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3x.Get-data-for-percent-cover.R
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3x.Get-data-for-percent-cover.R
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### ### ### ### ###
### Script to GET THE DATA to calculate percent cover of habitat classes ###
### Load libraries ----
library(ggplot2)
library(ggthemes)
library(cowplot)
library(sp)
library(spDta)
library(sf)
library(rgdal)
library(raster)
library(rgeos)
library(mapview)
library(tmap)
library(mapdata)
library(leaflet)
library(caTools)
library(reshape2)
library(tidyr)
library(car)
library(lattice)
library(latticeExtra)
library(dplyr)
library(raster)
library(rasterVis)
library(zoo)
library(sf)
library(fields)
library(geoR)
library(gstat)
library(ggsn)
library(ggspatial)
library(ggrepel)
library(patchwork)
#library(elsa)
#install.packages("corrplot")
#library(corrplot)
library(broman)
# Clear memory ----
rm(list=ls())
### Set directories ----
w.dir<- dirname(rstudioapi::getActiveDocumentContext()$path)
d.dir <- paste(w.dir, "data", sep='/')
dt.dir <- paste(w.dir, "data/tidy", sep='/')
s.dir <- paste(w.dir, "spatial_data", sep='/')
p.dir <- paste(w.dir, "plots", sep='/')
o.dir <- paste(w.dir, "outputs", sep='/')
# http://oswaldosantos.github.io/ggsn/
# Read gb cmr poly ----
gb <- st_read(dsn="C:/Users/00093391/Dropbox/UWA/Research Associate/PowAnalysis_for1sParksMeeting/Desktop/shapefiles")
gb <- readOGR(dsn="C:/Users/00093391/Dropbox/UWA/Research Associate/PowAnalysis_for1sParksMeeting/Desktop/shapefiles")
plot(gb)
levels(gb$ZoneName)
crs1 <- proj4string(gb) # "+proj=longlat +ellps=GRS80 +no_defs"
# for transformations --
gbu <- readOGR(dsn="G:/My Drive/Anita/Shapefiles/GeoBay_CMR_UTM.shp")
crs2 <- proj4string(gbu) # "+proj=utm +zone=50 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"
# get poly for each zone --
NPZ <- gbu[gbu$ZoneName=="National Park Zone",]
plot(NPZ)
HPZ <- gbu[gbu$ZoneName=="Habitat Protection Zone",]
MUZ <- gbu[gbu$ZoneName=="Multiple Use Zone",]
plot(MUZ)
SPZ <- gbu[gbu$ZoneName=="Special Purpose Zone (Mining Exclusion)",]
# Pick colors ----
sg <- brocolors("crayons")["Fern"] # "#78dbe2"
alg <- brocolors("crayons")["Raw Umber"] # "#1dacd6"
sand <- brocolors("crayons")["Unmellow Yellow"] # "#f75394"
pal1 <- c(sand, sg, alg )
## ## ## ## ## ##
#### GET DATA : FINE NPZ ####
#### BRUVs Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2, method ='ngb')
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine fine bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
fine.npz <- rbind(b, a, f, d)
head(fine.npz)
# add zone --
fine.npz$zone <- "NPZ"
#### GET DATA : FINE HPZ ####
#### BRUVs Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# HPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine fine bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
fine.hpz <- rbind(b, a, f, d)
head(fine.hpz)
# add zone --
fine.hpz$zone <- "HPZ"
fine.hpz
#### GET DATA : FINE MUZ ####
#### BRUVs Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine fine bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
fine.muz <- rbind(b, a, f, d)
head(fine.muz)
# add zone --
fine.muz$zone <- "MUZ"
fine.muz
#### GET DATA : FINE SPZ ####
#### BRUVs Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# SPZ ----
npzb <- mask(predu, SPZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# SPZ ----
npzb <- mask(predu, SPZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# SPZ ----
npzb <- mask(predu, SPZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Fine ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Fine-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# SPZ ----
npzb <- mask(predu, SPZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine fine bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
fine.spz <- rbind(b, a, f, d)
head(fine.spz)
# add zone --
fine.spz$zone <- "SPZ"
fine.spz
## ## ## ## ## ###
## Combine all fine data ----
fineall <- rbind(fine.npz, fine.hpz, fine.muz, fine.spz)
fineall
class(fineall)
# save --
write.csv(fineall, paste(dt.dir, "Areal-coverage-fine.csv", sep='/'))
### ### ### ### ### ###
#### GET DATA : COARSE NPZ ####
#### BRUVs Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
pred@data@values=1
# project --
predu <- projectRaster(pred, crs = crs2, method='ngb')
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, NPZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine Coarse bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
coarse.npz <- rbind(b, a, f, d)
head(coarse.npz)
# add zone --
coarse.npz$zone <- "NPZ"
coarse.npz
#### GET DATA : COARSE HPZ ####
#### BRUVs Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# HPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# NPZ ----
npzb <- mask(predu, HPZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine Coarse bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
coarse.hpz <- rbind(b, a, f, d)
head(coarse.hpz)
# add zone --
coarse.hpz$zone <- "HPZ"
coarse.hpz
#### GET DATA : COARSE MUZ ####
#### BRUVs Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-Bruvs.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
b <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
b
#### AUV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-AUV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
a <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
a
#### FTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-FTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
f <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
f
#### DTV Coarse ####
# Read data ----
pred <- raster(paste(o.dir, "GBpred-Coarse-DTV.tif", sep='/'))
plot(pred) # 1= algae, 2=seagrass, 3=Unveg
xx <- levels(pred[[1]])
xx
# project --
predu <- projectRaster(pred, crs = crs2)
plot(predu)
levels(predu) <- xx
# MUZ ----
npzb <- mask(predu, MUZ)
plot(npzb)
plot(gbu, add=T)
d <- as.data.frame(npzb) %>%
group_by(category) %>%
tally() %>%
mutate(area = n * res(npzb)[1] * res(npzb)[2])
d
## ## ## ## ## ## ##
#### Combine Coarse bathy data ####
b$method <- "Stereo-BRUVs"
b
a$method <- "AUV"
a
f$method <- "FTV"
f
d$method <- "DTV"
d
# join --
coarse.muz <- rbind(b, a, f, d)
head(coarse.muz)
# add zone --
coarse.muz$zone <- "MUZ"
coarse.muz