Nothing
R/nwfscMapping-internal.R
In nwfscMapping: Mapping functions for NWFSC
.addBubbles.ach <-
function (events, type = c("perceptual", "surface", "volume"),
z.max = NULL, max.size = 0.8, symbol.zero = "+", symbol.fg = rgb(0,
0, 0, 0.6), symbol.bg = rgb(0, 0, 0, 0.3), legend.pos = "bottomleft",
legend.breaks = NULL, show.actual = FALSE, legend.type = c("nested",
"horiz", "vert"), legend.title = "Abundance", legend.cex = 0.8,legend.title.cex=legend.cex+0.2,
...)
{
#A sligth modification from PBSmapping addBubbles to call a modified legend function (fixes an error)
events <- .validateEventData(events)
if (is.character(events))
stop(paste("Invalid EventData 'events'.\n", events, sep = ""))
if (!is.element("Z", names(events)))
stop("EventData is missing required column 'Z'.\n")
type <- match.arg(type)
if (!is.null(legend.pos))
legend.type <- match.arg(legend.type)
if (is.null(z.max) || is.na(z.max))
z.max <- max(events$Z, na.rm = TRUE)
if (is.null(legend.breaks) || is.na(legend.breaks))
legend.breaks <- pretty(range(events$Z), 3)[-1]
if (show.actual)
legend.breaks <- signif(legend.breaks/max(legend.breaks) *
max(events$Z, na.rm = TRUE), 3)
usr.xdiff <- par("usr")[2] - par("usr")[1]
usr.ydiff <- par("usr")[4] - par("usr")[3]
stand.rad <- (max.size/2)/par("pin")[1] * usr.xdiff
events <- events[order(events$Z, decreasing = TRUE), ]
type <- match.arg(type)
switch(type, volume = {
radii <- ((events$Z/z.max)^(1/3)) * stand.rad
radii.leg <- ((legend.breaks/z.max)^(1/3)) * stand.rad
}, surface = {
radii <- sqrt(events$Z/z.max) * stand.rad
radii.leg <- sqrt(legend.breaks/z.max) * stand.rad
}, perceptual = {
radii <- ((events$Z/z.max)^0.57) * stand.rad
radii.leg <- ((legend.breaks/z.max)^0.57) * stand.rad
})
isZero <- unlist(lapply(events$Z, all.equal, current = 0)) ==
"TRUE"
symbols(events$X[!isZero], events$Y[!isZero], circles = radii[!isZero],
inches = FALSE, bg = symbol.bg, fg = symbol.fg, add = TRUE)
if (any(isZero) && (!is.logical(symbol.zero) || symbol.zero)) {
if (is.logical(symbol.zero))
symbol.zero <- "+"
dots <- list(...)
if (!is.null(dots$pch))
stop("Specify 'pch' through 'symbol.zero'")
points(events$X[isZero], events$Y[isZero], pch = symbol.zero,
...)
}
if (!is.null(legend.pos)) {
if (!any(isZero))
symbol.zero <- FALSE
.addBubblesLegend.ach(radii.leg, usr.xdiff, usr.ydiff, symbol.zero,
symbol.fg, symbol.bg, legend.pos, legend.breaks,
legend.type, legend.title, legend.cex,legend.title.cex, ...)
}
invisible()
}
.addBubblesLegend.ach <-
function (radii.leg, usr.xdiff, usr.ydiff, symbol.zero, symbol.fg,
symbol.bg, legend.pos, legend.breaks, legend.type, legend.title,
legend.cex,legend.title.cex=legend.cex+0.2, ...)
{
#fixes an error in the vertical legend
ratio.y.x = (usr.ydiff/par("pin")[2])/(usr.xdiff/par("pin")[1])
gap.x <- par("cxy")[1] * legend.cex/2
gap.y <- par("cxy")[2] * legend.cex/2
radii.leg.y <- radii.leg * ratio.y.x
leg.tex.w <- strwidth(legend.breaks, units = "user") * legend.cex
title.w = strwidth(legend.title)
max.tex.w <- max(leg.tex.w)
switch(legend.type, nested = {
legend.height <- 2 * max(radii.leg.y) + 3 * gap.y
legend.width <- 2 * max(radii.leg) + gap.x + max.tex.w
}, horiz = {
legend.height <- 2 * max(radii.leg.y) + 3 * gap.y
legend.width <- 2 * sum(radii.leg) + (length(legend.breaks) -
1) * gap.x
}, vert = {
legend.height <- 2 * sum(radii.leg.y) + (length(legend.breaks) -
1) * gap.y + 3 * gap.y
legend.width <- 2 * max(radii.leg) + gap.x + max.tex.w
})
if (title.w > legend.width) {
w.adj <- (title.w - legend.width)/2
}
else {
w.adj <- 0
}
if (class(legend.pos) == "numeric") {
legend.loc <- legend.pos
}
else {
corners <- c("bottomleft", "bottomright", "topleft",
"topright")
if (legend.pos %in% corners) {
legend.loc <- switch(legend.pos, bottomleft = c(par("usr")[1] +
0.025 * usr.xdiff + w.adj, par("usr")[3] + 0.025 *
usr.ydiff + legend.height), bottomright = c(par("usr")[2] -
(0.025 * usr.xdiff + legend.width + w.adj), par("usr")[3] +
0.025 * usr.ydiff + legend.height), topleft = c(par("usr")[1] +
0.025 * usr.xdiff + w.adj, par("usr")[4] - 0.025 *
usr.ydiff), topright = c(par("usr")[2] - (0.025 *
usr.xdiff + legend.width + w.adj), par("usr")[4] -
0.025 * usr.ydiff))
}
}
switch(legend.type, nested = {
legend.loc[1] <- legend.loc[1] + max(radii.leg)
legend.loc[2] <- legend.loc[2] - legend.height
r <- rev(radii.leg)
bb <- rev(legend.breaks)
x.text.leg <- legend.loc[1] + max(r) + gap.x + max.tex.w
for (i in 1:length(r)) {
symbols(legend.loc[1], legend.loc[2] + r[i] * ratio.y.x,
circles = r[i], inches = FALSE, add = TRUE, bg = symbol.bg,
fg = symbol.fg)
lines(c(legend.loc[1], legend.loc[1] + r[1] + gap.x),
rep(legend.loc[2] + 2 * r[i] * ratio.y.x, 2))
text(x.text.leg, legend.loc[2] + 2 * r[i] * ratio.y.x,
bb[i], adj = c(1, 0.5), cex = legend.cex)
}
x.title.leg <- legend.loc[1] - max(radii.leg) + (legend.width/2)
text(x.title.leg, legend.loc[2] + legend.height, legend.title,
adj = c(0.5, 0.5), cex = legend.title.cex, col = "black")
zlab <- c(x.title.leg, legend.loc[2] + legend.height/4)
}, horiz = {
legend.loc[2] <- legend.loc[2] + max(radii.leg.y) - legend.height
offset <- vector()
for (i in 1:length(radii.leg)) offset[i] <- 2 * sum(radii.leg[1:i]) -
radii.leg[i] + (i - 1) * gap.x
symbols(legend.loc[1] + offset, rep(legend.loc[2], length(radii.leg)),
circles = radii.leg, inches = FALSE, bg = symbol.bg,
fg = symbol.fg, add = TRUE)
text(legend.loc[1] + offset, legend.loc[2] + radii.leg.y +
gap.y, legend.breaks, adj = c(0.5, 0.5), cex = legend.cex)
text(legend.loc[1] + legend.width/2, legend.loc[2] +
legend.height - max(radii.leg.y), legend.title, adj = c(0.5,
0.5), cex = legend.title.cex, col = "black")
zlab <- c(legend.loc[1], legend.loc[2] - legend.height/8)
}, vert = {
if (any(legend.pos == c("bottomleft", "topleft"))) legend.loc[1] <- legend.loc[1] +
0.05 * usr.xdiff
offset <- vector()
for (i in 1:length(legend.breaks)) offset[i] <- gap.y +
2 * sum(radii.leg.y[1:i]) - radii.leg.y[i] + i *
gap.y
symbols(rep(legend.loc[1], length(legend.breaks)), legend.loc[2] -
offset, circles = radii.leg, bg = symbol.bg, fg = symbol.fg,
inches = FALSE, add = TRUE)
x.text.leg <- legend.loc[1] + max(radii.leg) + gap.x +
max.tex.w
text(rep(x.text.leg, length(legend.breaks)), legend.loc[2] -
offset, legend.breaks, cex = legend.cex, adj = c(1,0.5), col = "black")
text(legend.loc[1] + legend.width/2 - max(radii.leg),
legend.loc[2], legend.title, adj = c(0.5, 0.5), cex = legend.title.cex, col = "black")
x.title.leg <- legend.loc[1] - max(radii.leg) + (legend.width/2) #ach
zlab <- c(x.title.leg, legend.loc[2])
})
if (!is.logical(symbol.zero))
legend(zlab[1], zlab[2], legend = "zero", pch = symbol.zero,
xjust = 0, yjust = 1, bty = "n", cex = 0.8, x.intersp = 0.5)
invisible()
}
.lat.to.km <-
function(lat){
# lat in degrees
lat.rad <- (lat * pi)/180
return(111.14 - 0.56 * cos(2 * lat.rad))
}
.long.to.km <-
function(lat){
# lat in degrees
lat.rad <- (lat * pi)/180
return(111.41 * cos(lat.rad) - 0.1 * cos(3 * lat.rad))
}
.Random.seed <-
c(403L, 10L, 2060855613L, -839351881L, -1855232418L, -124588136L,
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-1557257213L, -876343548L, -1912167630L, 402014599L, 1295427537L,
1859127638L, -781916364L, -1559508411L, -1232193905L, -231022584L,
341722150L, 803658963L, -51626443L, -239340142L, -719124128L,
916762825L, 932168699L, -2049137716L, 1188191834L, -1035713713L,
913627673L, -453404626L, 1356912188L, 1351675763L)
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.addBubbles.ach <-
function (events, type = c("perceptual", "surface", "volume"),
z.max = NULL, max.size = 0.8, symbol.zero = "+", symbol.fg = rgb(0,
0, 0, 0.6), symbol.bg = rgb(0, 0, 0, 0.3), legend.pos = "bottomleft",
legend.breaks = NULL, show.actual = FALSE, legend.type = c("nested",
"horiz", "vert"), legend.title = "Abundance", legend.cex = 0.8,legend.title.cex=legend.cex+0.2,
...)
{
#A sligth modification from PBSmapping addBubbles to call a modified legend function (fixes an error)
events <- .validateEventData(events)
if (is.character(events))
stop(paste("Invalid EventData 'events'.\n", events, sep = ""))
if (!is.element("Z", names(events)))
stop("EventData is missing required column 'Z'.\n")
type <- match.arg(type)
if (!is.null(legend.pos))
legend.type <- match.arg(legend.type)
if (is.null(z.max) || is.na(z.max))
z.max <- max(events$Z, na.rm = TRUE)
if (is.null(legend.breaks) || is.na(legend.breaks))
legend.breaks <- pretty(range(events$Z), 3)[-1]
if (show.actual)
legend.breaks <- signif(legend.breaks/max(legend.breaks) *
max(events$Z, na.rm = TRUE), 3)
usr.xdiff <- par("usr")[2] - par("usr")[1]
usr.ydiff <- par("usr")[4] - par("usr")[3]
stand.rad <- (max.size/2)/par("pin")[1] * usr.xdiff
events <- events[order(events$Z, decreasing = TRUE), ]
type <- match.arg(type)
switch(type, volume = {
radii <- ((events$Z/z.max)^(1/3)) * stand.rad
radii.leg <- ((legend.breaks/z.max)^(1/3)) * stand.rad
}, surface = {
radii <- sqrt(events$Z/z.max) * stand.rad
radii.leg <- sqrt(legend.breaks/z.max) * stand.rad
}, perceptual = {
radii <- ((events$Z/z.max)^0.57) * stand.rad
radii.leg <- ((legend.breaks/z.max)^0.57) * stand.rad
})
isZero <- unlist(lapply(events$Z, all.equal, current = 0)) ==
"TRUE"
symbols(events$X[!isZero], events$Y[!isZero], circles = radii[!isZero],
inches = FALSE, bg = symbol.bg, fg = symbol.fg, add = TRUE)
if (any(isZero) && (!is.logical(symbol.zero) || symbol.zero)) {
if (is.logical(symbol.zero))
symbol.zero <- "+"
dots <- list(...)
if (!is.null(dots$pch))
stop("Specify 'pch' through 'symbol.zero'")
points(events$X[isZero], events$Y[isZero], pch = symbol.zero,
...)
}
if (!is.null(legend.pos)) {
if (!any(isZero))
symbol.zero <- FALSE
.addBubblesLegend.ach(radii.leg, usr.xdiff, usr.ydiff, symbol.zero,
symbol.fg, symbol.bg, legend.pos, legend.breaks,
legend.type, legend.title, legend.cex,legend.title.cex, ...)
}
invisible()
}
.addBubblesLegend.ach <-
function (radii.leg, usr.xdiff, usr.ydiff, symbol.zero, symbol.fg,
symbol.bg, legend.pos, legend.breaks, legend.type, legend.title,
legend.cex,legend.title.cex=legend.cex+0.2, ...)
{
#fixes an error in the vertical legend
ratio.y.x = (usr.ydiff/par("pin")[2])/(usr.xdiff/par("pin")[1])
gap.x <- par("cxy")[1] * legend.cex/2
gap.y <- par("cxy")[2] * legend.cex/2
radii.leg.y <- radii.leg * ratio.y.x
leg.tex.w <- strwidth(legend.breaks, units = "user") * legend.cex
title.w = strwidth(legend.title)
max.tex.w <- max(leg.tex.w)
switch(legend.type, nested = {
legend.height <- 2 * max(radii.leg.y) + 3 * gap.y
legend.width <- 2 * max(radii.leg) + gap.x + max.tex.w
}, horiz = {
legend.height <- 2 * max(radii.leg.y) + 3 * gap.y
legend.width <- 2 * sum(radii.leg) + (length(legend.breaks) -
1) * gap.x
}, vert = {
legend.height <- 2 * sum(radii.leg.y) + (length(legend.breaks) -
1) * gap.y + 3 * gap.y
legend.width <- 2 * max(radii.leg) + gap.x + max.tex.w
})
if (title.w > legend.width) {
w.adj <- (title.w - legend.width)/2
}
else {
w.adj <- 0
}
if (class(legend.pos) == "numeric") {
legend.loc <- legend.pos
}
else {
corners <- c("bottomleft", "bottomright", "topleft",
"topright")
if (legend.pos %in% corners) {
legend.loc <- switch(legend.pos, bottomleft = c(par("usr")[1] +
0.025 * usr.xdiff + w.adj, par("usr")[3] + 0.025 *
usr.ydiff + legend.height), bottomright = c(par("usr")[2] -
(0.025 * usr.xdiff + legend.width + w.adj), par("usr")[3] +
0.025 * usr.ydiff + legend.height), topleft = c(par("usr")[1] +
0.025 * usr.xdiff + w.adj, par("usr")[4] - 0.025 *
usr.ydiff), topright = c(par("usr")[2] - (0.025 *
usr.xdiff + legend.width + w.adj), par("usr")[4] -
0.025 * usr.ydiff))
}
}
switch(legend.type, nested = {
legend.loc[1] <- legend.loc[1] + max(radii.leg)
legend.loc[2] <- legend.loc[2] - legend.height
r <- rev(radii.leg)
bb <- rev(legend.breaks)
x.text.leg <- legend.loc[1] + max(r) + gap.x + max.tex.w
for (i in 1:length(r)) {
symbols(legend.loc[1], legend.loc[2] + r[i] * ratio.y.x,
circles = r[i], inches = FALSE, add = TRUE, bg = symbol.bg,
fg = symbol.fg)
lines(c(legend.loc[1], legend.loc[1] + r[1] + gap.x),
rep(legend.loc[2] + 2 * r[i] * ratio.y.x, 2))
text(x.text.leg, legend.loc[2] + 2 * r[i] * ratio.y.x,
bb[i], adj = c(1, 0.5), cex = legend.cex)
}
x.title.leg <- legend.loc[1] - max(radii.leg) + (legend.width/2)
text(x.title.leg, legend.loc[2] + legend.height, legend.title,
adj = c(0.5, 0.5), cex = legend.title.cex, col = "black")
zlab <- c(x.title.leg, legend.loc[2] + legend.height/4)
}, horiz = {
legend.loc[2] <- legend.loc[2] + max(radii.leg.y) - legend.height
offset <- vector()
for (i in 1:length(radii.leg)) offset[i] <- 2 * sum(radii.leg[1:i]) -
radii.leg[i] + (i - 1) * gap.x
symbols(legend.loc[1] + offset, rep(legend.loc[2], length(radii.leg)),
circles = radii.leg, inches = FALSE, bg = symbol.bg,
fg = symbol.fg, add = TRUE)
text(legend.loc[1] + offset, legend.loc[2] + radii.leg.y +
gap.y, legend.breaks, adj = c(0.5, 0.5), cex = legend.cex)
text(legend.loc[1] + legend.width/2, legend.loc[2] +
legend.height - max(radii.leg.y), legend.title, adj = c(0.5,
0.5), cex = legend.title.cex, col = "black")
zlab <- c(legend.loc[1], legend.loc[2] - legend.height/8)
}, vert = {
if (any(legend.pos == c("bottomleft", "topleft"))) legend.loc[1] <- legend.loc[1] +
0.05 * usr.xdiff
offset <- vector()
for (i in 1:length(legend.breaks)) offset[i] <- gap.y +
2 * sum(radii.leg.y[1:i]) - radii.leg.y[i] + i *
gap.y
symbols(rep(legend.loc[1], length(legend.breaks)), legend.loc[2] -
offset, circles = radii.leg, bg = symbol.bg, fg = symbol.fg,
inches = FALSE, add = TRUE)
x.text.leg <- legend.loc[1] + max(radii.leg) + gap.x +
max.tex.w
text(rep(x.text.leg, length(legend.breaks)), legend.loc[2] -
offset, legend.breaks, cex = legend.cex, adj = c(1,0.5), col = "black")
text(legend.loc[1] + legend.width/2 - max(radii.leg),
legend.loc[2], legend.title, adj = c(0.5, 0.5), cex = legend.title.cex, col = "black")
x.title.leg <- legend.loc[1] - max(radii.leg) + (legend.width/2) #ach
zlab <- c(x.title.leg, legend.loc[2])
})
if (!is.logical(symbol.zero))
legend(zlab[1], zlab[2], legend = "zero", pch = symbol.zero,
xjust = 0, yjust = 1, bty = "n", cex = 0.8, x.intersp = 0.5)
invisible()
}
.lat.to.km <-
function(lat){
# lat in degrees
lat.rad <- (lat * pi)/180
return(111.14 - 0.56 * cos(2 * lat.rad))
}
.long.to.km <-
function(lat){
# lat in degrees
lat.rad <- (lat * pi)/180
return(111.41 * cos(lat.rad) - 0.1 * cos(3 * lat.rad))
}
.Random.seed <-
c(403L, 10L, 2060855613L, -839351881L, -1855232418L, -124588136L,
-748118277L, 461035161L, 788152104L, -857573930L, 354089553L,
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1366815317L, -584104596L, 78253506L, -1878659555L, 3110551L,
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1751976020L, 306568168L, 1263441658L, -2063144624L, 1133372204L,
885815156L, 140546962L, 1777694304L, 1321787276L, -936443040L,
128002018L, 1316188072L, -451445556L, -922178052L, -114979918L,
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1888604092L, 514781268L, 623920066L, -527834080L, 364973244L,
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971365840L, 849871852L, 164405140L, 1615195090L, 1164801888L,
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1047747516L, -156497072L, -1117183710L, 1536429384L, -1168254964L,
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2144536524L, -2144762116L, 1537617906L, -932938624L, 2098424052L,
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1316991981L, -1999029097L, 1333217120L, -183902402L, 678690827L,
852953229L, -794865222L, 2004942840L, -597509215L, -432818861L,
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698343787L, 1741131868L, -1680368246L, 1061448063L, -1130089271L,
1025411422L, -1605162484L, -427422243L, -853551897L, -20975344L,
-1222766546L, -701880613L, 1218305981L, 1397684522L, -180097592L,
-851873039L, 530046051L, -1628936092L, -1799511150L, -1465767833L,
-1475053519L, -15005322L, 496760468L, 27393189L, 1282302383L,
1294858856L, 1420608070L, 1977116659L, 830936917L, 678299954L,
-898261760L, 1746230761L, -1432950693L, 675297964L, 997074106L,
-1408965009L, -1359252487L, 1262017166L, -1687381156L, -512272435L,
1851234103L, 717931968L, 1282468510L, -168066197L, 579164909L,
-1993781414L, 1926333464L, 164135297L, -1732774093L, -1896403628L,
1091479394L, 813300727L, -1724349375L, 1177759942L, -2117698044L,
106248629L, -2068986209L, -1518893320L, -990745898L, -2027520157L,
1872512805L, 1273806018L, 1200077232L, -1270148647L, 317169483L,
34854332L, 1905919466L, 631669279L, -1024907095L, 421584958L,
-2050584276L, 1186225021L, -1541852729L, -1276615504L, 2041082574L,
-698816517L, -633278371L, 1676285834L, 32806824L, -378036975L,
-1557257213L, -876343548L, -1912167630L, 402014599L, 1295427537L,
1859127638L, -781916364L, -1559508411L, -1232193905L, -231022584L,
341722150L, 803658963L, -51626443L, -239340142L, -719124128L,
916762825L, 932168699L, -2049137716L, 1188191834L, -1035713713L,
913627673L, -453404626L, 1356912188L, 1351675763L)
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