Description Usage Arguments Details Value References Examples
Calculate diversity properties of a species abundance matrix: Gamma, Alpha, Beta, Halfchanges, Dust Bunny Index, others.
1 2 3 | mx_diversity(x, ...)
mx_profile(x, ...)
|
x |
array of species data, where rows = SUs and cols = species |
... |
further arguments passed to other methods |
Calculates eight measures of diversity in the matrix, and five row and column statistics. For an example applied to many simulated datasets, see Smith (2017).
'mx_diversity' returns a data.frame with 8 numeric values:
gamma = count of species in entire matrix
alpha = average count of species per SU
beta = Whittaker's beta diversity = [(gamma/alpha) - 1]
halfchanges = beta diversity by exponential transformation of average Sorenson dissimilarities (pg 31 of McCune & Grace 2002)
dbi = Dust Bunny Index of McCune and Root (2015)
prop0 = proportion of zero elements (McCune and Root 2015)
propnoshare = proportion of no-share SU pairs
N = number of SUs
'mx_profile' appends further items:
cv_rowtotals = coefficient of variation within rows
cv_coltotals = coefficient of variation within columns
mean_colskewness = mean of skewness within columns
min_nonzeroval = minimum nonzero value
min_nonzeroval = maximum nonzero value
McCune, B., and J. B. Grace. 2002. Analysis of Ecological Communities. MjM Software, Gleneden Beach, Oregon, USA. 304 pp.
McCune, B., and H.T. Root. 2015. Origin of the dust bunny distribution in ecological community data. Plant Ecology 216(5): 645-656.
Smith, R.J. 2017. Solutions for loss of information in high-beta-diversity community data. Methods in Ecology and Evolution 8(1): 68-74.
1 2 3 4 5 6 7 8 | # species abundance data
set.seed(1917)
spe <- data.frame(matrix(rnorm(30, 10, 50), 10, 3))
spe[spe < 0] <- 0
colnames(spe) <- c('Acer rubrum','Acer saccharum','Acer negundo')
spe
mx_diversity(spe)
mx_profile(spe)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.