depth: Calculate the depth of a light level

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

Description

This function uses the Lamberte-Beere law to predict the depth in metres a given proportion of surface Photosynthetically Active Radiation (PAR) penetrates to.

Usage

depth(light = seq(0.01, 1, length = 500), KdPAR = 0.05, shade = 1)

Arguments

light	The proportion of surface irradiance (PAR), between 0 and 1. Defaults to a vector of light values.
KdPAR	The average light attenuation coefficient of the water column above the reef. Defaults to 0.05.
shade	Additional shading at the seafloor, such as bathymetric effects, between 0 (no light available) and 1 (all light available). Defaults to 1 (all light available).

Details

The function takes the average light attenuation coefficient (KdPAR) of the water column above a reef and a proportion between 0 and 1 of surface PAR. The Lamberte-Beer law is then used to predict the depth in metres this light environment occurs at.

A shading parameter can be used to scale how much of the light which reaches the seafloor is available to the benthos. According to (Lesser et al., 2018) the shading effect of reef slope at a vertical wall is to limit surface irradiance to 25% (shade = 0.25). The default behaviour is for there to be no shading (Shade = 1). When shading is more severe, the function will return a shallower depth. This is as the function is predicting the depth you would find your specified light level in the shaded environment.

Leaving shade unspecified makes this function equivalent to the "Depth_function" in (Laverick et al. 2020).

Specifying shading makes this function equivalent to the "Shade_function" in (Laverick et al., 2020).

Value

A depth in metres. 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

Lamberte-Beer law

Lesser

Laverick

Examples

# Specifying a single light value and light
# attenuation returns a single depth.

   depth(light = 0.1, KdPAR = 0.03)


# By defualt there is no shading. You can
# switch this on by passing a value.

   depth(light = 0.1, KdPAR = 0.03, shade = 0.8)


# Specifying a vector of light values and light
# attenuation returns a vector of depths.

   depth(light = seq(0.0065, 1, length = 500), KdPAR = 0.03)

# By default the function uses the reference light
# environment from (Laverick et al., 2020) with no shade.

   depth()

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