describe.s
describe <- function(x, ...) UseMethod("describe")
describe.default <- function(x, descript, ...) {
if(missing(descript)) {
descript <- deparse(substitute(x))
}
if(is.matrix(x)) {
describe.matrix(x, descript, ...)
} else {
describe.vector(x, descript, ...)
}
}
describe.vector <- function(x, descript, exclude.missing=TRUE, digits=4,
listunique=0, listnchar=12,
weights=NULL, normwt=FALSE, minlength=NULL, ...)
{
oldopt <- options('digits')
options(digits=digits)
on.exit(options(oldopt))
weighted <- length(weights) > 0
if(! weighted) weights <- rep(1, length(x))
special.codes <- attr(x, "special.miss")$codes
labx <- attr(x,"label")
if(missing(descript)) descript <- as.character(sys.call())[2]
if(length(labx) && labx != descript) descript <- paste(descript,":",labx)
un <- attr(x, "units")
if(length(un) && un == '') un <- NULL
fmt <- attr(x, 'format')
if(length(fmt) && (is.function(fmt) || fmt == '')) fmt <- NULL
if(length(fmt) > 1)
fmt <- paste(as.character(fmt[[1]]), as.character(fmt[[2]]))
present <- if(all(is.na(x))) rep(FALSE, length(x))
else if(is.character(x)) x != "" & x != " " & ! is.na(x)
else ! is.na(x)
present <- present & ! is.na(weights)
if(length(weights) != length(x))
stop('length of weights must equal length of x')
if(normwt) {
weights <- sum(present) * weights / sum(weights[present])
n <- sum(present)
} else n <- sum(weights[present])
if(exclude.missing && n==0)
return(structure(list(), class="describe"))
missing <- sum(weights[! present], na.rm=TRUE)
atx <- attributes(x)
atx$names <- atx$dimnames <- atx$dim <- atx$special.miss <- NULL
atx$class <- atx$class[atx$class != 'special.miss']
isdot <- testDateTime(x,'either') # is date or time var
isdat <- testDateTime(x,'both') # is date and time combo var
x <- x[present, drop=FALSE]
x.unique <- sort(unique(x))
weights <- weights[present]
n.unique <- length(x.unique)
attributes(x) <- attributes(x.unique) <- atx
isnum <- (is.numeric(x) || isdot) && ! is.factor(x) # was isdat
timeUsed <- isdat && testDateTime(x.unique, 'timeVaries')
z <- list(descript=descript, units=un, format=fmt)
counts <- c(n,missing)
lab <- c("n","missing")
if(length(special.codes)) {
tabsc <- table(special.codes)
counts <- c(counts, tabsc)
lab <- c(lab, names(tabsc))
}
if(length(atx$imputed)) {
counts <- c(counts, length(atx$imputed))
lab <- c(lab, "imputed")
}
if(length(pd <- atx$partial.date)) {
if((nn <- length(pd$month)) > 0) {
counts <- c(counts, nn)
lab <- c(lab, "missing month")
}
if((nn <- length(pd$day)) > 0) {
counts <- c(counts, nn)
lab <- c(lab,"missing day")
}
if((nn <- length(pd$both)) > 0) {
counts <- c(counts, nn)
lab <- c(lab,"missing month,day")
}
}
if(length(atx$substi.source)) {
tabss <- table(atx$substi.source)
counts <- c(counts, tabss)
lab <- c(lab, names(tabss))
}
counts <- c(counts, n.unique)
lab <- c(lab, "distinct")
if(isnum) {
xnum <- unclass(x)
if(n.unique < 2) reff <- 0
else {
fp <- wtd.table(xnum, weights, normwt=FALSE, na.rm=FALSE, type='table') /
sum(weights)
reff <- (1 - sum(fp ^ 3)) / (1 - 1 / n / n)
}
counts <- c(counts, round(reff, 3))
lab <- c(lab, 'Info')
}
x.binary <- n.unique == 2 && isnum && x.unique[1] == 0 && x.unique[2] == 1
if(x.binary) {
counts <- c(counts, sum(weights[x == 1]))
lab <- c(lab, "Sum")
}
if(isnum) {
if(isdot) {
dd <- sum(weights * xnum) / sum(weights)
fval <- formatDateTime(dd, atx, ! timeUsed)
counts <- c(counts, fval)
} else counts <- c(counts, format(sum(weights * x) / sum(weights), ...))
lab <- c(lab, "Mean")
if(! weighted) {
gmd <- format(GiniMd(xnum), ...)
counts <- c(counts, gmd)
# counts <- c(counts, if(isdot) formatDateTime(gmd, atx, ! timeUsed)
# else
# format(gmd, ...))
lab <- c(lab, "Gmd")
}
} else if(n.unique == 1) {
counts <- c(counts, format(x.unique))
lab <- c(lab, "value")
}
if(n.unique >= 10 & isnum) {
q <-
if(any(weights != 1)) {
wtd.quantile(xnum, weights, normwt=FALSE, na.rm=FALSE,
probs=c(.05,.1,.25,.5,.75,.90,.95))
} else quantile(xnum,c(.05,.1,.25,.5,.75,.90,.95), na.rm=FALSE)
## Only reason to call quantile is that the two functions can give
## different results if there are ties, and users are used to quantile()
fval <-
if(isdot) formatDateTime(q, atx, ! timeUsed)
else format(q,...)
counts <- c(counts, fval)
lab <- c(lab,".05",".10",".25",".50",".75",".90",".95")
}
names(counts) <- lab
z$counts <- counts
tableIgnoreCaseWhiteSpace <- function(x) {
x <- gsub('\r',' ',x)
x <- gsub('^[[:space:]]+','',gsub('[[:space:]]+$','', x))
x <- gsub('[[:space:]]+',' ', x)
y <- tolower(x)
f <- table(y)
names(f) <- x[match(names(f), y)]
f
}
values <- NULL
if(! x.binary) {
if(inherits(x,'mChoice'))
z$mChoice <- summary(x, minlength=minlength)
else
if(n.unique <= listunique && ! isnum && ! is.factor(x) &&
max(nchar(x)) > listnchar)
values <- tableIgnoreCaseWhiteSpace(x)
else
if(isnum || n.unique <= 100) {
if(isnum) {
if(n.unique >= 100 ||
(n.unique > 20 &&
min(diff(sort(unique(xnum)))) < diff(range(xnum)) / 500)) {
pret <- pretty(xnum, if(n.unique >= 100) 100 else 500)
dist <- pret[2] - pret[1]
r <- range(pret)
xnum <- r[1] + dist * round((xnum - r[1]) / dist)
z$roundedTo <- dist
}
}
# values <- wtd.table(if(isnum) xnum else if(isdat) format(x) else x,
# weights, normwt=FALSE, na.rm=FALSE)
# values <- wtd.table(if(isdot) format(x) else if(isnum) xnum else x,
# weights, normwt=FALSE, na.rm=FALSE)
values <- wtd.table(if(isnum) xnum else x,
weights, normwt=FALSE, na.rm=FALSE)
vx <- values$x
cx <- intersect(atx$class,
c("Date", "POSIXt", "POSIXct", "dates", "times", "chron"))
class(vx) <- cx # restores as date, time, etc.
values <- list(value=vx, frequency=unname(values$sum.of.weights))
}
z$values <- values
if(n.unique >= 5) {
loandhi <- x.unique[c(1 : 5, (n.unique - 4) : n.unique)]
extremes <-
if(isdot && all(class(loandhi) %nin% 'timeDate')) {
formatDateTime(unclass(loandhi), at=atx, roundDay=! timeUsed)
} else if(isnum) loandhi else format(format(loandhi), ...)
names(extremes) <- c("L1","L2","L3","L4","L5","H5","H4","H3","H2","H1")
z$extremes <- extremes
}
}
structure(z, class="describe")
}
describe.matrix <- function(x, descript, exclude.missing=TRUE,
digits=4, ...)
{
if(missing(descript))
descript <- as.character(sys.call())[2]
nam <- dimnames(x)[[2]]
if(length(nam)==0)
stop('matrix does not have column names')
Z <- vector('list', length(nam))
names(Z) <- nam
d <- dim(x)
missing.vars <- NULL
for(i in 1:ncol(x)) {
z <- describe.vector(x[,i],nam[i],exclude.missing=exclude.missing,
digits=digits,...) #13Mar99
Z[[i]] <- z
if(exclude.missing && length(z)==0)
missing.vars <- c(missing.vars,nam[i])
}
attr(Z, 'descript') <- descript
attr(Z, 'dimensions') <- d
attr(Z, 'missing.vars') <- missing.vars
structure(Z, class="describe")
}
describe.data.frame <- function(x, descript, exclude.missing=TRUE,
digits=4, ...)
{
if(missing(descript))
descript <- as.character(sys.call())[2]
nam <- names(x)
Z <- list()
nams <- character(0)
i <- 0
missing.vars <- NULL
for(xx in x) {
mat <- is.matrix(xx)
i <- i+1
z <-
if(mat)
describe.matrix(xx,nam[i],exclude.missing=exclude.missing,
digits=digits,...)
else
describe.vector(xx,nam[i],exclude.missing=exclude.missing,
digits=digits,...)
all.missing <- length(z)==0
if(exclude.missing && all.missing)
missing.vars <- c(missing.vars, nam[i])
else {
Z <- c(Z, if(mat) z else list(z))
nams <- c(nams, if(mat) names(z) else nam[i])
}
}
names(Z) <- nams
attr(Z, 'descript') <- descript
attr(Z, 'dimensions') <- dim(x)
attr(Z, 'missing.vars') <- missing.vars
structure(Z, class="describe")
}
describe.formula <- function(x, descript, data, subset, na.action,
digits=4, weights, ...)
{
mf <- match.call(expand.dots=FALSE)
mf$formula <- x
mf$x <- mf$descript <- mf$file <- mf$append <- mf$... <- mf$digits <- NULL
if(missing(na.action))
mf$na.action <- na.retain
mf[[1]] <- as.name("model.frame")
mf <- eval(mf, sys.parent())
weights <- model.extract(mf, weights)
if(missing(descript)) {
ter <- attr(mf,"terms")
d <- as.character(x)
if(attr(ter,"response")==1) d <- c(d[2],d[1],d[-(1:2)])
else d <- d[-1]
d <- paste(d, collapse=" ")
descript <- d
}
Z <- describe.data.frame(mf, descript, digits=digits, weights=weights, ...)
if(length(z <- attr(mf,"na.action")))
attr(Z,'naprint') <- naprint(z)
Z
}
na.retain <- function(d) d
print.describe <-
function(x, ...)
{
if(prType() == 'html') return(html.describe(x, ...))
at <- attributes(x)
if(length(at$dimensions)) {
cat(at$descript,'\n\n',at$dimensions[2],' Variables ',at$dimensions[1],
' Observations\n')
if(length(at$naprint)) cat('\n',at$naprint,'\n')
w <- paste(rep('-', .Options$width), collapse='')
cat(w, '\n', sep='')
for(z in x) {
if(length(z)==0)
next
print.describe.single(z, ...)
cat(w, '\n', sep='')
}
if(length(at$missing.vars)) {
cat('\nVariables with all observations missing:\n\n')
print(at$missing.vars, quote=FALSE)
}
} else print.describe.single(x, ...)
invisible()
}
## Function to format part of describe.single output after description & counts
## verb=1 means verbatim mode open
formatdescribeSingle <-
function(x, condense=c('extremes', 'frequencies', 'both', 'none'),
lang=c('plain', 'latex', 'html'), verb=0, lspace=c(0, 0),
size=85, ...)
{
condense <- match.arg(condense)
lang <- match.arg(lang)
wide <- .Options$width
specs <- markupSpecs[[lang]]
bv <- function() {
if(lang == 'latex' && ! verb) '\\begin{verbatim}' else character()
}
vs <- if(lang == 'latex' && lspace[2] != 0)
function() cat('\\vspace{', -lspace[2], 'ex}\n',
sep='') else function() {}
vbtm <- if(lang == 'html')
function(x, omit1b=FALSE, ...)
htmlVerbatim(x, size=size, omit1b=omit1b, ...)
else
function(x, omit1b=NULL) capture.output(print(x, quote=FALSE, ...))
R <- character(0)
v <- x$values
is.standard <- length(v) && is.list(v) &&
all(names(v) == c('value', 'frequency'))
v_len <- if(is.standard) length(v$value)
if(is.standard && v_len > 0L && v_len <= 20L) {
# address GH issue #104
altv <- format(v$value)
altv[is.na(altv)] <- 'NA'
# check total width
print.freq <- sum(nchar(altv)) <= 200
} else print.freq <- FALSE
print.ext <- length(x$extremes) ## && ! print.freq
if(print.ext) {
val <- format(x$extremes)
w <- nchar(paste(val, collapse=' '))
R <- c(R, bv()); verb <- 1
if(condense %in% c('extremes', 'both')) {
if(lang == 'html') {
fsize <- specs$size
mnb <- function(x) specs$color(x, col='MidnightBlue')
spc <- specs$space
blo <- paste0(mnb('lowest'), spc, ':')
bhi <- paste0(mnb('highest'), ':')
if(w + 2 <= wide) {
low <- paste(blo, paste(val[1: 5], collapse=' '))
hi <- paste(bhi, paste(val[6:10], collapse=' '))
R <- c(R, fsize(paste(low, ', ', hi), pct=size))
} else {
low <- data.frame(name=blo, e1=val[1], e2=val[2], e3=val[3],
e4=val[4], e5=val[5])
hi <- data.frame(name=bhi, e1=val[6], e2=val[7], e3=val[8],
e4=val[9], e5=val[10])
tab <- html(rbind(low, hi, make.row.names=FALSE),
align='r',
header=NULL, border=0, size=size, file=FALSE)
R <- c(R, tab)
}
} # end lang='html'
else { # lang='plain' or 'latex'
low <- paste('lowest :', paste(val[1: 5], collapse=' '))
hi <- paste('highest:', paste(val[6:10], collapse=' '))
R <- c(R,
if(w + 2 <= wide)
c('', paste0(low, ', ', hi))
else c('', low, hi) )
}
} # end condense applicable to extremes
else
R <- c(R, if(lang != 'html') '', vbtm(val))
}
if(print.freq) {
R <- c(R, bv()); verb <- 1
val <- v$value
freq <- v$frequency
prop <- round(freq / sum(freq), 3)
## First try table output, if will fit in no more than 2 sets of 4 lines
condensed <- TRUE
if(condense %nin% c('frequencies', 'both')) {
fval <- if(is.numeric(val))
format(val) else format(val, justify='right')
ffreq <- format(freq)
fprop <- format(prop)
lval <- nchar(fval[1])
lfreq <- nchar(ffreq[1])
lprop <- nchar(fprop[1])
m <- max(lval, lfreq, lprop)
## Right justify entries in each row
bl <- ' '
fval <- paste0(substring(bl, 1, m - lval ), fval)
ffreq <- paste0(substring(bl, 1, m - lfreq), ffreq)
fprop <- paste0(substring(bl, 1, m - lprop), fprop)
w <- rbind(Value=fval, Frequency=ffreq, Proportion=fprop)
colnames(w) <- rep('', ncol(w))
out <- capture.output(print(w, quote=FALSE))
if(length(out) <= 8) {
R <- c(R, vbtm(w, omit1b=TRUE))
condensed <- FALSE
}
} # end condense frequencies (or both)
if(condensed) {
fval <- as.character(val)
ffreq <- as.character(freq)
fprop <- format(prop)
lval <- nchar(fval[1])
lfreq <- nchar(ffreq[1])
lprop <- nchar(fprop[1])
w <- paste0(fval, ' (', ffreq, ', ', fprop, ')')
w <- strwrap(paste(w, collapse=', '), width=wide)
R <- c(R, '', w)
}
if(length(x$roundedTo))
R <- c(R, '',
paste('For the frequency table, variable is rounded to the nearest',
format(x$roundedTo, scientific=3)))
} else if(length(v) && ! is.standard)
R <- c(R, '', vbtm(v))
if(length(x$mChoice)) {
R <- c(R, bv()); verb <- 1
R <- c(R, '', vbtm(x$mChoice, prlabel=FALSE))
}
if(lang == 'latex' && verb) R <- c(R, '\\end{verbatim}')
R
}
print.describe.single <-
function(x, ...)
{
wide <- .Options$width
des <- x$descript
if(length(x$units))
des <- paste0(des, ' [', x$units, ']')
if(length(x$format))
des <- paste0(des, ' Format:', x$format)
cat(des,'\n')
print(x$counts, quote=FALSE)
R <- formatdescribeSingle(x, lang='plain', ...)
cat(R, sep='\n')
invisible()
}
'[.describe' <- function(object, i, ...)
{
at <- attributes(object)
object <- '['(unclass(object),i)
structure(object, descript=at$descript,
dimensions=c(at$dimensions[1], length(object)),
class='describe')
}
latex.describe <-
function(object, title=NULL,
file=paste('describe',
first.word(expr=attr(object, 'descript')),
'tex', sep='.'),
append=FALSE, size='small',
tabular=TRUE, greek=TRUE, spacing=0.7, lspace=c(0,0), ...)
{
at <- attributes(object)
ct <- function(..., file, append=FALSE) {
if(file=='') cat(...)
else cat(..., file=file, append=append)
invisible()
}
spc <- if(spacing == 0) '' else
paste0('\\begin{spacing}{', spacing, '}\n')
ct(spc, file=file, append=append)
if(length(at$dimensions)) {
ct('\\begin{center}\\textbf{', latexTranslate(at$descript), '\\\\',
at$dimensions[2],'Variables~~~~~',at$dimensions[1],
'~Observations}\\end{center}\n', file=file, append=TRUE)
if(length(at$naprint))
ct(at$naprint,'\\\\\n', file=file, append=TRUE)
ct('\\smallskip\\hrule\\smallskip{\\',size,'\n',
sep='', file=file, append=TRUE)
vnames <- at$names
i <- 0
for(z in object) {
i <- i + 1
if(length(z)==0)
next
val <- z$values
potentiallyLong <-
length(val) && ! is.matrix(val) &&
length(val) != 10 || ! all(names(val)==
c("L1","L2","L3","L4","L5","H5","H4","H3","H2","H1"))
dovbox <- TRUE # was ! potentiallyLong
if(dovbox) cat('\\vbox{', file=file, append=TRUE)
latex.describe.single(z, vname=vnames[i],
file=file, append=TRUE,
tabular=tabular, greek=greek,
lspace=lspace, ...)
ct('\\smallskip\\hrule\\smallskip\n', file=file, append=TRUE)
if(dovbox) cat('}\n', file=file, append=TRUE)
}
if(length(mv <- at$missing.vars)) {
ct('\\smallskip\\noindent Variables with all observations missing:\\ \\smallskip\n',
file=file, append=TRUE)
mv <- latexTranslate(mv)
mv <- paste0('\\texttt{',mv,'}')
mv <- paste(mv, collapse=', ')
ct(mv, file=file, append=TRUE)
}
spc <- if(spacing == 0) '}\n' else '}\\end{spacing}\n'
ct(spc, file=file, append=TRUE)
}
else {
val <- object$values
potentiallyLong <-
length(val) && ! is.matrix(val) &&
length(val) != 10 || ! all(names(val)==
c("L1","L2","L3","L4","L5","H5","H4","H3","H2","H1"))
dovbox <- TRUE # was ! potentiallyLong
if(dovbox) cat('\\vbox{', file=file, append=TRUE)
latex.describe.single(object,
vname=first.word(expr=at$descript),
file=file, append=TRUE, size=size,
tabular=tabular, lspace=lspace, ...)
if(dovbox) cat('}\n', file=file, append=TRUE)
spc <- if(spacing == 0) '\n' else '\\end{spacing}\n'
ct(spc, file=file, append=TRUE)
}
structure(list(file=file, style=c('setspace','relsize')),
class='latex')
}
latex.describe.single <-
function(object, title=NULL, vname,
file, append=FALSE, size='small',
tabular=TRUE, greek=TRUE, lspace=c(0,0), ...)
{
ct <- function(..., file, append=FALSE) {
if(file=='') cat(...)
else cat(..., file=file, append=append)
invisible()
}
oldw <- options('width')
options(width=if(size == 'small') 95 else 85)
on.exit(options(oldw))
wide <- switch(size,
normalsize = 73, # was 66
small = 95, # was 73
scriptsize =110, # was 93
73)
Values <- object$values
## Put graph on its own line if length of label > 3.5 inches
## For normalsize there are 66 characters per 4.8 in. standard width
z <- latexTranslate(object$descript, '&', '\\&', greek=greek)
## If any math mode ($ not preceeded by \) don't put label part in bold
des <- if(! length(grep('[^\\]\\$', z)))
paste0('\\textbf{', z, '}')
else {
## Get text before : (variable name)
sp <- strsplit(z, ' : ')[[1]]
vnm <- sp[1]
rem <- paste(sp[-1], collapse=':')
paste0('\\textbf{', vnm, '}: ', rem)
}
if(length(object$units))
des <- paste0(des, '{\\smaller[1] [',
latexTranslate(object$units),']}')
if(length(object$format))
des <- paste0(des, '{\\smaller~~Format:', latexTranslate(object$format),
'}')
desbas <- paste(object$descript,
if(length(object$units))
paste0(' [', object$units, ']'),
if(length(object$format))
paste0(' Format:', object$format))
ct('\\noindent', des, sep='', file=file, append=append)
lco <- if(length(Values)) length(Values$frequency) else 0
if(lco > 2) {
counts <- Values$frequency
maxcounts <- max(counts)
## Scale distinct values to range from 1 : lco
va <- Values$value
if(! is.numeric(va)) va <- 1 : lco
else {
rang <- range(va)
va <- 1 + (lco - 1) * (va - rang[1]) / diff(rang)
}
## \mbox{~~~} makes \hfill work
ct(if(nchar(desbas)/(wide / 4.8) > (4.8 - 1.5))' \\\\ \\mbox{~~~} \n',
'\\setlength{\\unitlength}{0.001in}\\hfill',
'\\begin{picture}(1.5,.1)(1500,0)',
'\\linethickness{0.6pt}\n', sep='', file=file, append=TRUE)
## Todo: may need to label limits used since are pretty()'d versions
for(i in 1 : lco) {
ct('\\put(',
round(1000 * (va[i] - 1) * 1.5 / lco),',0){\\line(0,1){',
max(1, round(1000 * counts[i] / maxcounts * .1)), '}}\n',
sep='', file=file, append=TRUE)
}
ct('\\end{picture}\n', file=file, append=TRUE)
} else ct('\n', file=file, append=TRUE)
sz <- ''
if(tabular) {
ml <- nchar(paste(object$counts, collapse=' '))
if(ml > 90)
tabular <- FALSE
else if(ml > 80)
sz <- '[2]'
}
ct('\n{\\smaller', sz, '\n', sep='', file=file, append=TRUE)
if(tabular) {
if(lspace[1] != 0)
ct('\\vspace{', -lspace[1], 'ex}\n', sep='', file=file, append=TRUE)
ct('\\begin{tabular}{',
paste(rep('r',length(object$counts)),collapse=''),'}\n',
file=file, append=TRUE)
ct(paste(latexTranslate(names(object$counts)), collapse='&'), '\\\\\n',
file=file, append=TRUE)
ct(paste(latexTranslate(object$counts), collapse='&'), '\\end{tabular}\n',
file=file, append=TRUE)
}
vs <- if(lspace[2] != 0) function() ct('\\vspace{', -lspace[2], 'ex}\n',
sep='', file=file, append=TRUE) else function() {}
if(file != '')
sink(file, append=TRUE)
verb <- 0
if(! tabular) {
vs()
cat('\\begin{verbatim}\n'); verb <- 1
print(object$counts, quote=FALSE)
}
R <- formatdescribeSingle(object, lang='latex', verb=verb,
lspace=lspace, ...)
cat(R, sep='\n')
cat('}\n') ## ends \smaller
if(file != '') sink()
invisible()
}
html.describe <-
function(object, size=85,
tabular=TRUE, greek=TRUE, scroll=FALSE, rows=25, cols=100, ...)
{
at <- attributes(object)
m <- markupSpecs$html
center <- m$center
bold <- m$bold
code <- m$code
br <- m$br
lspace <- m$lspace
sskip <- m$smallskip
hrule <- m$hrulethin
fsize <- m$size
mnb <- function(x) m$color(x, col='MidnightBlue')
R <- c(m$unicode, m$style()) ## define thinhr (and others not needed here)
R <- c(R, paste0('<title>', at$descript, ' Descriptives</title>'))
if(length(at$dimensions)) {
R <- c(R,
mnb(center(bold(paste(htmlTranslate(at$descript), sskip,
at$dimensions[2], ' Variables', lspace,
at$dimensions[1],' Observations')))))
if(length(at$naprint)) R <- c(R, '', at$naprint)
R <- c(R, hrule)
vnames <- at$names
i <- 0
for(z in object) {
i <- i + 1
if(! length(z))
next
r <- html.describe.single(z, ## vname=vnames[i],
tabular=tabular, greek=greek, size=size, ...)
R <- c(R, r, hrule)
}
if(length(mv <- at$missing.vars)) {
R <- c(R, sskip, 'Variables with all observations missing:',
br, sskip)
mv <- paste(code(htmlTranslate(mv)), collapse=', ')
R <- c(R, mv)
}
if(scroll) R <- m$scroll(R, size=size, rows=rows, cols=cols,
name=at$descript)
}
else
R <- c(R, html.describe.single(object, tabular=tabular,
greek=greek, size=size, ...))
rendHTML(R)
}
html.describe.single <-
function(object, size=85,
tabular=TRUE, greek=TRUE, ...)
{
m <- markupSpecs$html
center <- m$center
bold <- m$bold
code <- m$code
br <- m$br
lspace <- m$lspace
sskip <- m$smallskip
fsize <- m$size
smaller<- m$smaller
pngfile <- paste(tempdir(), 'needle1234567890a.png', sep='/')
oldw <- options('width')
options(width=if(size < 90) 95 else 85)
on.exit(options(oldw))
wide <- if(size >= 90) 73 else if(size >= 75) 95 else 110
z <- htmlTranslate(object$descript, greek=greek)
des <- if(! length(grep(':', z))) bold(z)
else {
## Get text before : (variable name)
sp <- strsplit(z, ' : ')[[1]]
vnm <- sp[1]
rem <- paste(sp[-1], collapse=':')
paste0(bold(vnm), ': ', rem)
}
if(length(object$units))
des <- m$varlabel(des, htmlTranslate(object$units))
if(length(object$format))
des <- paste0(des, lspace,
smaller(paste0('Format:',
htmlTranslate(object$format))))
Values <- object$values
lco <- if(length(Values)) length(Values$frequency) else 0
if(lco > 2) {
counts <- Values$frequency
maxcounts <- max(counts)
counts <- counts / maxcounts
## Scale distinct values to range from 1 : lco
va <- Values$value
if(! is.numeric(va)) va <- 1 : lco
else {
rang <- range(va)
va <- 1 + (lco - 1) * (va - rang[1]) / diff(rang)
}
w <- if(lco >= 50) 150 / lco else 3
des <- paste0(des,
m$rightAlign(tobase64image(pngNeedle(counts,
x=va, w=w, h=13, lwd=2,
file=pngfile))))
}
R <- des
sz <- size
if(tabular) {
ml <- nchar(paste(object$counts, collapse=' '))
if(ml > 90)
tabular <- FALSE
else if(ml > 80)
sz <- round(0.875 * size)
}
if(tabular) {
d <- as.data.frame(as.list(object$counts))
colnames(d) <- names(object$counts)
tab <- html(d, file=FALSE, align='c',
align.header='c', bold.header=FALSE,
col.header='MidnightBlue', border=0,
translate=TRUE, size=sz)
R <- c(R, tab)
}
else
R <- c(R, htmlVerbatim(object$counts, size=sz))
R <- c(R, formatdescribeSingle(object, lang='html', ...))
R
}
dataDensityString <- function(x, nint=30)
{
x <- as.numeric(x)
x <- x[! is.na(x)]
if(length(x) < 2) return('')
r <- range(x)
x <- floor(nint * (x-r[1])/(r[2]-r[1]))
x <- pmin(tabulate(x), 37)
paste0(format(r[1]),' <',
paste(substring(' 1234567890abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ',
x+1,x+1), collapse=''),
'> ',format(r[2]))
}
contents <- function(object, ...) UseMethod('contents')
contents.data.frame <- function(object, sortlevels=FALSE,
id=NULL, range=NULL, values=NULL, ...)
{
dfname <- deparse(substitute(object))
nam <- names(object)
d <- dim(object)
n <- length(nam)
fl <- nas <- integer(n)
cl <- sm <- lab <- un <- longlab <- character(n)
Lev <- list()
for(i in 1:n) {
x <- object[[i]]
at <- attributes(x)
if(length(at$label)) lab[i] <- at$label
if(length(at$longlabel)) longlab[i] <- at$longlabel
if(length(at$units)) un[i] <- at$units
atl <- at$levels
fl[i] <- length(atl)
cli <- at$class[at$class %nin% c('labelled', 'factor')]
if(length(cli)) cl[i] <- cli[1]
sm[i] <- storage.mode(x)
nas[i] <- sum(is.na(x))
if(length(atl)) {
if(sortlevels) atl <- sort(atl)
if(length(Lev)) for(j in 1 : length(Lev)) {
w <- Lev[[j]]
if(! is.name(w) && is.logical(all.equal(w, atl))) {
atl <- as.name(names(Lev)[j])
break
}
}
Lev[[nam[i]]] <- atl
}
}
w <- list(Labels = if(any(lab != '')) lab,
Units = if(any(un != '')) un,
Levels = if(any(fl > 0)) fl,
Class = if(any(cl != '')) cl,
Storage= sm,
NAs = if(any(nas > 0)) nas )
w <- w[sapply(w, function(x)length(x) > 0)]
## R does not remove NULL elements from a list
structure(list(contents=data.frame(w, row.names=nam),
dim=d, maxnas=max(nas),
id=id, rangevar=range, valuesvar=values,
unique.ids = if(length(id) && id %in% nam)
length(unique(object[[id]])),
range = if(length(range) && range %in% nam)
paste(as.character(range(object[[range]], na.rm=TRUE)),
collapse='-'),
values = if(length(values) && values %in% nam)
paste(if(is.factor(object[[values]])) levels(object[[values]])
else sort(unique(object[[values]])), collapse=' '),
dfname=dfname,
Levels=Lev,
longLabels=if(any(longlab != ''))
structure(longlab, names=nam)),
class='contents.data.frame')
}
print.contents.data.frame <-
function(x, sort=c('none','names','labels','NAs'),
prlevels=TRUE, maxlevels=Inf, number=FALSE, ...)
{
sort <- match.arg(sort)
if(prType() == 'html')
return(html.contents.data.frame(x, sort=sort, prlevels=prlevels,
maxlevels=maxlevels, number=number, ...) )
d <- x$dim
maxnas <- x$maxnas
cat('\nData frame:', x$dfname, '\t', d[1],' observations and ', d[2],
' variables Maximum # NAs:', maxnas, '\n', sep='')
if(length(x$id)) cat('Distinct ', x$id, ':', x$unique.ids, '\t', sep='')
if(length(x$rangevar)) cat(x$rangevar, ' range:', x$range, '\t', sep='')
if(length(x$valuesvar))cat(x$valuesvar, ':', x$values, sep='')
cat('\n\n')
cont <- x$contents
nam <- row.names(cont)
if(number) row.names(cont) <- paste(format(1:d[2]), row.names(cont))
switch(sort,
names={
cont <- cont[order(nam),,drop=FALSE]
},
labels={
if(length(cont$Labels))
cont <- cont[order(cont$Labels, nam),, drop=FALSE]
},
NAs={
if(maxnas > 0)
cont <- cont[order(cont$NAs, nam),, drop=FALSE]
})
if(length(cont$Levels))
cont$Levels <- ifelse(cont$Levels == 0, '', format(cont$Levels))
print(cont)
if(prlevels && length(L <- x$Levels)) {
cat('\n')
nam <- names(L)
w <- .Options$width - max(nchar(nam)) - 5
reusingLevels <- sapply(L, is.name)
fullLevels <- which(! reusingLevels)
namf <- lin <- names(L[fullLevels])
## separate multiple lines per var with \n for print.char.matrix
j <- 0
for(i in fullLevels) {
j <- j + 1
varsUsingSame <- NULL
if(sum(reusingLevels)) {
for(k in which(reusingLevels))
if(L[[k]] == namf[j]) varsUsingSame <- c(varsUsingSame, nam[k])
if(length(varsUsingSame))
namf[j] <- paste(c(namf[j], varsUsingSame), collapse='\n')
}
Li <- L[[i]]
if(length(Li) > maxlevels) Li <- c(Li[1 : maxlevels], '...')
lin[j] <- paste(pasteFit(Li, width=w), collapse='\n')
}
z <- cbind(Variable=namf, Levels=lin)
print.char.matrix(z, col.txt.align='left', col.name.align='left',
row.names=TRUE, col.names=TRUE)
}
longlab <- x$longLabels
if(length(longlab)) {
if(existsFunction('strwrap'))
for(i in 1:length(longlab)) {
if(longlab[i] != '')
longlab[i] <- paste(strwrap(longlab[i],width=.85*.Options$width ),
collapse='\n')
}
i <- longlab != ''
nam <- names(longlab)
z <- cbind(Variable=nam[i], 'Long Label'=longlab[i])
print.char.matrix(z, col.names=TRUE, row.names=FALSE,
cell.align='left')
}
invisible()
}
html.contents.data.frame <-
function(object, sort=c('none', 'names', 'labels', 'NAs'), prlevels=TRUE,
maxlevels=Inf,
levelType=c('list', 'table'),
number=FALSE, nshow=TRUE, ...)
{
sort <- match.arg(sort)
levelType <- match.arg(levelType)
mu <- markupSpecs$html
lspace <- mu$lspace
lspace <- ' ' # override - browsers were not rendering correctly
hrule <- mu$hrule
d <- object$dim
maxnas <- object$maxnas
R <- paste0('<title>', object$dfname, ' Contents</title>')
if(nshow) {
R <- c(R,
paste0(hrule, '<h4>Data frame:', object$dfname,
'</h4>', d[1],
' observations and ', d[2],
' variables, maximum # NAs:',maxnas, lspace, lspace) )
if(length(object$id))
R <- paste0(R, 'Distinct ', object$id, ':', object$unique.ids,
lspace, lspace)
if(length(object$rangevar))
R <- paste0(R, object$rangevar, ' range:', object$range,
lspace, lspace)
if(length(object$valuesvar))
R <- paste0(R, object$valuesvar, ':', object$values,
lspace, lspace)
R <- c(R, hrule)
} else
R <- paste0(hrule, '<h4>Data frame:', object$dfname,
'</h4>', ' Variables:', d[2], hrule)
cont <- object$contents
nam <- row.names(cont)
if(number) {
rn <- paste(format(1:d[2]), row.names(cont))
nbsp <- htmlSpecial('nbsp')
rn <- sedit(rn, ' ', paste0(nbsp, nbsp))
row.names(cont) <- rn
}
switch(sort,
names={cont <- cont[order(nam),,drop=FALSE]},
labels={
if(length(cont$Labels))
cont <- cont[order(cont$Labels, nam),,drop=FALSE]
},
NAs={
if(maxnas>0) cont <- cont[order(cont$NAs,nam),,drop=FALSE]
})
link <- matrix('', nrow=nrow(cont), ncol=1+ncol(cont),
dimnames=list(dimnames(cont)[[1]], c('Name', dimnames(cont)[[2]])))
longlab <- object$longLabels
if(length(longlab)) {
longlab <- longlab[longlab != '']
link[names(longlab),'Name'] <- paste('#longlab',names(longlab),sep='.')
}
L <- object$Levels
Lnames <- names(L)
if(length(cont$Levels)) {
cont$Levels <- ifelse(cont$Levels==0, '', format(cont$Levels))
namUsed <- sapply(L, function(z) if(is.name(z)) as.character(z) else '')
reusingLevels <- namUsed != ''
fullLevels <- which(! reusingLevels)
namUsed <- ifelse(reusingLevels, namUsed, Lnames)
names(namUsed) <- Lnames
link[,'Levels'] <- ifelse(cont$Levels=='', '', paste('#levels',namUsed[nam],sep='.'))
}
adj <- rep('l', length(cont))
adj[names(cont) %in% c('NAs','Levels')] <- 'r'
if(! nshow) {
cont$NAs <- NULL
link <- link[, colnames(link) != 'NAs', drop=FALSE]
adj <- adj[names(adj) != 'NAs']
}
out <- html(cont, file=FALSE, rownames=TRUE,
link=link, border=2,
col.just=adj, ...)
R <- c(R, as.character(out), hrule)
if(prlevels && length(L) > 0) {
if(levelType=='list') {
R <- c(R, '<h5>Category Levels</h5>')
for(i in fullLevels) {
l <- L[[i]]
nami <- Lnames[i]
w <- nami
if(sum(reusingLevels))
for(k in which(reusingLevels))
if(L[[k]] == nami) w <- c(w, Lnames[k])
R <- c(R, paste0('<a name="levels.', nami, '"><h6>',
paste(w, collapse=', '), '</h6></a>'))
if(length(l) > maxlevels) l <- c(l[1 : maxlevels], '...')
for(k in l) R <- c(R, paste0('<li>', k, '</li>\n'))
}
}
else {
## Function to split a character vector x as evenly as
## possible into n elements, pasting multiple elements
## together when needed
evenSplit <- function(x, n) {
indent <- function(z) if(length(z) == 1) z else
c(z[1], paste0(' ', z[-1]))
m <- length(x)
if(m <= n) return(c(indent(x), rep('',n-m)))
totalLength <- sum(nchar(x)) + (m-1)*3.5
## add indent, comma, space
lineLength <- ceiling(totalLength/n)
y <- pasteFit(x, sep=', ', width=lineLength)
m <- length(y)
if(m > n) for(j in 1:10) {
lineLength <- round(lineLength*1.1)
y <- pasteFit(x, sep=', ', width=lineLength)
m <- length(y)
if(m <= n) break
}
## Take evasive action if needed
if(m == n) indent(y) else if(m < n)
c(indent(y), rep('', n - m)) else
c(paste(x, collapse=', '), rep('', n - 1))
}
nam <- names(L)
v <- lab <- lev <- character(0)
j <- 0
for(i in fullLevels) {
j <- j + 1
l <- L[[i]]
if(length(l) > maxlevels) l <- c(l[1 : maxlevels], '...')
nami <- nam[i]
v <- c(v, nami)
w <- nami
if(sum(reusingLevels))
for(k in which(reusingLevels)) if(L[[k]] == nam[i]) w <- c(w, nam[k])
lab <- c(lab, evenSplit(w, length(l)))
lev <- c(lev, l)
}
z <- cbind(Variable=lab, Levels=lev)
out <- html(z, file=FALSE,
link=ifelse(lab=='','',paste('levels',v,sep='.')),
linkCol='Variable', linkType='name', border=2,...)
R <- c(R, as.character(out), hrule)
}
}
i <- longlab != ''
if(any(i)) {
nam <- names(longlab)[i]
names(longlab) <- NULL
lab <- paste('longlab', nam, sep='.')
z <- cbind(Variable=nam, 'Long Label'=longlab[i])
out <- html(z, file=FALSE,
link=lab, linkCol='Variable', linkType='name', ...)
R <- c(R, as.character(out), hrule)
}
rendHTML(R)
}
contents.list <- function(object, dslabels=NULL, ...) {
nam <- names(object)
if(length(dslabels)) {
dslabels <- dslabels[nam]
names(dslabels) <- NULL
}
g <- function(w) {
if(length(w)==0 || is.null(w))
c(Obs=0, Var=if(is.null(w))
NA
else
length(w),
Var.NA=NA)
else
c(Obs=length(w[[1]]), Var=length(w),
Var.NA=sum(sapply(w, function(x) sum(is.present(x))==0)))
}
v <- t(sapply(object, g))
structure(list(contents=if(length(dslabels))
data.frame(Label=dslabels,Obs=v[,'Obs'],
Var=v[,'Var'],Var.NA=v[,'Var.NA'],
row.names=nam)
else
data.frame(Obs=v[,'Obs'],Var=v[,'Var'],
Var.NA=v[,'Var.NA'], row.names=nam)),
class='contents.list')
}
print.contents.list <-
function(x, sort=c('none','names','labels','NAs','vars'), ...)
{
sort <- match.arg(sort)
cont <- x$contents
nam <- row.names(cont)
cont <- cont[
switch(sort,
none=1:length(nam),
names=order(nam),
vars=order(cont$Var),
labels=order(cont$Label, nam),
NAs=order(cont$Var.NA,nam)),]
print(cont)
invisible()
}
