sample_quadrats: Plot-based samples from a spatially-explicit census

In mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

Plot-based samples from a spatially-explicit census

Description

This function allows to sample quadratic subplots from a spatially-explicit community. The output format are a sites x species abundance table and a sites x xy-coordinates table. The sites x species abundance is a classical data format used in community ecology. The table generated can be for instance be further analysed with the package vegan.

Usage

sample_quadrats(
  comm,
  n_quadrats = 20,
  quadrat_area = 0.01,
  plot = TRUE,
  method = "random",
  avoid_overlap = TRUE,
  x0 = 0,
  y0 = 0,
  delta_x = 0.1,
  delta_y = 0.1,
  seed = NULL
)

Arguments

comm	Community object from which the samples are generated
n_quadrats	(integer) Number of sampling quadrats
quadrat_area	(numeric) Area of the sampling quadrats
plot	(logical) Should the sampling design be plotted? default to TRUE.
method	(character) Available methods are "random", "transect", "grid"
avoid_overlap	(logical) For the random sampling try to generate a design without overlap of quadrats . Default is TRUE.
x0, y0	(numeric value) Lower left corner of the first quadrat in transect and grid sampling
delta_x	(numeric value) Distance between consecutive quadrats in transect and grid sampling in x-direction (the distance between the left sides is measured)
delta_y	(numeric value) Distance between consecutive quadrats in transect and grid sampling in y-direction (the distance between the lower sides is measured)
seed	(integer) Any integer passed to set.seed for reproducibility.

Value

A list with two items, spec_dat and xy_dat. spec_dat is a data.frame with sampling quadrats in rows and species abundances in columns, and xy_dat is a data.frame with sampling quadrats in rows and the xy-coordinates of the quadrats (lower left corner) in columns.

Examples

library(vegan)
sim_com1 <- sim_poisson_community(100, 10000)
comm_mat1 <- sample_quadrats(sim_com1, n_quadrats = 100,
quadrat_area = 0.002, method = "grid")
specnumber(comm_mat1$spec_dat)
diversity(comm_mat1$spec_dat, index = "shannon")

mobsim documentation built on May 29, 2024, 8:15 a.m.