comspat_plot: Within-Community Spatial Organization Plot

In jamestsakalos/ComSpat: Analysis of Within-Community Spatial Organization using Species Combinations

Within-Community Spatial Organization Plot

Description

The 'comspat_plot()' function makes use of core R graphics systems to display relationship between the Information Theory metrics (i.e. CD, NRC, etc.) and the length (default) or area of the sampling units. The 'comspat_plot()' does not calculate the Information Theory metrics, but it accepts results from the ['comspat()'] function.

Usage

comspat_plot(
  data = NULL,
  params = NULL,
  type = NULL,
  measure = NULL,
  su_size = NULL,
  unit = "Length",
  ymin = NULL,
  ymax = NULL,
  xmin = 0.01,
  xmax = 100,
  p_col = "black",
  p_cex = 0.75,
  cex_axis = 1,
  xaxt = TRUE,
  yaxt = TRUE,
  stats_output = FALSE,
  ci_type = NULL
)

Arguments

data	list of data frames or statistical output returned from comspat.
params	Data frame providing the secondary sampling information.
type	Character. Supply either '"Grid"' or '"Transect"'.
measure	Character. Supply one of '"CD"', '"NRC"', '"AS"'.
su_size	Numeric. Surface area of the smallest sampling unit (mm sq.).
unit	Character. Supply either '"Length"' or '"Area"'.
ymin	Numeric. Y axis lower limit.
ymax	Numeric. Y axis upper limit.
xmin	Numeric. Minimum x axis value (i.e. lower range).
xmax	Numeric. Maximum x axis value (i.e. upper range).
p_col	list of colors. Single or a vector matching data length.
p_cex	Numeric.
cex_axis	Numeric.
xaxt	TRUE or FALSE. Controls if x-axis text is displayed.
yaxt	TRUE or FALSE. Controls if y-axis text is displayed.
stats_output	'TRUE' or 'FALSE'. Controls if confidence intervals display.
ci_type	'"l"' or '"py"'. Confidence interval as line or polygon.

Details

'comspat_plot()' constructs the initial plot object. It has the functionality to return single or multiple outputs. When multiple outputs are returned the data must be supplied as a list; a single measure for each of the data frames will be added to the same plot. Confidence intervals generated from the use of null models (i.e. CSR and RS randomizations) can be added as lines or polygons (see the '"ci_type"' argument).

This function and makes use of core R graphics systems to explore the outputs of 'comspat_plot()'.

Value

The function does not return a value, rather it returns a plot object to assist users in interpreting the results.

Author(s)

James L. Tsakalos

See Also

The main ['comspat()'] function.

Examples

# Load the training data and parameter files
data("grid_random", library = "comspat")
data("param_grid", library = "comspat")

# Perform comspat calculations
temp_rand <- comspat(
  grid_random,
  param_grid[1:2, ],
  64,
  "Grid"
)

# Plot comspat results
comspat_plot(
  list(temp_rand),
  param_grid[1:2, ],
  "Grid",
  measure = "NRC",
  su_size = 0.01,
  ymin = 0,
  ymax = 65,
  p_col = list("red")
)

# Hint - several measures can be combined using par() commands

jamestsakalos/ComSpat documentation built on July 1, 2023, 3:52 p.m.