report5_VMS.R

library(icesTAF)
library(icesFO)
library(sf)
library(ggplot2)
library(dplyr)

mkdir("report")
## Run utilies
source("bootstrap/utilities.r")
###########
##Load data
###########

# read vms fishing effort
effort <-
  sf::st_read("vms_effort.csv",
               options = "GEOM_POSSIBLE_NAMES=wkt", crs = 4326)
effort <- dplyr::select(effort, -WKT)

# read vms swept area ratio
sar <-
  sf::st_read("vms_sar.csv",
               options = "GEOM_POSSIBLE_NAMES=wkt", crs = 4326)
sar <- dplyr::select(sar, -WKT)


#set range of years in plots

year_range <- "2018-2021"
cap_year <- 2022
ecoreg <- "BrS"

###########
## 3: VMS #
###########

#~~~~~~~~~~~~~~~#
# A. Effort map
#~~~~~~~~~~~~~~~#

# gears <- c("Static", "Midwater", "Otter", "Demersal seine", "Other")
gears <- c("Midwater", "Otter")
effort <-
    effort %>%
      dplyr::filter(fishing_category_FO %in% gears) %>%
      dplyr::mutate(
        fishing_category_FO =
          dplyr::recode(fishing_category_FO,
            # Static = "Static gears",
            Midwater = "Pelagic trawls and seines",
            Otter = "Bottom otter trawls"
            # `Demersal seine` = "Bottom seines",
            # Other = "Other"
            ),
          mw_fishinghours = as.numeric(mw_fishinghours)
        ) %>%
      filter(!is.na(mw_fishinghours))

# write layer
write_layer <- function(dat, fname) {
  sf::write_sf(dat, paste0("report/", fname, ".shp"))
  files <- dir("report", pattern = fname, full = TRUE)
  files <- files[tools::file_ext(files) != "png"]
  zip(paste0("report/", fname, ".zip"), files, extras = "-j")
  file.remove(files)
}
write_layer(effort, paste0(year_cap, "_", ecoreg,"_FO_VMS_effort"))

# save plot
plot_effort_map(effort, ecoregion) +
  ggtitle(paste0("Average MW Fishing hours ", year_range))

ggsave(file_name(cap_year,ecoreg,"VMS_effort", ext = "png", dir = "report"), width = 170, height = 200, units = "mm", dpi = 300)

#~~~~~~~~~~~~~~~#
# A. Swept area map
#~~~~~~~~~~~~~~~#

# write layer
write_layer(sar, paste0(year_cap, "_", ecoreg,"_FO_VMS_sar"))

plot_sar_map(sar, ecoregion, what = "surface") +
  ggtitle(paste0("Average surface swept area ratio ", year_range))

# ggplot2::ggsave(paste0(year_cap, "_", ecoreg,"_FO_VMS_sarA.png"), path = "report", width = 170, height = 200, units = "mm", dpi = 300)
ggsave(file_name(cap_year,ecoreg,"FO_VMS_sarA", ext = "png", dir = "report"), width = 170, height = 200, units = "mm", dpi = 300)


plot_sar_map(sar, ecoregion, what = "subsurface")+
  ggtitle(paste0("Average subsurface swept area ratio ", year_range))

ggsave(file_name(cap_year,ecoreg,"FO_VMS_sarB", ext = "png", dir = "report"), width = 170, height = 200, units = "mm", dpi = 300)