lhs.to.stats: Computes statistics on the centroid distances for...
In tlocoh.dev: Development package for tlocoh

Description Usage Arguments Details Value See Also

Computes statistics on the hull-to-hull centroid distance for time-overlapped hulls, with an option to plot and overlay the distribution of centroid distances for random pairs of hulls

lhs.to.stats(lhs, id1 = "all", id2 = "all", n = "all", iso.lower = NULL,
  iso.upper = NULL, iso.oz = TRUE, iso.sort.metric = "auto",
  to.comp.hist = TRUE, breaks = 20, to.mcd.outline.only = FALSE,
  lwd.outline = 3, hist.type = c("density", "counts")[1],
  col.to.mcd = "blue", col.h2h.cd = "red", title = NULL,
  title.show = TRUE, title.id.only = FALSE, title.sub.iso.enc = TRUE,
  mar = c(3, 3, if (title.show) 1.5 + (if (title.sub.iso.enc) 1.3 else 0) else
  0.5, 0.5), mgp = c(1.8, 0.5, 0), figs.per.page = 1, panel.num = NULL,
  panel.num.inside.plot = !title.show, png.dir = NULL,
  png.dir.make = TRUE, png.width = 800, png.height = png.width,
  png.overwrite = TRUE, png.pointsize = 12 + (png.width - 480)/80,
  status = TRUE, ...)

`lhs`	A LoCoH-hullset object
`id1`	Hullset 1 id value(s). Can also be `'all'`.
`id2`	Hullset 2 id value(s). Can also be `'all'`.
`n`	The number of randomly selected paired hulls to use as the NULL model of no association. Can also be "all"
`iso.lower`	The lower level isopleth for the isopleth filter
`iso.upper`	The upper level isopleth for the isopleth filter
`iso.oz`	Apply isopleth filter to hs1 using the isopleths from hs2. T/F.
`iso.sort.metric`	The name of a hull metric that was used to sort hulls in the construction of the isopleths to be used as filters. If `auto` (default) it will pick the default sort metric used for density isopleths (i.e., area for the k-method, and number of enclosed points for the a and r methods)
`to.comp.hist`	Draw a histogram of the centroid distances of temporally overlapping hulls
`breaks`	The number of breaks in the histgram (or another valid value for breaks, see `hist`).
`to.mcd.outline.only`	Show the outline only of the histogram of the mean centroid distance for temporally overlapping hulls. T/F.
`lwd.outline`	The line width of the histogram outline (ignored if `to.mcd.outline.only=F`).
`hist.type`	The type of histogram to plot: 'density' or 'counts'.
`col.to.mcd`	The color of the outline of the histogram of the distribution of the centroid distances of temporally overlapping hulls.
`col.h2h.cd`	The color of the outline of the histogram of the distribution of the centroid distances for randomly paired hulls.
`title`	The title to be displayed. Character. If NULL a title will be constructed.
`title.show`	Whether to show the title. T/F.
`title.id.only`	Whether to construct the title from the id values only. T/F. Ignored if `title` is passed or `title.show=FALSE`
`title.sub.iso.enc`	Whether to include the isopleth filter information as the second line of the title, T/F.
`mar`	The plot margins. A four item numeric vector
`mgp`	The distance away from the edge of the plot for the 1) label, 2) tick marks, and 3) axis line. A three-item numeric vector
`figs.per.page`	The number of plots per page.
`panel.num`	A number or letter to display in the upper left hand corner of the plot when the plot will be used as part of a multi-frame graphic (as in publications). Character
`panel.num.inside.plot`	Whether to display panel.num inside the plot area itself, as opposed to the title area. T/F
`png.dir`	The directory for a PNG file (filename will be constructed automatically). Ignored if png.fn is passed
`png.dir.make`	Whether to create png.dir if it doesn't exist. T/F
`png.width`	The width of the PNG image
`png.height`	The height of the PNG image
`png.overwrite`	Whether to overwrite an existing PNG file if it exists. T/F
`png.pointsize`	The pointsize (in pixels) for the PNG image, equivalent to the height or width of a character in pixels (increase to make labels appear larger)
`status`	Display status messages. T/F
`...`	Additional parameters that will be passed to the `plot` function

This returns a list object containing the centroid-to-centroid distances of a random selection of hulls from two individuals, which serves as a NULL model of no interaction. It can also plot the histogram of mean-centroid-distance of time-overlapped hulls with the outline of the centroid distance of random-pairs of hulls overlain on top, to visually see how close the distributions match.

It will also compute the Welch Two Sample t-test to see if the distribution for time-overlapped and randomly paired hulls have statistically significant means, and the Two-sample Kolmogorov-Smirnov test which tells you how likely the two distributions are the same.

Note that before you can use this function, the mean-centroid-distance for time-overlapped hulls must be computed using lhs.to.add

You can apply an isopleth filter by passing values for iso.lower and iso.upper. These should be the isopleth level (normally between 0 and 1) that the hull parent point must fall in to be included in the analysis. If, for example, you wanted to see whether association in the core area is significantly different from nuetral interaction, you would pass iso.upper=0.5 and leave iso.lower NULL. Note that the isopleths with matching isopleth levels must already be present.

A list object

lhs.to.add, lhs.iso.add

tlocoh.dev documentation built on May 2, 2019, 5:20 p.m.