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dotchartpl <- function(x, major=NULL, minor=NULL,
group=NULL, mult=NULL,
big=NULL, htext=NULL,
num=NULL, denom=NULL,
numlabel='', denomlabel='',
fun=function(x) x, ifun=function(x) x,
op='-',
lower=NULL, upper=NULL,
refgroup=NULL, sortdiff=TRUE, conf.int=0.95,
minkeep=NULL,
xlim=NULL, xlab='Proportion',
tracename=NULL, limitstracename='Limits',
nonbigtracename='Stratified Estimates',
dec=3, width=800, height=NULL,
col=colorspace::rainbow_hcl
) {
if (!requireNamespace("plotly"))
stop("This function requires the 'plotly' package.")
mu <- markupSpecs$html
bold <- mu$bold
if(! length(xlim)) xlim <- c(min(c(x, lower), na.rm=TRUE),
max(c(x, upper), na.rm=TRUE))
majorpres <- length(major) > 0
major <- if(majorpres) as.character(major) else rep(' ', length(x))
minorpres <- length(minor) > 0
if(! (majorpres || minorpres)) stop('must specify major or minor or both')
grouppres <- length(group) > 0 ## superpositioning variable
multpres <- length(mult) > 0
limspres <- length(lower) * length(upper) > 0
rgpres <- length(refgroup) > 0
if(minorpres) minor <- as.character(minor)
if(grouppres) group <- as.character(group)
if(multpres) mult <- as.character(mult)
ugroup <- if(grouppres) unique(group) else ''
fmt <- function(x) format(round(x, dec))
if(rgpres) {
if(! grouppres || multpres || length(big))
stop('when refgroup is given, group must be given and mult and big must not be used')
## big=TRUE for non-stratified estimates
if(length(ugroup) != 2)
stop('refgroup only works for 2 groups')
if(refgroup %nin% unique(group))
stop(paste('refgroup must be one of the following:',
paste(unique(group), collapse=', ')))
altgroup <- setdiff(ugroup, refgroup)
}
cols <- if(length(col)) {
if(! is.function(col)) col
else
if(grouppres) col(length(unique(group)))
else
col(1) }
if(! length(col) && ! grouppres) cols <- 'black'
dropped <- character(0)
D <- NULL
if(rgpres && minorpres) {
z <- pairUpDiff(x, major, minor, group,
refgroup=refgroup, lower=lower, upper=upper,
minkeep=minkeep, sortdiff=sortdiff, conf.int=conf.int)
Z <- z$X
D <- z$D
dropped <- z$dropped
i <- Z[,'subscripts']
x <- x[i]
major <- major[i]
minor <- minor[i]
group <- group[i]
if(length(num)) num <- num[i]
if(length(denom)) denom <- denom[i]
if(length(mult)) mult <- mult[i]
if(length(big)) big <- big[i]
if(length(lower)) lower <- lower[i]
if(length(upper)) upper <- upper[i]
if(length(htext)) htext <- htext[i]
} # end if(rgpres && ...
ht <- htext
if(numlabel != '') numlabel <- paste0(' ', numlabel)
if(denomlabel != '') denomlabel <- paste0(' ', denomlabel)
if(length(num))
ht <- paste0(ht, if(length(htext)) mu$lspace,
fmt(fun(x)), mu$lspace,
mu$frac(paste0(num, numlabel),
paste0(denom, denomlabel), size=95))
## if confidence interval for differences are not to be displayed,
## put point estimate confidence intervals in point hypertext
if(length(ugroup) != 2 && limspres)
ht <- paste0(ht, ' [',
fmt(fun(lower)), ', ',
fmt(fun(upper)), ']')
ht <- paste0(ht, if(length(ht)) '<br>',
if(majorpres) paste0(major, ': '))
if(minorpres) ht <- paste0(ht, minor)
if(grouppres) ht <- paste0(ht, '<br>',
gsub(' stratified<br>by .*', '', group))
if(multpres) ht <- paste0(ht, '<br>', mult)
n <- length(x)
minor <- if(minorpres) minor else rep('', n)
group <- if(grouppres) group else rep('', n)
mult <- if(multpres) mult else rep('', n)
if(! length(big)) big <- rep(TRUE, n)
w <- c(length(x), length(major), length(minor), length(group),
length(num), length(denom),
length(mult), length(big), length(htext),
length(lower), length(upper))
w <- w[w > 0]
if(diff(range(w)) > 0)
stop('x, major, minor, group, num, denom, mult, big, htext, lower, upper must all have same length when used')
y <- 1
X <- Y <- Ydiff <- Lower <- Upper <- numeric(0)
Group <- Htext <- Htextl <- character(0)
Big <- logical(0)
yl <- numeric(0); yt <- ytnb <- character(0)
difflower <- diffupper <- Diff <- numeric(0)
coldiff <- htdiff <- character(0)
lines <- 0
for(ma in unique(major)) {
y <- y - 1
yl <- c(yl, y)
yt <- c(yt, bold(ma))
ytnb <- c(ytnb, ma)
lminor <- unique(minor[major == ma])
y <- y + if(all(lminor == '')) 0.4 else 0
lines <- lines + 1
for(mi in lminor) {
y <- y - 0.4
lines <- lines + (mi != '')
j <- which(major == ma & minor == mi)
X <- c(X, x[j])
Y <- c(Y, ifelse(big[j], y, y - .14))
if(length(D)) {
k <- which(D$major == ma & D$minor == mi)
if(length(k) != 1)
stop('must have one observation for a major/minor/group combination')
diff <- D$diff[k]
coldiff <- c(coldiff,
ifelse(diff > 0,
paste0(altgroup, ' ',
htmlTranslate('>'), ' ', refgroup),
paste0(refgroup, ' ',
htmlTranslate('>='), ' ', altgroup)))
Ydiff <- c(Ydiff, y)
htd <- if(majorpres) paste0(ma, ': ') else ''
if(minorpres) htd <- paste0(htd, mi)
htd <- paste0(htd, '<br>', altgroup, ' ', op, ' ',
refgroup, ': ', fmt(fun(diff)))
if(! is.logical(conf.int) && limspres && length(D)) {
dlower <- fmt(fun(D$lower[k]))
dupper <- fmt(fun(D$upper[k]))
htd <- paste0(htd, '<br>', conf.int, ' C.L.: [', dlower,
', ', dupper, ']')
Diff <- c(Diff, diff)
difflower <- c(difflower, D$lowermid[k])
diffupper <- c(diffupper, D$uppermid[k])
}
htdiff <- c(htdiff, htd)
} # end if(length(D))
if(limspres && ! length(D)) {
Lower <- c(Lower, lower[j])
Upper <- c(Upper, upper[j])
Htextl <- c(Htextl,
paste0('[',
fmt(fun(lower[j])), ', ',
fmt(fun(upper[j])), ']' ) )
}
Group <- c(Group, group[j])
Big <- c(Big, big[j])
Htext <- c(Htext, ht[j])
if(mi != '') {
yl <- c(yl, y)
yt <- c(yt, mi)
ytnb <- c(ytnb, mi)
}
} # end mi in lminor
} # end ma in lmajor
d <- data.frame(X, Y, Group, Htext, Big)
if(limspres && ! length(D)) {
d$Lower <- Lower
d$Upper <- Upper
d$Htextl <- Htextl
}
if(! grouppres) d$Group <- NULL
if(any(d$Big)) {
db <- subset(d, Big) # non-stratified estimates
## For some reason, colors= in add_marker did not always take
if(! length(height)) height <- plotlyParm$heightDotchart(lines)
auto <- .Options$plotlyauto
if(length(auto) && auto) height <- width <- NULL
p <- plotly::plot_ly(data=db, colors=cols, height=height, width=width)
if(limspres && length(D)) {
ddiff <- data.frame(Diff, difflower, diffupper, Ydiff, coldiff, htdiff)
## Could not get color=coldiff to work; perhaps conflicted with
## earlier use of color =
nDiff <- Diff[! is.na(Diff)]
if(length(nDiff)) {
if(any(nDiff > 0))
p <- plotly::add_segments(p, data=subset(ddiff, Diff > 0),
x= ~ difflower, xend= ~ diffupper,
y= ~ Ydiff, yend= ~ Ydiff,
color = I('lightgray'),
text = ~ htdiff, hoverinfo='text',
name = paste0(htmlSpecial('half'),
' CL of difference<br>',
coldiff[Diff > 0][1]))
if(any(nDiff <= 0))
p <- plotly::add_segments(p, data=subset(ddiff, Diff <= 0),
x= ~ difflower, xend= ~ diffupper,
y= ~ Ydiff, yend= ~ Ydiff,
color = I('lavender'),
text = ~ htdiff, hoverinfo='text',
name = paste0(htmlSpecial('half'),
' CL of difference<br>',
coldiff[Diff <= 0][1]))
}
}
## tracename and limitstracename are used if groups not used
if(limspres && ! length(D)) ## && length(ugroup) == 2) why ??
p <- if(grouppres)
plotly::add_segments(p, data=db,
x=~ Lower, xend=~ Upper,
y=~ Y, yend=~ Y,
color=~ Group, text= ~ Htextl,
colors=cols, hoverinfo='text')
else
plotly::add_segments(p, x=~ Lower, xend=~ Upper,
y=~ Y, yend=~ Y,
text= ~ Htextl,
color=I('lightgray'), hoverinfo='text',
name=limitstracename)
p <- if(grouppres)
plotly::add_markers(p, x=~ X, y=~ Y,
color=~ Group, text=~ Htext,
colors=cols, hoverinfo='text')
else
plotly::add_markers(p, x=~ X, y=~ Y,
text=~ Htext, color=I('black'),
hoverinfo='text',
name=if(length(tracename)) tracename
else
if(any(! d$Big)) 'All' else '')
} else p <- plotly::plot_ly(colors=cols) # Big is not used
if(any(! d$Big)) {
dnb <- subset(d, ! Big) # stratified estimates
if(limspres)
p <- if(grouppres && length(ugroup) == 2)
plotly::add_segments(p, data=dnb,
x=~ Lower, xend=~ Upper,
y=~ Y, yend=~ Y,
color=~ Group, text=~ Htextl,
colors=cols, hoverinfo='text')
else plotly::add_segments(p, data=dnb,
x=~ Lower, xend=~ Upper,
y=~ Y, yend=~ Y,
text=~ Htextl,
color=I('lightgray'), hoverinfo='text',
name=limitstracename)
dnb$sGroup <- paste0(dnb$Group, '\nby ',
gsub('Stratified by\n', '', nonbigtracename))
## Don't understand why if use ~ sGroup right below the symbols no
## longer appear in the legend for the non-stratified estimates
p <- if(grouppres)
plotly::add_markers(p, data=dnb,
x=~ X, y=~ Y,
color=~ Group,
text=~ Htext,
colors=cols,
marker=list(opacity=0.45, size=4),
hoverinfo='text')
# name=nonbigtracename)
else
plotly::add_markers(p, data=dnb,
x=~ X, y=~ Y,
text=~ Htext,
marker=list(opacity=0.45, size=4),
color=I('black'), hoverinfo='text',
name=nonbigtracename)
} # end if(any(! Big))
leftmargin <- plotlyParm$lrmargin(ytnb)
tickvals <- pretty(fun(xlim), n=10)
xaxis <- list(title=xlab, range=xlim, zeroline=FALSE,
tickvals=ifun(tickvals), ticktext=format(tickvals))
yaxis <- list(title='',
range=c(min(Y) - 0.2, 0.2),
zeroline=FALSE, tickvals=yl, ticktext=yt)
p <- plotly::layout(p,
xaxis=xaxis,
yaxis=yaxis,
margin=list(l=leftmargin),
legend=list(traceorder=if(length(difflower))
'reversed' else 'normal'))
attr(p, 'levelsRemoved') <- dropped
p
}
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