plot.CAS.Rd
Create plots used to inspect one or more cumulative abundance profiles.
# S3 method for CAS
plot(x, plot=NULL, species=NULL, sizes1=NULL, sizes2 = NULL,
palette = colorRampPalette(c( "light blue","light green","white",
"yellow","orange","red")), zlim=NULL,...)
An object of class CAS
.
A string indicating the plot record whose surface is to be drawn.
A string indicating the species whose profile is to be drawn.
A vector containing the size values associated to each primary size class. If NULL
the x-axis will be defined using the primary size class order in x
.
A vector containing the size values associated to each secondary size class. If NULL
the y-axis will be defined using the secondary size class order in x
.
Color palette for z values.
The limits for the z-axis.
Additional plotting parameters for function persp
.
De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of ecological communities. Methods in Ecology and Evolution 4: 1167-1177.
## Create synthetic tree data
pl = rep(1,100) # All trees in the same plot
sp = ifelse(runif(100)>0.5,1,2) # Random species identity (species 1 or 2)
h=rgamma(100,10,2) # Heights (m)
d = rpois(100, lambda=h^2) # Diameters (cm)
m = data.frame(plot=pl,species=sp, height=h,diameter=d)
m$ba = pi*(m$diameter/200)^2
print(head(m))
#> plot species height diameter ba
#> 1 1 1 5.031797 21 0.03463606
#> 2 1 1 4.562974 18 0.02544690
#> 3 1 2 7.091567 49 0.18857410
#> 4 1 1 5.523011 32 0.08042477
#> 5 1 2 3.604555 12 0.01130973
#> 6 1 2 4.069347 15 0.01767146
## Size classes
heights = seq(0,4, by=.25)^2 # Quadratic classes
diams = seq(0,130, by=5) # Linear classes
## Stratify tree data
X<-stratifyvegdata(m, sizes1=heights, sizes2=diams,
plotColumn = "plot", speciesColumn = "species",
size1Column = "height", size2Column = "diameter",
abundanceColumn = "ba")
## Build cummulative abundance surface
Y = CAS(X)
## Plot the surface of species '1' in plot '1' using heights and diameters
plot(Y, species=1, sizes1=heights[-1], xlab="height (m)",
ylab="diameter (cm)", sizes2=diams[-1], zlab="Basal area (m2)",
zlim = c(0,6), main="Species 1")