sloss: Calculation of SLOSS-Curves and -Index

In kamapu/Lexiguel: Miscellaneous Functions

Calculation of SLOSS-Curves and -Index

Description

Calculation of SLOSS curves and SLOSS index according to Quinn & Harrison (1988).

This function uses a vegetation matrix with presence or abundance of species in units (units as rows and species as columns). If table is a data frame, it will be coerced to a matrix.

If area provided as a vector, then env is not necessary. This function assumes that the sorting of units in area (or in env) is the same as the sorting in table.

This function also calculates the SLOSS-index as the ratio of surfaces below the SLOSS-curves (small to large divided by large to small), following Quinn & Harrison (1988) and Vargas et al. (2013).

The function curve_area() calculates the area below a curve by the trapezoidal rule.

The argument bottom can be adjusted to the minimum observed values an will be particularly useful when values of y are negative.

Curves going bellow the bottom value will get a negative value of area and therefore subtracted when y cuts the bottom value.

This function was originally written as internal function for the calculations done by sloss.

Usage

sloss(table, env = data.frame(), area)

curve_area(x, y, bottom = 0)

Arguments

table	A matrix or data frame with the species abundance in units.
env	A data frame containing the units' sizes (e.g. as surface).
area	Symbol, vector or character value indicating the size of units.
x	A numerical vector with the ordinate values.
y	A numerical vector with the abscissa values.
bottom	A numerical value indicating the bottom for area calculation. It can be adjusted to the minimum observed values an will be particularly useful when values of y are negative.

Value

sloss() returns an object of class SLOSS, which is a list with following elements:

SL

two vectors (area and species), showing the cumulative increase on species versus cumulative area accounting from smallest to largest unit.

LS

two vectors (area and species), showing the cumulative increase on species versus cumulative area accounting from largest to smallest unit.

Index

Numeric value with the calculated SLOSS-index.

Author(s)

Miguel Alvarez ([e-mail]).

References

Quinn JF, Harrison SP (1988). Effects on habitat fragmentation and isolation on species richness: Evidence from biogeographic patterns. Oecologia 75: 132-140.

Vargas RI, Gärtner S, Alvarez M, Hagen E, Reif A (2013). Does restoration help the conservation of the threatened forest of Robinson Crusoe Island? The impact of forest gap attributes on endemic plant species richness and exotic invasions. Biodiversity and Conservation 22: 1283-1300.

See Also

plot.SLOSS().

Examples

## Load gaps from the Robinson Crusoe Island
data(rc_gaps)
data(rc_gaps.env)

## Calculation of curves
rc_curves <- sloss(rc_gaps, rc_gaps.env, area)

## Plot the curves
plot(rc_curves, show.legend = TRUE)

## Calculation of curves
rc_curves <- sloss(rc_gaps, rc_gaps.env, area)

## Area calculated by function
rc_curves$Index

## Cross-check
with(rc_curves$SL, curve_area(area, species)) / with(
  rc_curves$LS,
  curve_area(area, species)
)

kamapu/Lexiguel documentation built on May 14, 2024, 9:14 a.m.