shallow: Calculate the shallow community value for a given light level

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

Description

This function captures the preferred light environment of the "shallow" coral community.

Usage

shallow(light = seq(0.01, 100, length = 500), Vm = 0.393, K = 13.5)

Arguments

light	The percentage of surface irradiance (PAR) reaching a reef, positive and up to 100%.
Vm	The maximum similarity of a reef patch to the idealised shallow reef community, between 0 and 1. Defaults to (Tamir et al., 2019).
K	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.

Details

A Michaelis-Menten equation is used to represent the relationship between shallow coral communities and light. We assume shallow corals are light-limited beneath a light threshold, and that community values (how similar a reef patch is to the idealised shallow community) increase asymptotically with increasing light.

This relationship has been verified in the Red Sea (Tamir et al., 2019), but certainly needs more research!

Value

A shallow community indicator value, as discussed in (Laverick et al., 2017). 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., 2017)

See Also

Other Community relationships: mesophotic()

Examples

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

   shallow(light = 10)


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

   shallow(light = seq(0.0065, 100, length = 500))


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

   shallow()


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

   shallow(Vm = 0.2, K = 11)

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