pairwise: Compute Pairwise Competition Indices

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/pairwise.R

Description

This function computes competition indices based on pairs of plants, ignoring higher-order interactions.

Usage

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pairwise(plants, maxN = NULL, maxR = NULL, select = NULL, selpar =
         NULL, kernel, kerpar = NULL)

Arguments

plants

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

maxN

Maximum number of nearest neighbors to include as potential competitors. Default is NULL (no restriction).

maxR

Maximum radius to search for potential competitors. Default is NULL (no restriction).

select

Optional user-supplied selection function for choosing competitors. Must take arguments (imarks, jmarks, dists, dranks) or (imarks, jmarks, dists, dranks, par), where imarks are the marks for the subject plant (a 1-row data frame), jmarks is a data frame with the marks of the potential competitors, dists is a vector distances between subject plant and the potential competitors, dranks are the distance ranks, and par receives the value of the selpar argument if not NULL. It must return a logical vector with the same length as dists. Examples are provided in the functions powlinear_sel(), etc. (see select). Default is NULL (no selection).

selpar

Parameter(s) for select, usually a list or vector. Default: NULL.

kernel

Competition kernel function for computing the effect of competitor j on the subject plant i. Must yake arguments (imarks, jmarks, dists, dranks) or (imarks, jmarks, dists, dranks, par), where imarks are the marks for the subject plant (a 1-row data frame), jmarks is a data frame with the marks of the potential competitors, dists is a vector of distances between subject plant and the potential competitors, dranks are the distance ranks, and par receives the value of the kerpar argument if not NULL. It must return a numeric vector with the same length as dists. Examples are provided in the functions powers_ker(), etc. (see kernel).

kerpar

Parameter(s) for kernel, usually a list or vector. Default: NULL.

Details

Traditionally, the competition index for a subject plant i is obtained in two stages: (1) Choose a set of competitors of i by some selection rule. (2) Compute a measure of the effect of each competitor j on plant i, and add over j. This effect of j on i is normally a function of the sizes of both plants and of the distance between them, which we call a competition kernel. The kernel may depend on other plant attributes, like species, and in some rare instances on the distance ranks or on the number of competitors. Conceptually, the first stage is not strictly necessary, it could be replaced by specifying zero kernel values (the effect of the selection is usually to truncate the kernel function beyond some distance). However, a separate selection rule may be more transparent, and may reduce the computational effort in searching for neighbors.

Some simple selection rules can be implemented by giving a value to maxN and/or maxR. In any case, reasonable limits on these variables may be advisable for reducing computation.

More complex rules can be specified by the select function, with parameters in selpar. See select for examples. If more than one of maxN, maxR or select are given, the intersection of the selection criteria is used.

Kernel computation is specified by the kernel function and the parameters in kerpar. See kernel for examples.

Value

Returns the input point pattern plants, with the marks replaced by a data frame containing the original marks followed by the competition index in a column named cindex.

Note

Requires the spatstat package.

Author(s)

Oscar García.

References

https://github.com/ogarciav/siplab

García, O. “Siplab, a spatial individual-based plant modelling system”. Computational Ecology and Software 4(4), 215-222. 2014.

See Also

select, kernel, edges

Examples

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# Hegyi (1974) index (no distance offset, as usual)
summary(pairwise(finpines, maxR = 6, kernel=powers_ker))

Example output

Loading required package: spatstat
Loading required package: spatstat.data
Loading required package: nlme
Loading required package: rpart

spatstat 1.64-1       (nickname:Help you I can, yes!) 
For an introduction to spatstat, typebeginnerNote: spatstat version 1.64-1 is out of date by more than a year; we strongly recommend upgrading to the latest version.

Attaching package:siplabThe following object is masked frompackage:spatstat:

    edges

Marked planar point pattern:  126 points
Average intensity 1.26 points per square metre

Coordinates are given to 13 decimal places

Mark variables: diameter, height, cindex
Summary:
    diameter         height          cindex      
 Min.   :0.000   Min.   :0.800   Min.   :  5.28  
 1st Qu.:1.000   1st Qu.:1.825   1st Qu.: 21.09  
 Median :2.000   Median :2.850   Median : 36.28  
 Mean   :2.532   Mean   :2.828   Mean   : 57.95  
 3rd Qu.:3.000   3rd Qu.:3.600   3rd Qu.: 73.57  
 Max.   :7.000   Max.   :5.400   Max.   :489.61  
                                 NA's   :8       

Window: rectangle = [-5, 5] x [-8, 2] metres
                    (10 x 10 metres)
Window area = 100 square metres
Unit of length: 1 metre
Warning message:
some mark values are NA in the point pattern object 

siplab documentation built on Sept. 4, 2020, 5:07 p.m.