Section 4 Mapping Elephant Movement
4.1 Load libraries
4.2 Load data
4.2.1 Prepare extent
4.2.2 Load movement data
4.2.3 Load boundary data
# get kruger data
kruger <- st_read("data/kruger_clip/kruger_clip.shp")
kruger <- st_transform(kruger, 32736)
# get inversion
kruger_invert <- st_difference(
st_as_sfc(st_bbox(kruger)),
kruger
)
# get kruger point -- this is hardcoded but could also be a centroid
kruger_point <- st_point(c(31.5, -24))
kruger_point <- st_sfc(kruger_point, crs = 4326)
kruger_point <- st_transform(kruger_point, 32736)# get rivers
rivers <- st_read("data/rivers_kruger.gpkg")
rivers <- st_transform(rivers[is.na(rivers$seasonal), ], 32736)
# waterholes
waterholes <- st_read("data/waterholes/waterpoints_zambatis_2011.shp")# get temperature
if (!file.exists("data/kruger_temp_200m.tif")) {
res_init <- res(raster("data/kruger_temperature_UTM.tif"))
res_final <- res_init * 200 / res_init
gdalUtils::gdalwarp(
srcfile = "data/kruger_temperature_UTM.tif",
dstfile = "data/kruger_temp_200m.tif",
tr = c(res_final), r = "average",
te = c(bbox(raster("data/kruger_temperature_UTM.tif")))
)
}
# read in cropped raster
temp <- raster("data/kruger_temp_200m.tif")
temp <- raster::crop(temp, as(bbox_sf, "Spatial"))
temp <- cbind(coordinates(temp), values(temp))
temp <- data.table(temp)
temp <- temp[V3 > 22, ]
setnames(temp, "V3", "temp")4.3 Make Africa Inset
fig_inset_a <-
ggplot() +
geom_sf(
data = africa,
fill = "tan",
show.legend = F,
col = NA
) +
geom_sf(
data = africa[africa$name == "South Africa", ],
fill = "sienna",
col = NA
) +
geom_sf(
data = kruger_point,
size = 5,
fill = NA,
shape = 21,
colour = "grey20",
stroke = 1
) +
scale_y_continuous(
breaks = seq(-22, -34, -6)
) +
theme_void(base_size = 8) +
theme(
panel.background = element_rect(
fill = "powderblue",
colour = "grey20"
),
plot.margin = unit(rep(2, 4), "mm")
) +
coord_sf(
expand = T
)4.4 Make Kruger Inset
pal <- scico(7, palette = "turku")
fig_inset_b <-
ggplot() +
geom_sf(
data = kruger,
fill = "tan",
alpha = 0.8,
col = NA,
lwd = 0.3
) +
geom_sf(
data = data,
lwd = c(0.1),
lty = 1,
alpha = c(0.3),
col = pal[2]
) +
annotate(
geom = "rect",
fill = NA,
col = "grey20",
lwd = 0.3,
xmin = bbox["xmin"],
xmax = bbox["xmax"],
ymin = bbox["ymin"],
ymax = bbox["ymax"]
) +
annotation_scale(
bar_cols = c("grey50", "grey70"),
height = unit(1, units = "mm"),
text_family = "IBM Plex Sans"
) +
theme_void() +
coord_sf(
crs = 32736,
expand = FALSE,
xlim = c(325000, NA)
) +
theme(
panel.background = element_rect(
fill = "grey75"
),
panel.border = element_rect(
colour = "grey20",
fill = NA
),
plot.margin = unit(rep(1, 4), "mm")
)4.5 Make Main Figure
4.5.1 Prepare textbox
textbox <- glue(
"**Kruger Elephants Shuttle to Water**
African elephants move as they please, \\
ignoring park boundaries when it suits them. \\
Yet they need water to help them \\
through the thermal landscape (_blue: cool, orange: warm_; LANDSAT 5 \\
2007 -- 2009 average). \\
In Kruger, elephants frequent water sources during the afternoon, the \\
hottest part of the day; arriving and leaving at high speed. \\
Here, elephant _AM253_ (red) and her herd seem anchored to specific \\
water sources, tracing loops to and from them, \\
while avoiding other herds (grey). \\
Elephants apparently also avoid the cooler conditions of _Acacia_ woodland, \\
seen here as the central blue patch. \\
Read more: _Thaker, Gupte, et al. (2019). Front. Ecol. Evol._"
)
# texttitle = "Elephants Shuttle to Water"
textdata <- data.table(
x = bbox["xmin"] + 5000,
y = bbox["ymax"] - 9000,
label = textbox
)4.5.2 Prepare movement plot
# make plot
fig_main <-
ggplot() +
geom_sf(
data = kruger,
col = NA,
fill = "antiquewhite",
) +
geom_tile(
data = temp,
aes(x, y, fill = temp),
show.legend = F,
alpha = 0.4
) +
geom_sf(
data = rivers[is.na(rivers$seasonal), ],
lwd = 1,
col = blue,
alpha = 0.35
) +
geom_sf(
data = data_rest,
lwd = c(0.15),
lty = 1,
alpha = c(0.2, 0.7, 0.3, 0.15),
col = pal[c(2, 3, 2, 3)]
) +
geom_sf(
data = data_253,
lwd = 0.2,
alpha = 1,
col = scico::scico(7,
palette = "bilbao"
)[6]
) +
geom_sf(
data = waterholes,
col = blue,
alpha = 0.45
) +
geom_sf(
data = kruger,
col = "grey50",
lwd = 0.3,
fill = NA,
lty = 2
) +
geom_sf(
data = kruger_invert,
fill = alpha("grey80", 0.35),
col = NA
) +
coord_sf(
xlim = bbox[c("xmin", "xmax")],
ylim = bbox[c("ymin", "ymax")],
expand = FALSE
)4.5.3 Add decoration
fig_main <-
fig_main +
annotation_north_arrow(
style = north_arrow_minimal(
text_family = "IBM Plex Sans",
text_size = 10,
text_col = "grey50",
line_col = "grey50",
fill = "grey50"
),
location = "br"
) +
annotation_scale(
bar_cols = c("grey50", "grey90"),
height = unit(1, units = "mm"),
text_family = "IBM Plex Sans"
) +
theme_void() +
theme(
panel.background = element_rect(
colour = "grey",
fill = alpha("grey", 0.5)
),
plot.margin = unit(rep(5, 4), "mm")
)4.5.4 Add insets
fig_main <-
fig_main +
annotation_custom(
grob = ggplotGrob(
fig_inset_b
),
xmin = bbox[c("xmin")] + 1000,
xmax = bbox[c("xmin")] + 7500,
ymax = bbox["ymin"] + 13500,
ymin = bbox["ymin"] + 1000
) +
annotation_custom(
grob = ggplotGrob(
fig_inset_a
),
xmin = bbox[c("xmin")] + 1000,
xmax = bbox[c("xmin")] + 7500,
ymax = bbox["ymin"] + 21000,
ymin = bbox["ymin"] + 13600
)4.5.5 Add text box
4.5.6 Add some labels
fig_main <-
fig_main +
annotate(
geom = "text",
x = bbox[c("xmin")] +
c(20000, 30000),
y = bbox["ymin"] +
c(12600, 15400),
label = c(
"Private\nNature\nReserves",
"Kruger\nNational\nPark"
),
fontface = "italic",
family = "IBM Plex Serif",
alpha = c(0.55, 0.5),
size = c(4, 5)
) +
geom_text(
data = textlabels,
aes(x, y,
label = label
),
fontface = "italic",
family = "IBM Plex Serif",
alpha = c(0.5, 0.5),
size = c(3, 3)
)4.5.7 Make options
# op1 = fig_main +
# scale_fill_gradientn(
# colours = scico(20,
# palette = "romaO",
# direction = -1,
# begin = 0., end = 1
# )
# )
#
# op2 = fig_main +
# scale_fill_distiller(
# palette = "RdYlBu"
# )
fig_main <- fig_main +
scale_fill_gradientn(
colours = scico(20,
palette = "vikO",
direction = 1,
begin = 0., end = 1
)
)