JostDiversity: Jost diversity from 'vegetarian' Package

In walterxie/ComMA: Community Matrix Analysis

Description

Data input t.community.matrix is a transposed matrix of community matrix we defined in ComMA. Community matrix from file is a matrix where rows are OTUs or individual species and columns are sites or samples. See ComMA.

Usage

diversityTable(t.community.matrix, named.vector = FALSE)

summaryCMPerSample(t.community.matrix, hasTotal = TRUE, digits = 2,
  sort = "descending", comma.in.number = TRUE)

Arguments

t.community.matrix	is abundances argument in vegetarian d, which is a transposed matrix of community matrix, where rows are plots (Use plots instead of subplots.), columns are OTUs.
named.vector	Logical, if TRUE, then return a named vector instead of data.frame.
hasTotal	If TRUE, then display the Total. Default to TRUE.
sort	Sort abundance column by "descending", "ascending", or do nothing for any other string.
comma.in.number	If TRUE, then add comma to bug numbers. Default to TRUE.
digit	The digits of Shannon index. Default to 2.

Details

diversityTable creates a data frame or named vector of Jost diversity measurement.

summaryCMPerSample creates a brief summary table of diversities per sample.

Value

diversityTable returns a 3x3 data frame: columns are levels of diversity c("gamma", "alpha", "beta"), rows are orders of the diversity measure c(0, 1, 2). For example,

	$q=0$	$q=1$	$q=1$
$D_\gamma(q)$	13922.000000	2501.693162	601.509610
$D_\alpha(q)$	2238.392857	880.944977	251.127187
$D_\beta(q)$	6.219641	2.839784	2.395239

summaryCMPerSample returns a summary data frame: columns are types of diversity c("abundance", "richness", "shannon"), rows are samples. For example,

	$q=0$	$q=1$	$q=1$
Total	688,733	16,860	NA
sample1	32,837	508	23.02
sample2	25,023	181	7.9

Examples

diversity.table <- diversityTable(t.community.matrix)

summary.t.cm <- summaryCMPerSample(t.community.matrix)

walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.