# growth.pp: Limitation Growth primary producers In Atlantis-Ecosystem-Model/ReactiveAtlantis: Multiple Reactive HTML tools to help in the calibration of the Atlantis ecosystem model (AEM)

## Description

This function helps you visualize what are the possible factors that limit the growth of primary producers. Primary producers in Atlantis are limited in their biomass by variables such as: nutrients, light, space, and by processes such as acidification and the presence of eddies (Audijyontze et al. 2017). In this function, most of these factors are analyzed, except for the acidification process and the spatial limitation.

• Nutrient limitation: The nutrients limitation scalar (δ_{nutrients}) in the case of species limited only by nitrogen is calculated as:

δ_{nutrients} = \frac{DIN}{KN + DIN}

were DIN is the concentration of NH_{3} + NO_{3} and KN is the half-saturation constant of nutrient uptake.
For species that are limited for multiple nutrients like diatoms that can be limited by silicate Si and nitrogen you have 3 different options to choose on Atlantis (flagnut) and the nutrient limitation can have different options:

• Leibig limitation flagnut = 0

δ_{nutrients} = min(\frac{DIN}{KN + DIN}, \frac{Si}{KS + Si})

• multiplicative limitation flagnut = 1

δ_{nutrients} = √{\frac{DIN}{KN + DIN} * \frac{Si}{KS + Si}}

• ERSEM WQI limitation flagnut = 2

δ_{nutrients} = \frac{2}{\frac{DIN}{KN + DIN} * \frac{Si}{KS + Si}}

were KS is the growth half-saturation constant for the functional group.

• Light limitation: In Atlantis photosynthesis in primary producers can be limited by light. The light limitation factor δ_{light} is calculated by:

δ_{light} = min(\frac{IRR}{KI}, 1)

were IRR is irradiance or available light andKI is the light saturation coefficient.
In Atlantis there is a second option flaglight = 1 that allows the calculation of the light limitation factor allowing for light adaptation. This is intended to capture the ability of the primary producers to rapidly adapt to different light conditions (Audijyontze et al. 2017). This option was not considered in this version of the tool but would be implemented in future updates.

• Effect of eddies on primary production: The eddy effect on primary produces δ_{eddy} is calculated by multiplying the scale parameter eddy_{scale} (eddy_scale on Atlantis) by the eddy strength eddy_{strength}.

δ_{eddy} = eddy_{scale} * eddy_{strength}

## Usage

 1 growth.pp(ini.nc.file, grp.file, prm.file, out.nc.file) 

## Arguments

 ini.nc.file Character string with the path to the netcdf file to read in. This netcdf file contains the initial conditions for the Atlantis model usually ends in .nc. grp.file Character string with the path to the Groups *.csv file (Atlantis input file). prm.file Character string with the path to the biology parameter file *.prm. out.nc.file Character string with the path to the netcdf file to read in. This netcdf file is a generic output from an Atlantis run and usually starts with output and ends in .nc.

## Value

A reactive HTML with graphical output by functional group, for layer and box of the following variables:

• Growth: This variable is the Primary producer growth (G_{pp}) which is determined by the biomass for the primary producer (Biom_{pp}), the maximum effective growth (mum) and the limiting factors: Light limitation (δ_{light}), Nutrients limitation δ_{nutrients}, and Eddy scalar (δ_{eddy}).

G_{pp} = Biom_{pp} * mum * δ_{light} * δ_{nutrients} * δ_{eddy}

• Light limitation: The available light by box and layer. This option uses only the basic formula (δ_{light}, described before) and currently does not use the light adaptation option. The light attenuation values used for the calculations are the values estimated by Atlantis and reported in the out.nc.file.

• Nutrient limitation: Nutrient limitation is calculated by layer and by box, using the option chosen by the user in the Atlantis run (flagnut = 0, 1 or 2).

• Eddy scalar: This value is calculated by functional group and by box. The values of eddies strength (eddy_{strength}) used are from the Atlantis output and the value of eddy scale (eddy_{scale}) is read from the Atlantis configuration file.

## Author(s)

Demiurgo

Atlantis-Ecosystem-Model/ReactiveAtlantis documentation built on Dec. 7, 2018, 7:59 a.m.