neighbordens.1sp {CTFS} | R Documentation

## Create File of Neighbor Attributes for a Single Species

### Description

Calculates the number and summed basal area of conspecific and heterospecific trees within defined distances of all individuals of a given species. The resulting data frame can be used for analysis of the effect of neighbors on the population characteristics of a species.

### Usage

    neighbordens.1sp(spname, census.quad, census.spp, distbreak =
            c(0, 5, 10, 20, 30), gridsize = 20, plotdim = c(1000, 500))

### Arguments

`spname` | species code name (aka target species), in quotes
`census.quad` | data file as a list with quadrates as names
`census.spp` | data file as a list with species as names
`distbreak` | vector of radii for neighborhood annuli
`gridsize` | gridsize that `census.quad` was created with
`plotdim` | dimensions of plot

### Details

This function finds all trees within a given distance for each individual tree of the target species. It computes the number of individuals and their total basal area for two groups: conspecifics and heterospecifics. This is done for each neighborhood size. These values are returned for each individuals of the target species in a data frame with the identification number of the target species trees.

The function requires a two versions of the tree data file. One is a list of data frames of the trees in each quadrate. The second is a list of data frames of trees in each species. See `CTFS.datafiles` for structure and definitions of these data files and `link{CTFS.groupcats}` for how to make these data files. Briefly it requires creating a vector of quadrate number for each tree using `sep.quadinfo` and then using `sep.vct.data` to create the list.

In order to minimize the time it takes to identify trees that are within the defined neighborhood distances, the potential neighbors of a target species are first identified by using the quadrate number of the target individual and its bordering quadrates. This is why `census.quad` is needed to run the functions. It is the source of the neighboring tree data. `census.spp` provides the data for individuals for each target species.

Distance classes are defined as larger than and including the low value to smaller than and not including the high value of the distance classes provided by `distbreak`.

If the neighborhood annulus does not lie entirely within the plot then no information is accumulated for this target tree at that neighborhood distance (values are set to NA).

Remember that the neighborhoods computed are ANNULI so that the cummulative number of individuals (or basal area) within a given neighborhood distance is computed by summing the annuli values up to that distance.

Remember that the returned values are NOT densities, but counts. Therefore, if densities are needed, then the area of the annuli needs to be taken into account. However, if the same neighborhood distances are used for all species being investigated, then the counts are comparable since the neighborhood annuli are all of the same sizes for all species.

All trees that are alive or alive but broken are included as valid neighbors for the computation of neighborhood attributes.

For more information on how to change the selection criteria for neighbors or the attributed computed, see `CTFS.densdepend`.

### Value

Returns a dataframe of neighborhood attributes for each tree of a single species. This data frame matches the order and number of trees of a species as found in `census.spp`. The following values are produced for each distance class in `distbreak`. Numbers and basal area are for the annuli as defined by `distbreak`. See `socrex90.neigh` for an example result.

`Ncon` | Number of conspecific individuals
`BAcon` | Total basal area (m^2) of conspecific individuals
`Nhet` | Number of heterospecific individuals
`BAhet` | Total basal area (m^2) of heterospecific individuals

The labels for each variable are created from the dist breaks.

### Author(s)

Rick Condit and Pamela Hall

### See Also

`CTFS.densdepend`, `CTFS.datafiles`, `CTFS.groupcats`, `socrex90.neigh`

### Examples

    ## Not run:

    socrex90.neigh <- neighbordens.1sp("socrex",tst.bci90.quad,tst.bci90.spp)
    socrex90.neigh[1:10,]
    ## End(Not run)

[Package CTFS version 1.00 Index]