Last data update: 2014.03.03

 R: Hydrodynamic model output (getm) of Sylt-Romo Bight
Sylt data setR Documentation

Hydrodynamic model output (getm) of Sylt-Romo Bight

Description

3D Sylt-tidal simulation model output generated by the GETM model version 2.2.2.

The Sylt-Romo bight is a Wadden Sea embayment in the North Sea, between the Danish island Romo and the German island Sylt at about 55 dg N and 8 dg E, an area of approximately 300 km^2.

  • Sylttran contains (x, sigma, time) data from an E-W transect.

  • Syltsurf contains 2-D surface data, at 5 time intervals.

  • Sylt3D contains 3-D (x, y, z) data, at 2 time intervals.

Usage

data(Sylttran)
data(Syltsurf)
data(Sylt3D)

Format

  • Sylttran is a data.frame with (x, sigma, time) data from an E-W transect (8.1 - 17.9 km) taken at km 18.5. There are 50 x-values, 21 sigma levels and 21 model output times.

    It contains:

    • x, y, the positions in km, of length 50 and 1 respectively.

    • time, the model output time in hours, of length 21.

    • visc, the viscosity (getm variable num), (50 x 21 x 21), m2/s.

    • tke, the turbulent kinetic energy (getm variable tke), (50 x 21 x 21), m2/s2.

    • u, v, the zonal and meridional velocity, (50 x 21 x 21), m/s.

    • sigma, the depth of the sigma coordinates (50 x 21 x 21), metres.

  • Syltsurf contains 2-D surface data of the entire model domain, at 5 time intervals (hour 24.7 to 37.1). It is a data.frame with:

    • x, y, the positions in km, of length 135 and 160 respectively.

    • time, the output time in hours, of length 5.

    • u, v, the vertically averaged zonal and meridional velocity (135 x 160 x 5), m/s.

    • elev, tidal elevation (135 x 160 x 5), metres.

    • depth, the bathymetry (135 x 160), metres.

  • Sylt3D contains 3-D (x, y, z) data, at 2 time intervals (hour 0 and 9.94). The box extends from x inbetween [12.1, 14.9] and from y inbetween [12.7 - 16.3]; there are 21 sigma levels.

    It is a data.frame with:

    • x, y, the positions in km, of length 15 and 19 respectively.

    • time, the output time in hours, of length 2.

    • visc, the viscosity (getm model variable num), (55 x 19 x 21 x 2), m2/s.

    • sigma, the sigma depth levels, (55 x 19 x 21 x 2), m2/s. metres.

    • depth, the bathymetry (15 x 19), metres.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

References

Hans Burchard and Karsten Bolding, 2002. GETM, A General Estuarine Transport Model, Scientific Documentation. EUR 20253 EN.

http://www.getm.eu

See Also

image2D for plotting images, package plot3D.

ImageOcean for an image of the ocean's bathymetry, package plot3D.

scatter2D for making scatterplots, package plot3D.

Oxsat for a 3-D data set, package plot3D.

Examples

# save plotting parameters
 pm <- par("mfrow")
 mar <- par("mar")
   
## =============================================================================
## Show position of transect and 3D box in bathymetry
## =============================================================================  

 par(mfrow = c(2, 2))
 par(mar = c(4, 4, 4, 4))

 x <- Syltsurf$x ; y <- Syltsurf$y ; depth <- Syltsurf$depth
 image2D(z = depth, x = x, y = y, clab = c("depth", "m"))

# position of transect 
 with (Sylttran, points (x, rep(y, length(x)), 
         pch = 16, col = "grey"))
# position of 3-D area
 with (Sylt3D, rect(x[1], y[1], x[length(x)], y[length(y)], lwd = 3))
         
 image2D(z = depth, x = x, y = y, clab = c("depth", "m"), log = "z")

# sigma coordinates of the transect (at time = 10)
 matplot(Sylttran$x, Sylttran$sigma[,,10], type = "l", 
         main = "sigma", ylim = c(25, -2), col = "black", lty = 1)

# perspective view - reduce resolution for speed
 ix <- seq(1, length(x), by = 3)
 iy <- seq(1, length(y), by = 3)
 
 par(mar = c(1, 1, 1, 2))
 persp3D(z = -depth[ix, iy], x = x[ix], y = y[iy], 
   scale = FALSE, expand = 0.2, ticktype = "detailed", 
   col = "grey", shade = 0.6, bty = "f",
   plot = FALSE)

# add 3-D region; small amount added to z so that it is visible in rgl   
 persp3D(z = -Sylt3D$depth + 1e-3, x = Sylt3D$x, y = Sylt3D$y, 
   col = alpha.col("red", alpha = 0.4), add = TRUE,
   plot = FALSE)

# transect
 with (Sylttran, points3D(x = x, y = rep(y, length(x)), 
   z = rep(0, length(x)), pch = 16, add = TRUE, colkey = FALSE))

## Not run: 
 plotrgl()
 plotrgl(lighting = TRUE, new = FALSE, smooth = TRUE)

## End(Not run)

## =============================================================================
## Data Syltsurf: Surface elevation
## =============================================================================  

 par(mfrow = c(2, 2), mar = c(0, 0, 1, 0))
# reduce resolution for speed
 ix <- seq(1, length(x), by = 3)
 iy <- seq(1, length(y), by = 3)

 clim <- range(Syltsurf$elev, na.rm = TRUE)
 for (i in 1:3) 
   persp3D(z = -depth[ix, iy], colvar = Syltsurf$elev[ix,iy,i], 
     x = x[ix], y = y[iy], clim = clim, inttype = 2,  d = 2, 
     scale = FALSE, expand = 0.1, colkey = FALSE, shade = 0.5, 
       main = paste(format(Syltsurf$time[i], digits = 3), " hr"))
 par(mar = c(3, 3, 3, 3))
 colkey(clim = clim, clab = c("elevation", "m")) 
  
# can also be done using shaded image2D plots, faster
 par(mfrow = c(2, 2), mar = c(3, 3, 3, 3))
 clim <- range(Syltsurf$elev, na.rm = TRUE)
 for (i in 1:3) 
   image2D(z = -depth[ix, iy], colvar = Syltsurf$elev[ix,iy,i], 
     x = x[ix], y = y[iy], clim = clim, 
     colkey = FALSE, shade = 0.3, resfac = 2,
       main = paste(format(Syltsurf$time[i], digits = 3), " hr"))
 colkey(clim = clim, clab = c("elevation", "m")) 

## =============================================================================
## Data Syltsurf: Surface currents
## =============================================================================  
 
 par(mfrow = c(1, 1))
 Speed <- sqrt(Syltsurf$u[,,2]^2 + Syltsurf$v[,,2]^2)

 with (Syltsurf,
   quiver2D(x = x, y = y, u = u[,,2], v = v[,,2], col = gg.col(100),
     xlim = c(5, 20), ylim = c(10, 25), by = 3, 
     colvar = Speed, clab = c("speed", "m/s"), 
     main = paste(formatC(time[1]), " hr"), scale = 1.5, 
     image = list(z = depth, x = x, y = y, col = "white",  #background
       NAcol = "darkblue"),
     contour = list(z = depth, x = x, y = y, col = "black",#depth 
       lwd = 2)
     )
  )

## =============================================================================
## Data Sylttran: plot a transect
## =============================================================================

 par(mfrow = c(1, 1), mar = c(4, 4, 4, 2))
 D   <- seq(-1, 20, by = 0.02)

 visc <- mapsigma (Sylttran$visc [ , ,1], x = Sylttran$x, 
     sigma = Sylttran$sigma[ , ,1], depth = D, resfac = 2)

 image2D(visc$var, x = visc$x, y = -visc$depth, ylim = c(-20, 1),
     main = "eddy viscosity", ylab = "m", xlab = "hour", 
     clab = "m2/s")
     
# show position of timeseries in next example
 abline(v = visc$x[45])  

## =============================================================================
## Data Sylttran: plot a time-series
## =============================================================================

 par(mfrow = c(1, 1), mar = c(5, 4, 4, 3))
 ix <- 45 

 visct <-  Sylttran$visc  [ix, ,]
 sig   <-  Sylttran$sigma [ix, ,]  

# sigma coordinates are first dimension (signr)
 visc <- mapsigma(visct, sigma = sig, signr = 1, 
   x = Sylttran$time, numdepth = 100, resfac = 3)
 D    <- -visc$depth

 image2D(t(visc$var), x = visc$x, y = D, NAcol = "black", 
   ylim = range(D), main = "eddy viscosity", 
   ylab = "m", xlab = "hour", clab = "m2/s")

## =============================================================================
## Data Sylt3D: increase resolution and map from sigma to depth
## =============================================================================

# select a time series point
 it <- 1
 par(mfrow = c(1, 1))
 sigma  <- Sylt3D$sigma[,,,it]
 visc   <- Sylt3D$visc [,,,it]  
 (D <- dim(sigma))     # x, y, z
 
# remap the data from sigma coordinates to depth coordinates
# depth from max in first box to max in last box
 depth <- seq(max(sigma[,,D[3]], na.rm = TRUE), 
              max(sigma[,,1   ], na.rm = TRUE), length.out = 20)

# Step-bystep mapping, increasing the resolution
 z    <- 1:21
 x    <- Sylt3D$x
 y    <- Sylt3D$y

 xto <- seq(min(x), max(x), length.out = 30)
 yto <- seq(min(y), max(y), length.out = 30)

# higher resolution 
 Sigma <- remap(sigma, x, y, z, xto, yto, zto = z)$var
 Visc  <- remap(visc, x, y, z, xto, yto, zto = z)$var

# viscosity in sigma coordinates
 visc_sig <- mapsigma(Visc, sigma = Sigma, depth = depth)

## =============================================================================
## The 3-D data set - plotted as slices
## =============================================================================

 slice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
   scale = FALSE, expand = 0.1, NAcol = "transparent", 
   ys = yto[seq(1, length(yto), length.out = 10)], plot = FALSE, 
   colkey = list(side = 1))
 persp3D(x = x, y = y, z = -Sylt3D$depth, add = TRUE, 
   border = "black", facets = NA, colkey = FALSE)

# visualise it in rgl window
 plotrgl()

## the same, as a movie

 persp3Drgl(x = x, y = y, z = -Sylt3D$depth, smooth = TRUE, 
   col = "grey", lighting = TRUE)

 movieslice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
   add = TRUE, ys = yto)

# in order to wait inbetween slice drawings until a key is hit:
## Not run: 
 persp3Drgl(x = x, y = y, z = -Sylt3D$depth, smooth = TRUE, 
   col = "grey", lighting = TRUE)
 movieslice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, add = TRUE, 
   ask = TRUE, ys = yto)

## End(Not run)

## =============================================================================
## The 3-D data set - plotted as isosurfaces
## =============================================================================

 isosurf3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
   level = c(0.005, 0.01, 0.015), col = c("red", "blue", "green"), 
   scale = FALSE, expand = 0.1, ticktype = "detailed", 
   main = "viscosity", clab = "m2/s", 
   plot = FALSE, colkey = list(side = 1))
 persp3D(x = x, y = y, z = -Sylt3D$depth, border = "black", 
   col = "white", add = TRUE, plot = FALSE)


## Not run: 
 plotdev(alpha = 0.3, phi = 30)         # this is slow

## End(Not run)
 plotrgl(alpha = 0.3)

# reset plotting parameters
 par(mar = mar)
 par(mfrow = pm)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OceanView)
Loading required package: plot3D
Loading required package: plot3Drgl
Loading required package: rgl
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/OceanView/Sylt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Sylt data set
> ### Title: Hydrodynamic model output (getm) of Sylt-Romo Bight
> ### Aliases: Syltsurf Sylttran Sylt3D
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # save plotting parameters
>  pm <- par("mfrow")
>  mar <- par("mar")
>    
> ## =============================================================================
> ## Show position of transect and 3D box in bathymetry
> ## =============================================================================  
> 
>  par(mfrow = c(2, 2))
>  par(mar = c(4, 4, 4, 4))
> 
>  x <- Syltsurf$x ; y <- Syltsurf$y ; depth <- Syltsurf$depth
>  image2D(z = depth, x = x, y = y, clab = c("depth", "m"))
> 
> # position of transect 
>  with (Sylttran, points (x, rep(y, length(x)), 
+          pch = 16, col = "grey"))
> # position of 3-D area
>  with (Sylt3D, rect(x[1], y[1], x[length(x)], y[length(y)], lwd = 3))
>          
>  image2D(z = depth, x = x, y = y, clab = c("depth", "m"), log = "z")
Warning message:
In log(z) : NaNs produced
> 
> # sigma coordinates of the transect (at time = 10)
>  matplot(Sylttran$x, Sylttran$sigma[,,10], type = "l", 
+          main = "sigma", ylim = c(25, -2), col = "black", lty = 1)
> 
> # perspective view - reduce resolution for speed
>  ix <- seq(1, length(x), by = 3)
>  iy <- seq(1, length(y), by = 3)
>  
>  par(mar = c(1, 1, 1, 2))
>  persp3D(z = -depth[ix, iy], x = x[ix], y = y[iy], 
+    scale = FALSE, expand = 0.2, ticktype = "detailed", 
+    col = "grey", shade = 0.6, bty = "f",
+    plot = FALSE)
> 
> # add 3-D region; small amount added to z so that it is visible in rgl   
>  persp3D(z = -Sylt3D$depth + 1e-3, x = Sylt3D$x, y = Sylt3D$y, 
+    col = alpha.col("red", alpha = 0.4), add = TRUE,
+    plot = FALSE)
> 
> # transect
>  with (Sylttran, points3D(x = x, y = rep(y, length(x)), 
+    z = rep(0, length(x)), pch = 16, add = TRUE, colkey = FALSE))
> 
> ## Not run: 
> ##D  plotrgl()
> ##D  plotrgl(lighting = TRUE, new = FALSE, smooth = TRUE)
> ## End(Not run)
> 
> ## =============================================================================
> ## Data Syltsurf: Surface elevation
> ## =============================================================================  
> 
>  par(mfrow = c(2, 2), mar = c(0, 0, 1, 0))
> # reduce resolution for speed
>  ix <- seq(1, length(x), by = 3)
>  iy <- seq(1, length(y), by = 3)
> 
>  clim <- range(Syltsurf$elev, na.rm = TRUE)
>  for (i in 1:3) 
+    persp3D(z = -depth[ix, iy], colvar = Syltsurf$elev[ix,iy,i], 
+      x = x[ix], y = y[iy], clim = clim, inttype = 2,  d = 2, 
+      scale = FALSE, expand = 0.1, colkey = FALSE, shade = 0.5, 
+        main = paste(format(Syltsurf$time[i], digits = 3), " hr"))
>  par(mar = c(3, 3, 3, 3))
>  colkey(clim = clim, clab = c("elevation", "m")) 
>   
> # can also be done using shaded image2D plots, faster
>  par(mfrow = c(2, 2), mar = c(3, 3, 3, 3))
>  clim <- range(Syltsurf$elev, na.rm = TRUE)
>  for (i in 1:3) 
+    image2D(z = -depth[ix, iy], colvar = Syltsurf$elev[ix,iy,i], 
+      x = x[ix], y = y[iy], clim = clim, 
+      colkey = FALSE, shade = 0.3, resfac = 2,
+        main = paste(format(Syltsurf$time[i], digits = 3), " hr"))
>  colkey(clim = clim, clab = c("elevation", "m")) 
> 
> ## =============================================================================
> ## Data Syltsurf: Surface currents
> ## =============================================================================  
>  
>  par(mfrow = c(1, 1))
>  Speed <- sqrt(Syltsurf$u[,,2]^2 + Syltsurf$v[,,2]^2)
> 
>  with (Syltsurf,
+    quiver2D(x = x, y = y, u = u[,,2], v = v[,,2], col = gg.col(100),
+      xlim = c(5, 20), ylim = c(10, 25), by = 3, 
+      colvar = Speed, clab = c("speed", "m/s"), 
+      main = paste(formatC(time[1]), " hr"), scale = 1.5, 
+      image = list(z = depth, x = x, y = y, col = "white",  #background
+        NAcol = "darkblue"),
+      contour = list(z = depth, x = x, y = y, col = "black",#depth 
+        lwd = 2)
+      )
+   )
> 
> ## =============================================================================
> ## Data Sylttran: plot a transect
> ## =============================================================================
> 
>  par(mfrow = c(1, 1), mar = c(4, 4, 4, 2))
>  D   <- seq(-1, 20, by = 0.02)
> 
>  visc <- mapsigma (Sylttran$visc [ , ,1], x = Sylttran$x, 
+      sigma = Sylttran$sigma[ , ,1], depth = D, resfac = 2)
> 
>  image2D(visc$var, x = visc$x, y = -visc$depth, ylim = c(-20, 1),
+      main = "eddy viscosity", ylab = "m", xlab = "hour", 
+      clab = "m2/s")
>      
> # show position of timeseries in next example
>  abline(v = visc$x[45])  
> 
> ## =============================================================================
> ## Data Sylttran: plot a time-series
> ## =============================================================================
> 
>  par(mfrow = c(1, 1), mar = c(5, 4, 4, 3))
>  ix <- 45 
> 
>  visct <-  Sylttran$visc  [ix, ,]
>  sig   <-  Sylttran$sigma [ix, ,]  
> 
> # sigma coordinates are first dimension (signr)
>  visc <- mapsigma(visct, sigma = sig, signr = 1, 
+    x = Sylttran$time, numdepth = 100, resfac = 3)
>  D    <- -visc$depth
> 
>  image2D(t(visc$var), x = visc$x, y = D, NAcol = "black", 
+    ylim = range(D), main = "eddy viscosity", 
+    ylab = "m", xlab = "hour", clab = "m2/s")
> 
> ## =============================================================================
> ## Data Sylt3D: increase resolution and map from sigma to depth
> ## =============================================================================
> 
> # select a time series point
>  it <- 1
>  par(mfrow = c(1, 1))
>  sigma  <- Sylt3D$sigma[,,,it]
>  visc   <- Sylt3D$visc [,,,it]  
>  (D <- dim(sigma))     # x, y, z
[1] 15 19 21
>  
> # remap the data from sigma coordinates to depth coordinates
> # depth from max in first box to max in last box
>  depth <- seq(max(sigma[,,D[3]], na.rm = TRUE), 
+               max(sigma[,,1   ], na.rm = TRUE), length.out = 20)
> 
> # Step-bystep mapping, increasing the resolution
>  z    <- 1:21
>  x    <- Sylt3D$x
>  y    <- Sylt3D$y
> 
>  xto <- seq(min(x), max(x), length.out = 30)
>  yto <- seq(min(y), max(y), length.out = 30)
> 
> # higher resolution 
>  Sigma <- remap(sigma, x, y, z, xto, yto, zto = z)$var
>  Visc  <- remap(visc, x, y, z, xto, yto, zto = z)$var
> 
> # viscosity in sigma coordinates
>  visc_sig <- mapsigma(Visc, sigma = Sigma, depth = depth)
> 
> ## =============================================================================
> ## The 3-D data set - plotted as slices
> ## =============================================================================
> 
>  slice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
+    scale = FALSE, expand = 0.1, NAcol = "transparent", 
+    ys = yto[seq(1, length(yto), length.out = 10)], plot = FALSE, 
+    colkey = list(side = 1))
>  persp3D(x = x, y = y, z = -Sylt3D$depth, add = TRUE, 
+    border = "black", facets = NA, colkey = FALSE)
> 
> # visualise it in rgl window
>  plotrgl()
> 
> ## the same, as a movie
> 
>  persp3Drgl(x = x, y = y, z = -Sylt3D$depth, smooth = TRUE, 
+    col = "grey", lighting = TRUE)
> 
>  movieslice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
+    add = TRUE, ys = yto)
> 
> # in order to wait inbetween slice drawings until a key is hit:
> ## Not run: 
> ##D  persp3Drgl(x = x, y = y, z = -Sylt3D$depth, smooth = TRUE, 
> ##D    col = "grey", lighting = TRUE)
> ##D  movieslice3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, add = TRUE, 
> ##D    ask = TRUE, ys = yto)
> ## End(Not run)
> 
> ## =============================================================================
> ## The 3-D data set - plotted as isosurfaces
> ## =============================================================================
> 
>  isosurf3D(xto, yto, -visc_sig$depth, colvar = visc_sig$var, 
+    level = c(0.005, 0.01, 0.015), col = c("red", "blue", "green"), 
+    scale = FALSE, expand = 0.1, ticktype = "detailed", 
+    main = "viscosity", clab = "m2/s", 
+    plot = FALSE, colkey = list(side = 1))
>  persp3D(x = x, y = y, z = -Sylt3D$depth, border = "black", 
+    col = "white", add = TRUE, plot = FALSE)
> 
> 
> ## Not run: 
> ##D  plotdev(alpha = 0.3, phi = 30)         # this is slow
> ## End(Not run)
>  plotrgl(alpha = 0.3)
> 
> # reset plotting parameters
>  par(mar = mar)
>  par(mfrow = pm)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO