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Sea_level_map.R
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Sea_level_map.R
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### MAP of different sea levels ---
### Load libraries ----
library(ggplot2)
library(ggthemes)
library(cowplot)
library(sp)
library(spData)
library(sf)
library(rgdal)
library(raster)
library(rgeos)
library(mapview)
library(tmap)
library(tmaptools)
library(maptools)
library(mapdata)
library(leaflet)
library(caTools)
library(reshape2)
library(tidyr)
library(car)
library(lattice)
library(latticeExtra)
library(dplyr)
library(rasterVis)
library(zoo)
library(fields)
library(geoR)
library(gstat)
library(ggsn)
library(ggspatial)
library(ggrepel)
library(patchwork)
#library(elsa)
#install.packages("corrplot")
#library(corrplot)
library(broman)
library(viridis)
library(smoothr)
library(units)
library(RColorBrewer)
# Clear memory ----
rm(list=ls())
### Set directories ----
m.dir <- dirname(rstudioapi::getActiveDocumentContext()$path)
w.dir <- "Y:/mbh-d3-swc-fish"
p.dir <- paste(m.dir, "plots", sep = '/')
d.dir <- paste(m.dir, "data", sep='/')
s.dir <- paste(m.dir, "shapefiles", sep='/')
r.dir <- paste(m.dir, "rasters", sep='/')
### Read sw cmr polys ----
cmr <- readOGR(paste(s.dir, "AustraliaNetworkMarineParks.shp",sep='/'))
plot(cmr)
names(cmr)
head(cmr)
cmr$ZoneName <- as.factor(cmr$ZoneName)
cmr$ResName <- as.factor(cmr$ResName)
levels(cmr$ZoneName)
crs1 <- proj4string(sw)
levels(cmr$ZoneName)
dfcmr <- as.data.frame(cmr)
# get poly for each zone --
NPZ <- cmr[cmr$ZoneName=="National Park Zone",]
HPZ <- cmr[cmr$ZoneName=="Habitat Protection Zone",]
MUZ <- cmr[cmr$ZoneName=="Multiple Use Zone",]
SPZ <- cmr[cmr$ZoneName=="Special Purpose Zone",]
# read Australia poly ----
wa <- readOGR(paste(s.dir, "WA_wgs84.shp",sep='/'))
plot(wa)
# read state reserves ----
wamp <- readOGR(paste(s.dir, "All_StateReserves.shp", sep='/'))
wamp
plot(wamp)
# read coastal waters ----
cw <- readOGR(paste(s.dir, "amb_coastal_waters_limit.shp", sep='/'))
cw
plot(cw)
## Read Bathy ----
bathy <- raster(paste(r.dir, "Bathy.tif", sep='/'))
#bathy <- raster(paste(r.dir, "WA_500m_Bathy.tif", sep='/'))
plot(bathy)
#values(bathy)[values(bathy) < -2500] = NA
#plot(bathy)
plot(cmr, add=T)
# set extent --
#ext1 <- extent( 114.1401 , 115.8426, -34.64244, -32.87244)
# e <- drawExtent()
# e
ext1 <- extent(113.1145 , 114.4722, -23.40797 , -21.48672 )
# crop polys ----
cmr1 <- crop(cmr, ext1)
wa1 <- crop(wa, ext1)
wamp1 <- crop(wamp, ext1)
bathy1 <- crop(bathy, ext1)
cw1 <- crop(cw, ext1)
# check
plot(bathy1)
plot(cmr1, add=T)
# Polygons of different sealevels ----
ybf70k <- bathy1
ybf70k[ybf70k < (-70)] <- NA
plot(ybf70k, add=T)
plot(ybf70k, col="black")
ybf70k[ybf70k > (-70)] <- 1
ybf21k <- bathy1
ybf21k[ybf21k < (-125)] <- NA
plot(ybf21k, col="blue")
ybf21k[ybf21k > (-125)] <- 1
ybf11k <- bathy1
ybf11k[ybf11k < (-40)] <- NA
plot(ybf11k, col="red")
#plot(wa1, add=T)
ybf11k[ybf11k > (-40)] <- 1
plot(ybf21k, col="blue")
plot(ybf70k, col="green", add=T)
plot(ybf11k, col="red", add=T)
#bathy2 <- bathy
#bathy2[bathy2 > (-125)] <- NA
#plot(bathy2)
## to polys --
k70 <- rasterToPolygons(ybf70k, na.rm =T, dissolve=T)
plot(k70)
k21 <- rasterToPolygons(ybf21k, na.rm =T, dissolve=T)
plot(k21)
k11 <- rasterToPolygons(ybf11k, na.rm =T, dissolve=T)
plot(k11)
## TRYING SOME STUFF ----
# k11$OBJECTID <- '1'
# wa2 <- wa1
# wa2$OBJECTID <- '11'
# wa2 <- wa2[,-c(2:7)]
# plot(wa2)
# k11 <- k11[,-1]
# k11a <- raster::merge(k11, wa1)
# plot(k11a)
# k11a$OBJECTID
# k <- k11a[k11a$OBJECTID.1 == 1,]
# plot(k)
# w <- k11a[k11a$OBJECTID.2 == 11,]
# plot(w)
# k11b <- raster::aggregate(rbind(wa2,k11))
# plot(k11b, col='red')
# k11b$OBJECTID
# Read land locations ----
df <- read.csv(paste(s.dir, "Locations.csv", sep = '/'))
df
dfs <- df
coordinates(dfs) <- ~Longitude+Latitude
#plot(dfs)
### Map ----
## Colours ----
sg <- brocolors("crayons")["Spring Green"]
y1 <- brocolors("crayons")["Canary"]
g1 <- brocolors("crayons")["Asparagus"]
g2 <- brocolors("crayons")["Fern"]
g3 <- brocolors("crayons")["Tropical Rainforest"]
g4 <- brocolors("crayons")["Yellow Green"]
g5 <- brocolors("crayons")["Pine Green"]
g6 <- brocolors("crayons")["Electric Lime"]
map <- tm_shape(cmr1) + tm_borders(col ='white', lwd = 1.5) +
tm_compass(type = "arrow", position = c(0.1, 0.1), size = 2) +
#tm_fill(col ='ZONENAME', palette=c('yellow', 'red'), alpha = 0.1) +
tm_scale_bar(breaks = c(0, 10, 20), text.size = 0.5, position = c(0.08, 0.02)) +
#tm_graticules(ticks = FALSE) +
tm_grid(n.x = 3, n.y = 3, labels.size = 1.5, lines = FALSE)
map
map0 <- map + tm_shape(bathy2) + tm_raster(palette=viridis(40, direction =-1), style = 'cont', legend.reverse = TRUE) +
tm_layout(legend.text.size = 1.7,
legend.outside = TRUE,
legend.outside.position = 'right',
#legend.position = c(1, 0.05),
legend.title.size = 0.5,
legend.title.color = 'white',
legend.width = 1)
map0
map1 <- map0 + tm_shape(k21) + tm_borders(col = g2, lwd = 2) + tm_fill(col=g2) +
tm_add_legend(type = 'fill', labels = "21,000 years ago", col = g2, lwd = 2, size = 2)
map1
map2 <- map1 + tm_shape(k70) + tm_borders(col = g5, lwd = 2) + tm_fill(col=g5) +
tm_add_legend(type = 'fill', labels = "70,000 years ago", col = g5, lwd = 2, size = 2)
map2
map3 <- map2 + tm_shape(k11) + tm_borders(col = g4, lwd = 2) + tm_fill(g4) +
tm_add_legend(type = 'fill', labels = "11,000 years ago", col = g4, lwd = 2, size = 2)
map3
map4 <- map3 + tm_shape(wa1) + tm_borders(col = 'black', lwd = 2) + tm_fill(col=sg) +
tm_add_legend(type = 'fill', labels = "Coastline today", col = sg, lwd = 2, size = 2)
map4
map5 <- map4 + tm_shape(dfs) + tm_symbols(col = 'black', size = 0.2) +
tm_text("Location", size = 0.8, xmod = 1.5, ymod = -0.5)
map5
map55 <- map5 + tm_shape(cmr1) + tm_borders(col = 'black', lwd = 1.5)
map55
# Option 1 ----
map6 <- map55 + tm_shape(SPZ) + tm_borders(col = 'black', lwd = 1.5) +
tm_add_legend(type = 'line', labels = "Special Purpose Zone", col = 'black', lwd = 2, size = 2)
map6
map7 <- map55 + tm_shape(MUZ) + tm_borders(col = 'gray', lwd = 1.5) +
tm_add_legend(type = 'line', labels = "Mutiple Use Zone", col = 'gray', lwd = 2, size = 2, lty ='33')
map7
map8 <- map7 + tm_shape(HPZ) + tm_borders(col = 'red', lwd = 1.5, lty ='33') +
tm_add_legend(type = 'line', labels = "Habitat Protection Zone", col = 'red', lwd = 2, size = 2, lty ='33')
map8
map9 <- map8 + tm_shape(NPZ) + tm_borders(col = 'green', lwd = 1.5, lty ='33') +
tm_add_legend(type = 'line', labels = "National Park Zone", col = 'green', lwd = 2, size = 2, lty ='33')
map9
# Option 2 ----
map6 <- map55 + tm_shape(SPZ) + tm_borders(col = 'black', lwd = 1.5)
#tm_add_legend(type = 'line', labels = "Special Purpose Zone", col = 'black', lwd = 2, size = 2)
map6
map7 <- map6 + tm_shape(NPZ) + tm_borders(col = 'green', lwd = 1.5, lty ='33') +
tm_add_legend(type = 'line', labels = "National Park Zone", col = 'green', lwd = 2, size = 2, lty ='33')
map7
map8 <- map7 + tm_shape(wamp1) + tm_borders(col = 'black', lwd = 1.5, lty ='33') + tm_fill(col='pink', alpha = 0.3) +
tm_add_legend(type = 'fill', col = 'pink', alpha = 0.4, labels = 'State Sanctuary Zones')
map8
####
# Bathy options
map0 <- map + tm_shape(bathy2) + tm_raster( style= "quantile", n=7, palette=get_brewer_pal("Blues", n = 7, plot=FALSE), legend.reverse = T) +
tm_layout(legend.text.size = 1.7,
legend.outside = TRUE,
legend.outside.position = 'right',
#legend.position = c(1, 0.05),
legend.title.size = 0.5,
legend.title.color = 'white',
legend.width = 1)
map0
map0 <- map + tm_shape(bathy2) + tm_raster(title = 'Depth (m)', palette=get_brewer_pal("Blues", plot=FALSE), style='cont', legend.reverse = T) +
tm_layout(legend.text.size = 1,
legend.outside = TRUE,
#legend.outside.position = 'right',
legend.outside.position = 'bottom',
#legend.position = c(1, 0.05),
legend.title.size = 1.5,
legend.title.color = 'black',
legend.width = 1)
map0
# save ----
tmap_save(
tm = map8,
filename = paste(p.dir, "SW-Sea-level1.png", sep ='/'),
#width = NA,
#height = NA,
#units = NA,
dpi = 300)
### VERSION TWO -----
# smooth polygons ---
k11sm <- st_as_sf(k11)
k11sm <- drop_crumbs(k11sm, set_units(2, km^2))
plot(k11sm)
k11sm <- fill_holes(k11sm, set_units(201, km^2))
k11sm <- smoothr::smooth(k11sm, method = "ksmooth", smoothness = 15)
k21sm <- st_as_sf(k21)
k21sm <- drop_crumbs(k21sm, set_units(2, km^2))
k21sm <- fill_holes(k21sm, set_units(201, km^2))
k21sm <- smooth(k21sm, method = "ksmooth", smoothness = 10)
plot(k21sm)
wa1sm <- st_as_sf(wa1)
wa1sm <- smoothr::drop_crumbs(wa1sm, set_units(2, km^2))
#wa1sm <- fill_holes(wa1sm, set_units(201, km^2))
wa1sm2 <- smoothr::smooth(wa1sm, method = 'ksmooth')
plot(wa1sm2) # THIS ISN'T WORKING
map <- tm_shape(cmr1, bbox=ext1) + tm_borders(col ='white', lwd = 1.5) +
tm_compass(type = "arrow", position = c(0.23, 0.1), size = 2) +
#tm_fill(col ='ZONENAME', palette=c('yellow', 'red'), alpha = 0.1) +
tm_scale_bar(breaks = c(0, 25, 50), text.size = 0.5, position = c(0.2, 0.02))
#tm_graticules(ticks = FALSE) +
#tm_grid(n.x = 3, n.y = 3, labels.size = 1.5, lines = FALSE)
map
map0 <- map + tm_shape(bathy1) + tm_raster(title = 'Depth (m)', palette=get_brewer_pal("Blues", plot=FALSE), style='cont', legend.reverse = T) +
#tm_add_legend(type = 'fill', labels = "xxx", col = g2, lwd = 2, size = 2) +
tm_layout(outer.margins = 0.01,
inner.margins = 0,
legend.text.size = 1,
#legend.outside = FALSE,
#legend.outside.position = 'right',
#legend.outside.position = 'right',
#legend.stack = 'horizontal',
#legend.is.protrait = TRUE,
legend.position = c(0.01, 0.72),
legend.title.size = 1.5,
legend.title.color = 'black',
legend.width = 1)
map0
map1 <- map0 + tm_shape(k21sm) + tm_borders(col = g2, lwd = 2) + tm_fill(col=g2)
#tm_add_legend(type = 'fill', labels = "21,000 years ago", col = g2, lwd = 2, size = 2)
map1
#map2 <- map1 + tm_shape(k70) + tm_borders(col = g5, lwd = 2) + tm_fill(col=g5) +
# tm_add_legend(type = 'fill', labels = "70,000 years ago", col = g5, lwd = 2, size = 2)
#map2
map3 <- map1 + tm_shape(k11sm) + tm_borders(col = g4, lwd = 2) + tm_fill(g4)
# tm_add_legend(type = 'fill', labels = "11,000 years ago", col = g4, lwd = 2, size = 2)
map3
map4 <- map3 + tm_shape(wa1sm) + tm_borders(col = 'grey70', lwd = 2) + tm_fill(col=sg)
#tm_add_legend(type = 'fill', labels = "Coastline today", col = sg, lwd = 2, size = 2)
map4
#map5 <- map4 + tm_shape(dfs) + tm_symbols(col = 'black', size = 0.2) +
# tm_text("Location", size = 0.8, xmod = 1.5, ymod = -0.5)
#map5
map55 <- map4 + tm_shape(cmr1) + tm_borders(col = 'grey55', lwd = 0.5)
map55
#map6 <- map55 + tm_shape(SPZ) + tm_borders(col = 'black', lwd = 1.5)
#tm_add_legend(type = 'line', labels = "Special Purpose Zone", col = 'black', lwd = 2, size = 2)
#map6
map7 <- map55 + tm_shape(NPZ) + tm_borders(col = "#006600", lwd = 2)
#tm_add_legend(type = 'fill', labels = "National Park Zone and State Sanctuary Zones", col = 'white', border.col= "#006600", border.lwd = 3, size = 2)
map7
map71 <- map7 + tm_shape(dfs) + tm_symbols(col = 'black', size = 0.2) +
tm_text("Location", size = 0.8, xmod = 1.4, ymod = -0.5)
map71
map8 <- map71 + tm_shape(wamp1) + tm_borders(col = "#006600", lwd = 2) #+ tm_fill(col='pink', alpha = 0.4) +
#tm_add_legend(type = 'fill', col = 'white', border.col = 'white', labels = 'State Sanctuary Zones')
map8
map9 <- map8 + tm_shape(cw1) + tm_lines(col = 'red', lwd = 1)
# #tm_add_legend(type = 'fill', col = 'white', border.col = 'red', border.lwd =3, labels = 'Commonwealth/State waters boundary') +
# tm_layout(#outer.margins = 0.1,
# legend.text.size = 1,
# #legend.outside = TRUE,
# #legend.outside.position = 'right',
# #legend.outside.position = 'right',
# #legend.only = TRUE,
# legend.title.size = 1.5,
# legend.title.color = 'black',
# legend.width = 1) +
# tm_add_legend(type = 'fill', labels = "21,000 years ago (-125 metres)", col = g2, lwd = 2, size = 2) +
# tm_add_legend(type = 'fill', labels = "11,000 years ago (-40 metres)", col = g4, lwd = 2, size = 2) +
# tm_add_legend(type = 'fill', labels = "Coastline today", col = sg, lwd = 2, size = 2) +
# tm_add_legend(type = 'fill', col = 'white', border.col = 'red', border.lwd =3, labels = 'Commonwealth/State waters boundary', size = 3) +
# tm_add_legend(type = 'fill', labels = "National Park Zone and State Sanctuary Zones", col = 'white', border.col= "#006600", border.lwd = 3, size = 2)
map9
map.leg <- tm_shape(cmr1) + tm_borders(col ='white', lwd = 1.5) +
#tm_shape(cw1) + tm_lines(col = 'red', lwd = 1) +
tm_layout(#outer.margins = 0.1,
legend.text.size = 2,
#legend.outside = TRUE,
# #legend.outside.position = 'right',
# #legend.outside.position = 'right',
legend.only = TRUE) +
# legend.title.size = 1.5,
# legend.title.color = 'black',
#legend.width = 1) +
tm_add_legend(type = 'fill', labels = "21,000 years ago (-125 metres)", col = g2, lwd = 2, size = 4) +
tm_add_legend(type = 'fill', labels = "11,000 years ago (-40 metres)", col = g4, lwd = 2, size = 4) +
tm_add_legend(type = 'fill', labels = "Coastline today", col = sg, lwd = 2, size = 4) +
tm_add_legend(type = 'fill', col = 'white', border.col = 'red', border.lwd =3, labels = 'Commonwealth/State waters boundary', size = 4) +
tm_add_legend(type = 'fill', labels = "National Park Zone and State Sanctuary Zones", col = 'white', border.col= "#006600", border.lwd = 3, size = 4)
map.leg
####
# save ----
tmap_save(
tm = map9,
filename = paste(p.dir, "Ningaloo-Sea-level.png", sep ='/'),
#width = 2000,
#height = 2200,
#units = NA,
scale = 1,
dpi = 300)
tmap_save(
tm = map.leg,
filename = paste(p.dir, "Ningaloo-Sea-level-legend.png", sep ='/'),
#width = 2000,
#height = 2200,
#units = NA,
scale = 1,
dpi = 300)
#### To create the inset map ----
### 1. define area of interest: part of WA ####
sw_region <- st_bbox(ext1,
crs = st_crs(bathy1)) %>%
st_as_sfc()
### 1.1 define area of interest: Rottnest Island ####
extent(ri)
ri_region <- st_bbox(c(xmin = 115.4242, xmax = 115.5675,
ymin = -32.06073 , ymax = -31.97739),
crs = st_crs(ri)) %>%
st_as_sfc()
### 2.1 create a base map: Austalia ###
# read Australia shapefile ----
a <- readOGR(paste(s.dir, "STE11aAust.shp", sep='/'))
plot(a)
asm <- st_as_sf(a)
asm <- drop_crumbs(asm, set_units(10, km^2))
plot(asm)
asm2 <- fill_holes(asm, set_units(20, km^2))
asm3 <- smoothr::smooth(asm2, method = "ksmooth", smoothness = 20)
plot(asm3)
a_map <- tm_shape(wa, bbox = wa_region) + tm_polygons(border.col = "black")
wa2_map