ComStructIndices: Community Structure Integrity Indices

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Community Structure Integrity Indices

Description

Calculates indices of community integrity compared to a reference community according to Jaunatre et al. (2013).

Usage

ComStructIndices(REF, ASSESS, rar = 1)

Arguments

REF	is the reference community data matrix
ASSESS	is the assessed community data matrix
rar	(facultative) Minimum number of samples in which species have to be present to be taken into account in the calculation of indices. Default value is 1. It should not be used in the indices calculation, but it can be useful to reduce the number of species with the structure.plot() function.

Value

Comb	A combined community data matrix of reference and assessed communities
Nam_Tot	A list of species names corresponding to the Comb matrix
Nam_Tar	A list of the target species names
REF_Tab	Reference community data matrix (with zero values for species which were absent in the reference community)
ASSESS_Tab	Assessed community data matrix (with zero values for species which were absent in the assessed community)
SumMeanAbREF	Sum of mean abundances
SumAbASSESS	A list of sum of species abundance for each sample
Diff	Matrix of differences, for each species, between mean abundance in the reference samples and abundance in each assessed community samples
SumNeg	Sum of negative differences issued from Diff, i.e. sum of 'higher abundances' in each of assessed community sample
SumPos	Sum of positive differences issued from Diff, i.e. sum of 'missing abundances' in each of assessed community sample
CSII	A list of Community Integrity Index in each assessed community sample
HAI	A list of Higher Abundance Index in each of assessed community sample
CSIInorm	A list of Normalized Community Integrity Index in each assessed community sample
AbMeanREFOnly	A list of mean abundances of target species in reference samples
ASSESSTarOnly_Tab	An assessed community data matrix with target species only
HigherOnly_Tab	An assessed community data matrix with non-target species only

See Also

structure.plot for graphical output

RenaudJau/Renaudpack2 documentation built on Feb. 16, 2025, 7:33 p.m.