GLEON 2021 R Spatial Workshop

gleon2021_rspatial.R

library(sf)
library(mapview)

erie_outline <- st_read("data/erie_outline.shp")

st_geometry_type(erie_outline)

st_crs(erie_outline)

st_bbox(erie_outline)

library(ggplot2)
# install.packages("ggplot2")

plot(erie_outline$geometry)

ggplot() +
  geom_sf(data = erie_outline, fill="cyan", size=1.5) +
  ggtitle("Lake Erie Outline")

mapview(erie_outline)

st_write(erie_outline, "data/erie_outline.gpkg")

erie_outline

erie_zones <- st_read("data/erie_zones.shp")

erie_zones

View(erie_zones)

names(erie_zones)

head(erie_zones)


zone_5 <- dplyr::filter(erie_zones, MGMTUNIT == "MU5")

mapview(erie_zones) + mapview(zone_5)

ggplot() +
  geom_sf(data = zone_5) 

mapview(erie_zones, zcol = "MGMTUNIT")

ggplot() +
  geom_sf(data = erie_zones, aes(color = MGMTUNIT)) +
  ggtitle("Managment Units", subtitle = "colored by zone") +
  labs(color = "Unit ID")

ggplot() +
  geom_sf(data = erie_zones, aes(color = MGMTUNIT, size = MGMTUNIT)) +
  scale_size_manual(values = c(1, 2, 3, 4, 1))

fish_tracks <- read.csv("data/fish_tracks.csv")
View(fish_tracks)

st_crs(erie_outline)

fish_locations <- st_as_sf(fish_tracks, coords = c("X", "Y"), crs = st_crs(4326))

st_crs(fish_locations)

mapview(fish_locations)

table(fish_locations$animal_id)

ggplot() +
  geom_sf(data = fish_locations)

mapview(erie_outline) + mapview(fish_locations, zcol = "animal_id")

library(raster)
library(rgdal)

GDALinfo("data/erie_bathy.tif")

erie_bathy <- raster("data/erie_bathy.tif")

summary(erie_bathy)

mapview(erie_bathy)

plot(erie_bathy)

minValue(erie_bathy)

maxValue(erie_bathy)

erie_bathy_df <- as.data.frame(erie_bathy, xy = TRUE)
View(erie_bathy)

ggplot() +
  geom_raster(data = erie_bathy_df, aes(x = x, y = y, fill = erie_bathy)) +
  scale_fill_viridis_c(na.value = "deeppink")

ggplot() +
  geom_histogram(data = erie_bathy_df, aes(erie_bathy))

fish_tracks_bathy <- extract(x = erie_bathy, 
              y = as(fish_locations, "Spatial"), df = TRUE)
View(fish_tracks_bathy)
summary(fish_tracks_bathy$erie_bathy)

ggplot() +
  geom_histogram(data = fish_tracks_bathy, aes(x = erie_bathy))

erie_bathy_cropped <- crop(x = erie_bathy, y = as(erie_outline, "Spatial"))


mapview(erie_bathy) + mapview(erie_bathy_cropped)