Commit upstream/3.14-6 - hmisc

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DESCRIPTION less more

0	0	Package: Hmisc
1		Version: 3.14-5
2		Date: 2014-09-11
	1	Version: 3.14-6
	2	Date: 2014-11-16
3	3	Title: Harrell Miscellaneous
4	4	Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
5	5	contributions from Charles Dupont and many others.

17	17	LazyLoad: Yes
18	18	URL: http://biostat.mc.vanderbilt.edu/Hmisc,
19	19	https://github.com/harrelfe/Hmisc
20		Packaged: 2014-09-11 21:00:20 UTC; harrelfe
	20	Packaged: 2014-11-21 18:05:11 UTC; harrelfe
21	21	NeedsCompilation: yes
22	22	Repository: CRAN
23		Date/Publication: 2014-09-12 15:50:33
	23	Date/Publication: 2014-11-22 00:42:24

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MD5 less more

0	0	16f8ea43efba90112351c5ecb33021c4 *COPYING
1		28b724e3db7594714c1ab685e1b877f3 *DESCRIPTION
	1	3c38884e849267c86148b87c6e843631 *DESCRIPTION
2	2	17da8e77284bb353c8e685a3c47a669d *INDEX
3		6b76cfc1cd8c7205a7a46f26c3a2f18d *NAMESPACE
4		716a51594604fcc74f0aa34a8ca7a118 *NEWS
	3	a8b838ef66b469e2b6ae849e3f96f74a *NAMESPACE
	4	57f1318c607746fb3bd8c6ec3c4a9c11 *NEWS
5	5	76f90acbe9bf8ad2eaaa6b8813eb7c82 *R/AFirst.lib.s
6	6	62ef16fc333551d6c65f15dedfb5a697 *R/Cs.s
7	7	387ca68eeb2830ad1d19cdbd979cef6e *R/Key.s

21	21	8c002470a851e0d14571cfda085e6c42 *R/confbar.s
22	22	1274fe9b36deb504e596de1fc99cdbcb *R/consolidate.s
23	23	c04e31869fdc5107eb6af6886eadb566 *R/cpower.s
24		a0d62412137930c872a577dc5ea139c2 *R/curveRep.s
	24	45de10ab5edf3d2a193a8617fe6128f4 *R/curveRep.s
25	25	5da6635f342086cedeee652e296ce9e1 *R/cut2.s
26	26	25c501e1db065dacd0b7ebbc9918254e *R/data.frame.labelled.s
27	27	97dc5dcc48cb719088b817833067352c *R/dataRep.s
28	28	8ef7d2efc9aa8c82dcdb3073d48477ae *R/dates.s
29	29	3f02d2486d14e095a96fe5ee10e483c7 *R/deff.s
30		1e1f95133698fda2a768f668e276e98d *R/describe.s
	30	c836746571a4ea73ad482de3c552debe *R/describe.s
31	31	6cb5b3a77860b605f102bb528e84a071 *R/discrete.s
32	32	a96e8a7c59626e7cb975f79eb869b025 *R/dotchart3.s
33	33	01ac1a5622f257498eefc940f11c8615 *R/ecdf.s

51	51	8cf9e0a10997c59a5be3f19a39c73684 *R/james.stein.s
52	52	88c72d01c0b5a4f5d40f919918bfbd00 *R/labcurve.s
53	53	df6cc0711c0f32bd8524560fc403dbff *R/label.s
54		8fc31a2fcfe7d0aa1abc9dd2e5188eae *R/latex.s
	54	f20844d838120469e5167a1933e90071 *R/latex.s
55	55	15f9f1d9ce01c4624523182f7a514244 *R/latexDotchart.s
56	56	9fafa76ce37fa2f42c27236c9bbcfb9d *R/latexTabular.s
57	57	330de4a4106a11330d54434e2d7a8c32 *R/latexTherm.s

61	61	e21c3cbb9b9c17b07223d4f805433395 *R/makeNstr.s
62	62	e5f0eef89d954522d56fb5399066a6d3 *R/mask.s
63	63	f4cc097babcda3c1edcd60f516713ff2 *R/matxv.s
64		f0d3e83235352d62cc0714846821c68e *R/mdb.get.s
	64	c43b31317d74ac389aff80c7adf7efa5 *R/mdb.get.s
65	65	1c430f0b7f3caed1b15359483136509d *R/minor.tick.s
66	66	32a369e847b95005134970ac15b4ba73 *R/model.frame.default.s
67	67	fc71dbaeeb57983dcfa3ac0497ed837b *R/mtitle.s

76	76	215f9a06ffc6df02fb67576ad0da83b9 *R/panel.abwplot.s
77	77	35e90e268046316b9369585f790bdd9a *R/panel.bpplot.s
78	78	1630c1be85251dac0e8cd0243bedd201 *R/pc1.s
79		187f93b46f9d3d54258618f1cb7a1333 *R/plsmo.s
	79	b4c352cd36449e5ec442b9badb45c9d2 *R/plsmo.s
80	80	ce22555a4a09e120b39f9eec3320b37c *R/popower.s
81	81	9a1119c7949407c39968645e921a87a6 *R/print.char.list.s
82	82	afe3fb9a3b0fa665e0811fd2b1ace401 *R/pstamp.s

109	109	b42e6d7953adef86625842fa4bdbe291 *R/strwrap.s
110	110	055ef617ac4b0362b6466e6436ba69fb *R/subplot.s
111	111	14e533b635192fae8b28ca81b9c86f5d *R/substi.s
112		fb4587629a1bb412968b1c55092900c3 *R/summary.formula.s
113		e820a611b7ad0ef9fa7c8a4751a74839 *R/summaryM.s
	112	abcd76fbff84661c057ae17869fecc40 *R/summary.formula.s
	113	da2e1714f9e6874e265dedf924bb2fb5 *R/summaryM.s
114	114	7968792139f8f165a2725d04be6d7600 *R/summaryP.s
115	115	dc27150ba262b8c3844ce46d36f1e492 *R/summaryRc.s
116	116	598051fb147f0879ecb04ad4a0dfe54f *R/summaryS.s

125	125	91c82b7b8e9ad8cff084bf7b2069d11b *R/units.s
126	126	25b2e4d51ba3475a3e2bd22da07305ad *R/valueTags.s
127	127	ce9c8d4ed31e5172583f329e103dcbe4 *R/varclus.s
128		02c2c59f781d8c3433c0b4ffae2f54d4 *R/wtd.stats.s
	128	6fb48df83188e5a99022fdcfb106cb0e *R/wtd.stats.s
129	129	fafd82249f6870351f42d4ad6c3757c5 *R/xYplot.s
130	130	ceb40edad1b482275efde229ce48cdea *R/xtfrm.labelled.s
131	131	b72b2ab287d4c1af9d741022300a18bb *R/xy.group.s

142	142	d04e0431bff384660d258b2e2e405b32 *man/Hmisc-internal.Rd
143	143	a8d3213ffdeb74c3f50bb2d54a8b9ab5 *man/Lag.Rd
144	144	1dcfad836f562a867431ea9225ef009d *man/Misc.Rd
145		81e0509297dea67156903a55e89339b4 *man/Overview.Rd
	145	0beff88dfa85ab0fd7b4306272170a8f *man/Overview.Rd
146	146	0b14624c4cf49f60e6447e2792b227c6 *man/Save.Rd
147	147	6512b9f5df15df6558a987169ebbc216 *man/abs.error.pred.Rd
148	148	ccb2959a926f28700383197d9496151d *man/addMarginal.Rd

160	160	d787d413eeb83e8f9cd809d4630a9f99 *man/ciapower.Rd
161	161	4202bd798ad52004eec93d91b0a8d945 *man/cnvrt.coords.Rd
162	162	00db76a86189178fe8385d5aaeda346b *man/consolidate.Rd
163		214346eb5560c930d14d2318c26959d9 *man/contents.Rd
	163	e94ba9a8822c12a12ed1fa3c5f3526f2 *man/contents.Rd
164	164	11c78317d89330da550b16617b3b96a6 *man/cpower.Rd
165	165	5673d004d5398e681cc11521217a38ca *man/csv.get.Rd
166		588c98170b6ff457695cfe40cc409f78 *man/curveRep.Rd
	166	3189e5ba69e3ed68dfbe16b8272837eb *man/curveRep.Rd
167	167	8837df3d98894a30648d941bed708600 *man/cut2.Rd
168	168	3f0207be8386db756a98655b26cc21be *man/data.frame.create.modify.check.Rd
169	169	2ead582aeae9e126400a6b4ad683e264 *man/dataRep.Rd

195	195	216bb0989ebf4378cb87841082451438 *man/inc-dec.Rd
196	196	40974ee6be081e636f57e6649b6fde38 *man/labcurve.Rd
197	197	c9a14ef836c70a6c1ba034f40505006b *man/label.Rd
198		c7bdf4b6b293f2382bd9cb95884e5f4c *man/latex.Rd
	198	acb1fe98c820d282892d7a63cb1ee43c *man/latex.Rd
199	199	211c0afb26e58d9aee079d5ee9bebc95 *man/latexDotchart.Rd
200	200	27998cfcd912e12c8ca2a0ae72a0f3fb *man/latexTabular.Rd
201	201	0bc6e69386de30a3e231170b3d19a218 *man/latexTherm.Rd

204	204	7a3ad23a76192d3d91b2995a098bfabb *man/mApply.Rd
205	205	6aaa5648e29fa7bbbffcc6abb94a003e *man/mChoice.Rd
206	206	c2c3d7fd7b6118a5480308fcacb57afa *man/makeNstr.Rd
207		15299005b391107453578c49e8b3f75a *man/mdb.get.Rd
	207	7b897bfa6c2c3500b188ef4db8b3c112 *man/mdb.get.Rd
208	208	02d1f868b81a79ca95f29a1237ffea4e *man/mgp.axis.Rd
209	209	3808e059fc503259824eb5cc2bc0b621 *man/minor.tick.Rd
210	210	d513cb5e98a79934c27f37e090d9c849 *man/mtitle.Rd

258	258	9a4cac30cfc22acf2afa062a30b62d9c *man/stringDims.Rd
259	259	bbd0b4524bd9a4e350d6a7ad4aca3a0a *man/subplot.Rd
260	260	5f57bda18966651336d67c9815a4a735 *man/summarize.Rd
261		0944ea9a5cd83e6c55f5101b72b16510 *man/summary.formula.Rd
262		c993d780a236a0b93067be0df044df6e *man/summaryM.Rd
	261	f01235c13973dda377b308305ef2c522 *man/summary.formula.Rd
	262	5280d7d8d537e0bde0b0628e742b337c *man/summaryM.Rd
263	263	83d5ba5f470f16b143e9dc9505789054 *man/summaryP.Rd
264	264	7ca4294ccd0452d806afe92197d4b6c5 *man/summaryRc.Rd
265	265	e82661d26ccd2ab7689b3cb63113c65d *man/summaryS.Rd

278	278	05327becfe12abbbc92e8f5c342197a5 *man/valueTags.Rd
279	279	5b38e2511ce2b1f47cbb217211b5a803 *man/varclus.Rd
280	280	bc5f53ee64bd18f64dd31271902608ca *man/windows/sas.get.Rd
281		3829ebdffaf2cff78fb395416b9dbb5f *man/wtd.stats.Rd
	281	bb8aba91aba23e8359f046a3cf7854ad *man/wtd.stats.Rd
282	282	7bcbae4f32d3a80d4bcd721f45aa9ede *man/xYplot.Rd
283	283	13c3f8a542f16076e346f9d6cc7904c3 *man/xtfrm.labelled.Rd
284	284	83b8f2732a6c378785187242ff93b26a *man/xy.group.Rd

324	324	bc723e6e82c91373f2c3f142bbe0be59 *tests/inverseFunction.r
325	325	573465e16901912adb87c138b62056c6 *tests/largest.empty.r
326	326	a1e0437dadc110e13e67c1f72235bfb5 *tests/latex.s
327		665a97c81e3fafa665ec1365a9997242 *tests/latex.summaryM.Rnw
	327	969b3b3132b54e2b4a174e8c251338b0 *tests/latex.summaryM.Rnw
328	328	86bb29e3df2c4cc1dab74549971ca150 *tests/latexTherm.Rnw
329	329	2a119079fd599b3fd6f64b6f579de087 *tests/latexTherm.r
330	330	c0668a4323dcc6d83736668c00456d23 *tests/minor.tick.r

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NAMESPACE less more

22	22	S3method(plot, summaryS)
23	23	S3method(label, default)
24	24	S3method(label, data.frame)
	25	S3method('label<-', default)
	26	S3method('label<-', data.frame)
	27	S3method('[', labelled)
	28	S3method(print, labelled)
25	29	S3method(label, Surv)
26	30	S3method(units, default)
27	31	S3method(units, Surv)

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NEWS less more

	0	Changes in version 3.14-6 (2014-11-16)
	1	* wtd.rank: fixed bug in no weights case (thanks: DPlat)
	2	* latex.summaryM, latex.summary.formula.reverse: added npct='slash' to present numerators and denominators horizontally instead of vertically
	3	* plsmo: put derivation of ylab earlier so will use original attributes
	4	* NAMESPACE: exported more S3 methods for label
	5	* contents: added arguments id, range, values
	6	* print.contents.data.frame, html.contents.data.frame: added maxlevels argument
	7	* curveRep: added option to have the color of frequencies displayed match line colors. Thanks: jstat10
	8	* curveRep: changed call to strwidth to use units instead of unit argument
	9	* contents.data.frame: corrected omission in help file
	10	* wtd.var: corrected denominator. Thanks: Shan Huang
	11	* latex.default: changed to use colheads=FALSE to suppress column headings. Thanks: Michael Rose
	12	* mdb.get: added system option -b strip to mdb-export to skip binary output
	13
0	14	Changes in version 3.14-5 (2014-09-11)
1	15	* latex.summaryM: fixed bug in caption with test=TRUE. Thanks: Yonghao Pua
2	16	* csv.get: uses data.table package's fread in place of read.csv if data.table is in effect

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R/curveRep.s less more

0		## $Id$
1	0	curveRep <- function(x, y, id, kn=5, kxdist=5, k=5, p=5, force1=TRUE,
2	1	metric=c('euclidean','manhattan'),
3	2	smooth=FALSE, extrap=FALSE, pr=FALSE) {

143	142	nx=NULL, fill=TRUE,
144	143	idcol=NULL, freq=NULL, plotfreq=FALSE,
145	144	xlim=range(x), ylim=range(y),
146		xlab='x', ylab='y', ...) {
	145	xlab='x', ylab='y', colorfreq=FALSE, ...) {
147	146	method <- match.arg(method)
148	147	ncuts <- x$ncuts
149	148	res <- x$res; id <- x$id; y <- x$y; k <- x$k; x <- x$x

235	234	return()
236	235	}
237	236	txt <- paste(names(tab), tab, sep=':')
	237	txt2 <- txt
238	238	paste(txt, collapse=';')
239	239	} else {
240	240	size <- sizecluster[subscripts[1]]
241	241	paste('N=',size,sep='')
242	242	}
243		grid.text(txt, x=.005, y=.99, just=c(0,1),
244		gp=gpar(fontsize=9, col=gray(.25)))
	243	if (!colorfreq \| is.null(idcol) \| is.null(freq)) #Do same as original
	244	{
	245	grid.text(txt, x = 0.005, y = 0.99, just = c(0, 1),
	246	gp = gpar(fontsize = 9, col = gray(0.25)))
	247	}
	248	else #color freq text using idcol
	249	{
	250	mycolors<-data.frame(idcol,freq)
	251	mycolors<-unique(mycolors)
	252	curtext<-txt2[1]
	253	curtrt<-strsplit(curtext,':')[[1]][1]
	254	curcol<-as.character( mycolors[ curtrt==as.character( mycolors[,2]) ,1] )
	255
	256	grid.text(curtext,
	257	x = 0.005,
	258	y = 0.99,
	259	just = c(0, 1),
	260	gp = gpar(fontsize = 9, col =curcol)
	261	)
	262	emspace<-2*strwidth('M', units="figure")
	263	for (i in 2:length(txt2))
	264	{
	265	curtext<-txt2[i]
	266	curtrt<-strsplit(curtext,':')[[1]][1]
	267	curcol<-as.character( mycolors[ curtrt==as.character( mycolors[,2]) ,1] )
	268
	269	grid.text(curtext,
	270	x = emspace+strwidth(txt2[i-1], units="figure") ,
	271	y = 0.99, just = c(0, 1),
	272	gp = gpar(fontsize = 9, col = curcol)
	273	)
	274	}
	275	}
245	276	}
246	277	pan <- if(length(idcol))
247	278	function(x, y, subscripts, groups, type, ...) {

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R/describe.s less more

685	685
686	686	contents <- function(object, ...) UseMethod('contents')
687	687
688		contents.data.frame <- function(object, sortlevels=FALSE, ...)
	688	contents.data.frame <- function(object, sortlevels=FALSE,
	689	id=NULL, range=NULL, values=NULL, ...)
689	690	{
690	691	dfname <- deparse(substitute(object))
691	692	nam <- names(object)

697	698	for(i in 1:n) {
698	699	x <- object[[i]]
699	700	at <- attributes(x)
700		if(length(at$label))
701		lab[i] <- at$label
702		if(length(at$longlabel))
703		longlab[i] <- at$longlabel
704
705		if(length(at$units))
706		un[i] <- at$units
	701	if(length(at$label)) lab[i] <- at$label
	702	if(length(at$longlabel)) longlab[i] <- at$longlabel
	703
	704	if(length(at$units)) un[i] <- at$units
707	705
708	706	atl <- at$levels
709	707	fl[i] <- length(atl)
710		cli <- at$class[at$class %nin% c('labelled','factor')]
711		if(length(cli))
712		cl[i] <- cli[1]
	708	cli <- at$class[at$class %nin% c('labelled', 'factor')]
	709	if(length(cli)) cl[i] <- cli[1]
713	710
714	711	sm[i] <- storage.mode(x)
715	712	nas[i] <- sum(is.na(x))
716	713	if(length(atl)) {
717	714	if(sortlevels) atl <- sort(atl)
718		if(length(Lev)) for(j in 1:length(Lev)) {
	715	if(length(Lev)) for(j in 1 : length(Lev)) {
719	716	w <- Lev[[j]]
720	717	if(!is.name(w) && is.logical(all.equal(w, atl))) {
721	718	atl <- as.name(names(Lev)[j])

726	723	}
727	724	}
728	725
729		w <- list(Labels=if(any(lab!='')) lab,
730		Units=if(any(un!='')) un,
731		Levels=if(any(fl>0)) fl,
732		Class=if(any(cl!='')) cl,
733		Storage= sm,
734		NAs=if(any(nas>0)) nas )
735
736		w <- w[sapply(w, function(x)length(x)>0)]
	726	w <- list(Labels = if(any(lab != '')) lab,
	727	Units = if(any(un != '')) un,
	728	Levels = if(any(fl > 0)) fl,
	729	Class = if(any(cl != '')) cl,
	730	Storage= sm,
	731	NAs = if(any(nas > 0)) nas )
	732
	733	w <- w[sapply(w, function(x)length(x) > 0)]
737	734
738	735	## R does not remove NULL elements from a list
739	736	structure(list(contents=data.frame(w, row.names=nam),
740		dim=d, maxnas=max(nas), dfname=dfname,
	737	dim=d, maxnas=max(nas),
	738	id=id, rangevar=range, valuesvar=values,
	739	unique.ids = if(length(id) && id %in% nam)
	740	length(unique(object[[id]])),
	741	range = if(length(range) && range %in% nam)
	742	paste(as.character(range(object[[range]], na.rm=TRUE)),
	743	collapse='-'),
	744	values = if(length(values) && values %in% nam)
	745	paste(if(is.factor(object[[values]])) levels(object[[values]])
	746	else sort(unique(object[[values]])), collapse=' '),
	747	dfname=dfname,
741	748	Levels=Lev,
742		longLabels=if(any(longlab!='')) structure(longlab, names=nam)),
	749	longLabels=if(any(longlab!=''))
	750	structure(longlab, names=nam)),
743	751	class='contents.data.frame')
744	752	}
745	753
746	754
747	755	print.contents.data.frame <-
748	756	function(x, sort=c('none','names','labels','NAs'),
749		prlevels=TRUE, number=FALSE, ...)
	757	prlevels=TRUE, maxlevels=Inf, number=FALSE, ...)
750	758	{
751	759	sort <- match.arg(sort)
752	760	d <- x$dim
753	761	maxnas <- x$maxnas
754		cat('\nData frame:',x$dfname,'\t',d[1],' observations and ',d[2],
755		' variables Maximum # NAs:',maxnas,'\n\n',sep='')
	762	cat('\nData frame:', x$dfname, '\t', d[1],' observations and ', d[2],
	763	' variables Maximum # NAs:', maxnas, '\n', sep='')
	764	if(length(x$id)) cat('Unique ', x$id, ':', x$unique.ids, '\t', sep='')
	765	if(length(x$rangevar)) cat(x$rangevar, ' range:', x$range, '\t', sep='')
	766	if(length(x$valuesvar))cat(x$valuesvar, ':', x$values, sep='')
	767	cat('\n\n')
756	768	cont <- x$contents
757	769	nam <- row.names(cont)
758	770	if(number) row.names(cont) <- paste(format(1:d[2]), row.names(cont))

763	775	},
764	776	labels={
765	777	if(length(cont$Labels))
766		cont <- cont[order(cont$Labels, nam),,drop=FALSE]
	778	cont <- cont[order(cont$Labels, nam),, drop=FALSE]
767	779	},
768	780	NAs={
769		if(maxnas>0)
770		cont <- cont[order(cont$NAs,nam),,drop=FALSE]
	781	if(maxnas > 0)
	782	cont <- cont[order(cont$NAs, nam),, drop=FALSE]
771	783	})
772	784
773	785	if(length(cont$Levels))
774		cont$Levels <- ifelse(cont$Levels==0,'',format(cont$Levels))
	786	cont$Levels <- ifelse(cont$Levels == 0, '', format(cont$Levels))
775	787
776	788	print(cont)
777	789
778	790	if(prlevels && length(L <- x$Levels)) {
779	791	cat('\n')
780	792	nam <- names(L)
781		w <- .Options$width-max(nchar(nam))-5
	793	w <- .Options$width - max(nchar(nam)) - 5
782	794	reusingLevels <- sapply(L, is.name)
783		fullLevels <- which(!reusingLevels)
	795	fullLevels <- which(!reusingLevels)
784	796	namf <- lin <- names(L[fullLevels])
785	797	## separate multiple lines per var with \n for print.char.matrix
786	798	j <- 0
787		for(i in fullLevels)
788		{
789		j <- j + 1
790		varsUsingSame <- NULL
791		if(sum(reusingLevels))
792		{
793		for(k in which(reusingLevels)) if(L[[k]] == namf[j])
794		varsUsingSame <- c(varsUsingSame, nam[k])
795		if(length(varsUsingSame))
796		namf[j] <- paste(c(namf[j], varsUsingSame), collapse='\n')
797		}
798		lin[j] <- paste(pasteFit(L[[i]], width=w), collapse='\n')
	799	for(i in fullLevels) {
	800	j <- j + 1
	801	varsUsingSame <- NULL
	802	if(sum(reusingLevels)) {
	803	for(k in which(reusingLevels))
	804	if(L[[k]] == namf[j]) varsUsingSame <- c(varsUsingSame, nam[k])
	805	if(length(varsUsingSame))
	806	namf[j] <- paste(c(namf[j], varsUsingSame), collapse='\n')
799	807	}
	808	Li <- L[[i]]
	809	if(length(Li) > maxlevels) Li <- c(Li[1 : maxlevels], '...')
	810	lin[j] <- paste(pasteFit(Li, width=w), collapse='\n')
	811	}
800	812	z <- cbind(Variable=namf, Levels=lin)
801	813	print.char.matrix(z, col.txt.align='left', col.name.align='left',
802	814	row.names=TRUE, col.names=TRUE)

822	834
823	835
824	836	html.contents.data.frame <-
825		function(object, sort=c('none','names','labels','NAs'), prlevels=TRUE,
826		file=paste('contents',object$dfname,'html',sep='.'),
827		levelType=c('list','table'),
	837	function(object, sort=c('none', 'names', 'labels', 'NAs'), prlevels=TRUE,
	838	maxlevels=Inf, file=paste('contents',object$dfname, 'html', sep='.'),
	839	levelType=c('list', 'table'),
828	840	append=FALSE, number=FALSE, nshow=TRUE, ...)
829	841	{
830	842	sort <- match.arg(sort)
831	843	levelType <- match.arg(levelType)
832	844	d <- object$dim
833	845	maxnas <- object$maxnas
834		if(nshow)
	846	if(nshow) {
835	847	cat('<hr><h2>Data frame:',object$dfname,
836	848	'</h2>',d[1],
837	849	' observations and ',d[2],
838		' variables, maximum # NAs:',maxnas,'<hr>\n',sep='',
839		file=file, append=append)
840		else
	850	' variables, maximum # NAs:',maxnas, '&nbsp&nbsp&nbsp&nbsp',
	851	sep='', file=file, append=append)
	852	if(length(object$id)) cat('Unique ', object$id, ':', object$unique.ids,
	853	'&nbsp&nbsp&nbsp&nbsp',
	854	sep='', file=file, append=TRUE)
	855	if(length(object$rangevar)) cat(object$rangevar, ' range:', object$range,
	856	'&nbsp&nbsp&nbsp&nbsp', sep='', file=file, append=TRUE)
	857	if(length(object$valuesvar))cat(object$valuesvar, ':', object$values,
	858	'&nbsp&nbsp&nbsp&nbsp', sep='', file=file, append=TRUE)
	859	cat('<hr>\n', file=file, append=TRUE)
	860	} else
841	861	cat('<hr><h2>Data frame:',object$dfname,
842	862	'</h2>', ' Variables:', d[2], '<hr>\n', sep='',
843	863	file=file, append=append)

893	913
894	914	cat('<hr>\n', file=file, append=TRUE)
895	915
896		if(prlevels && length(L)) {
	916	if(prlevels && length(L) > 0) {
897	917	if(levelType=='list') {
898	918	cat('<h2 align="center">Category Levels</h2>\n', file=file, append=TRUE)
899	919	for(i in fullLevels) {

907	927	paste(w, collapse=', '), '</h3>\n', sep='',
908	928	file=file, append=TRUE)
909	929	cat('<ul>\n', file=file, append=TRUE)
	930	if(length(l) > maxlevels) l <- c(l[1 : maxlevels], '...')
910	931	for(k in l) cat('<li>', k, '</li>\n', sep='',
911	932	file=file, append=TRUE)
912	933	cat('</ul>\n', file=file, append=TRUE)

917	938	## possible into n elements, pasting multiple elements
918	939	## together when needed
919	940	evenSplit <- function(x, n) {
920		indent <- function(z) if(length(z)==1)z else
921		c(z[1], paste('&nbsp&nbsp&nbsp',z[-1],sep=''))
	941	indent <- function(z) if(length(z) == 1) z else
	942	c(z[1], paste('&nbsp&nbsp&nbsp', z[-1], sep=''))
922	943	m <- length(x)
923	944	if(m <= n) return(c(indent(x), rep('',n-m)))
924	945	totalLength <- sum(nchar(x)) + (m-1)*3.5

933	954	if(m <= n) break
934	955	}
935	956	## Take evasive action if needed
936		if(m==n) indent(y) else if(m < n)
937		c(indent(y), rep('', n-m)) else
938		c(paste(x, collapse=', '), rep('',n-1))
	957	if(m == n) indent(y) else if(m < n)
	958	c(indent(y), rep('', n - m)) else
	959	c(paste(x, collapse=', '), rep('', n - 1))
939	960	}
940	961	nam <- names(L)
941	962	v <- lab <- lev <- character(0)

943	964	for(i in fullLevels) {
944	965	j <- j + 1
945	966	l <- L[[i]]
	967	if(length(l) > maxlevels) l <- c(l[1 : maxlevels], '...')
946	968	nami <- nam[i]
947	969	v <- c(v, nami)
948	970	w <- nami

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381	381	double.slash=double.slash, ...)
382	382	if (missing(rowname))
383	383	rowname <- dimnames(cx)[[1]]
	384
	385	nocolheads <- length(colheads) == 1 && is.logical(colheads) && ! colheads
384	386
385	387	if (!length(colheads))
386	388	colheads <- dimnames(cx)[[2]]

742	744	labs <- colheads
743	745	if (length(colnamesTexCmd))
744	746	labs <- paste(sl, colnamesTexCmd, " ", labs, sep="")
	747	if(nocolheads) colheads <- labs <- NULL
745	748	header <- NULL
746	749	if(length(labs)) {
747	750	if(!length(extracolheads)) {

754	757	if(multicol)
755	758	colheads <- paste(slmc1, cvbar, "}{", colheads, "}", sep="")
756	759
757		header <- paste(colheads, collapse='&')
	760	header <- if(length(colheads)) paste(colheads, collapse='&')
758	761	if(length(extracolheads)) {
759	762	extracolheads <- ifelse(extracolheads == ''\| extracolsize == '',
760	763	extracolheads,

768	771	extracolheads <- ifelse(extracolheads == '',extracolheads,
769	772	paste(extracolheads,sep=''))
770	773
771		header <- paste(header, eol, paste(extracolheads, collapse='&'), sep='')
	774	header <- if(length(header))
	775	paste(header, eol, paste(extracolheads, collapse='&'), sep='')
772	776	}
773	777
774		cat(header, eog, file=file, sep='', append=file!='')
	778	if(length(header)) cat(header, eog, file=file, sep='', append=file!='')
775	779
776	780	if(ctable)
777	781	cat(midrule, file=file, append=file!='')

791	795	cat(midrule, sep="",file=file, append=file!='')
792	796	if(length(cgroupheader))
793	797	cat(cgroupheader, file=file, append=file!='')
794		cat(header, file=file, sep="&", append=file!='')
	798	if(length(header)) cat(header, file=file, sep="&", append=file!='')
795	799	cat(eog, midrule, sl, "endhead", '\n', midrule,
796	800	sep="", file=file, append=file!='')
797	801	if(length(insert.bottom)) {

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22	22	if(lowernames) vnames <- casefold(vnames)
23	23	types <- sapply(s, function(x)x[length(x)])
24	24	datetime <- vnames[grep('DateTime', s)]
25		system(paste('mdb-export', file, shQuote(tab), '>', f))
	25	system(paste('mdb-export -b strip', file, shQuote(tab), '>', f))
26	26	d <- csv.get(f, datetimevars=datetime,
27	27	lowernames=lowernames, allow=allow,
28	28	dateformat=dateformat, ...)

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9	9	gfun <- ordGridFun(grid)
10	10	nam <- as.character(sys.call())[2 : 3]
11	11	method <- match.arg(method)
	12	if(missing(ylab))
	13	ylab <- label(y, units=TRUE, plot=TRUE, default=nam[2])
12	14	Y <- as.matrix(y)
13	15	p <- ncol(Y)
14	16	if(!missing(subset)) {

83	85	else {
84	86	if(missing(xlab))
85	87	xlab <- label(x, units=TRUE, plot=TRUE, default=nam[1])
86		if(missing(ylab))
87		ylab <- label(Y, units=TRUE, plot=TRUE, default=nam[2])
88
	88
89	89	if(missing(xlim)) xlim <- c(xmin, xmax)
90	90	if(missing(ylim)) ylim <- c(ymin, ymax)
91	91	plot(xmin, ymin, xlim=xlim, ylim=ylim,

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1469	1469	switch(npct,
1470	1470	numerator=paste('{\\',npct.size,' (',format(tab),')}',sep=''),
1471	1471	denominator=paste('{\\',npct.size,' of',denom.rep,'}'),
1472		both=paste('{\\',npct.size,' $\\frac{',
1473		format(tab),'}{',denom.rep,
1474		'}$}',sep=''))
	1472	both=paste('{\\', npct.size, ' $\\frac{', format(tab),'}{',
	1473	denom.rep,'}$}',sep=''),
	1474	slash=paste('~{\\', npct.size, ' ', format(tab),
	1475	'\\,/\\,', # \, = LaTeX thin space
	1476	denom.rep, '}', sep='')
	1477	)
1475	1478	else
1476	1479	switch(npct,
1477	1480	numerator=paste('(',format(tab),')',sep=''),

1754	1757	function(object, title=first.word(deparse(substitute(object))),
1755	1758	digits, prn = any(n!=N), pctdig=0,
1756	1759	what=c('%', 'proportion'),
1757		npct=c('numerator','both','denominator','none'),
	1760	npct=c('numerator','both','denominator','slash','none'),
1758	1761	npct.size='scriptsize', Nsize='scriptsize',
1759	1762	exclude1=TRUE, vnames=c("labels","names"), prUnits=TRUE,
1760	1763	middle.bold=FALSE, outer.size="scriptsize",

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557	557	file=paste(title, 'tex', sep='.'), append=FALSE,
558	558	digits, prn = any(n!=N),
559	559	what=c('proportion', '%'), pctdig=if(what=='%') 0 else 2,
560		npct=c('numerator','both','denominator','none'),
	560	npct=c('numerator','both','denominator','slash','none'),
561	561	npct.size='scriptsize', Nsize='scriptsize',
562	562	exclude1=TRUE, vnames=c("labels","names"), prUnits=TRUE,
563	563	middle.bold=FALSE, outer.size="scriptsize",

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24	24	}
25	25
26	26	if(normwt)
27		weights <- weights*length(x)/sum(weights)
28
29		xbar <- sum(weights*x)/sum(weights)
30		sum(weights*((x - xbar)^2)) / (sum(weights) - 1)
	27	weights <- weights * length(x) / sum(weights)
	28
	29	sw <- sum(weights)
	30	xbar <- sum(weights * x) / sw
	31	sum(weights*((x - xbar)^2)) / (sw - sum(weights ^ 2) / sw)
31	32	}
32	33
33	34

182	183	wtd.rank <- function(x, weights=NULL, normwt=FALSE, na.rm=TRUE)
183	184	{
184	185	if(!length(weights))
185		return(rank(x),na.last=if(na.rm)NA else TRUE)
	186	return(rank(x, na.last=if(na.rm) NA else TRUE))
186	187
187	188	tab <- wtd.table(x, weights, normwt=normwt, na.rm=na.rm)
188	189

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46	46	bsamsize \tab Sample size requirements for test of 2 proportions\cr
47	47	bystats \tab Statistics on a single variable by levels of >=1 factors\cr
48	48	bystats2 \tab 2-way statistics\cr
49		calltree \tab Calling tree of functions \cr
50		\tab (David Lubinsky, \email{david@hoqax.att.com})\cr
51	49	character.table \tab Shows numeric equivalents of all latin characters\cr
52	50	\tab Useful for putting many special chars. in graph titles\cr
53	51	\tab (Pierre Joyet, \email{pierre.joyet@bluewin.ch})\cr

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29	29	}
30	30	\usage{
31	31	contents(object, \dots)
32		\method{contents}{data.frame}(object, sortlevels=FALSE, \dots)
	32	\method{contents}{data.frame}(object, sortlevels=FALSE, id=NULL,
	33	range=NULL, values=NULL, \dots)
33	34	\method{print}{contents.data.frame}(x,
34		sort=c('none','names','labels','NAs'), prlevels=TRUE, number=FALSE, \dots)
	35	sort=c('none','names','labels','NAs'), prlevels=TRUE, maxlevels=Inf,
	36	number=FALSE, \dots)
35	37	\method{html}{contents.data.frame}(object,
36		sort=c('none','names','labels','NAs'), prlevels=TRUE,
	38	sort=c('none','names','labels','NAs'), prlevels=TRUE, maxlevels=Inf,
37	39	file=paste('contents',object$dfname,'html',sep='.'),
38	40	levelType=c('list','table'),
39	41	append=FALSE, number=FALSE, nshow=TRUE, \dots)

51	53	variables use the same levels but in different orders. They will
52	54	still be recognized by the \code{html} method as having identical
53	55	levels if sorted.}
	56	\item{id}{an optional subject ID variable name that if present in
	57	\code{object} will cause the number of unique IDs to be printed in
	58	the contents header}
	59	\item{range}{an optional variable name that if present in \code{object}
	60	will cause its range to be printed in the contents header}
	61	\item{values}{an optional variable name that if present in
	62	\code{object} will cause its unique values to be printed in the
	63	contents header}
54	64	\item{x}{
55	65	an object created by \code{contents}
56	66	}

66	76	\item{prlevels}{
67	77	set to \code{FALSE} to not print all levels of \code{factor} variables
68	78	}
	79	\item{maxlevels}{maximum number of levels to print for a \code{factor} variable}
69	80	\item{number}{
70	81	set to \code{TRUE} to have the \code{print} and \code{latex} methods
71	82	number the variables by their order in the data frame

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62	62	m=NULL, probs=c(.5, .25, .75), nx=NULL, fill=TRUE,
63	63	idcol=NULL, freq=NULL, plotfreq=FALSE,
64	64	xlim=range(x), ylim=range(y),
65		xlab='x', ylab='y', \dots)
	65	xlab='x', ylab='y', colorfreq=FALSE, \dots)
66	66	curveSmooth(x, y, id, p=NULL, pr=TRUE)
67	67
68	68	}

133	133	Applies only to \code{method = "lattice"}. By default the largest bar
134	134	is 0.1 times the length of a panel's x-axis. Specify
135	135	\code{plotfreq = 0.5} for example to make the longest bar half this long.}
	136	\item{colorfreq}{set to \code{TRUE} to color the frequencies printed by
	137	\code{plotfreq} using the colors provided by \code{idcol}.}
136	138	\item{xlim, ylim, xlab, ylab}{plotting parameters. Default ranges are
137	139	the ranges in the entire set of raw data given to \code{curveRep}.}
138	140	\item{\dots}{arguments passed to other functions.}

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313	313	justification for labels for column groups. Defaults to \code{"c"}.
314	314	}
315	315	\item{colheads}{a character vector of column headings if you don't want
316		to use \code{dimnames(object)[[2]]}. Specify \code{colheads=NULL} to
	316	to use \code{dimnames(object)[[2]]}. Specify \code{colheads=FALSE} to
317	317	suppress column headings.}
318	318	\item{extracolheads}{
319	319	an optional vector of extra column headings that will appear under the

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31	31	}
32	32	\details{
33	33	Uses the \code{mdbtools} package executables \code{mdb-tables},
34		\code{mdb-schema}, and \code{mdb-export}. In Debian/Ubuntu Linux run
	34	\code{mdb-schema}, and \code{mdb-export} (with option \code{-b strip}
	35	to drop any binary output). In Debian/Ubuntu Linux run
35	36	\code{apt get install mdbtools}.
36	37	\code{cleanup.import} is invoked by \code{csv.get} to transform
37	38	variables and store them as efficiently as possible.

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130	130
131	131	\method{latex}{summary.formula.reverse}(object, title = first.word(deparse(substitute(object))), digits,
132	132	prn = any(n != N), pctdig = 0, what=c('\%', 'proportion'),
133		npct = c("numerator", "both", "denominator", "none"),
	133	npct = c("numerator", "both", "denominator", "slash", "none"),
134	134	npct.size = 'scriptsize', Nsize = "scriptsize", exclude1 = TRUE,
135	135	vnames=c("labels", "names"), prUnits = TRUE, middle.bold = FALSE,
136	136	outer.size = "scriptsize", caption, rowlabel = "",

416	416	specifies which counts are to be printed to the right of percentages.
417	417	The default is to print the frequency (numerator of the percent) in
418	418	parentheses. You can specify \code{"both"} to print both numerator and
419		denominator, \code{"denominator"}, or \code{"none"}.
	419	denominator, \code{"denominator"}, \code{"slash"} to
	420	typeset horizontally using a forward slash, or \code{"none"}.
420	421	}
421	422	\item{npct.size}{
422	423	the size for typesetting \code{npct} information which appears after percents.

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78	78	file=paste(title, 'tex', sep='.'), append=FALSE, digits,
79	79	prn = any(n != N), what=c('proportion', '\%'),
80	80	pctdig = if(what == '\%') 0 else 2,
81		npct = c('numerator', 'both', 'denominator', 'none'),
	81	npct = c('numerator', 'both', 'denominator', 'slash', 'none'),
82	82	npct.size = 'scriptsize', Nsize = 'scriptsize', exclude1 = TRUE,
83	83	vnames=c("labels", "names"), prUnits = TRUE, middle.bold = FALSE,
84	84	outer.size = "scriptsize", caption, rowlabel = "",

237	237	specifies which counts are to be printed to the right of percentages.
238	238	The default is to print the frequency (numerator of the percent) in
239	239	parentheses. You can specify \code{"both"} to print both numerator and
240		denominator, \code{"denominator"}, or \code{"none"}.
	240	denominator as a fraction, \code{"denominator"}, \code{"slash"} to
	241	typeset horizontally using a forward slash, or \code{"none"}.
241	242	}
242	243	\item{npct.size}{
243	244	the size for typesetting \code{npct} information which appears after

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162	162	Gatz DF, Smith L (1995): The standard error of a weighted mean
163	163	concentration--II. Estimating confidence intervals. Atmospheric Env
164	164	29:1195-1200.
	165
	166	http://en.wikipedia.org/wiki/Weighted_arithmetic_mean
165	167	}
166	168	\seealso{
167	169	\code{\link{mean}}, \code{\link{var}}, \code{\link{quantile}}, \code{\link{table}}, \code{\link{rank}}, \code{\link{loess.smooth}}, \code{\link{lowess}},

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46	46	<<echo=FALSE, results='asis'>>=
47	47	latex(summaryM(age + height + type ~ sex , data=dbase, overall=TRUE, test=TRUE),
48	48	size='small', where="ht",
49		long=TRUE, prmsd = TRUE,
	49	long=TRUE, prmsd = TRUE, npct='slash',
50	50	caption="Descriptive Statistics",
51	51	msdsize='scriptsize', round = 2, digits=2, prtest='P', pdig =2, file='',
52	52	label="table:summary")

64	64	caption="Descriptive stats and tests of between-group differences for all primary and secondary neuroimaging outcomes",
65	65	label= "tbl:descrOutcomes",
66	66	exclude1=FALSE, digits=2, long=TRUE, prmsd=TRUE,
67		npct="both", size="tiny",
	67	npct="slash", size="tiny", npct.size='tiny',
68	68	center="centering")
69	69	@
	70
	71	Put a complex table in an external \texttt{.tex} file for conversion
	72	to \texttt{html} using \texttt{htlatex}:
	73	<<extex>>=
	74	## Example taken from help file for summaryM
	75	options(digits=3)
	76	set.seed(173)
	77	sex <- factor(sample(c("m","f"), 500, rep=TRUE))
	78	country <- factor(sample(c('US', 'Canada'), 500, rep=TRUE))
	79	age <- rnorm(500, 50, 5)
	80	sbp <- rnorm(500, 120, 12)
	81	label(sbp) <- 'Systolic BP'
	82	units(sbp) <- 'mmHg'
	83	treatment <- factor(sample(c("Drug","Placebo"), 500, rep=TRUE))
	84	treatment[1]
	85	sbp[1] <- NA
	86
	87	# Generate a 3-choice variable; each of 3 variables has 5 possible levels
	88	symp <- c('Headache','Stomach Ache','Hangnail',
	89	'Muscle Ache','Depressed')
	90	symptom1 <- sample(symp, 500,TRUE)
	91	symptom2 <- sample(symp, 500,TRUE)
	92	symptom3 <- sample(symp, 500,TRUE)
	93	Symptoms <- mChoice(symptom1, symptom2, symptom3, label='Primary Symptoms')
	94	table(as.character(Symptoms))
	95	# Produce separate tables by country
	96	f <- summaryM(age + sex + sbp + Symptoms ~ treatment + country,
	97	groups='treatment', test=TRUE)
	98	fi <- '/tmp/z.tex'
	99	cat('\\documentclass{report}\\begin{document}\n', file=fi)
	100	w <- latex(f, file=fi, npct='slash', middle.bold=TRUE, prmsd=TRUE, append=TRUE)
	101	cat('\\end{document}\n', file=fi, append=TRUE)
	102	## In /tmp run htlatex z.tex to produce z.html
	103	## To get htlatex install the linux tex4ht package
	104	## You may also need to install the tth package
	105	## See http://biostat.mc.vanderbilt.edu/SweaveConvert
	106	@
	107
70	108	\end{document}