R/uwtv_bubble_plot_v2.R
In ices-tools-dev/NephAssess: SG Nephrops assessment functions
Defines functions
uwtv_bubble_plot
uwtv_bubble_plot <- function(
dat = NULL,
wk.dir,
year = NA,
orientation = c("Landscape", "Portrait"),
style = c("new", "old"),
stratum_legend = FALSE,
elevation = FALSE,
jura = NULL){
# Coefficient of variation function
CV <- function(x){
(sd(x)/mean(x))
}
# Function to create new plot names
get.fname <- function(base.name){
fname <- function(i){paste(base.name, i, ".jpeg", sep = "")}
out <- fname(i <- 1)
while(file.exists(out))
out <- fname(i <- i + 1)
return(out)
}
# Function to capitalize first letter of each word
simpleCap <- function(x){
x <- tolower(x)
s <- strsplit(x, " ")[[1]]
paste(toupper(substring(s, 1, 1)), substring(s, 2),
sep = "", collapse = " ")
}
## evaluate orientation
# orientation <- orientation(members)
orientation <- match.arg(orientation)
style <- match.arg(style)
## Plotting colour palettes
# 3 sediment types
sedimentCol <- c("#009E73", "#E69F00", "#56B4E9")
bubbleFill <- c(rgb(0, 158, 115, 50, maxColorValue = 255),
rgb(230, 159, 0, 50, maxColorValue = 255),
rgb(86, 180, 233, 50, maxColorValue = 255))
# 2 sediment types
sedimentCol2 <- sedimentCol[c(2,3)]
bubbleFill2 <- bubbleFill[c(2,3)]
# Fladen
fladenCol <- c("#009E73", "#E69F00", "#56B4E9", "#CC79A7")
fladenFill <- c(rgb(0, 158, 115, 50, maxColorValue = 255),
rgb(230, 159, 0, 50, maxColorValue = 255),
rgb(86, 180, 233, 50, maxColorValue = 255),
rgb(204, 121, 167, 50, maxColorValue = 255))
### FU7
if(unique(dat$FU) == "Fladen"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Strata as factor
dat$strata_type <- factor(dat$strata_type, levels = c("C", "MC", "MF", "F"))
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU7_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-2.1, 2),
ylim = c(57.4, 60.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r7, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#dadada")
segments(-1, 60.5, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#dadada")
lapply(fladenSedimentsList, polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = fladenCol[as.factor(nz$strata_type)],
bg = fladenFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10,10,10,-10), y = c(50,50,70,70), col = "#c9e9f6")
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#000000")
segments(-1, 60.5, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#000000")
lapply(fladen.surfer.poly[c(17:20,24,25)], polygon, col = "olivedrab", border = NA)
lapply(fladen.surfer.poly[c(1,2,3,4,23)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(5,7,9,14)], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[10], polygon, col = "darkgreen", border = NA)
lapply(fladen.surfer.poly[12], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[c(13,22)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(6,8,11,15,16,21)], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(1, 60.2, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1,
cex.axis = 1.5,
at = c(-1.5, 0, 1.5),
labels = c(expression("1.5"^o*W),
expression("0"^o),
expression("1.5"^o*E)))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(58, 60, by = 1), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(58, 60, by = 1)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(1.2, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.2", cex = 0.5)
stW <- strwidth(c("1.2","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-1.25, 3), rep(59.4, 3) + 2*heightAdj,
x1 = rep(-1.5, 3), y1 = rep(59.4, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-1.25, 3), rep(59.4, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-1.6, 3) - 0.5*stWdiff, rep(59.4, 3) + 2*heightAdj,
c("1.2", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-1.25, 59.15,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-7.8, 57,
legend = levels(as.factor(dat$strata_type)),
col = fladenCol,
pt.bg = fladenFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU7_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-2.1, 2),
ylim = c(57.4, 60.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r7, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#dadada")
segments(-1, 60.5, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#dadada")
lapply(fladenSedimentsList, polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = fladenCol[as.factor(nz$strata_type)],
bg = fladenFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10,10,10,-10), y = c(50,50,70,70), col = "#c9e9f6")
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#000000")
segments(-1, 60.5, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#000000")
lapply(fladen.surfer.poly[c(17:20,24,25)], polygon, col = "olivedrab", border = NA)
lapply(fladen.surfer.poly[c(1,2,3,4,23)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(5,7,9,14)], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[10], polygon, col = "darkgreen", border = NA)
lapply(fladen.surfer.poly[12], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[c(13,22)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(6,8,11,15,16,21)], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(1, 60.2, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1,
cex.axis = 1.5,
at = c(-1.5, 0, 1.5),
labels = c(expression("1.5"^o*W),
expression("0"^o),
expression("1.5"^o*E)))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(58, 60, by = 1), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(58, 60, by = 1)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(1.2, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.2", cex = 0.5)
stW <- strwidth(c("1.2","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-1.25, 3), rep(59.4, 3) + 2*heightAdj,
x1 = rep(-1.5, 3), y1 = rep(59.4, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-1.25, 3), rep(59.4, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-1.6, 3) - 0.5*stWdiff, rep(59.4, 3) + 2*heightAdj,
c("1.2", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-1.25, 59.15,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-5.7, 57,
legend = levels(as.factor(dat$strata_type)),
col = fladenCol,
pt.bg = fladenFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU8
if(unique(dat$FU) == "Firth of Forth"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU8_bubble_plot_ls.")),
width = 380, height = 200, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-3.5, -1.95),
ylim = c(55.85, 56.35),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r8, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU8 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
segments(-2, 56.5, -2, 55.5, lty = 2, col = "#dadada")
# FU8 strata
lapply(forth.poly[5:16], polygon, col = NA, border = "#dadada")
lapply(forth.poly[23:53], polygon, col = NA, border = "#dadada")
lapply(forth.poly[54:66], polygon, col = NA, border = "#dadada")
lapply(forth.poly[17:22], polygon, col = NA, border = "#dadada")
lapply(forth.poly[1:4], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol2[as.factor(nz$strata_type)],
bg = bubbleFill2[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-5, 0, 0,-5), y = c(55, 55, 60, 60), col = "#c9e9f6")
lines(x = c(-2, -2), y = c(56.5, 55.5), lty = 2)
lines(x = c(-3, -2), y = c(56.5, 56.5), lty = 2)
lapply(forth.poly[5:16], polygon, col = "olivedrab", border = NA)
lapply(forth.poly[23:53], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[54:66], polygon, col = "green", border = NA)
lapply(forth.poly[17:22], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[1:4], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.45, 55.9, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-3.2, -2.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.2, -2.2, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(56, 56.2, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56, 56.2, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(3.3, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("3.3", cex = 0.5)
stW <- strwidth(c("3.3","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.2, 3), rep(56.25, 3) + 2*heightAdj,
x1 = rep(-3.3, 3), y1 = rep(56.25, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.2, 3), rep(56.25, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.33, 3) - 0.5*stWdiff, rep(56.25, 3) + 2*heightAdj,
c("3.3", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.2, 56.2,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-6, 55.8,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol2,
pt.bg = bubbleFill2,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU8_bubble_plot_po.")),
width = 360, height = 260, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-3.5, -1.95),
ylim = c(55.85, 56.35),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r8, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU8 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
segments(-2, 56.5, -2, 55.5, lty = 2, col = "#dadada")
# FU8 strata
lapply(forth.poly[5:16], polygon, col = NA, border = "#dadada")
lapply(forth.poly[23:53], polygon, col = NA, border = "#dadada")
lapply(forth.poly[54:66], polygon, col = NA, border = "#dadada")
lapply(forth.poly[17:22], polygon, col = NA, border = "#dadada")
lapply(forth.poly[1:4], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol2[as.factor(nz$strata_type)],
bg = bubbleFill2[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-5, 0, 0,-5), y = c(55, 55, 60, 60), col = "#c9e9f6")
lines(x = c(-2, -2), y = c(56.5, 55.5), lty = 2)
lines(x = c(-3, -2), y = c(56.5, 56.5), lty = 2)
lapply(forth.poly[5:16], polygon, col = "olivedrab", border = NA)
lapply(forth.poly[23:53], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[54:66], polygon, col = "green", border = NA)
lapply(forth.poly[17:22], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[1:4], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.45, 55.9, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-3.2, -2.3, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.2, -2.3, by = 0.3)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(56, 56.2, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56, 56.2, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(3.3, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("3.3", cex = 0.5)
stW <- strwidth(c("3.3","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.2, 3), rep(56.25, 3) + 2*heightAdj,
x1 = rep(-3.3, 3), y1 = rep(56.25, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.2, 3), rep(56.25, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.33, 3) - 0.5*stWdiff, rep(56.25, 3) + 2*heightAdj,
c("3.3", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.2, 56.2,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-5, 55.8,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol2,
pt.bg = bubbleFill2,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU9
if(unique(dat$FU) == "Moray Firth"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
dat <- dat[!is.na(dat$average_density),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
# Set as factor
dat$strata_type <- as.factor(dat$strata_type)
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU9_bubble_plot_ls.")),
width = 380, height = 200, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4.1, -1.6),
ylim = c(57.6, 58.2),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r9, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU9 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
# FU9 strata
lapply(moray.poly[2:8], polygon, col = NA, border = "#dadada")
segments(-2, 57.96422, -2, 57.80697, lty = 1, col = "#ffffff")
lapply(moray.poly[9:20], polygon, col = NA, border = "#dadada")
lapply(moray.poly[21:25], polygon, col = NA, border = "#dadada")
lapply(moray.poly[1], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -2), y = c(58.5, 58.5), lwd = 1, lty = 2)
lines(x = c(-2, -2), y = c(58.5, 58), lwd = 1, lty = 2)
lines(x = c(-2, -1), y = c(58, 58), lwd = 1, lty = 2)
lines(x = c(-1, -1), y = c(58, 57.5), lwd = 1, lty = 2)
lines(x = c(-1, -2), y = c(57.5, 57.5), lwd = 2, lty = 2)
lapply(moray.poly[2:8], polygon, col = "olivedrab", border = NA)
lapply(moray.poly[9:20], polygon, col = "#c9e9f6", border = NA)
lapply(moray.poly[21:25], polygon, col = "green", border = NA)
lapply(moray.poly[1], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-4, 58.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-3.6, -2, by = 0.8), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.6, -2, by = 0.8)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(57.7, 58.1, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.7, 58.1, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-8)]){
legdens <- c(1.37, 0.75, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.35", cex = 0.5)
stW <- strwidth(c("1.35","0.75","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-2.1, 3), rep(58.05, 3) + 2*heightAdj,
x1 = rep(-2.3, 3), y1 = rep(58.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-2.1, 3), rep(58.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-2.375, 3) - 0.5*stWdiff, rep(58.05, 3) + 2*heightAdj,
c("1.35","0.75","0.1"),
col = "#000000",
cex = 0.75)
text(-2.1, 58,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8.5, 57.55,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU9_bubble_plot_po.")),
width = 300, height = 260, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4.1, -1.6),
ylim = c(57.6, 58.2),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r9, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU9 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
# FU9 strata
lapply(moray.poly[2:8], polygon, col = NA, border = "#dadada")
segments(-2, 57.96422, -2, 57.80697, lty = 1, col = "#ffffff")
lapply(moray.poly[9:20], polygon, col = NA, border = "#dadada")
lapply(moray.poly[21:25], polygon, col = NA, border = "#dadada")
lapply(moray.poly[1], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -2), y = c(58.5, 58.5), lwd = 1, lty = 2)
lines(x = c(-2, -2), y = c(58.5, 58), lwd = 1, lty = 2)
lines(x = c(-2, -1), y = c(58, 58), lwd = 1, lty = 2)
lines(x = c(-1, -1), y = c(58, 57.5), lwd = 1, lty = 2)
lines(x = c(-1, -2), y = c(57.5, 57.5), lwd = 2, lty = 2)
lapply(moray.poly[2:8], polygon, col = "olivedrab", border = NA)
lapply(moray.poly[9:20], polygon, col = "#c9e9f6", border = NA)
lapply(moray.poly[21:25], polygon, col = "green", border = NA)
lapply(moray.poly[1], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-4, 58.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-3.6, -2, by = 0.8), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.6, -2, by = 0.8)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(57.7, 58.1, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.7, 58.1, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-9)]){
legdens <- c(1.37, 0.75, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.35", cex = 0.5)
stW <- strwidth(c("1.35","0.75","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-2.1, 3), rep(58.05, 3) + 2*heightAdj,
x1 = rep(-2.3, 3), y1 = rep(58.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-2.1, 3), rep(58.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-2.375, 3) - 0.5*stWdiff, rep(58.05, 3) + 2*heightAdj,
c("1.35","0.75","0.1"),
col = "#000000",
cex = 0.75)
text(-2.1, 58,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-7, 57.55,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU10
if(unique(dat$FU) == "Noup"){
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.2
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU10_bubble_plot.")),
width = 280, height = 190, units = "mm", res = 350)
par(mfrow = c(2, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in tail(unique(dat$year),6)){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4, -3),
ylim = c(59, 59.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r10, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU10 strata
lapply(noup.poly[1:2], polygon, col = NA, border = "#dadada")
lapply(noup.poly[3:5], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[2],
bg = bubbleFill[2],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -3), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-3, -3), y = c(59, 59.5), lwd = 1, lty = 2)
lines(x = c(-4, -3), y = c(59.5, 59.5), lwd = 1, lty = 2)
lines(x =c(-4, -4), y = c(59, 59.5), lwd = 1, lty = 2)
lapply(noup.poly[1:2], polygon, col = "olivedrab", border = NA)
lapply(noup.poly[3:5], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.3, 59.6, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% tail(unique(dat$year),3)){
axis(1, at = seq(-3.8, -3.2, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.8, -3.2, by = 0.3)), "W")))
}
# y-axes
if(i %in% matrix(tail(unique(dat$year),6),nrow=2,byrow=T)[,1]){
axis(2, at = c(59.2, 59.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(c(59.2, 59.5)), "N")))
}
# Bubble Legend
if(i == tail(unique(dat$year),1)){
legdens <- c(0.9, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1", cex = 0.5)
stW <- strwidth(c("1","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.7, 3), rep(59.05, 3) + 2*heightAdj,
x1 = rep(-3.78, 3), y1 = rep(59.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.7, 3), rep(59.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.8, 3) - 0.5*stWdiff, rep(59.05, 3) + 2*heightAdj,
c("1", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.7, 59,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU10_bubble_plot.")),
width = 200, height = 280, units = "mm", res = 350)
par(mfrow = c(3, 2), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in tail(unique(dat$year),6)){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4, -3),
ylim = c(59, 59.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r10, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU10 strata
lapply(noup.poly[1:2], polygon, col = NA, border = "#dadada")
lapply(noup.poly[3:5], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[2],
bg = bubbleFill[2],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -3), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-3, -3), y = c(59, 59.5), lwd = 1, lty = 2)
lines(x = c(-4, -3), y = c(59.5, 59.5), lwd = 1, lty = 2)
lines(x =c(-4, -4), y = c(59, 59.5), lwd = 1, lty = 2)
lapply(noup.poly[1:2], polygon, col = "olivedrab", border = NA)
lapply(noup.poly[3:5], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.3, 59.6, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% tail(unique(dat$year),2)){
axis(1, at = seq(-3.8, -3.2, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.8, -3.2, by = 0.3)), "W")))
}
# y-axes
if(i %in% matrix(tail(unique(dat$year),6),nrow=3,byrow=T)[,1]){
axis(2, at = c(59.2, 59.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(c(59.2, 59.5)), "N")))
}
# Bubble Legend
if(i == tail(unique(dat$year),1)){
legdens <- c(0.9, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1", cex = 0.5)
stW <- strwidth(c("1","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.7, 3), rep(59.05, 3) + 2*heightAdj,
x1 = rep(-3.78, 3), y1 = rep(59.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.7, 3), rep(59.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.8, 3) - 0.5*stWdiff, rep(59.05, 3) + 2*heightAdj,
c("1", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.7, 59,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
dev.off()
}
}
### FU11 Bubble Plots
if(unique(dat$FU) == "North Minch"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU11_bubble_plot_ls.")),
width = 350, height = 250, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-7.1, -5.3),
ylim = c(57.4, 58.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU11 boundaries
segments(-7, 57.5, -5, 57.5, lty = 2, col = "#dadada")
segments(-7, 57.5, -7, 59, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU11 strata
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-7, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-7, -5), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-7, -7), y = c(57.5, 59), lwd = 1, lty = 2)
lines(x = c(-5, -5), y = c(57.5, 59), lwd = 1, lty = 2)
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(poly_union_2007_2011_nm.rda)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and label
box()
text(-5.75, 57.64, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c((year-3):year)){
axis(1, at = seq(-6.5, -5.75, by = 0.75), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6.5, -5.75, by = 0.75)), "W")))
}
# y-axes
if(i %in% c((year-11), (year-7), (year-3))){
axis(2, at = seq(57.6, 58.4, by = 0.4), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.6, 58.4, by = 0.4)), "N")))
}
# Bubble Legend
if(i == (year-3)){
legdens <- c(2.8, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-6.73, 3), rep(58.45, 3) + 2*heightAdj,
x1 = rep(-6.83, 3), y1 = rep(58.45, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-6.73, 3), rep(58.45, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.87, 3) - 0.5*stWdiff, rep(58.45, 3) + 2*heightAdj,
c("2.8", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-6.73, 58.35,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-9.25, 57.3,
legend = "VMS",
col = "#CC79A7",
pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU11_bubble_plot_po.")),
width = 280, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-7.1, -5.3),
ylim = c(57.4, 58.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU11 boundaries
segments(-7, 57.5, -5, 57.5, lty = 2, col = "#dadada")
segments(-7, 57.5, -7, 59, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU11 strata
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-7, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-7, -5), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-7, -7), y = c(57.5, 59), lwd = 1, lty = 2)
lines(x = c(-5, -5), y = c(57.5, 59), lwd = 1, lty = 2)
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(poly_union_2007_2011_nm.rda)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and label
box()
text(-5.75, 57.64, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c((year-2):year)){
axis(1, at = seq(-6.5, -5.75, by = 0.75), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6.5, -5.75, by = 0.75)), "W")))
}
# y-axes
if(i %in% c((year-11), (year-8), (year-5), (year-2))){
axis(2, at = seq(57.6, 58.4, by = 0.4), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.6, 58.4, by = 0.4)), "N")))
}
# Bubble Legend
if(i == (year-2)){
legdens <- c(2.8, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-6.73, 3), rep(58.45, 3) + 2*heightAdj,
x1 = rep(-6.83, 3), y1 = rep(58.45, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-6.73, 3), rep(58.45, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.87, 3) - 0.5*stWdiff, rep(58.45, 3) + 2*heightAdj,
c("2.8", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-6.73, 58.35,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8.25, 57.3,
legend = "VMS",
col = "#CC79A7",
pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU12 Bubble Plots
if(unique(dat$FU) == "South Minch"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU12_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-8, -5.5),
ylim = c(56, 57.5),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU12 area strata
segments(-6.75, 56.6, -6.75, 57.16,
lty = 2,
col = "#dadada")
segments(-6.75, 57.16, -6.51, 57.33,
lty = 2,
col = "#dadada")
segments(-6.75, 56.6, -8, 56.4, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# FU12 Boundary
segments(-8, 57.5, -8, 56, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r12, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-8, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-8, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lines(x = c(-8, -8), y = c(57.5, 56), lwd = 1, lty = 2)
lapply(south.minch.poly[17:50], polygon, col = "olivedrab", border = NA)
lapply(south.minch.poly[51], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[53:72], polygon, col = "green", border = NA)
lapply(south.minch.poly[52], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[1:16], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-8, 57.3, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-7.5, -6, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-7.5, -6, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(56.5, 57, by=0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.5, 57, by=0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(2.5, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.5", cex = 0.5)
stW <- strwidth(c("2.5","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-7.5, 3), rep(56.1, 3) + 2*heightAdj,
x1 = rep(-7.75, 3), y1 = rep(56.1, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-7.5, 3), rep(56.1, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-7.8, 3) - 0.5*stWdiff, rep(56.1, 3) + 2*heightAdj,
c("2.5", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-7.5, 56,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-12.8, 55.85,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU12_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-8, -5.5),
ylim = c(56, 57.5),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU12 area strata
segments(-6.75, 56.6, -6.75, 57.16,
lty = 2,
col = "#dadada")
segments(-6.75, 57.16, -6.51, 57.33,
lty = 2,
col = "#dadada")
segments(-6.75, 56.6, -8, 56.4, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# FU12 Boundary
segments(-8, 57.5, -8, 56, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r12, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-8, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-8, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lines(x = c(-8, -8), y = c(57.5, 56), lwd = 1, lty = 2)
lapply(south.minch.poly[17:50], polygon, col = "olivedrab", border = NA)
lapply(south.minch.poly[51], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[53:72], polygon, col = "green", border = NA)
lapply(south.minch.poly[52], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[1:16], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-8, 57.3, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-7.5, -6, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-7.5, -6, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(56.5, 57, by=0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.5, 57, by=0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(2.5, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.5", cex = 0.5)
stW <- strwidth(c("2.5","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-7.5, 3), rep(56.1, 3) + 2*heightAdj,
x1 = rep(-7.75, 3), y1 = rep(56.1, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-7.5, 3), rep(56.1, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-7.8, 3) - 0.5*stWdiff, rep(56.1, 3) + 2*heightAdj,
c("2.5", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-7.5, 56,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-10.8, 55.85,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU13
if(unique(dat$FU) == "Clyde"){
# Is Jura provided?
if(is.null(jura) == FALSE){
dat13 <- rbind(dat, jura)
} else {dat13 <- dat}
# Get years
mfys <- unique(dat13$year)
dat13 <- dat13[dat13$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat13$radii <- sqrt(dat13$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat13 <- dat13[dat13$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU13_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat13[dat13$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-6.2, -4.6),
ylim = c(55, 56),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU13 Boundary
segments(-6, 55, -6, 56, lty = 2, col = "#dadada")
segments(-6, 56, -4, 56, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r13, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU13 strata
lapply(clyde.poly[26:35], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[1:16], polygon, col = NA, border = "#dadada")
lapply(clyde.poly[44:49], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[17:25], polygon, col = NA, border = "#dadada")
lapply(jura.poly[3:4], polygon, col = NA, border = "#dadada")
lapply(jura.poly[7], polygon, col = NA, border = "#dadada")
lapply(jura.poly[5:6], polygon, col = NA, border = "#dadada")
lapply(jura.poly[1], polygon, col = NA, border = "#dadada")
lapply(jura.poly[2], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-6, -6), y = c(56, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5), y = c(55, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lapply(clyde.poly[26:35], polygon, col = "olivedrab", border = NA)
lapply(clyde.poly[1:16], polygon, col = "#c9e9f6", border = NA)
lapply(clyde.poly[44:49], polygon, col = "green", border = NA)
lapply(clyde.poly[17:25], polygon, col = "darkgreen", border = NA)
if(is.null(jura) == FALSE){
lapply(jura.poly[3:4], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[7], polygon, col = "green", border = NA)
lapply(jura.poly[5:6], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[1], polygon, col = "#c9e9f6", border = NA)
lapply(jura.poly[2], polygon, col = "darkgreen", border = NA)
}
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-5, 55.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-6, -5, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6, -5, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(55.2, 55.8, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(55.2, 55.8, by = 0.3)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(2.83, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat13$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","1","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-5.88, 3), rep(55.15, 3) + 2*heightAdj,
x1 = rep(-6, 3), y1 = rep(55.15, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-5.88, 3), rep(55.15, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.04, 3) - 0.5*stWdiff, rep(55.15, 3) + 2*heightAdj,
c("2.8", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-5.88, 55.05,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-9, 54.9,
legend = sapply(levels(as.factor(dat13$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU13_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat13[dat13$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-6.2, -4.6),
ylim = c(55, 56),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU13 Boundary
segments(-6, 55, -6, 56, lty = 2, col = "#dadada")
segments(-6, 56, -4, 56, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r13, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU13 strata
lapply(clyde.poly[26:35], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[1:16], polygon, col = NA, border = "#dadada")
lapply(clyde.poly[44:49], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[17:25], polygon, col = NA, border = "#dadada")
lapply(jura.poly[3:4], polygon, col = NA, border = "#dadada")
lapply(jura.poly[7], polygon, col = NA, border = "#dadada")
lapply(jura.poly[5:6], polygon, col = NA, border = "#dadada")
lapply(jura.poly[1], polygon, col = NA, border = "#dadada")
lapply(jura.poly[2], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-6, -6), y = c(56, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5), y = c(55, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lapply(clyde.poly[26:35], polygon, col = "olivedrab", border = NA)
lapply(clyde.poly[1:16], polygon, col = "#c9e9f6", border = NA)
lapply(clyde.poly[44:49], polygon, col = "green", border = NA)
lapply(clyde.poly[17:25], polygon, col = "darkgreen", border = NA)
if(is.null(jura) == FALSE){
lapply(jura.poly[3:4], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[7], polygon, col = "green", border = NA)
lapply(jura.poly[5:6], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[1], polygon, col = "#c9e9f6", border = NA)
lapply(jura.poly[2], polygon, col = "darkgreen", border = NA)
}
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-5, 55.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-6, -5, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6, -5, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(55.2, 55.8, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(55.2, 55.8, by = 0.3)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(2.83, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat13$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-5.88, 3), rep(55.15, 3) + 2*heightAdj,
x1 = rep(-6, 3), y1 = rep(55.15, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-5.88, 3), rep(55.15, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.04, 3) - 0.5*stWdiff, rep(55.15, 3) + 2*heightAdj,
c("2.8", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-5.88, 55.05,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8, 54.9,
legend = sapply(levels(as.factor(dat13$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU11 Bubble Plots
if(unique(dat$FU) == "Devil's Hole"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-9):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU34_bubble_plot_ls.")),
width = 350, height = 160, units = "mm", res = 350)
par(mfrow = c(2, 5), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-9):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-0.5, 2.5),
ylim = c(55.9, 57.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
# Add terrestrial map
# if(elevation == FALSE){
# polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
# } else {
# plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
# plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
# }
# FU11 strata
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#000000")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(devils.hole.vms.poly)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and year label
box()
if(style == "old"){
polygon(x = c(-0.1, 0.1, 0.1, -0.1), y = c(56.02, 56.02, 56.2, 56.2),
col = "#c9e9f6", border = "#c9e9f6")
}
text(-0.45, 56.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% mfys[c((match(year, mfys) - seq(4, 0, by = -1)))]){
axis(1, at = seq(0, 2, by = 1), cex.axis = 1.5,
labels = c(0, parse(text = sprintf("%s^o*%s",
abs(seq(1, 2, by = 1)), "W"))))
}
# y-axes
if(i %in% mfys[c((match(year, mfys) - seq(9, 4, by = -5)))]){
axis(2, at = seq(56.2, 57.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.2, 57.2, by = 0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys) - 4)]){
legdens <- c(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1), 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(0.7, 3), rep(57.2, 3) + 2*heightAdj,
x1 = rep(0.4, 3), y1 = rep(57.2, 3) + 2*heightAdj,
col="#000000")
symbols(rep(0.7, 3), rep(57.2, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(0.3, 3) - 0.5*stWdiff, rep(57.2, 3) + 2*heightAdj,
c(as.character(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1)),
"0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(0.7, 57.075,
bty = "n",
col = "#000000",
cex = 0.9,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
# if(stratum_legend == TRUE & style == "new"){
# legend(-9.25, 57.3,
# legend = "VMS",
# col = "#CC79A7",
# pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
# horiz = TRUE,
# xpd = NA,
# pch = 21,
# cex = 2,
# pt.cex = 2,
# pt.lwd = 2,
# bty = "n")
# }
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU34_bubble_plot_po.")),
width = 150, height = 320, units = "mm", res = 350)
par(mfrow = c(5, 2), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-9):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-0.5, 2.5),
ylim = c(55.9, 57.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
# FU11 strata
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#000000")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(devils.hole.vms.poly)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and year label
box()
if(style == "old"){
polygon(x = c(-0.1, 0.1, 0.1, -0.1), y = c(56.02, 56.02, 56.2, 56.2),
col = "#c9e9f6", border = "#c9e9f6")
}
text(-0.45, 56.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% mfys[c((match(year, mfys) - seq(1, 0, by = -1)))]){
axis(1, at = seq(0, 2, by = 1), cex.axis = 1.5,
labels = c(0, parse(text = sprintf("%s^o*%s",
abs(seq(1, 2, by = 1)), "W"))))
}
# y-axes
if(i %in% mfys[c((match(year, mfys) - seq(9, 1, by = -2)))]){
axis(2, at = seq(56.2, 57.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.2, 57.2, by = 0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys) - 1)]){
legdens <- c(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1), 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(0.7, 3), rep(57.2, 3) + 2*heightAdj,
x1 = rep(0.4, 3), y1 = rep(57.2, 3) + 2*heightAdj,
col="#000000")
symbols(rep(0.7, 3), rep(57.2, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(0.3, 3) - 0.5*stWdiff, rep(57.2, 3) + 2*heightAdj,
c(as.character(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1)),
"0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(0.7, 57.075,
bty = "n",
col = "#000000",
cex = 0.9,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
# if(stratum_legend == TRUE & style == "new"){
# legend(-8.25, 57.3,
# legend = "VMS",
# col = "#CC79A7",
# pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
# horiz = TRUE,
# xpd = NA,
# pch = 21,
# cex = 2,
# pt.cex = 2,
# pt.lwd = 2,
# bty = "n")
# }
# Close File Connection
dev.off()
}
}
}
ices-tools-dev/NephAssess documentation built on Oct. 19, 2024, 6:33 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions uwtv_bubble_plot
uwtv_bubble_plot <- function(
dat = NULL,
wk.dir,
year = NA,
orientation = c("Landscape", "Portrait"),
style = c("new", "old"),
stratum_legend = FALSE,
elevation = FALSE,
jura = NULL){
# Coefficient of variation function
CV <- function(x){
(sd(x)/mean(x))
}
# Function to create new plot names
get.fname <- function(base.name){
fname <- function(i){paste(base.name, i, ".jpeg", sep = "")}
out <- fname(i <- 1)
while(file.exists(out))
out <- fname(i <- i + 1)
return(out)
}
# Function to capitalize first letter of each word
simpleCap <- function(x){
x <- tolower(x)
s <- strsplit(x, " ")[[1]]
paste(toupper(substring(s, 1, 1)), substring(s, 2),
sep = "", collapse = " ")
}
## evaluate orientation
# orientation <- orientation(members)
orientation <- match.arg(orientation)
style <- match.arg(style)
## Plotting colour palettes
# 3 sediment types
sedimentCol <- c("#009E73", "#E69F00", "#56B4E9")
bubbleFill <- c(rgb(0, 158, 115, 50, maxColorValue = 255),
rgb(230, 159, 0, 50, maxColorValue = 255),
rgb(86, 180, 233, 50, maxColorValue = 255))
# 2 sediment types
sedimentCol2 <- sedimentCol[c(2,3)]
bubbleFill2 <- bubbleFill[c(2,3)]
# Fladen
fladenCol <- c("#009E73", "#E69F00", "#56B4E9", "#CC79A7")
fladenFill <- c(rgb(0, 158, 115, 50, maxColorValue = 255),
rgb(230, 159, 0, 50, maxColorValue = 255),
rgb(86, 180, 233, 50, maxColorValue = 255),
rgb(204, 121, 167, 50, maxColorValue = 255))
### FU7
if(unique(dat$FU) == "Fladen"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Strata as factor
dat$strata_type <- factor(dat$strata_type, levels = c("C", "MC", "MF", "F"))
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU7_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-2.1, 2),
ylim = c(57.4, 60.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r7, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#dadada")
segments(-1, 60.5, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#dadada")
lapply(fladenSedimentsList, polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = fladenCol[as.factor(nz$strata_type)],
bg = fladenFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10,10,10,-10), y = c(50,50,70,70), col = "#c9e9f6")
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#000000")
segments(-1, 60.5, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#000000")
lapply(fladen.surfer.poly[c(17:20,24,25)], polygon, col = "olivedrab", border = NA)
lapply(fladen.surfer.poly[c(1,2,3,4,23)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(5,7,9,14)], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[10], polygon, col = "darkgreen", border = NA)
lapply(fladen.surfer.poly[12], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[c(13,22)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(6,8,11,15,16,21)], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(1, 60.2, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1,
cex.axis = 1.5,
at = c(-1.5, 0, 1.5),
labels = c(expression("1.5"^o*W),
expression("0"^o),
expression("1.5"^o*E)))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(58, 60, by = 1), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(58, 60, by = 1)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(1.2, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.2", cex = 0.5)
stW <- strwidth(c("1.2","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-1.25, 3), rep(59.4, 3) + 2*heightAdj,
x1 = rep(-1.5, 3), y1 = rep(59.4, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-1.25, 3), rep(59.4, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-1.6, 3) - 0.5*stWdiff, rep(59.4, 3) + 2*heightAdj,
c("1.2", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-1.25, 59.15,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-7.8, 57,
legend = levels(as.factor(dat$strata_type)),
col = fladenCol,
pt.bg = fladenFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU7_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-2.1, 2),
ylim = c(57.4, 60.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r7, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#dadada")
segments(-1, 60.5, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -1, 59, lty = 2, col = "#dadada")
segments(-2, 59, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -2, 58, lty = 2, col = "#dadada")
segments(-1, 58, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#dadada")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#dadada")
lapply(fladenSedimentsList, polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = fladenCol[as.factor(nz$strata_type)],
bg = fladenFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10,10,10,-10), y = c(50,50,70,70), col = "#c9e9f6")
# FU7 strata & sediments
segments(-1, 60.5, 2, 60.5, lty = 2, col = "#000000")
segments(-1, 60.5, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -1, 59, lty = 2, col = "#000000")
segments(-2, 59, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -2, 58, lty = 2, col = "#000000")
segments(-1, 58, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, -1, 57.5, lty = 2, col = "#000000")
segments(2, 57.5, 2, 60.5, lty = 2, col = "#000000")
lapply(fladen.surfer.poly[c(17:20,24,25)], polygon, col = "olivedrab", border = NA)
lapply(fladen.surfer.poly[c(1,2,3,4,23)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(5,7,9,14)], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[10], polygon, col = "darkgreen", border = NA)
lapply(fladen.surfer.poly[12], polygon, col = "lightgreen", border = NA)
lapply(fladen.surfer.poly[c(13,22)], polygon, col = "green", border = NA)
lapply(fladen.surfer.poly[c(6,8,11,15,16,21)], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r7, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(1, 60.2, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1,
cex.axis = 1.5,
at = c(-1.5, 0, 1.5),
labels = c(expression("1.5"^o*W),
expression("0"^o),
expression("1.5"^o*E)))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(58, 60, by = 1), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(58, 60, by = 1)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(1.2, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.2", cex = 0.5)
stW <- strwidth(c("1.2","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-1.25, 3), rep(59.4, 3) + 2*heightAdj,
x1 = rep(-1.5, 3), y1 = rep(59.4, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-1.25, 3), rep(59.4, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-1.6, 3) - 0.5*stWdiff, rep(59.4, 3) + 2*heightAdj,
c("1.2", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-1.25, 59.15,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-5.7, 57,
legend = levels(as.factor(dat$strata_type)),
col = fladenCol,
pt.bg = fladenFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU8
if(unique(dat$FU) == "Firth of Forth"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU8_bubble_plot_ls.")),
width = 380, height = 200, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-3.5, -1.95),
ylim = c(55.85, 56.35),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r8, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU8 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
segments(-2, 56.5, -2, 55.5, lty = 2, col = "#dadada")
# FU8 strata
lapply(forth.poly[5:16], polygon, col = NA, border = "#dadada")
lapply(forth.poly[23:53], polygon, col = NA, border = "#dadada")
lapply(forth.poly[54:66], polygon, col = NA, border = "#dadada")
lapply(forth.poly[17:22], polygon, col = NA, border = "#dadada")
lapply(forth.poly[1:4], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol2[as.factor(nz$strata_type)],
bg = bubbleFill2[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-5, 0, 0,-5), y = c(55, 55, 60, 60), col = "#c9e9f6")
lines(x = c(-2, -2), y = c(56.5, 55.5), lty = 2)
lines(x = c(-3, -2), y = c(56.5, 56.5), lty = 2)
lapply(forth.poly[5:16], polygon, col = "olivedrab", border = NA)
lapply(forth.poly[23:53], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[54:66], polygon, col = "green", border = NA)
lapply(forth.poly[17:22], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[1:4], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.45, 55.9, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-3.2, -2.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.2, -2.2, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(56, 56.2, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56, 56.2, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(3.3, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("3.3", cex = 0.5)
stW <- strwidth(c("3.3","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.2, 3), rep(56.25, 3) + 2*heightAdj,
x1 = rep(-3.3, 3), y1 = rep(56.25, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.2, 3), rep(56.25, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.33, 3) - 0.5*stWdiff, rep(56.25, 3) + 2*heightAdj,
c("3.3", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.2, 56.2,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-6, 55.8,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol2,
pt.bg = bubbleFill2,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU8_bubble_plot_po.")),
width = 360, height = 260, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-3.5, -1.95),
ylim = c(55.85, 56.35),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r8, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU8 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
segments(-2, 56.5, -2, 55.5, lty = 2, col = "#dadada")
# FU8 strata
lapply(forth.poly[5:16], polygon, col = NA, border = "#dadada")
lapply(forth.poly[23:53], polygon, col = NA, border = "#dadada")
lapply(forth.poly[54:66], polygon, col = NA, border = "#dadada")
lapply(forth.poly[17:22], polygon, col = NA, border = "#dadada")
lapply(forth.poly[1:4], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol2[as.factor(nz$strata_type)],
bg = bubbleFill2[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-5, 0, 0,-5), y = c(55, 55, 60, 60), col = "#c9e9f6")
lines(x = c(-2, -2), y = c(56.5, 55.5), lty = 2)
lines(x = c(-3, -2), y = c(56.5, 56.5), lty = 2)
lapply(forth.poly[5:16], polygon, col = "olivedrab", border = NA)
lapply(forth.poly[23:53], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[54:66], polygon, col = "green", border = NA)
lapply(forth.poly[17:22], polygon, col = "#c9e9f6", border = NA)
lapply(forth.poly[1:4], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r8, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.45, 55.9, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-3.2, -2.3, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.2, -2.3, by = 0.3)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(56, 56.2, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56, 56.2, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(3.3, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("3.3", cex = 0.5)
stW <- strwidth(c("3.3","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.2, 3), rep(56.25, 3) + 2*heightAdj,
x1 = rep(-3.3, 3), y1 = rep(56.25, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.2, 3), rep(56.25, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.33, 3) - 0.5*stWdiff, rep(56.25, 3) + 2*heightAdj,
c("3.3", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.2, 56.2,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-5, 55.8,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol2,
pt.bg = bubbleFill2,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU9
if(unique(dat$FU) == "Moray Firth"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
dat <- dat[!is.na(dat$average_density),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
# Set as factor
dat$strata_type <- as.factor(dat$strata_type)
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU9_bubble_plot_ls.")),
width = 380, height = 200, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4.1, -1.6),
ylim = c(57.6, 58.2),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r9, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU9 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
# FU9 strata
lapply(moray.poly[2:8], polygon, col = NA, border = "#dadada")
segments(-2, 57.96422, -2, 57.80697, lty = 1, col = "#ffffff")
lapply(moray.poly[9:20], polygon, col = NA, border = "#dadada")
lapply(moray.poly[21:25], polygon, col = NA, border = "#dadada")
lapply(moray.poly[1], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -2), y = c(58.5, 58.5), lwd = 1, lty = 2)
lines(x = c(-2, -2), y = c(58.5, 58), lwd = 1, lty = 2)
lines(x = c(-2, -1), y = c(58, 58), lwd = 1, lty = 2)
lines(x = c(-1, -1), y = c(58, 57.5), lwd = 1, lty = 2)
lines(x = c(-1, -2), y = c(57.5, 57.5), lwd = 2, lty = 2)
lapply(moray.poly[2:8], polygon, col = "olivedrab", border = NA)
lapply(moray.poly[9:20], polygon, col = "#c9e9f6", border = NA)
lapply(moray.poly[21:25], polygon, col = "green", border = NA)
lapply(moray.poly[1], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-4, 58.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-3.6, -2, by = 0.8), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.6, -2, by = 0.8)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(57.7, 58.1, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.7, 58.1, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-8)]){
legdens <- c(1.37, 0.75, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.35", cex = 0.5)
stW <- strwidth(c("1.35","0.75","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-2.1, 3), rep(58.05, 3) + 2*heightAdj,
x1 = rep(-2.3, 3), y1 = rep(58.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-2.1, 3), rep(58.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-2.375, 3) - 0.5*stWdiff, rep(58.05, 3) + 2*heightAdj,
c("1.35","0.75","0.1"),
col = "#000000",
cex = 0.75)
text(-2.1, 58,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8.5, 57.55,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU9_bubble_plot_po.")),
width = 300, height = 260, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4.1, -1.6),
ylim = c(57.6, 58.2),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r9, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU9 strata
segments(-4, 56.5, -2, 56.5, lty = 2, col = "#dadada")
# FU9 strata
lapply(moray.poly[2:8], polygon, col = NA, border = "#dadada")
segments(-2, 57.96422, -2, 57.80697, lty = 1, col = "#ffffff")
lapply(moray.poly[9:20], polygon, col = NA, border = "#dadada")
lapply(moray.poly[21:25], polygon, col = NA, border = "#dadada")
lapply(moray.poly[1], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -2), y = c(58.5, 58.5), lwd = 1, lty = 2)
lines(x = c(-2, -2), y = c(58.5, 58), lwd = 1, lty = 2)
lines(x = c(-2, -1), y = c(58, 58), lwd = 1, lty = 2)
lines(x = c(-1, -1), y = c(58, 57.5), lwd = 1, lty = 2)
lines(x = c(-1, -2), y = c(57.5, 57.5), lwd = 2, lty = 2)
lapply(moray.poly[2:8], polygon, col = "olivedrab", border = NA)
lapply(moray.poly[9:20], polygon, col = "#c9e9f6", border = NA)
lapply(moray.poly[21:25], polygon, col = "green", border = NA)
lapply(moray.poly[1], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r9, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-4, 58.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-3.6, -2, by = 0.8), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.6, -2, by = 0.8)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(57.7, 58.1, by = 0.2), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.7, 58.1, by = 0.2)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-9)]){
legdens <- c(1.37, 0.75, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1.35", cex = 0.5)
stW <- strwidth(c("1.35","0.75","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-2.1, 3), rep(58.05, 3) + 2*heightAdj,
x1 = rep(-2.3, 3), y1 = rep(58.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-2.1, 3), rep(58.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-2.375, 3) - 0.5*stWdiff, rep(58.05, 3) + 2*heightAdj,
c("1.35","0.75","0.1"),
col = "#000000",
cex = 0.75)
text(-2.1, 58,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-7, 57.55,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU10
if(unique(dat$FU) == "Noup"){
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.2
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU10_bubble_plot.")),
width = 280, height = 190, units = "mm", res = 350)
par(mfrow = c(2, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in tail(unique(dat$year),6)){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4, -3),
ylim = c(59, 59.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r10, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU10 strata
lapply(noup.poly[1:2], polygon, col = NA, border = "#dadada")
lapply(noup.poly[3:5], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[2],
bg = bubbleFill[2],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -3), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-3, -3), y = c(59, 59.5), lwd = 1, lty = 2)
lines(x = c(-4, -3), y = c(59.5, 59.5), lwd = 1, lty = 2)
lines(x =c(-4, -4), y = c(59, 59.5), lwd = 1, lty = 2)
lapply(noup.poly[1:2], polygon, col = "olivedrab", border = NA)
lapply(noup.poly[3:5], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.3, 59.6, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% tail(unique(dat$year),3)){
axis(1, at = seq(-3.8, -3.2, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.8, -3.2, by = 0.3)), "W")))
}
# y-axes
if(i %in% matrix(tail(unique(dat$year),6),nrow=2,byrow=T)[,1]){
axis(2, at = c(59.2, 59.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(c(59.2, 59.5)), "N")))
}
# Bubble Legend
if(i == tail(unique(dat$year),1)){
legdens <- c(0.9, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1", cex = 0.5)
stW <- strwidth(c("1","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.7, 3), rep(59.05, 3) + 2*heightAdj,
x1 = rep(-3.78, 3), y1 = rep(59.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.7, 3), rep(59.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.8, 3) - 0.5*stWdiff, rep(59.05, 3) + 2*heightAdj,
c("1", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.7, 59,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU10_bubble_plot.")),
width = 200, height = 280, units = "mm", res = 350)
par(mfrow = c(3, 2), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in tail(unique(dat$year),6)){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-4, -3),
ylim = c(59, 59.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r10, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU10 strata
lapply(noup.poly[1:2], polygon, col = NA, border = "#dadada")
lapply(noup.poly[3:5], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[2],
bg = bubbleFill[2],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-4, -3), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-3, -3), y = c(59, 59.5), lwd = 1, lty = 2)
lines(x = c(-4, -3), y = c(59.5, 59.5), lwd = 1, lty = 2)
lines(x =c(-4, -4), y = c(59, 59.5), lwd = 1, lty = 2)
lapply(noup.poly[1:2], polygon, col = "olivedrab", border = NA)
lapply(noup.poly[3:5], polygon, col = "#c9e9f6", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r10, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-3.3, 59.6, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% tail(unique(dat$year),2)){
axis(1, at = seq(-3.8, -3.2, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-3.8, -3.2, by = 0.3)), "W")))
}
# y-axes
if(i %in% matrix(tail(unique(dat$year),6),nrow=3,byrow=T)[,1]){
axis(2, at = c(59.2, 59.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(c(59.2, 59.5)), "N")))
}
# Bubble Legend
if(i == tail(unique(dat$year),1)){
legdens <- c(0.9, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("1", cex = 0.5)
stW <- strwidth(c("1","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-3.7, 3), rep(59.05, 3) + 2*heightAdj,
x1 = rep(-3.78, 3), y1 = rep(59.05, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-3.7, 3), rep(59.05, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-3.8, 3) - 0.5*stWdiff, rep(59.05, 3) + 2*heightAdj,
c("1", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-3.7, 59,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
dev.off()
}
}
### FU11 Bubble Plots
if(unique(dat$FU) == "North Minch"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU11_bubble_plot_ls.")),
width = 350, height = 250, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-7.1, -5.3),
ylim = c(57.4, 58.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU11 boundaries
segments(-7, 57.5, -5, 57.5, lty = 2, col = "#dadada")
segments(-7, 57.5, -7, 59, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU11 strata
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-7, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-7, -5), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-7, -7), y = c(57.5, 59), lwd = 1, lty = 2)
lines(x = c(-5, -5), y = c(57.5, 59), lwd = 1, lty = 2)
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(poly_union_2007_2011_nm.rda)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and label
box()
text(-5.75, 57.64, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c((year-3):year)){
axis(1, at = seq(-6.5, -5.75, by = 0.75), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6.5, -5.75, by = 0.75)), "W")))
}
# y-axes
if(i %in% c((year-11), (year-7), (year-3))){
axis(2, at = seq(57.6, 58.4, by = 0.4), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.6, 58.4, by = 0.4)), "N")))
}
# Bubble Legend
if(i == (year-3)){
legdens <- c(2.8, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-6.73, 3), rep(58.45, 3) + 2*heightAdj,
x1 = rep(-6.83, 3), y1 = rep(58.45, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-6.73, 3), rep(58.45, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.87, 3) - 0.5*stWdiff, rep(58.45, 3) + 2*heightAdj,
c("2.8", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-6.73, 58.35,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-9.25, 57.3,
legend = "VMS",
col = "#CC79A7",
pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU11_bubble_plot_po.")),
width = 280, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-7.1, -5.3),
ylim = c(57.4, 58.7),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU11 boundaries
segments(-7, 57.5, -5, 57.5, lty = 2, col = "#dadada")
segments(-7, 57.5, -7, 59, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU11 strata
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-7, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-7, -5), y = c(59, 59), lwd = 1, lty = 2)
lines(x = c(-7, -7), y = c(57.5, 59), lwd = 1, lty = 2)
lines(x = c(-5, -5), y = c(57.5, 59), lwd = 1, lty = 2)
plot(poly_union_2007_2011_nm.rda, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(poly_union_2007_2011_nm.rda)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and label
box()
text(-5.75, 57.64, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c((year-2):year)){
axis(1, at = seq(-6.5, -5.75, by = 0.75), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6.5, -5.75, by = 0.75)), "W")))
}
# y-axes
if(i %in% c((year-11), (year-8), (year-5), (year-2))){
axis(2, at = seq(57.6, 58.4, by = 0.4), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(57.6, 58.4, by = 0.4)), "N")))
}
# Bubble Legend
if(i == (year-2)){
legdens <- c(2.8, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-6.73, 3), rep(58.45, 3) + 2*heightAdj,
x1 = rep(-6.83, 3), y1 = rep(58.45, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-6.73, 3), rep(58.45, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.87, 3) - 0.5*stWdiff, rep(58.45, 3) + 2*heightAdj,
c("2.8", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-6.73, 58.35,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8.25, 57.3,
legend = "VMS",
col = "#CC79A7",
pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU12 Bubble Plots
if(unique(dat$FU) == "South Minch"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU12_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-8, -5.5),
ylim = c(56, 57.5),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU12 area strata
segments(-6.75, 56.6, -6.75, 57.16,
lty = 2,
col = "#dadada")
segments(-6.75, 57.16, -6.51, 57.33,
lty = 2,
col = "#dadada")
segments(-6.75, 56.6, -8, 56.4, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# FU12 Boundary
segments(-8, 57.5, -8, 56, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r12, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-8, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-8, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lines(x = c(-8, -8), y = c(57.5, 56), lwd = 1, lty = 2)
lapply(south.minch.poly[17:50], polygon, col = "olivedrab", border = NA)
lapply(south.minch.poly[51], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[53:72], polygon, col = "green", border = NA)
lapply(south.minch.poly[52], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[1:16], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-8, 57.3, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-7.5, -6, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-7.5, -6, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(56.5, 57, by=0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.5, 57, by=0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(2.5, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.5", cex = 0.5)
stW <- strwidth(c("2.5","0.5","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-7.5, 3), rep(56.1, 3) + 2*heightAdj,
x1 = rep(-7.75, 3), y1 = rep(56.1, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-7.5, 3), rep(56.1, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-7.8, 3) - 0.5*stWdiff, rep(56.1, 3) + 2*heightAdj,
c("2.5", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-7.5, 56,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-12.8, 55.85,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU12_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-8, -5.5),
ylim = c(56, 57.5),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU12 area strata
segments(-6.75, 56.6, -6.75, 57.16,
lty = 2,
col = "#dadada")
segments(-6.75, 57.16, -6.51, 57.33,
lty = 2,
col = "#dadada")
segments(-6.75, 56.6, -8, 56.4, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# FU12 Boundary
segments(-8, 57.5, -8, 56, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r12, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-8, -5), y = c(57.5, 57.5), lwd = 1, lty = 2)
lines(x = c(-8, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lines(x = c(-8, -8), y = c(57.5, 56), lwd = 1, lty = 2)
lapply(south.minch.poly[17:50], polygon, col = "olivedrab", border = NA)
lapply(south.minch.poly[51], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[53:72], polygon, col = "green", border = NA)
lapply(south.minch.poly[52], polygon, col = "#c9e9f6", border = NA)
lapply(south.minch.poly[1:16], polygon, col = "darkgreen", border = NA)
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r12, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-8, 57.3, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-7.5, -6, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-7.5, -6, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(56.5, 57, by=0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.5, 57, by=0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(2.5, 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.5", cex = 0.5)
stW <- strwidth(c("2.5","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-7.5, 3), rep(56.1, 3) + 2*heightAdj,
x1 = rep(-7.75, 3), y1 = rep(56.1, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-7.5, 3), rep(56.1, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-7.8, 3) - 0.5*stWdiff, rep(56.1, 3) + 2*heightAdj,
c("2.5", "0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(-7.5, 56,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-10.8, 55.85,
legend = sapply(levels(as.factor(dat$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU13
if(unique(dat$FU) == "Clyde"){
# Is Jura provided?
if(is.null(jura) == FALSE){
dat13 <- rbind(dat, jura)
} else {dat13 <- dat}
# Get years
mfys <- unique(dat13$year)
dat13 <- dat13[dat13$year %in% c(mfys[(match(year, mfys)-11):match(year, mfys)]),]
# Calculate bubble radii
dat13$radii <- sqrt(dat13$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat13 <- dat13[dat13$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU13_bubble_plot_ls.")),
width = 380, height = 230, units = "mm", res = 350)
par(mfrow = c(3, 4), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat13[dat13$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-6.2, -4.6),
ylim = c(55, 56),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU13 Boundary
segments(-6, 55, -6, 56, lty = 2, col = "#dadada")
segments(-6, 56, -4, 56, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r13, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU13 strata
lapply(clyde.poly[26:35], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[1:16], polygon, col = NA, border = "#dadada")
lapply(clyde.poly[44:49], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[17:25], polygon, col = NA, border = "#dadada")
lapply(jura.poly[3:4], polygon, col = NA, border = "#dadada")
lapply(jura.poly[7], polygon, col = NA, border = "#dadada")
lapply(jura.poly[5:6], polygon, col = NA, border = "#dadada")
lapply(jura.poly[1], polygon, col = NA, border = "#dadada")
lapply(jura.poly[2], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-6, -6), y = c(56, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5), y = c(55, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lapply(clyde.poly[26:35], polygon, col = "olivedrab", border = NA)
lapply(clyde.poly[1:16], polygon, col = "#c9e9f6", border = NA)
lapply(clyde.poly[44:49], polygon, col = "green", border = NA)
lapply(clyde.poly[17:25], polygon, col = "darkgreen", border = NA)
if(is.null(jura) == FALSE){
lapply(jura.poly[3:4], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[7], polygon, col = "green", border = NA)
lapply(jura.poly[5:6], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[1], polygon, col = "#c9e9f6", border = NA)
lapply(jura.poly[2], polygon, col = "darkgreen", border = NA)
}
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-5, 55.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-3):match(year, mfys)])){
axis(1, at = seq(-6, -5, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6, -5, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-7)],
mfys[(match(year, mfys)-3)])){
axis(2, at = seq(55.2, 55.8, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(55.2, 55.8, by = 0.3)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-3)]){
legdens <- c(2.83, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat13$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","1","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(-5.88, 3), rep(55.15, 3) + 2*heightAdj,
x1 = rep(-6, 3), y1 = rep(55.15, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-5.88, 3), rep(55.15, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.04, 3) - 0.5*stWdiff, rep(55.15, 3) + 2*heightAdj,
c("2.8", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-5.88, 55.05,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-9, 54.9,
legend = sapply(levels(as.factor(dat13$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU13_bubble_plot_po.")),
width = 300, height = 320, units = "mm", res = 350)
par(mfrow = c(4, 3), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-11):match(year, mfys)]){
xx <- dat13[dat13$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-6.2, -4.6),
ylim = c(55, 56),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU13 Boundary
segments(-6, 55, -6, 56, lty = 2, col = "#dadada")
segments(-6, 56, -4, 56, lty = 2, col = "#dadada")
segments(-6.75, 56.6, -5, 56.6, lty = 2, col = "#dadada")
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
plot(r13, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
}
# FU13 strata
lapply(clyde.poly[26:35], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[1:16], polygon, col = NA, border = "#dadada")
lapply(clyde.poly[44:49], polygon, col = NA, border = "#dadada")
#lapply(clyde.poly[17:25], polygon, col = NA, border = "#dadada")
lapply(jura.poly[3:4], polygon, col = NA, border = "#dadada")
lapply(jura.poly[7], polygon, col = NA, border = "#dadada")
lapply(jura.poly[5:6], polygon, col = NA, border = "#dadada")
lapply(jura.poly[1], polygon, col = NA, border = "#dadada")
lapply(jura.poly[2], polygon, col = NA, border = "#dadada")
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = sedimentCol[as.factor(nz$strata_type)],
bg = bubbleFill[as.factor(nz$strata_type)],
lwd = 2,
add = TRUE)
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
lines(x = c(-6, -6), y = c(56, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5), y = c(55, 55), lwd = 1, lty = 2)
lines(x = c(-6, -5.5), y = c(56, 56), lwd = 1, lty = 2)
lapply(clyde.poly[26:35], polygon, col = "olivedrab", border = NA)
lapply(clyde.poly[1:16], polygon, col = "#c9e9f6", border = NA)
lapply(clyde.poly[44:49], polygon, col = "green", border = NA)
lapply(clyde.poly[17:25], polygon, col = "darkgreen", border = NA)
if(is.null(jura) == FALSE){
lapply(jura.poly[3:4], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[7], polygon, col = "green", border = NA)
lapply(jura.poly[5:6], polygon, col = "olivedrab", border = NA)
lapply(jura.poly[1], polygon, col = "#c9e9f6", border = NA)
lapply(jura.poly[2], polygon, col = "darkgreen", border = NA)
}
# Add terrestrial map
if(elevation == FALSE){
polygon(uk.coast$lons, uk.coast$lats, col = "#cccccc", border = "#000000")
} else {
plot(r13, add = TRUE, col = grey(51:100/100), legend = FALSE)
}
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
}
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
# Box and label
box()
text(-5, 55.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% c(mfys[(match(year, mfys)-2):match(year, mfys)])){
axis(1, at = seq(-6, -5, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(-6, -5, by = 0.5)), "W")))
}
# y-axes
if(i %in% c(mfys[(match(year, mfys)-11)],
mfys[(match(year, mfys)-8)],
mfys[(match(year, mfys)-5)],
mfys[(match(year, mfys)-2)])){
axis(2, at = seq(55.2, 55.8, by = 0.3), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(55.2, 55.8, by = 0.3)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys)-2)]){
legdens <- c(2.83, 1, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat13$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","1","0.1"), cex=0.75)
stWdiff <- stW - stW[1]
segments(rep(-5.88, 3), rep(55.15, 3) + 2*heightAdj,
x1 = rep(-6, 3), y1 = rep(55.15, 3) + 2*heightAdj,
col="#000000")
symbols(rep(-5.88, 3), rep(55.15, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat13$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(-6.04, 3) - 0.5*stWdiff, rep(55.15, 3) + 2*heightAdj,
c("2.8", "1", "0.1"),
col = "#000000",
cex = 0.75)
text(-5.88, 55.05,
bty = "n",
col = "#000000",
cex = 1.2,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
if(stratum_legend == TRUE & style == "new"){
legend(-8, 54.9,
legend = sapply(levels(as.factor(dat13$strata_type)), simpleCap),
col = sedimentCol,
pt.bg = bubbleFill,
horiz = TRUE,
xpd = NA,
pch = 21,
cex = 2,
pt.cex = 2,
pt.lwd = 2,
bty = "n")
}
# Close File Connection
dev.off()
}
}
### FU11 Bubble Plots
if(unique(dat$FU) == "Devil's Hole"){
# Get years
mfys <- unique(dat$year)
dat <- dat[dat$year %in% c(mfys[(match(year, mfys)-9):match(year, mfys)]),]
# Calculate bubble radii
dat$radii <- sqrt(dat$average_density/pi)
# SymbolScaling
symbolScaling <- 0.15
# Remove FALSE strata
dat <- dat[dat$strata_type != "FALSE",]
## Landscape Orientation
if(orientation == "Landscape"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU34_bubble_plot_ls.")),
width = 350, height = 160, units = "mm", res = 350)
par(mfrow = c(2, 5), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-9):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-0.5, 2.5),
ylim = c(55.9, 57.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
# Add terrestrial map
# if(elevation == FALSE){
# polygon(uk.coast$lons, uk.coast$lats, col = "#dadada", border = "#dadada")
# } else {
# plot(r11, add = TRUE, col = grey(51:100/100), legend = FALSE)
# plot(r11, add = TRUE, alpha = 0.2, col = terrain.colors(255), legend = FALSE)
# }
# FU11 strata
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#000000")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(devils.hole.vms.poly)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and year label
box()
if(style == "old"){
polygon(x = c(-0.1, 0.1, 0.1, -0.1), y = c(56.02, 56.02, 56.2, 56.2),
col = "#c9e9f6", border = "#c9e9f6")
}
text(-0.45, 56.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% mfys[c((match(year, mfys) - seq(4, 0, by = -1)))]){
axis(1, at = seq(0, 2, by = 1), cex.axis = 1.5,
labels = c(0, parse(text = sprintf("%s^o*%s",
abs(seq(1, 2, by = 1)), "W"))))
}
# y-axes
if(i %in% mfys[c((match(year, mfys) - seq(9, 4, by = -5)))]){
axis(2, at = seq(56.2, 57.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.2, 57.2, by = 0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys) - 4)]){
legdens <- c(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1), 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(0.7, 3), rep(57.2, 3) + 2*heightAdj,
x1 = rep(0.4, 3), y1 = rep(57.2, 3) + 2*heightAdj,
col="#000000")
symbols(rep(0.7, 3), rep(57.2, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(0.3, 3) - 0.5*stWdiff, rep(57.2, 3) + 2*heightAdj,
c(as.character(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1)),
"0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(0.7, 57.075,
bty = "n",
col = "#000000",
cex = 0.9,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
# if(stratum_legend == TRUE & style == "new"){
# legend(-9.25, 57.3,
# legend = "VMS",
# col = "#CC79A7",
# pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
# horiz = TRUE,
# xpd = NA,
# pch = 21,
# cex = 2,
# pt.cex = 2,
# pt.lwd = 2,
# bty = "n")
# }
# Close File Connection
dev.off()
## Portrait Orientation
} else if(orientation == "Portrait"){
# Open File Connection
jpeg(get.fname(paste0(wk.dir, "FU34_bubble_plot_po.")),
width = 150, height = 320, units = "mm", res = 350)
par(mfrow = c(5, 2), mar = c(0, 0, 0, 0), oma = c(5.5, 3, 0.2, 0.2))
for(i in mfys[(match(year, mfys)-9):match(year, mfys)]){
xx <- dat[dat$year == i,]
# Get scaling for bubble plot
bubbleScale <- max(xx$radii, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)
# Get zero/non-zero data
nz <- xx[xx$average_density>0,]
ind <- rev(order(nz$average_density))
nz <- nz[ind,]
zDat <- xx[xx$average_density==0,]
# Plot
plot(1, 1,
xlim = c(-0.5, 2.5),
ylim = c(55.9, 57.6),
xaxs = "i",
yaxs = "i",
type = "n",
xlab = "",
ylab = "",
axes = FALSE)
# New style map
if(style == "new"){
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#dadada")
# FU11 strata
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = NA, border = "#dadada"))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#CC79A7",
bg = rgb(204, 121, 167, 50, maxColorValue = 255),
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#ff0000")
} else if(style == "old"){
polygon(x = c(-10, 10, 10, -10), y = c(50, 50, 70, 70), col = "#c9e9f6")
# FU34 boundaries
lines(x = c(0, 2), y = c(57.5, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 2), y = c(56.0, 56.0), lwd = 2, lty = 2, col = "#000000")
lines(x = c(2, 2), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
lines(x = c(0, 0), y = c(56, 57.5), lwd = 2, lty = 2, col = "#000000")
plot(devils.hole.vms.poly, add = TRUE,
poly.args = list(col = 2, border = NA))
# plot holes
pts <- get.pts(devils.hole.vms.poly)
logic.pts.hole <- lapply(1:length(pts), function(x){pts[[x]]$hole == TRUE})
pts.hole <- pts[logic.pts.hole == TRUE]
pts.hole <- new("gpc.poly", pts=pts.hole)
plot(pts.hole, add = TRUE, poly.args = list(col = "#c9e9f6", border = NA))
# Bubbles
symbols(nz$lons, nz$lats,
circles = nz$radii,
inches = symbolScaling * bubbleScale,
fg = "#000000",
bg = NA,
lwd = 2,
add = TRUE)
# Zeroes
points(zDat$lons, zDat$lats,
pch = "x",
cex = 2,
lwd = 2,
col = "#000000")
}
# Box and year label
box()
if(style == "old"){
polygon(x = c(-0.1, 0.1, 0.1, -0.1), y = c(56.02, 56.02, 56.2, 56.2),
col = "#c9e9f6", border = "#c9e9f6")
}
text(-0.45, 56.1, labels = i, cex = 3, font = 2, pos = 4)
# x-axes
if(i %in% mfys[c((match(year, mfys) - seq(1, 0, by = -1)))]){
axis(1, at = seq(0, 2, by = 1), cex.axis = 1.5,
labels = c(0, parse(text = sprintf("%s^o*%s",
abs(seq(1, 2, by = 1)), "W"))))
}
# y-axes
if(i %in% mfys[c((match(year, mfys) - seq(9, 1, by = -2)))]){
axis(2, at = seq(56.2, 57.2, by = 0.5), cex.axis = 1.5,
labels = parse(text = sprintf("%s^o*%s",
abs(seq(56.2, 57.2, by = 0.5)), "N")))
}
# Bubble Legend
if(i == mfys[(match(year, mfys) - 1)]){
legdens <- c(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1), 0.5, 0.1)
legRad <- sqrt(legdens/pi)
hin <- par("pin")[2]
ydiff <- par("usr")[c(4,3)]
densPerInch <- abs(ydiff[2]-ydiff[1]) / hin
radPerInch <- sqrt(max(dat$average_density)/pi)/symbolScaling
heightAdj <- legRad/radPerInch*densPerInch
# Get some adjustment values
tAdj <- strheight("2.8", cex = 0.5)
stW <- strwidth(c("2.8","0.5","0.1"), cex = 0.75)
stWdiff <- stW - stW[1]
segments(rep(0.7, 3), rep(57.2, 3) + 2*heightAdj,
x1 = rep(0.4, 3), y1 = rep(57.2, 3) + 2*heightAdj,
col="#000000")
symbols(rep(0.7, 3), rep(57.2, 3) + heightAdj,
circles = legRad,
inches = symbolScaling * (max(legRad, na.rm = TRUE)/max(dat$radii, na.rm = TRUE)),
fg = "#000000",
add = TRUE)
text(rep(0.3, 3) - 0.5*stWdiff, rep(57.2, 3) + 2*heightAdj,
c(as.character(round(max(FU34_tvdata$average_density, na.rm = TRUE), 1)),
"0.5", "0.1"),
col = "#000000",
cex = 0.75)
text(0.7, 57.075,
bty = "n",
col = "#000000",
cex = 0.9,
labels = expression(atop(Mean~Burrows~per~m^2)))
}
}
# Sediment Type Legend
# if(stratum_legend == TRUE & style == "new"){
# legend(-8.25, 57.3,
# legend = "VMS",
# col = "#CC79A7",
# pt.bg = rgb(204, 121, 167, 50, maxColorValue = 255),
# horiz = TRUE,
# xpd = NA,
# pch = 21,
# cex = 2,
# pt.cex = 2,
# pt.lwd = 2,
# bty = "n")
# }
# Close File Connection
dev.off()
}
}
}
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