neighbordens.1sp {CTFS} | R Documentation |
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.
neighbordens.1sp(spname, census.quad, census.spp, distbreak = c(0, 5, 10, 20, 30), gridsize = 20, plotdim = c(1000, 500))
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 |
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
.
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.
Rick Condit and Pamela Hall
CTFS.densdepend
,
CTFS.datafiles
, CTFS.groupcats
,
socrex90.neigh
## Not run: socrex90.neigh <- neighbordens.1sp("socrex",tst.bci90.quad,tst.bci90.spp) socrex90.neigh[1:10,] ## End(Not run)