Arch_schem: A schematic figure of the archetypes

In vitaliskim/msco: Multi-Species Co-Occurrence Analyses

A schematic figure of the archetypes

Description

A schematic diagram illustrating nine possible archetypes (from the null model test) of the patterns of species co-occurrences in ecological communities. The archetypes are denoted \{Ai: i \in (1:9)\}. See the details below.

Usage

Arch_schem()

Value

The Arch_schem function returns a schematic diagram of the archetypes of species co-occurrence patterns (denoted by \{Ai: i \in (1:9)\}), with the following components:

Archetype	Description/Interpretation
A1	The joint occupancy value of the observed community matrix (observed; dark solid line) is above the null model. This means the null hypothesis (i.e. a statement that imply any change in the observed patterns do not reflect any community assembly process as underlying cause) should be rejected, confirming the presence of a mechanism of interest being tested (Lagat et al., 2021a). It is typical of a community whose species are positively associated (or aggregated) more often than would be expected by chance. Such patterns of community structure may arise from a number of ecological mechanisms including environmental filtering or shared habitat requirements (Cordero and Jackson, 2019).
A2	The observed is greater than null expectation for i = 2 but within null expectation for i \ge 3. This implies a pairwise metric detects a non-random pattern of the community structure, but when higher order species are considered, a random pattern is produced. This is typical of a community whose species are aggregated more often than by chance in sites with few species than in sites with many species (Lagat et al., 2021a).
A3	The observed is greater than null expectation for lower orders, within null expectation for medium orders, and less than null expectation for higher orders. This means species co-occur more often than by chance in sites with few species, but are segregated more often than by chance in sites with many species, depicting a community structured by two different community assembly processes (Lagat et al., 2021a).
A4	The observed is within null expectation for i = 2 but greater than null expectation for i \ge 3. This means when use pairwise co-occurrence is used, the null hypothesis is not rejected, but when joint occupancy is used, the same null hypothesis is rejected. I.e., pairwise co-occurrence fails at detecting patterns of aggregation for sites with many species, i.e. a type II error or false negative (Lagat et al., 2021a).
A5	The observed is within the null expectation for all orders i \ge 2, implying the test is not statistically significant. This has been ecologically inferred to mean ecological communities are random and that no community assembly processes or mechanisms influence their structure (Lagat et al., 2021a; Cordero and Jackson, 2019; Gotelli and Sounding, 2001).
A6	The observed is within the null expectation for i = 2 but less than the null expectation for i \ge 3. This means when use pairwise co-occurrence is used, the null hypothesis is not rejected, but when joint occupancy is used, the same null hypothesis is rejected. I.e., pairwise co-occurrence fails at detecting patterns of segregation for sites with many species, i.e. a type II error or false negative (Lagat et al., 2021a).
A7	The observed is less than null expectation for lower orders, within null expectation for medium orders, and greater than null expectation for higher orders. Implying species are segregated more often than would be expected by chance in sites with few species, but co-occur more often than by chance in sites with many species, depicting a community structured by two different community assembly processes (Lagat et al., 2021a).
A8	The observed is less than null expectation for i = 2 but within null expectation for i \ge 3. This means a pairwise metric detects a non-random pattern of the community structure, but when higher order species are considered, a random pattern is produced. This is typical of a community whose species are segregated more often than by chance in sites with few species than in sites with many species (Lagat et al., 2021a).
A9	The joint occupancy value of the observed community matrix (dark solid line) is below the null model. This means the null hypothesis should be rejected, confirming the presence of a mechanism of interest being tested (Lagat et al., 2021a). It is typical of a community structured by inter-specific competition or limiting similarity, though predation might also generate similar patterns (Hein et al. 2014).

Note

Arch_schem is not a generic function which can take in any dataset and give the outputs, but a path to a schematic diagram saved in this package. A representational figure from empirical, simulated or any known .csv binary data matrices can be accessed with Jo.plots function.

References

1. Cordero, R.D. and Jackson, D.A. (2019). Species-pair associations, null models, and tests of mechanisms structuring ecological communities. Ecosphere 10. https://doi.org/10.1002/ecs2.2797

2. Gotelli, N. J. and Sounding, E. (2001). Research frontiers in null model analysis. Glob. Ecol. Biogeogr. 10, 337-343. https://doi.org/10.1046/j.1466-822X.2001.00249.x

3. Hein et al. (2014). Fish introductions reveal the temperature dependence of species interactions. Proc. R. Soc. B Biol. Sci. 281. https://doi.org/10.1098/rspb.2013.2641

4. Lagat, V. K., Latombe, G. and Hui, C. (2021a). A multi-species co-occurrence index to avoid type II errors in null model testing. DOI: ⁠<To be added>⁠.

vitaliskim/msco documentation built on Sept. 29, 2023, 9:22 p.m.