Diversity across sites.

Source: R/site_diversity.r

Calculates a diversity measure as a function of adding samples, and uses permutation to obtain a confidence interval.

site_diversity(Dat, factor, group, divfun = total_richness, nperm = 20)

Arguments

Dat

A Dataset object
factor

String representing the name of the variable to be used for grouping samples. Must correspond to a header name in the Mat portion of the Dataset object.
group

Value of the variable defined in factor to extract. See examples.
divfun

Function that returns a diversity estimate given a matrix of samples. See total_richness and examples to see how to define your function.
nperm

Number of permutations to perform.

Value

A data.frame of class site.diversity which contains the following variables:

mean

Mean diversity value of all permutations

sd

Standard deviation of the diversity estimates estimated from the permutations.

nsites

Number of sites (ie. samples).

group

Variable used for selecting the samples.

See also

compare_site_diversity, total_richness

Examples

data(Rhizo)
data(Rhizo.map)
data(Rhizo.tax)
Dat <- create_dataset(Rhizo,Rhizo.map,Rhizo.tax)

soil.sitediv <- site_diversity(Dat = Dat,
                               factor = "accession",
                               group = "Soil")
col.sitediv <- site_diversity(Dat = Dat,
                              factor = "accession",
                              group = "Col")
plotgg(soil.sitediv)
plotgg(col.sitediv)

# The following function requires the vegan package installed
# and can be used with the site_diversity function.
#divfun <- function(x){
#  if(!is.null(ncol(x)))
#    x <- rowSums(x)
#  s <- vegan::diversity(x)
#  return(s)
#}