Vpyramid3d: 3d trophic level volume pyramid

In marchtaylor/EwEvis: Ecopath with Ecosim visualization

Description

Produces a trophic pyramid where the vertical seperations are trophic levels, with volume being biomass or (more typically) throuput. The pyramid angle is inversely proportional to the mean transfer efficiency (TEgm). V and TEgm arguments are passed to the V2Pdim function, which calculates the pyramid geometry. Output is a 3d model plotted with the rgl package.

Usage

Vpyramid3d(V, TEgm, col = seq(V), alpha = 0.2,
  col.bases.only = FALSE, add.scale = TRUE, scale.len = 10,
  shift = c(0, 0, 0), draw = TRUE)

Arguments

V	vector of volumes (i.e. biomass, throughput) from lowest to highest trophic level (TL). Pyramid plots usually extend to highest TL (e.g. TL 8 in EwE output). Passed to V2Pdim.
TEgm	geometric mean transfer efficiency (TLs 2-4). Passed to V2Pdim.
col	vector of colors for each volume (V). If shorter than V, colors will be cycled.
alpha	alpha of V (single value (0-1))
col.bases.only	Logical. Color bases of trophic levels only?
add.scale	logical (TRUE / FALSE) adds scale (cube) to right of box plot.
scale.len	length of side of scale cube (units of V).
shift	shift location of plot (x,y,z). Useful in comparitive plots.
draw	Logical. Produce plot (Default: draw = TRUE)

Value

rgl output

Examples

### data from Tam et al (2008) - Northern Humboldt Current Ecosystem (1995-1996)

# data
TEgm <- 0.1014
Ts <- c(27165, 22349, 1658, 266.3, 17.45, 0.607, 0.00515, 6e-06)
Bs <- c(62.84, 147.1, 70.05, 20.61, 1.658, 0.084, 0.000657, 1e-06, 0)
res <- V2Pdim(V = Ts, TEgm=TEgm)
pal <- colorRampPalette(c("green", "yellow", "red"), bias=3)



# single plot of biomasses by TL
rgl::open3d()
res <- Vpyramid3d(V=Bs, TEgm = TEgm, col=pal(9), scale.len = 1)

# single plot of throughput by TL
rgl::open3d()
res <- Vpyramid3d(V=Ts[2:8], TEgm = TEgm, col=2:7, scale.len = 10)

# color bases only
rgl::open3d()
res <- Vpyramid3d(V=Ts[2:8], TEgm = TEgm, col=8, alpha=0.5, col.bases.only = TRUE, scale.len = 10)


# how to set-up a comparison plot (throughout example)
rgl::open3d()
tmp <- Vpyramid3d(V=Ts[2:8], TEgm = TEgm, alpha=0, add.scale = FALSE)
Vpyramid3d(V=Ts[2:8], TEgm = TEgm, col=2:7, 
  shift=c(dist(tmp[[1]]$vb[1,1:2])+5,0,0), scale.len = 10
)

# illustration of the effect of TEgm on top angle
rgl::open3d()
tmp <- Vpyramid3d(V=Ts[2:8], TEgm = 0.07, col=2:7, 
    add.scale = FALSE
)
tmp2 <- Vpyramid3d(V=Ts[2:8], TEgm = 0.1, col=2:7,
   shift=c(dist(tmp[[1]]$vb[1,1:2])*1.1,0,0),
   add.scale = FALSE
)
tmp3 <- Vpyramid3d(V=Ts[2:8], TEgm = 0.15, col=2:7,
  shift=c(dist(tmp[[1]]$vb[1,1:2])*1.1*2,0,0),
  add.scale = TRUE, scale.len = 1000^(1/3)
)

# add labels
pos <- data.frame(rbind(
  rowMeans(tmp[[7]]$vb),
  rowMeans(tmp2[[7]]$vb),
  rowMeans(tmp3[[7]]$vb)
))
names(pos) <- c("x", "y", "z", "w")

rgl::text3d(pos$x, y=pos$y, z = pos$z+3,
          text=paste("TE =", c("7%", "10%", "15%")),
       color="black", font=2
) 

 

marchtaylor/EwEvis documentation built on Dec. 2, 2019, 4:44 p.m.