hist.locoh.lhs: Plot histograms of hull metrics

Description Usage Arguments Value Note

Description

Plot histograms of hull metrics

Usage

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## S3 method for class 'locoh.lhs'
hist(x, lhs, id = NULL, k = NULL, r = NULL,
  a = NULL, s = NULL, hs.names = NULL, metric = "area",
  include.missing.hulls = TRUE, hmap = NULL, hmap.in.title = TRUE,
  hs.name.in.title = TRUE, title = NULL, title.show = TRUE,
  figs.per.page = NULL, mar = c(3, 3, if (title.show) 2.8 else 0.7,
  0.5), mgp = c(1.8, 0.5, 0), same.axes.for.all = FALSE, ufat = TRUE,
  breaks = "Sturges", col = "gray80", lo.margins.set, lo.save = TRUE,
  png.dir = NULL, png.dir.make = TRUE, png.width = 800,
  png.height = png.width, png.overwrite = TRUE, png.pointsize = 12 +
  (png.width - 480)/80, title.two.id = FALSE,
  indicate.missing.hulls.in.axis.lbl = TRUE, panel.num = NULL,
  panel.num.inside.plot = !title.show, ...)

Arguments

x

A LoCoH-hullset object

lhs

Deprecated, use x instead

id

The names of the individual(s) to include in the plot.

k

The k value(s) of the hullset(s) to include in the plot. Numeric vector or comma-delimited character object.

r

The r value(s) of the hullset(s) to include in the plot. Numeric vector or comma-delimited character object.

a

The a value(s) of the hullset(s) to include in the plot. Numeric vector or comma-delimited character object.

s

The s value(s) of the hullset(s) to include in the plot. Numeric vector or comma-delimited character object.

hs.names

The name(s) of saved hullsets to include in the plot

metric

The name(s) of hull metric(s); one histogram will be created for each hull metric.

include.missing.hulls

Whether to include missing hulls on the histogram (using the default value assigned to missing hulls by the hull metrics). T/F

hmap

A named list of hull metric auxillary parameters, the name of each list element is the name of the variable.

hmap.in.title

Include the hmap value(s) in the plot subtitle. T/F

hs.name.in.title

Include the name of the hullset in the plot subtitle. T/F

title

A title for the plot (over-writes the construction of a title)

title.show

Whether to add a title on the plot. T/F

figs.per.page

Number of plots per page

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

same.axes.for.all

Whether to use the same range on the axes for all histograms generated (helps to visually see differences)

ufat

User-friendly axis title. T/F

breaks

Number of breaks or a clustring function. See hist.

col

Color value for the bars

lo.margins.set

Deprecated, use lo.save instead

lo.save

Whether to set the plot device options (margins, rows and columns). T/F.

png.dir

The directory for a PNG file (filename will be constructed automatically).

png.dir.make

Whether to create png.dir if it doesn't exist. T/F

png.width

The width of the PNG image. Ignored if png.fn is passed.

png.height

The height of the PNG image. Ignored if png.fn is passed.

png.overwrite

Whether to overwrite an existing PNG file if it exists. T/F

png.pointsize

The pointsize (in pixels) for the PNG image (increase to make labels appear larger). Determines the height or width of a character in pixels.

title.two.id

Construct a title with the names of two ids (for so.* and to.* assocation metrics). T/F

indicate.missing.hulls.in.axis.lbl

Specify whether missing hulls are excluded in the axes label, T/F

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. Ignored if panel.num is NULL. T/F

...

Other parameters, including any auxillary parameters to specify particular hull metrics

Value

A named list of values of the hull metrics. There is one list element for each metric.

Note

To see the names of hull metrics, type hm.expr(). Only hull metrics which have been computed can be plotted.


tlocoh documentation built on May 2, 2019, 5:27 p.m.