Add SST data and other environmental layers

[quantifish]

Add SST data and other environmental layers

[quantifish]

I've added mfe_average_sst but the projection looks wrong. Needs some work.

Jim got me some different SST data for the PHC project. See the files ERA5_data_script.R etc for how to get and plot these data. I used this code:

library(ecmwfr)

library(raster)
library("ncdf4")

library("ncdf.tools")

library(ggplot2)

library(ggthemes)

library(sf)
library(nzsf)

ncfile <- "era5-nz_sst_to_2020.nc"
rr <- brick(x = ncfile)
rr <- stack(x = ncfile)
nlayers(rr)
rr
raster::plot(rr)

df <- rasterToPoints(rr) %>%
data.frame() %>%
pivot_longer(cols = c(-x, -y)) %>%
separate(col = name, into = c("year", "month", "day", "hr", "min", "sec"), sep = "\.") %>%
mutate(year = gsub("X", "", year), value = value - 273.15)

p <- ggplot(data = df %>% filter(year == "2000")) +
geom_raster(aes(x = .data$x, y = .data$y, fill = .data$value)) +
facet_wrap(year ~ month)
p

r1 <- rr[[1]]
sf_stat <- get_statistical_areas("CRA") %>%
filter(area %in% c(901:907)) %>%
st_transform(crs = crs(rr), check = TRUE) %>%
dplyr::select(MFISH_ID, area)
average_temperature <- raster::extract(x = rr, y = sf_stat, df = TRUE) %>%
full_join(data.frame(sf_stat), by = c("ID" = "MFISH_ID")) %>%
dplyr::select(-geometry, -ID) %>%
pivot_longer(-area) %>%
separate(col = name, into = c("year", "month", "day", "hr", "min", "sec"), sep = "\.") %>%
mutate(year = gsub("X", "", year), value = value - 273.15) %>%
group_by(year, month, area) %>%
summarise(temp = mean(value, na.rm = TRUE))
save(average_temperature, file = "average_temperature.rda")

[quantifish]

Not sure what is wrong with the MFE raster. Think I will drop it as the projection looks buggered.