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Matrix of biogeographic events

Source: R/node_test.R
biogeography_matrix.Rd

Codes the events of node_test() from the area of each site, for example the refugium, basin or island where it lies. Each event gets 1 for sites on one side, -1 for sites on the other and 0 for sites on neither.

Usage

biogeography_matrix(
  area,
  contrast = "others",
  outside = c("zero", "other"),
  min_sites = 5
)

Arguments

area

Area of each site, with NA for sites outside all areas, or a matrix or data frame with one row per site and one column per area, with 1 or TRUE for the sites of each area. Polygons can give it with sf::st_join() or sf::st_intersects().

contrast

Named list of events, each a list with the areas of the two sides, or "others" for one event per area.

outside

For contrast = "others", sites outside all areas are left out of each event with "zero" or count as the other side with "other".

min_sites

A warning is given for events with fewer sites on one side. This is a rule of thumb, not a value from the literature.

Value

Matrix with one row per site and one column per event, with values of 1, -1 and 0.

Details

Events should come from a hypothesis stated in advance. Leibold et al. (2010) contrasted areas on the two sides of historical barriers, and Leibold & Chase (2018, chapter 9) a published biogeographic hypothesis. A named list in contrast gives this design, and nested events are written as nested groups of areas. contrast = "others" compares each area with the rest, which does not need that hypothesis, but asks a different question and is better seen as exploratory.

A site on both sides of an event gets 0.

The sites of an area are often neighbours, so their number overstates the information in an event. See site_permutations in node_test().

References

Leibold, M. A., & Chase, J. M. (2018). Metacommunity Ecology. Monographs in Population Biology 59. Princeton University Press. doi:10.2307/j.ctt1wf4d24

Leibold, M. A., Economo, E. P., & Peres-Neto, P. (2010). Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography. Ecology Letters, 13, 1290–1299. doi:10.1111/j.1461-0248.2010.01523.x

Examples

area <- rep(c("north", "centre", "south", NA), c(8, 6, 6, 10))

# a barrier between the north and the rest, and a later one between centre and south
events <- list(barrier = list("north", c("centre", "south")),
               river = list("centre", "south"))
colSums(biogeography_matrix(area, events) == 1)
#> barrier   river 
#>       8       6 

# each area against the others
head(biogeography_matrix(area, "others"))
#>      centre north south
#> [1,]     -1     1    -1
#> [2,]     -1     1    -1
#> [3,]     -1     1    -1
#> [4,]     -1     1    -1
#> [5,]     -1     1    -1
#> [6,]     -1     1    -1