sep='/'), file)
1674		file.edit(file)
	1676	if(requireNamespace('rstudioapi', quietly=TRUE) &&
	1677	rstudioapi::isAvailable()) rstudioapi::navigateToFile(file)
	1678	else file.edit(file)
1675	1679	invisible()
1676	1680	}
1677	1681

1835	1839
1836	1840
1837	1841	grType <- function() {
1838		if('plotly' %nin% utils::installed.packages()[,1]) return('base')
	1842	if(! length(find.package('plotly', quiet=TRUE))) return('base')
1839	1843	if(length(g <- .Options$grType) && g == 'plotly') 'plotly' else 'base'
1840	1844	}
1841	1845

1948	1952	}
1949	1953
1950	1954	restoreHattrib <- function(obj, attribs) {
	1955	nam <- names(obj)
1951	1956	for(n in names(attribs)) {
1952	1957	a <- attribs[[n]]
1953	1958	if(length(a)) {
1954	1959	sv <- n == '.single.variable.'
1955		x <- if(sv) obj else obj[[n]]
1956		if(length(a$label)) label(x) <- a$label
1957		if(length(a$units)) units(x) <- a$units
1958		if(sv) return(x)
1959		obj[[n]] <- x
	1960	if(sv \|\| n %in% nam) {
	1961	x <- if(sv) obj else obj[[n]]
	1962	if(length(a$label)) label(x) <- a$label
	1963	if(length(a$units)) units(x) <- a$units
	1964	if(sv) return(x)
	1965	obj[[n]] <- x
	1966	}
1960	1967	}
1961	1968	}
1962	1969	obj

+1

-1

R/describe.s less more

222	222	if(n.unique >= 5) {
223	223	loandhi <- x.unique[c(1 : 5, (n.unique - 4) : n.unique)]
224	224	extremes <-
225		if(isdot && (class(loandhi) %nin% 'timeDate')) {
	225	if(isdot && all(class(loandhi) %nin% 'timeDate')) {
226	226	formatDateTime(unclass(loandhi), at=atx, roundDay=! timeUsed)
227	227	} else if(isnum) loandhi else format(format(loandhi), ...)
228	228	names(extremes) <- c("L1","L2","L3","L4","L5","H5","H4","H3","H2","H1")

+1

-1

R/latex.s less more

568	568
569	569	## pandoc used by R Markdown gets fooled by LaTeX comments
570	570	olc <- getOption('omitlatexcom')
571		if(! length(olc) \|\| ! olc)
	571	if(length(olc) && olc)
572	572	cat("%", deparse(sys.call()), "%\n", file=file, append=file != '', sep='')
573	573
574	574	if(dcolumn) {

+38

-11

R/mChoice.s less more

0		# $Id$
1	0	mChoice <- function(..., label='',
2	1	sort.levels=c('original','alphabetic'),
3		add.none=FALSE, drop=TRUE)
	2	add.none=FALSE, drop=TRUE, ignoreNA=TRUE)
4	3	{
5	4	sort.levels <- match.arg(sort.levels)
6	5	dotlist <- list(...)

8	7	if (drop)
9	8	lev <- unique(as.character(unlist(dotlist)))
10	9	else
11		lev <- unique(unlist(lapply(dotlist, function(x)levels(as.factor(x)))))
12
	10	lev <- unique(unlist(lapply(dotlist, function(x) levels(as.factor(x)))))
	11	if(ignoreNA) lev <- setdiff(lev, NA)
13	12	if(sort.levels=='alphabetic') lev <- sort(lev)
14	13
15	14	lev <- setdiff(lev,'')
16	15
17	16	vcall <- as.character(sys.call())[-1]
18
19		dotlist <- lapply(dotlist, FUN=match, table=lev, nomatch=0)
20
	17	dotlist <- lapply(dotlist, FUN=match, table=lev) #, nomatch=0)
	18
21	19	g <- function(...) {
22	20	set <- c(...)
23	21	set <- set[!is.na(set)]
24
25	22	if(!length(set)) return('')
26	23
27	24	paste(sort(unique(set)), collapse=';')

154	151	X
155	152	}
156	153
	154	nmChoice <- function(object) {
	155	y <- gsub('[^;]', '', object)
	156	nchoices <- nchar(y) + 1
	157	nchoices[object == ''] <- 0
	158	nchoices
	159	}
	160
157	161	summary.mChoice <- function(object, ncombos=5, minlength=NULL,
158	162	drop=TRUE, ...) {
159	163	nunique <- length(unique(object))

208	212	# inmChoice <- function(x, values) {
209	213	# match.mChoice(values, x, nomatch=0) > 0
210	214	# }
211		inmChoice <- function(x, values) {
	215	inmChoice <- function(x, values, condition=c('any', 'all')) {
	216	condition <- match.arg(condition)
212	217	lev <- attr(x, 'levels')
213	218	if(is.character(values)) {
214	219	v <- match(values, lev)

218	223	}
219	224	x <- paste(';', unclass(x), ';', sep='')
220	225	values <- paste(';', values, ';', sep='')
221		res <- rep(FALSE, length(x))
	226	res <- rep(condition != 'any', length(x))
222	227	for(j in 1:length(values)) {
223	228	i <- grep(values[j], x)
224		if(length(i)) res[i] <- TRUE
	229	if(length(i)) {
	230	if(condition == 'any') res[i] <- TRUE
	231	else
	232	res[-i] <- FALSE
	233	} else if(condition == 'all') res[] <- FALSE
225	234	}
226	235	res
227	236	}
228	237
	238	inmChoicelike <- function(x, values, condition=c('any', 'all'),
	239	ignore.case=FALSE, fixed=FALSE) {
	240	condition <- match.arg(condition)
	241	if(! is.character(values)) stop('values must be a character vector')
	242	x <- as.character(x)
	243	res <- rep(condition != 'any', length(x))
	244	for(j in 1 : length(values)) {
	245	i <- grep(values[j], x, ignore.case=ignore.case, fixed=fixed)
	246	if(length(i)) {
	247	if(condition == 'any') res[i] <- TRUE
	248	else
	249	res[-i] <- FALSE
	250	} else if(condition == 'all') res[] <- FALSE
	251	}
	252	res
	253	}
	254
	255
229	256	is.mChoice <- function(x) inherits(x, 'mChoice')

+9

-3

R/transcan.s less more

1287	1287	lab=lab, type='transform'))
1288	1288	}
1289	1289	}
	1290
	1291	# scale*manual calls are from David Norris
	1292	# The implicit (alphabetical) order of 'imputed' and 'transform'
	1293	# reverses the intended symbol & color assignments. But naming
	1294	# the vectors corrects this.
	1295
1290	1296	ggplot(data, aes(x=x, y=y, color=type, shape=type, size=type)) + geom_point() +
1291	1297	facet_wrap(~ X, scales=if(scale) 'free_x' else 'free', ...) +
1292	1298	xlab(NULL) + ylab('Transformed') +
1293		scale_color_manual(values=c('#00000059', '#FF000059')) +
1294		scale_shape_manual(values=c(1, 3)) +
1295		scale_size_manual(values=c(1.3, 2.25)) +
	1299	scale_color_manual(values = c(transform="#00000059", imputed="#FF000059")) +
	1300	scale_shape_manual(values = c(transform=1, imputed=3)) +
	1301	scale_size_manual(values = c(transform=1.3, imputed=2.25)) +
1296	1302	theme(legend.position='none') +
1297	1303	geom_text(data=adata, aes(label=lab), parse=TRUE, size=1.65, col='black')
1298	1304	}

+7

-2

man/all.is.numeric.Rd less more

6	6	numeric vector. Leading and trailing blanks in \code{x} are ignored.
7	7	}
8	8	\usage{
9		all.is.numeric(x, what = c("test", "vector"), extras=c('.','NA'))
	9	all.is.numeric(x, what = c("test", "vector", "nonnum"), extras=c('.','NA'))
10	10	}
11	11	\arguments{
12	12	\item{x}{a character vector}
13	13	\item{what}{specify \code{what="vector"} to return a numeric vector if
14		it passes the test, or the original character vector otherwise}
	14	it passes the test, or the original character vector otherwise, the
	15	default \code{"test"} to return \code{FALSE} if there are no
	16	non-missing non-\code{extra} values of \code{x} or there is at least
	17	one non-numeric value of \code{x}, or \code{"nonnum"} to return the
	18	vector of non-\code{extra}, non-NA, non-numeric values of \code{x}.}
15	19	\item{extras}{a vector of character strings to count as numeric
16	20	values, other than \code{""}.}
17	21	}

24	28	all.is.numeric(c('1','1.2','3'),'vector')
25	29	all.is.numeric(c('1','1.2','3a'),'vector')
26	30	all.is.numeric(c('1','',' .'),'vector')
	31	all.is.numeric(c('1', '1.2', '3a'), 'nonnum')
27	32	}
28	33	\keyword{character}

+1

-4

man/getRs.Rd less more

35	35	minor categories available. Specify a character string to list
36	36	all scripts whose major category contains the string (ignoring
37	37	case).}
38		\item{put}{Leave at the default (\code{'rstudio'}) to load \code{file}
39		into the RStudio script editor window. Use \code{put='source'} to
40		\code{source()} the file. This is useful when the file just defines
41		a function you want to use in the session.}
	38	\item{put}{Leave at the default (\code{'source'}) to \code{source()} the file. This is useful when the file just defines a function you want to use in the session. Use load \code{put='rstudio'} to load the file into the RStudio script editor window using the \code{rstudioapi} \code{navigateToFile} function. If RStudio is not running, \code{file.edit()} is used instead.}
42	39	}
43	40	\value{a data frame or list, depending on arguments}
44	41	\author{Frank Harrell and Cole Beck}

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man/hidingTOC.Rd less more

45	45	\details{
46	46	\code{hidingTOC} creates a table of contents in a Rmd document that
47	47	can be hidden at the press of a button. It also generate buttons that allow
48		the hiding or unhiding of the diffrent level depths of the table of contents.
	48	the hiding or unhiding of the diffrent level depths of the table of
	49	contents. For \code{quarto}-related methods see \url{https://stackoverflow.com/questions/73999697}.
49	50	}
50	51	\examples{
51	52	\dontrun{

+3

-3

man/latex.Rd less more

547	547	commands which are assumed to be in the system path.
548	548	}
549	549	\details{
550		\command{latex.default} outputs a LaTeX comment containing the calling
551		statement. To suppress outputting this comment, run
552		\command{options(omitlatexcom=TRUE)} before running. This is helpful
	550	\command{latex.default} optionally outputs a LaTeX comment containing the calling
	551	statement. To output this comment, run
	552	\command{options(omitlatexcom=FALSE)} before running. The default behavior or suppressing the comment is helpful
553	553	when running RMarkdown to produce pdf output using LaTeX, as this uses
554	554	\command{pandoc} which is fooled into try to escape the percent
555	555	comment symbol.

+31

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man/mChoice.Rd less more

5	5	\alias{as.character.mChoice}
6	6	\alias{as.double.mChoice}
7	7	\alias{inmChoice}
	8	\alias{inmChoicelike}
	9	\alias{nmChoice}
8	10	\alias{match.mChoice}
9	11	\alias{[.mChoice}
10	12	\alias{print.summary.mChoice}

49	51	contains at least one of the codes or value labels in the second
50	52	argument.
51	53
52		\code{match.mChoice} creats an integer vector of the indexes of all
	54	\code{match.mChoice} creates an integer vector of the indexes of all
53	55	elements in \code{table} which contain any of the speicified levels
	56
	57	\code{nmChoice} returns an integer vector of the number of choices
	58	that were made
54	59
55	60	\code{is.mChoice} returns \code{TRUE} is the argument is a multiple
56	61	choice variable.

58	63	\usage{
59	64	mChoice(\dots, label='',
60	65	sort.levels=c('original','alphabetic'),
61		add.none=FALSE, drop=TRUE)
	66	add.none=FALSE, drop=TRUE, ignoreNA=TRUE)
62	67
63	68	\method{format}{mChoice}(x, minlength=NULL, sep=";", \dots)
64	69

77	82
78	83	match.mChoice(x, table, nomatch=NA, incomparables=FALSE)
79	84
80		inmChoice(x, values)
	85	inmChoice(x, values, condition=c('any', 'all'))
	86
	87	inmChoicelike(x, values, condition=c('any', 'all'),
	88	ignore.case=FALSE, fixed=FALSE)
	89
	90	nmChoice(object)
81	91
82	92	is.mChoice(x)
83	93

119	129	set \code{drop=FALSE} to keep unused factor levels as columns of the matrix
120	130	produced by \code{mChoice}
121	131	}
	132	\item{ignoreNA}{set to \code{FALSE} to keep any \code{NA}s present in
	133	data as a real level. Prior to Hmisc 4.7-2 \code{FALSE} was the default.}
122	134	\item{x}{
123	135	an object of class \code{"mchoice"} such as that created by
124	136	\code{mChoice}. For \code{is.mChoice} is any object.

153	165	\item{values}{
154	166	a scalar or vector. If \code{values} is integer, it is
155	167	the choice codes, and if it is a character vector, it is assumed to
156		be value labels.
157		}
	168	be value labels. For \code{inmChoicelike} \code{values} must be
	169	character strings which are pieces of choice labels.
	170	}
	171	\item{condition}{set to \code{'all'} for \code{inmChoice} to require
	172	that all choices in \code{values} be present instead of the default of
	173	any of them present.}
	174	\item{ignore.case}{set to \code{TRUE} to have \code{inmChoicelike}
	175	ignore case in the data when matching on \code{values}}
	176	\item{fixed}{see \code{grep}}
158	177	}
159	178	\value{
160	179	\code{mChoice} returns a character vector of class \code{"mChoice"}
161	180	plus attributes \code{"levels"} and \code{"label"}.
162	181	\code{summary.mChoice} returns an object of class
163		\code{"summary.mChoice"}. \code{inmChoice} returns a logical vector.
	182	\code{"summary.mChoice"}. \code{inmChoice} and \code{inmChoicelike}
	183	return a logical vector.
164	184	\code{format.mChoice} returns a character vector, and
165	185	\code{as.double.mChoice} returns a binary numeric matrix.
	186	\code{nmChoice} returns an integer vector
166	187	}
167	188	\author{
168	189	Frank Harrell

197	218	print(Symptoms, long=TRUE)
198	219	format(Symptoms[1:5])
199	220	inmChoice(Symptoms,'Headache')
	221	inmChoicelike(Symptoms, 'head', ignore.case=TRUE)
200	222	levels(Symptoms)
201	223	inmChoice(Symptoms, 3)
	224	# Find all subjects with either of two symptoms
202	225	inmChoice(Symptoms, c('Headache','Hangnail'))
203	226	# Note: In this example, some subjects have the same symptom checked
204	227	# multiple times; in practice these redundant selections would be NAs
205	228	# mChoice will ignore these redundant selections
	229	# Find all subjects with both symptoms
	230	inmChoice(Symptoms, c('Headache', 'Hangnail'), condition='all')
206	231
207	232	meanage <- N <- numeric(5)
208	233	for(j in 1:5) {

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man/popower.Rd less more

41	41
42	42	\code{multEventChart} uses \code{\link{ggplot2}} to plot event charts
43	43	showing state transitions, account for absorbing states/events. It is
44		based on code written by Lucy D'Agostino McGowan posted at \url{https://livefreeordichotomize.com/2020/05/21/survival-model-detective-1}.
	44	based on code written by Lucy D'Agostino McGowan posted at \url{https://livefreeordichotomize.com/posts/2020-05-21-survival-model-detective-1/}.
45	45
46	46	}
47	47	\usage{

+3

-12

src/ranksort.c less more

0	0	#include "R.h"
1	1
2		void sort2(np,ra,rb)
3		int *np;
4		double ra[];
5		int rb[];
	2	void sort2(int *np, double ra[], int rb[])
6	3	{
7	4	int l,j,ir,i,n,rrb,*xrb;
8	5	double rra,*xra;

45	42	}
46	43
47	44
48		void crank(np, w)
49		int *np;
50		double w[];
51
	45	void crank(int *np, double w[])
52	46	{
53	47	int n,j=1,ji,jt;
54	48	double rank,*xw;

72	66	}
73	67
74	68
75		void F77_SUB(rank)(np, x, w, ix, r)
76		int *np, ix[];
77		double x[],r[],w[];
78
	69	void F77_SUB(rank)(int *np, double x[], double w[], int ix[], double r[])
79	70	{
80	71	int n, *xix, i;
81	72	double xx, xr, *xw;