reef: Calculate the whole-reef community value for a given light...

In Jack-H-Laverick/MCE: Modelling Community Transitions Across Coral Reef Depth Gradients

Description

This function returns the community value for the whole reef community at a light level, given shallow and mesophotic community light relationships.

Usage

reef(
  light = seq(0.01, 1, length = 500),
  Vm = 0.393,
  K = 13.5,
  a = 1.54,
  b = 8.92
)

Arguments

light	The proportion of surface irradiance (PAR), between 0 and 1.
Vm	Passed to shallow. The maximum similarity of a reef patch to the idealised shallow reef community, between 0 and 1. Defaults to (Tamir et al., 2019).
K	Passed to shallow. The light value where the community value = Vmax/2, between 0 and 100. Defaults to (Tamir et al., 2019). This can be interpreted as the light level at which shallow reef communities become light limited.
a	Passed to mesophotic. The scale parameter of a Weibull distribution, defaults to (Tamir et al., 2019). a describes the spread of the data, or ‘the peakyness’. Larger numbers create a flatter, wider, curve. Varying a will simultaneously change the width of the preferred light environment of mesophotic taxa, and the maximum similarity a reef patch is expected to achieve in comparison to the idealised mesophotic community.
b	Passed to mesophotic. The shape parameter of a Weibull distribution, defaults to (Tamir et al., 2019). A value of 3 approximates a normal distribution. Values larger than 3 introduce a left-skew to the curve. This means mesophotic taxa can be light-limited, while keeping mesophotic communities in low-light environments. Varying b shifts the preferred light environment of mesophotic communities.

Details

The function assumes a tradeoff, where an observed patch of reef can approach a mesophotic or shallow community. A patch of reef cannot simultaneously look like the exemplar mesophotic and shallow reef patch. This is achieved by subtracting the shallow community value from the mesophotic community value.

Essentially this function is a wrapper for mesophotic() - shallow(), but it is neccessary for use in boundary when calculating the light level the communities switch at.

Value

A reef wide community indicator value. This is the basis of the model presented in (Laverick et al., 2020). When a single light value is provided, a single value is returned. You can pass a vector of light levels for a vector of depths.

References

(Tamir et al., 2019)

(Laverick et al., 2020)

See Also

shallow

mesophotic

Other Zonation functions: reef_boundary()

Examples

# Specifying a single light value
# returns a single community value.

   reef(light = 10)


# Specifying a vector of light values
# returns a vector of community values.

   reef(light = seq(0.0065, 1, length = 500))


# By default the function uses the shallow and mesophotic
# community light relationships from (Tamir et al., 2019)
# for a range of light values.

   reef()


# You can specify your own community light relationships
# by setting parameters explicitly

   reef(Vm = 0.2, K = 11, a = 1.2, b = 8)

Jack-H-Laverick/MCE documentation built on May 9, 2020, 3:58 p.m.