recruitment.cal: Estimation of Recruitment and primary producer growth

In Atlantis-Ecosystem-Model/ReactiveAtlantis: Multiple Reactive HTML tools to help in the calibration of the Atlantis ecosystem model (AEM)

Estimation of Recruitment and primary producer growth

Description

This function helps to estimate the recruitment for age structured functional groups and the primary and secondary production.

• Recruits and young of the year (YOY): This option shows the parameter values and the recruitment equation for the chosen functional groups (i.e. Ricker or Beverton-holt). Based on the larval survival and the biomass at each reproductive time step the function allows the user to re-calculate the recruitment based on a new set of parameters provided by the user.

• Primary production and light limitation: This option provides a view of the primary production (phytoplankton, seagrass and macroalgae), light and secondary production (zooplankton) by box and layer. This helps to calibrate the growth of primary producers and the consumption of light.

Usage

recruitment.cal(
  ini.nc.file,
  out.nc.file,
  yoy.file,
  grp.file,
  prm.file,
  quiet = TRUE
)

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 and usually ends in .nc.
out.nc.file	Character string with the path to the netcdf file to read in. This netcdf file contains a generic output from an Atlantis run usually starting with output and ending in .nc.
yoy.file	Character string with the path to Young of the Year (YOY) standard output file. Usually the name for this file is : output[YOUR_MODEL]YOY.txt where [YOUR_MODEL] is the name of your Atlantis model.
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 (Atlantis input file).
quiet	(Default = TRUE) this parameter helps during the process of debugging.

Value

The outputs of this function are divided into 3 tabs:

• Recruits and YOY: Shows the recruitment and YOY curves from the Atlantis output for each functional group and provides the option to test different parameter values to obtain new recruitment and YOY curves.

• Growth Zoo and PP's: Allows the user to check the light levels and biomass values for primary producers (PP's) and zooplankton (Zoo) by box and layer. The user has the option to set those values as a proportion by box, proportion by layer, or their logarithmic value.

• Help: Shows information about the inputs, parameter values and output. It also, provides an overview of the different options for the user.

Author(s)

Demiurgo

Atlantis-Ecosystem-Model/ReactiveAtlantis documentation built on April 16, 2024, 6:27 a.m.