simba (version 0.3-4)

CqN: Probabilistic multiple-plot similarity indices following Chao et al. (2008). Strictly preliminary.

Description

The two functions follow different approaches to the probabilistic multiple-plot similarity indices as developed by Chao et al. (2008). Both are in alpha state.

Usage

CqN(x, q = 2, method = "pi.a")
CqNa(x, q = 0, base = exp(1), ...)

Arguments

x

Species x sites matrix.

q

Integer. Specifies the order of the diversity (see References).

method

Character string. How the proportional abundances (pi) are to be calculated. Following the gamma-, omega- or alpha-classification in the sense of Tuomisto 2010a,b. Possible are "pi.a" – pi are calculated against the sums per site, "pi.ga" - pi are calcula

base

In CqNa there is logarithm calculation involved. Per default the general default of R for the base (exp(1)) is taken, but it can be changed if wanted via base.

...

Further arguments to trudi.

Value

• CqN returns the value and a correct description. For instance when using q = 3 on a species x sites matrix with 5 sites the result will be named "C35".

  CqNa returns a named vector with values for the overlap measure based on CqN (naming follows the same path as described above), the homogeneity measure sensu MacArthur (1965) based on CqN, and the relative homogeneity measure based on CqN.

encoding

UTF-8

Details

Both function are approaches to the family of multiple-plot similarity measures suggested by Chao et al. (2008) including measures of overlap and homogeneity. Strictly preliminary. Basically included at this stage because C27 was also calculated in Jurasinski et al. 2011 as one of many different multiple-plot similarity indices. Currently CqN is not defined at q < 2.

CqNa bases its calculations on calculations of trudi for the respective order q.

References

see References in trudi

See Also

trudi

Examples

# get data
data(bernina)
# run CqNa on the first time step in the summit data
CqNa(veg[1:7,], q=1)
# vary q to see what is happening when you lay more emphasis on rare (0) 
# or common (2) species
CqNa(veg[1:7,], q=0)
CqNa(veg[1:7,], q=0)

# check the development of multiple plot similarity on the summits in time
ans <- c(rep(1907,7), rep(1985,7), rep(2003,7))
by(veg, ans, function(x) CqNa(x, q=1))