growth.pp | R Documentation |
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
(\delta_{nutrients}
) in the case of species limited only by nitrogen is
calculated as:
\delta_{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
\delta_{nutrients} = min(\frac{DIN}{KN + DIN}, \frac{Si}{KS + Si})
multiplicative limitation flagnut = 1
\delta_{nutrients} = \sqrt{\frac{DIN}{KN + DIN} * \frac{Si}{KS + Si}}
ERSEM WQI limitation flagnut = 2
\delta_{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 \delta_{light}
is calculated by:
\delta_{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 \delta_{eddy}
is calculated by multiplying the scale parameter eddy_{scale}
(eddy_scale on Atlantis) by the eddy strength eddy_{strength}
.
\delta_{eddy} = eddy_{scale} * eddy_{strength}
growth.pp(ini.nc.file, grp.file, prm.file, out.nc.file)
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. |
A shiny::reactive shiny::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 (\delta_{light}
),
Nutrients limitation \delta_{nutrients}
, and Eddy scalar (\delta_{eddy}
).
G_{pp} = Biom_{pp} * mum * \delta_{light} * \delta_{nutrients} *
\delta_{eddy}
Light limitation: The available light by box and layer. This option
uses only the basic formula (\delta_{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.
Demiurgo
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