Compare diversity accross sites and groups of samples.

Performs permuation to estimate diversity as a function of adding sites. And does this for samples grouped according to a factor.

compare_site_diversity(...)

# S3 method for default
compare_site_diversity(Tab, Map, factor,
  divfun = total_richness, nperm = 20)

# S3 method for Dataset
compare_site_diversity(Dat, factor, divfun = total_richness,
  nperm = 20)

Arguments

Tab	A numeric matrix of samples as columns and taxa as rows.
Map	A data.frame containing the variables to be modelled as columns and samples as rows. The rows should be named with sample IDs and must correspond to the column names from x if an abundance matrix was passed
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.
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.
Dat	A Dataset object.

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

site_diversity, total_richness

Examples

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

sitediv.accession <- compare_site_diversity(Dat = Dat,factor = "accession", divfun = total_richness, 20)
plotgg(sitediv.accession)

# The following code requires the vegan package
# divfun <- function(x){
#  if(!is.null(ncol(x)))
#    x <- rowSums(x)
#  s <- vegan::diversity(x)
#  return(s)
# }

# sitediv.accession <- compare_site_diversity(Dat = Dat,
#                                             factor = "accession",
#                                             divfun = divfun, 20)
# plotgg(sitediv.accession, alpha = 0.3) +
#   scale_color_brewer(palette = "Set3") +
#   scale_fill_brewer(palette = "Set3")