Simpson_r: Spatially Explicit Simpson's Entropy

In EricMarcon/SpatDiv: Spatially Explicit Measures of Diversity

Spatially Explicit Simpson's Entropy

Description

Simpson's entropy of the neighborhood of individuals, up to a distance \insertCiteShimatani2001SpatDiv.

Usage

Simpson_r(
  spCommunity,
  r = NULL,
  spCorrection = "isotropic",
  CheckArguments = TRUE
)

Simpson_rEnvelope(
  spCommunity,
  r = NULL,
  NumberOfSimulations = 100,
  Alpha = 0.05,
  spCorrection = "isotropic",
  SimulationType = "RandomLabeling",
  Global = FALSE,
  CheckArguments = TRUE
)

Arguments

spCommunity	A spatialized community (A wmppp.object with PointType values as species names.)
r	A vector of distances. If NULL accumulation is along n, else neighbors are accumulated in circles of radius r.
spCorrection	The edge-effect correction to apply when estimating the K function with Kest. Default is "isotropic".
CheckArguments	If TRUE (default), the function arguments are verified. Should be set to FALSE to save time in simulations for example, when the arguments have been checked elsewhere.
NumberOfSimulations	The number of simulations to run, 100 by default.
Alpha	The risk level, 5% by default.
SimulationType	A string describing the null hypothesis to simulate. The null hypothesis may be "RandomPosition": points are drawn in a Poisson process (default); "RandomLabeling": randomizes point types, keeping locations unchanged.
Global	Logical; if TRUE, a global envelope sensu \insertCiteDuranton2005SpatDiv is calculated.

Value

Simpson_r returns an object of class fv, see fv.object. There are methods for print and plot for this class. It contains the value of the spatially explicit Simpson's entropy for each distance in r.

Simpson_rEnvelope returns an envelope object envelope. There are methods for print and plot for this class. It contains the observed value of the function, its average simulated value and the confidence envelope.

References

\insertAllCited

Examples

# Generate a random community
spCommunity <- rSpCommunity(1, size=1000, S=3)
# Calculate the entropy and plot it
autoplot(Simpson_r(spCommunity))

# Generate a random community
spCommunity <- rSpCommunity(1, size=1000, S=3)
# Calculate the entropy and plot it
autoplot(Simpson_rEnvelope(spCommunity, NumberOfSimulations=10))

EricMarcon/SpatDiv documentation built on May 25, 2023, 12:54 p.m.