plot_indicator_taxa: Plot indicator taxa

In alexology/biomonitoR: biomonitoring indices and metrics

Plot indicator taxa

Description

A sankey plot of indicator taxa.

Usage

plot_indicator_taxa(
  x,
  clusters = NULL,
  tax_lev = "Taxa",
  nmax = 10,
  thresh = 25,
  method = "ward.D2",
  parent = "Order",
  opacity = 0.8,
  color = NULL
)

Arguments

x	Result of aggregate_taxa().
clusters	Sites clusters. If NULL an automatic clustering procedure will be used. Otherwise, provide a data.frame with 2 columns, the first called sites where store sites name while the second called clusters where store cluster groups. Please avoid groups with numeric values.
tax_lev	Taxonomic level to be plotted.
nmax	Maximum number of clusters when clusters is NULL.
thresh	Threshold to identify indicator taxa, ranging from 0 to 100.
method	Clustering method if clusters is NULL.
parent	Parent taxonomic level. It must be coarser than tax_lev.
opacity	Set the opacity of the color link.
color	Set the color link.

Details

Indicator Taxa Analysis (IndVal; Dufrene and Legendre, 1997) is a method to find indicator species and species assemblages characterizing groups of sites. The function plot_indicator_taxa implements the group-equalized IndVal for both presence-absence and abundance data (De Caceres and Legendre, 2009). Please consider that plot_indicator_taxa is intended to visualize the main trends present in the data. For having more control on the IndVal calculation consider the indicspecies package (De Caceres and Legendre, 2009).

References

Dufrene, M., & Legendre, P. (1997). Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological monographs, 67(3), 345-366.

De Caceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566-3574.

Examples

data(macro_ex)
data_bio <- as_biomonitor(mi_prin)
data_agr <- aggregate_taxa(data_bio)
plot_indicator_taxa(data_agr)

alexology/biomonitoR documentation built on Oct. 10, 2024, 12:02 a.m.