gridinfer {SyNet} | R Documentation |
Produces a sympatry matrix from distributional data organized as tables of species vs. pre-defined spatial units.
gridinfer(file = NULL, dntable = NULL, sp_row = TRUE)
file |
Character string naming the ASCII file to read it. The file is read
by read.table and contains an species-by-grids matrix of presence/absence.
Entries must be non-negative and scores higher than zero are interpreted as presence. |
dntable |
A matrix or data frame object with non-negative entries. It is an species-by-grids distributional table. Entries must be non-negative and scores higher than zero are interpreted as presence. |
sp_row |
Logical. If TRUE rows are interpreted as species and columns as
grids, otherwise the opposite is considered. |
Species are sympatric if their ranges overlap, while they are allopatric if their ranges show spatial disjunction. Inference of sympatry can be addressed over raw distributional data (i. e., dot maps or coordinates of species records) or over distributional tables (i. e., tables of species vs. pre-defined areas that indicates occupancy or not).
In case of punctual data, sympatry is inferred by the interaction of geographical proximity and interpenetration of sets of species records. Thus, sympatry is proposed when records are close together, sharing a subjacent area of unknown boundary. A step by step explanation of the procedure can be found in the source code. In case of distributional data based on grids, sympatry is inferred by co-occurrence of species in at least one pre-defined spatial unit.
The first approach uses the evidence of distribution without appealing to a priori delimited areas. It avoids the conversion of records into ranges as a preliminar step to infer sympatry.
The second approach encodes the distribtuion of species in terms of area occupancy. It is prone to obtain results biased by the size (scale effect) and shape of spatial units considered.
An object of class gridinference
, which is a list with components:
sm |
An adjacency matrix that reflects the existence (1) or not (0) of a sympatric link between species. |
Label |
Character vector of species labels. |
Dngrid |
Distributional table of species-by-grids. |
Given a distribuional matrix D, where rows are species and columns grids, the sympatry matrix S is firstly inferred through the matrix mulplication of D with its transpose. Then, entries are dichotomized, becoming S in a binary matrix.
Daniel A. Dos Santos
Dos Santos, D.A., Fernandez, H.R., Cuezzo, M.G., Dominguez, E. Sympatry Inference and Network Analysis in Biogeography. Systematic Biology (in press).
Objects of class gridinference
can be submitted to functions outgrid
and nam
.
data(sciobius2x2) gridinfer(dntable = sciobius2x2)$sm # Displays the sympatry matrix