6 Terrain mapping, caves and water samples in a karst

Sinking Cove, Tennessee is a karst valley system carved into the Cumberland Plateau, a nice place to explore mapping alternatives employing basemaps and environmental measurement point symbolization, from a hydrologic and geochemical study (Davis and Brook 1993) of karst and cave development (Figures 6.1, 6.2, and 6.3).

  • We’ll build static maps in tmap’s “plot” mode by creating our own basemap from a hillshade (created with terra’s terrain function) combined with hypsometric tinting of elevation using the terrain.color palette.
  • We’ll also employ maptiles to download an online basemap into a raster to continue using a static map.
  • We’ll build interactive maps with tmap’s leaflet-based “view” mode, allowing us to zoom in as well as select alternative online basemaps.
Cave Cove Cave Entrance

FIGURE 6.1: Cave Cove Cave Entrance

Sinking Cove Cave

FIGURE 6.2: Sinking Cove Cave

Sinking Cove Cave spring

FIGURE 6.3: Sinking Cove Cave spring

6.1 Creating a basemap from a DEM, using hillshade and terrain shading

We’ll read in a digital elevation model (DEM) derived from USGS data, and use it to build a terrain basemap, using a hillshade and hypsometric coloring with a 24-level terrain.color palette, and start with a map showing the overall Sinking Cove Area (Figure ??).

Sinking Cove Area map, using terra rasters in tmap

FIGURE 6.4: Sinking Cove Area map, using terra rasters in tmap 

tmap_mode("plot")
DEM <- rast(ex("SinkingCove/DEM_SinkingCoveUTM.tif"))
slope <- terrain(DEM, v='slope')
aspect <- terrain(DEM, v='aspect')
hillsh <- shade(slope/180*pi, aspect/180*pi, angle=40, direction=330)
# Need to crop a bit since grid north != true north 
bbox0 <- st_bbox(DEM)
xrange <- bbox0$xmax - bbox0$xmin
yrange <- bbox0$ymax - bbox0$ymin
bbox1 <- bbox0
crop <- 0.05
bbox1[1] <- bbox0[1] + crop * xrange # xmin
bbox1[3] <- bbox0[3] - crop * xrange # xmax
bbox1[2] <- bbox0[2] + crop * yrange # ymin
bbox1[4] <- bbox0[4] - crop * yrange # ymax
bboxPoly <- bbox1 %>% st_as_sfc() # makes a polygon
#
tm_shape(hillsh, bbox=bboxPoly) +
  tm_raster(palette="-Greys",legend.show=F,n=20) +
  tm_shape(DEM) +
  tm_raster(palette=terrain.colors(24), alpha=0.5) +
  tm_graticules(lines=F)

First we’ll prep some data on the caves and water samples.

library(igisci); library(terra)
library(sf); library(tidyverse); library(readxl); library(tmap)
caves <- st_read(ex("SinkingCove/caves.shp"))
ents <- st_read(ex("SinkingCove/CaveEntrances.shp"))
geology <- st_read(ex("SinkingCove/geology.shp"))
wChemData <- read_excel(ex("SinkingCove/SinkingCoveWaterChem.xlsx")) %>%
  mutate(siteLoc = str_sub(Site,start=1L, end=1L))
wChemTrunk <- wChemData %>% filter(siteLoc == "T") %>% mutate(siteType = "trunk")
wChemDrip <- wChemData %>% filter(siteLoc %in% c("D","S")) %>% mutate(siteType = "dripwater")
wChemTrib <- wChemData %>% filter(siteLoc %in% c("B", "F", "K", "W", "P")) %>% 
  mutate(siteType = "tributary")
wChemData <- bind_rows(wChemTrunk, wChemDrip, wChemTrib) %>%
  mutate(carbonate_ppm = TH)
sites <- read_csv(ex("SinkingCove/SinkingCoveSites.csv"))
wChem <- wChemData %>%
  left_join(sites, by = c("Site" = "site")) %>%
  st_as_sf(coords = c("longitude", "latitude"), crs = 4326)
DEM <- rast(ex("SinkingCove/DEM_SinkingCoveUTM.tif"))   
slope <- terrain(DEM, v='slope')
aspect <- terrain(DEM, v='aspect')
hillsh <- shade(slope/180*pi, aspect/180*pi, 40, 330) 
bounds <- st_bbox(wChem)
tmap_mode("plot")
xrange <- bounds$xmax - bounds$xmin
yrange <- bounds$ymax - bounds$ymin
xMIN <- as.numeric(bounds$xmin - xrange/10)
xMAX <- as.numeric(bounds$xmax + xrange/10)
yMIN <- as.numeric(bounds$ymin - yrange/10)
yMAX <- as.numeric(bounds$ymax + yrange/10)
newbounds <- st_bbox(c(xmin=xMIN, xmax=xMAX, ymin=yMIN, ymax=yMAX), crs= st_crs(4326))

Then we’ll zoom into upper Sinking Cove, where we have some significant caves (Figure 6.5).

hillshCol <- tm_scale_continuous(values = "-brewer.greys")
labeledCaves <- caves |> filter(!is.na(CaveLabel))
tm_graticules(labels.cardinal=F) +
  tm_shape(hillsh,bbox=newbounds) +
    tm_raster(col.scale=hillshCol, col.legend = tm_legend(show=F)) +
  tm_shape(DEM) + 
    tm_raster(col.scale=terrainCol, col_alpha=0.5,col.legend = tm_legend(show=F)) +
  tm_shape(caves) + tm_lines(lwd=2) + 
  tm_shape(labeledCaves) + tm_text("CaveLabel", size=0.7, col_alpha=0.5) +  #, just="left") + #, xmod=0.75) +
  tm_shape(ents) + tm_symbols(fill="Formation", shape=17, size=0.33)# + #, title.col ="Geologic unit of entrance") + #col_alpha=.75,
Upper Sinking Cove caves and entrances

FIGURE 6.5: Upper Sinking Cove caves and entrances 

  # tm_layout(legend.position = c("left", "bottom"))

Or the same map on Geology (Figure 6.6)

geol_bounds <- st_bbox(geology)
tm_graticules(labels.cardinal=F) +
  tm_shape(hillsh,bbox=geol_bounds) +
    tm_raster(col.scale=hillshCol, col.legend = tm_legend(show=F)) +
  tm_shape(geology) + 
    tm_polygons(fill="ElevGeol", fill_alpha=0.5, 
    fill.legend = tm_legend(reverse=T, title="Elevation and Geology")) +
  tm_shape(caves) + tm_lines(lwd=2) + 
  tm_shape(labeledCaves) + tm_text("CaveLabel", size=0.7, col_alpha=0.5) +  
  tm_shape(ents) + tm_symbols(fill="Formation", shape=17, size=0.33, 
                  fill.legend=tm_legend(title="Cave Entrance Formation"))
Upper Sinking Cove geology with caves

FIGURE 6.6: Upper Sinking Cove geology with caves

We’ve studied the water chemistry in cave passages and surface water features to look at limestone solution processes (Figure 6.7).

tm_shape(hillsh,bbox=geol_bounds) +
  tm_raster(palette="-Greys",legend.show=F,n=20) +
  #tm_shape(DEM) + tm_raster(palette=terrain.colors(24), alpha=0.5,legend.show=F) +
  tm_shape(caves) + tm_lines(lwd=2) +
  tm_shape(geology) + tm_fill(fill="ElevGeol", alpha=0.5, title="Geology by base elev(m)", legend.reverse=T) +
  tm_shape(wChem) + tm_symbols(col="siteType", size="carbonate_ppm", border.col="black", scale=2, alpha=0.66) + #col="navy", 
  tm_layout(legend.outside=TRUE) +
  tm_graticules(lines=F)
Upper Sinking Cove water sample results, with major caves as black lines

FIGURE 6.7: Upper Sinking Cove water sample results, with major caves as black lines

6.2 Using topographic basemap with contours

Using maptiles with tmap in plot mode may produce the most informative map. We could have created contours from the DEM, but it’s easier to use a basemap, as long as the internet connection works. The Esri.WorldTopoMap in employing USGS labels works well in the US, though elevations are in feet (Figure 6.8).

# library(maptiles)
# upperSinkingCove <- get_tiles(wChem, provider="Esri.WorldTopoMap", forceDownload=T)

  # tm_shape(upperSinkingCove) + tm_rgb() + 
  tm_shape(caves) + tm_lines(lwd=2) + #
  tm_shape(wChem) + 
  tm_symbols(size="carbonate_ppm", col="Lithology", scale=2, shape="siteType", col_alpha=0.5) +
  # tm_graticules(lines=F) +
  tm_basemap(server="Esri.WorldTopoMap")
Upper Sinking Cove static map with maptiles

FIGURE 6.8: Upper Sinking Cove static map with maptiles 

library(maptiles)
# basemap <- get_tiles(wChem, provider="Esri.WorldTopoMap", forceDownload=T)
tmap_mode("view")
tm_graticules(lines=F) +
  tm_basemap("Esri.WorldTopoMap") +
  # tm_shape(basemap) + tm_rgb() + 
  tm_shape(caves, bbox=geol_bounds) + tm_lines(lwd=2) +
  tm_shape(wChem) + 
  tm_symbols(size="carbonate_ppm", col="Lithology", scale=2, shape="siteType", col_alpha=0.5)
# +
#   tm_layout(legend.position = tm_pos_in("right"c("left", "bottom"))

References

Davis, Jerry D, and George A Brook. 1993. “Geomorphology and Hydrology of Upper Sinking Cove, Cumberland Plateau, Tennessee.” Earth Surface Processes and Landforms 18 (4): 339–62. https://doi.org/10.1002/esp.3290180404.