kfunc {riverdist} | R Documentation |
Plotting K-functions for a Set of Surveys
Description
Plots K-functions for locations in each of a set of surveys. In this implementation, this can be interpreted as the proportion of additional fish within a given distance. This will increase as a function of distance, and may provide evidence of clustering or dispersion features, particularly if the envelope is used.
Usage
kfunc(
seg,
vert,
survey = NULL,
rivers,
lwd = 2,
envelope = TRUE,
envreps = 1000,
envcol = "grey80",
envborder = NA,
maxdist = NULL,
xlab = "Distance",
ylab = "% within",
showN = TRUE,
whichplots = NULL,
returnoutput = FALSE,
...
)
Arguments
seg |
A vector of river locations (segment) |
vert |
A vector of river locations (vertex) |
survey |
A vector of survey IDs corresponding to the values of
|
rivers |
The river network object to use |
lwd |
Line width used for plotting. Defaults to 2. |
envelope |
Whether to construct and display a 95 percent confidence
envelope (see note.) Defaults to |
envreps |
Number of bootstrap replicates to use for envelope calculation. Defaults to 1000. |
envcol |
Color to use for envelope plotting. Defaults to
|
envborder |
Border color to use for envelope plotting. Defaults to
|
maxdist |
Maximum distance (x-axis value) for plotting. The default
value ( |
xlab |
X-coordinate label for plotting |
ylab |
Y-coordinate label for plotting |
showN |
Whether to show the sample size for each survey in each plot
title. Defaults to |
whichplots |
A vector of plots to produce, if multiple plots are
produced. For example, specifying |
returnoutput |
Whether to return output instead of producing a plot. Defaults to |
... |
Additional plotting parameters. |
Note
K-function envelopes for each survey are constructed by bootstrapping all within-survey distances, that is, the distances between all individuals within each survey, for all surveys. This results in a confidence envelope under the assumption that spacing is independent of survey; therefore a survey K-function outside the envelope provides evidence of clustering or dispersal in that survey that is outside the typical range. An envelope is not available if only one survey is plotted.
A K-function above the envelope for a given distance range provides evidence of a greater number of individuals than expected at that distance range (clustering); A K-function below the envelope for a given distance range provides evidence of a smaller number of individuals than expected at that distance range (dispersal).
This function is distance-computation intensive, and will be extremely slow-running if a river network is used that does not have segment routes and/or distance lookup tables for fast distance computation. See buildsegroutes and/or buildlookup for more information.
Author(s)
Matt Tyers
Examples
data(Gulk, fakefish)
# # 10 plots will be created - recommend calling
# # par(mfrow=c(3,4))
kfunc(seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk, survey=fakefish$flight,
envreps=100, maxdist=200000)
# # This shows relatively high amounts of clustering for surveys 1 and 8,
# # and relatively high amounts of dispersal in surveys 5 and 6.
# # plotting the survey locations that led to this calculation, for comparison
# # 10 plots will be created - recommend calling
# # par(mfrow=c(3,4))
for(i in 1:10) {
plot(x=Gulk, segmentnum=FALSE, color=FALSE, main=i)
riverpoints(seg=fakefish$seg[fakefish$flight==i],
vert=fakefish$vert[fakefish$flight==i], rivers=Gulk, col=2, pch=15)
}