asbio (version 0.2-1)

veg.table: Summarized constancy/cover vegetation tables (not vegetables)

Description

Calcutes vegetation cover and constancy within groups (factor) for species at a defined minimum constancy,then converts constancy and cover to codes. Three different cover classes systems can be specified. A method developed by Aho (2006), Daubenmire cover classes, and Braun-Blanquet cover classes.

Usage

veg.table(Y, cat, min.const = 0.3, method = "aho", cover.only = FALSE)

Arguments

Y

A site x species (n x p) community matrix.

cat

An n x 1 vector of categorical assignments. Must be a factor.

min.const

A constancy cutoff. To help distill information data will be subset into two components species with >= min.const in at least one group, and < min.const across all groups. min.const=0

method

The type of cover codes to use. The choices are possible aho, daub, and braun

cover.only

Logical. If only cover output is desired then stipulate cover.only = TRUE

Value

• A list with two of three possible components is returned. The components will change depending what is specified in cover.only
• const.cover
  A matrix with constancy and cover ciphers containing species with >= 30 percent constancy in at least one group
• const.cover_less.than.min.const
  A matrix with constancy and cover ciphers containing species which do not have >= 30 percent constancy in at least one group
• cover
  A matrix with constancy and cover ciphers containing species with >= 30 percent constancy in at least one group

Details

The function assumes that responses in the community matrix are percent cover, i.e. responses are generally in the range 0 - 100 (although responses greater than 100 are allowed). For constancy: 0 percent = ".", 0-10 = +, 10-20 = 1, 20-30 = 2, 30-40 = 3, 40-50 = 4, 50-60 = 5, 60-70 = 6,70-80 = 7, 80-90 = 8, 90-100 = 9. Three different cover class systems can be specified. Aho, i.e. method = aho cover classes use the following codes: 0 percent = ".", 0-0.01 = +, 0.01-1 = A, 1-2 = B, 2-5 = C, 5-25 = D, >25 = E. Daubenmire,i.e. daub cover classes are as follows: 0 percent = ".", 0-5 percent = 1, 5-25 = 2, 25-50 = 3, 50-75 = 4, 75-95 = 5, >95 = 6. Braun-Blanquet, i.e. braun cover classes are as follows: 0 percent = ".", 0-0.1 = "r", 0.1-1 = "+", 1-5 = 1, 5-25 = 2, 25-50 = 3, 50-75 = 4, >75 = 5. The argument min.const allows creation of two summary cover and constancy matrices. The first contains species which have >= min.const within at least one of the categories/clusters. The second contains cover and constancy summaries for all other species

References

Aho, K. (2006) Alpine ecology and subalpine cliff ecology in the Northern Rocky Mountains. Doctoral dissertation, Montana State University, 458 pgs. Gurevitch, J., Scheiner, S. M., and Fox, G. A. (2006) The ecology of Plants. Sinauer.

See Also

const

Examples

data(dune)
data(dune.env)
veg.table(Y=dune,cat=dune.env[,3])