siplab (version 1.0)

assimilation: Compute Assimilation Indices

Description

This is the main function in siplab for computing assimilation indices. Optionally, it computes also a free-growing index, and/or the assimilation centroid.

Usage

assimilation(plants, pixsize = 0.1, resource = 1, influence = gnomon.inf,
  infpar = list(a = 1, b = 4, smark = 1), partpar = Inf, efficiency = flat.eff,
  effpar = NULL, plot = TRUE, afree = FALSE, centroid = FALSE)
assimilation.pix(plants, pixsize = 0.1, resource = 1, influence = gnomon.inf,
  infpar = list(a = 1, b = 4, smark = 1), partpar = Inf, efficiency = flat.eff,
  effpar = NULL, plot = TRUE, afree = FALSE, centroid = FALSE)

Arguments

plants

A spatstat point pattern object (class ppp), containing the plants coordinates and marks with the plant size and possibly other attributes.

pixsize

Resolution, approximate step size in the pixel grid. Default 0.1.

resource

Either a pixel image (class im), or a function, or other object that can be converted to a pixel image, specifying the spatial distribution of resource availability. If an image, it should cover the plants window. It is adjusted

influence

User-supplied influence function for computing influence values. Must have arguments (dx, dy, marks, par), where dx is a vector of points-to plant x-distances, dy is a vector of points-to plant y-distances, mar

infpar

Parameter(s) for influence, usually a list or vector. Default: list(a=1, b=4, smark=1). Note that smark=1 indicates that the plant size variable is the first or only item in marks.

partpar

Exponent $\theta$ in the partition function. Default is Inf, which produces a tesselation.

efficiency

User-supplied efficiency function for weighting the point resource uptake. Must have arguments (dx, dy, marks, par), where dx is a vector of points-to plant x-distances, dy is a vector of points-to plant y-distances,

effpar

Parameter(s) for efficiency, usually a list or vector.

plot

If TRUE, the denominator of the partition function is graphed as a pixel image, to visualize competition pressure (default).

afree

If TRUE, the free-growing assimilation is also computed. Default is FALSE.

centroid

If TRUE, the centroid of the plant assimilation distribution is also computed. Default is FALSE.

Value

• Returns the point pattern plants with the results appended to the marks(plants) data frame. The additional marks are the assimilation indices in the column aindex, and optionally the free-growing index in afree, and/or the x and y centroid coordinates in cx and cy.

encoding

UTF-8

Details

assimilation and assimilation.pix are functionally equivalent, but the code in assimilation.pix is somewhat clearer and slower. It may be useful for documentation purposes, and as a basis for user modification.

Computation starts with a resource intensity grid at a spatial resolution of pixsize, which is typically assumed to be uniform, Plants exert competitive pressure depending on size and distance, described by the influence function. The resource available at each pixel is allocated to plants according to their influence and to a partition rule parametrized by partpar. Finally, the resource uptake is weighted by the efficiency function, and is spatially integrated to obtain the plant's assimilation index.

References

http://forestgrowth.unbc.ca/siplab

García{Garcia}, O. (2013) A generic approach to spatial individual-based modelling and simulation of plant communities. Manuscript in review.

See Also

influence, efficiency, edges

Examples

a <- assimilation(finpines, infpar=list(a=1, b=4,
     smark="height"), afree=TRUE)
head(marks(a))
system.time(assimilation.pix(finpines))
system.time(assimilation(finpines))