Description Usage Arguments Details See Also
Identify the values of s that result in proportion p of hulls being time-selected
1 2 3 4 5 6 7 8 | lxy.ptsh.add(lxy, id = NULL, k = 10, n = 200, samp.idx = NULL,
sinit = 0.005, ptsh.target = 1:9/10, ptsh.max = 0.98,
ptsh.buf = 0.01, max.iter = 15, max.loops = 15,
max.reached = c("warning", "stop")[1], time.term = c("vmax",
"dif")[1], FNN.algorithm = c("cover_tree", "kd_tree", "VR", "CR")[2],
use.nn = FALSE, plotme = TRUE, save = TRUE, nn.add = FALSE,
use.pb.n = 200, ptsh.exists = c("replace", "append")[2],
beep = FALSE, status = TRUE)
|
lxy |
A LoCoH-xy object |
id |
The name(s) of individuals to analyze |
k |
Value for the k-method that will be used to create hulls for the sample points (and then used to find the proportion of time-selected hulls) |
n |
Number of randomly selected points to use as samples (ignored if |
samp.idx |
A vector of indices of the points to use as samples |
sinit |
The initial value of s that will be used to start the iteration to find that value of s that produces a proportion of time selected hulls >= ptsh.max |
ptsh.target |
A vector of values 0..1 that will serve as the target ptsh values. For each ptsh target, script will
try to find a value of s that generates the targeted proportion of time selected hulls (within |
ptsh.max |
The highest value of ptsh for which a value of s will be computed. It is generally recommended that this be less than 1. |
ptsh.buf |
The level of accuracy or precison to which the found values of 's' return the targetted ptsh. |
max.iter |
The maximum number of times the script will double sinit in an effort to find the value of s that produces ptsh.max |
max.loops |
The maximum number of intermediate values of s the script will try when 'zooming' in on the target ptsh levels |
max.reached |
What to do if the maximum number of iterations is reached, |
time.term |
The space-time transformation to use in the TSD distance metric: |
FNN.algorithm |
The algorithm to be used in the get.knnx() function in the package FNN |
use.nn |
Whether to use saved nearest neighbor sets for the ptsh computations. T/F |
plotme |
Whether to plot the ptsh vs. s curve. T/F |
save |
Whether to save the ptsh-s table in the LoCoH-xy object. T/F |
nn.add |
Whether to also identify and save nearest neighbor sets for all points for k= |
use.pb.n |
The sample size (i.e., |
ptsh.exists |
What to do if there is already a ptsh table in the LoCoH-xy object: |
beep |
Whether to beep when done. T/F |
status |
Display status messages. T/F |
When s=0, nearest neighbors are space-selected (i.e., point-to-point distance is merely Euclidean distance). For large values of s, nearest neighbors are effectively time-selected (e.g., temporally contiguous). One approach to selecting a value of s between these two ends of the spectrum is to pick a s value that returns an intermediate proportion of time-selected-hulls representing the desired balance between space and time selection (which in turn is shaped by the research question / objective). This function will find the value(s) of s that produce a desired proportion of time-selected-hulls using a randomly-selected subset of points. A general rule of thumb is to pick a value of s that results in a proportion of time-selected hulls from 0.4 to 0.6.
The script iteratively tries a variety of s values until it finds one that produces the desired
proportion of time-selected hulls within a tolerance of ptsh.buf
. If for example the vector of target
values ptsh.target
includes 0.5, and ptsh.buf = 0.01
, the script will try to find a
value of s that results in a proportion of time-selected hulls between 0.49 and 0.51.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.