accum_sp: Spatial Accumulation of Diversity

In divent: Entropy Partitioning to Measure Diversity

Spatial Accumulation of Diversity

Description

A spatial accumulation is a measure of diversity with respect to the distance from individuals.

Usage

## S3 method for class 'accum_sp'
plot(
  x,
  ...,
  q = dimnames(x$accumulation)$q[1],
  type = "l",
  main = "accumulation of ...",
  xlab = "Sample size...",
  ylab = "Diversity...",
  ylim = NULL,
  show_h0 = TRUE,
  line_width = 2,
  col_shade = "grey75",
  col_border = "red"
)

## S3 method for class 'accum_sp'
autoplot(
  object,
  ...,
  q = dimnames(object$accumulation)$q[1],
  main = "Accumulation of ...",
  xlab = "Sample size...",
  ylab = "Diversity...",
  ylim = NULL,
  show_h0 = TRUE,
  col_shade = "grey75",
  col_border = "red"
)

plot_map(
  accum,
  q = as.numeric(dimnames(accum$accumulation)$q[1]),
  neighborhood = as.numeric(dplyr::last(colnames(accum$neighborhoods))),
  sigma = spatstat.explore::bw.scott(accum$X, isotropic = TRUE),
  allow_jitter = TRUE,
  weighted = FALSE,
  adjust = 1,
  dim_x = 128,
  dim_y = 128,
  main = "",
  col = grDevices::terrain.colors(256),
  contour = TRUE,
  contour_levels = 10,
  contour_col = "dark red",
  points = FALSE,
  pch = 20,
  point_col = "black",
  suppress_margins = TRUE,
  ...,
  check_arguments = TRUE
)

Arguments

x	an accum_sp object.
...	Additional arguments to be passed to plot, or, in plot_map(), to spatstat.explore::bw.smoothppp and spatstat.explore::density.ppp to control the kernel smoothing and to spatstat.geom::plot.im to plot the image.
q	a number: the order of diversity.
type	plotting parameter. Default is "l".
main	main title of the plot.
xlab	X-axis label.
ylab	Y-axis label.
ylim	limits of the Y-axis, as a vector of two numeric values.
show_h0	if TRUE, the values of the null hypothesis are plotted.
line_width	width of the Diversity Accumulation Curve line.
col_shade	The color of the shaded confidence envelope.
col_border	The color of the borders of the confidence envelope.
object	an accum_sp object.
accum	an object to map.
neighborhood	The neighborhood size, i.e. the number of neighbors or the distance to consider.
sigma	the smoothing bandwidth. The standard deviation of the isotropic smoothing kernel. Either a numerical value, or a function that computes an appropriate value of sigma.
allow_jitter	if TRUE, duplicated points are jittered to avoid their elimination by the smoothing procedure.
weighted	if TRUE, the weight of the points is used by the smoothing procedure.
adjust	force the automatically selected bandwidth to be multiplied by adjust. Setting it to values lower than one (1/2 for example) will sharpen the estimation.
dim_x	the number of columns (pixels) of the resulting map, 128 by default.
dim_y	the number of rows (pixels) of the resulting map, 128 by default.
col	the colors of the map. See spatstat.geom::plot.im for details.
contour	if TRUE, contours are added to the map.
contour_levels	the number of levels of contours.
contour_col	the color of the contour lines.
points	if TRUE, the points that brought the data are added to the map.
pch	the symbol used to represent points.
point_col	the color of the points. Standard base graphic arguments such as main can be used.
suppress_margins	if TRUE, the map has reduced margins.
check_arguments	if TRUE, the function arguments are verified. Should be set to FALSE to save time when the arguments have been checked elsewhere.

Details

Objects of class accum_sp contain the value of diversity (accum_sp_diversity objects), entropy (accum_sp_entropy objects) or mixing (accum_sp_mixing objects) at distances from the individuals.

These objects are lists:

• X contains the dbmss::wmppp point pattern,

• accumulation is a 3-dimensional array, with orders of diveristy in rows, neighborhood size (number of points or distance) in columns and a single slice for the observed entropy, diversity or mixing.

• neighborhoods is a similar 3-dimensional array with one slice per point of X.

They can be plotted or mapped.

Value

plot.accum_sp() returns NULL.

autoplot.accum_sp() returns a ggplot2::ggplot object.

plot_map returns a spatstat.geom::im object that can be used to produce alternative maps.

Examples

# Generate a random community
X <- rspcommunity(1, size = 50, species_number = 10)
# Calculate the species accumulation curve
accum <- accum_sp_hill(X, orders = 0, r = c(0, 0.2), individual = TRUE)
# Plot the local richness at distance = 0.2
plot_map(accum, q = 0, neighborhood = 0.2)

divent documentation built on April 3, 2025, 7:40 p.m.