ecopart.pair: Partitioning pairwise dissimilarity

In CommunityEcologist/ecopart: Partitioning the Temporal Changes in Beta Diversity into Extinction and Colonization Components

Partitioning pairwise dissimilarity

Description

ecopart.pair patitions the temporal changes in pairwise dissimilarity (Jaccard, Sorensen, Ruzicka, and Bray-Curtis indices) into dynamic components based on methods proposed by Tatsumi et al. (2021, 2022)

Usage

ecopart.pair(d1, d2, index = "sorensen", components = "four")

Arguments

d1	A matrix or dataframe at time 1. Rows are a pair of sites (sites 1 and 2), columns are species, and elements are presence-absence (01) or abundances of species.
d2	A matrix or dataframe at time 2. Note that d1 and d2 must have exactly the same sites and species in the same order.
index	Type of dissimilarity measure. Options are "jaccard", "sorensen", "ruzicka", and "bray-curtis". "jaccard" and "sorensen" These indices are based on presence-absence data (Jaccard 1912, Sorensen 1948). When d1 and d2 are abundance data, the elements are automatically converted to presence-absence data by replacing non-zero values with 1. "ruzicka" and "bray-curtis" These indices are based on abundance data (Bray & Curtis 1957, Ruzicka 1958). When d1 and d2 are presence-absence data, Ruzicka and Bray-Curtis indices are equivalent to the Jaccard and Sorensen indices, respectively.
components	Types of components into which the total change in beta diversity is partitioned. Options are "two", "four", "six", and "sp". "two" Calculates extinction and colonization components (when index = "jaccard" or index = "sorensen") or subtractive and additive components (when "ruzicka" or "bray-curtis"). "four" Calculates extinction- and colonization-induced homogenization and differentiation (when index = "jaccard" or index = "sorensen") or subtractive and additive homogenization and differentiation (when "ruzicka" or "bray-curtis"). "six" Calculates six components that represent (1) homogenization by decrease in U, (2) differentiation by decrease in C, (3) differentiation by change from C to U, (4) differentiation by increase in U, (5) homogenization by increase in C, and (6) homogenization by change from U to C, where U is the existance or abundance of species unique to either site and C is the existance or abundance of species common to both sites. "sp" Same with "four" but the components are further partitioned down to the species-level.

Value

The ecopart.pair function returns a vector or matrix object containing the partitioned components of beta diversity.

• When components = "two" was specified, the function returns a vector object with two elements: extinction and colonization components (when index = "jaccard" or index = "sorensen") or subtractive and additive components (when index = "ruzicka" or index = "bray-curtis"). The extinction and colonization components represent temporal changes in beta diversity that result from local species extinctions and colonizations. The subtractive and additive components represent temporal changes in beta diversity that result from local losses and gains in species abundances.

• When components = "four" was specified, the function returns a vector object with four elements: extinction- and colonization-induced homogenization and differentiation (when index = "jaccard" or index = "sorensen") or subtractive and additive homogenization and differentiation (when index = "ruzicka" or index = "bray-curtis"). Homogenization and differentiation indicate decreases and increases in beta diversity, respectively.

• When components = "six" was specified, the function returns a vector object with six elements: (1) homogenization by decrease in U, (2) differentiation by decrease in C, (3) differentiation by change from C to U, (4) differentiation by increase in U, (5) homogenization by increase in C, and (6) homogenization by change from U to C.

• When components = "sp" was specified, the function returns a matrix object. The rows represent the four components that are equivalent to when components = "four" was specified. The columns represent species.

Author(s)

Shinichi Tatsumi

References

• Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27(4): 325-349.

• Jaccard P (1912) The distribution of the flora in the alphine zone. New Phytologist 11(2): 37-50.

• Ruzicka M (1958) Anwendung mathematisch-statisticher Methoden in der Geobotanik (synthetische Bearbeitung von Aufnahmen). Biologia, Bratislava 13: 647-661.

• Sorensen T (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskab 5(4): 1-34.

• Tatsumi S, Iritani R, Cadotte MW (2021) Temporal changes in spatial variation: partitioning the extinction and colonisation components of beta diversity. Ecology Letters 24(5): 1063-1072.

• Tatsumi S, Iritani R, Cadotte MW (2022) Partitioning the temporal changes in abundance-based beta diversity into loss and gain components. Methods in Ecology and Evolution: in press

CommunityEcologist/ecopart documentation built on July 8, 2023, 11:41 p.m.