compare: Compare Outputs

View source: R/compare.R

compareR Documentation

Compare Outputs

Description

This function allows visualization of either the output from a simulation or comparison between two different Atlantis simulations. The user can compare biomasses, abundance, structural or reserve nitrogen between two different outputs. The user is also able to check the changes is these variables by age for the different functional groups.

Usage

compare(nc.out.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths)

Arguments

nc.out.current

Current netcdf output file. Character string with the path to the netcdf file to read in. This netcdf file contains a generic output from an Atlantis run and usually starts with output and ends in .nc.

nc.out.old

(Default = NULL) This is the character string with the path to the second netcdf output file to read in (used only for comparisons). This netcdf file contains a generic output from an Atlantis run and usually starts with output and ends in .nc.

grp.csv

Character string with the path to the Groups *.csv file (Atlantis input file).

bgm.file

Character string with the path to the XY coordinates Atlantis input file *.bgm with the information in metres.

cum.depths

Cumulative depth of the Atlantis model

Value

A shiny::reactive shiny::HTML that is divided in 3 different panels:

  • Biomass: This panel shows the results for:

    • Total Biomass which displays the changes in total biomass for each functional group.

    • Relative Biomass which displays the variation of the total biomass relative to the initial biomass (B_{0}).

    If only one netcdf file is read in it provides a single output, which expands two sub-panels in the case of comparisons.

  • Total: This function shows the changes in the variables (i.e. Biomass, Numbers and Structural and reserve nitrogen) for the entire population over time. If a second output is provided the function allows comparison of the outputs. In this function the user is able to:

    • Visualize any combination of variables, that allows the user to activate and deactivate variables from the visualization. This provides increased flexibility and comparing between variables.

    • Scaled, this option allows for visualization of the values normalized by the value in the initial conditions (this option is very helpful for checking the main changes in variables during the calibration process).

    • Limit-axis, indicating whether the user desires total or normalized values, this option allows for the y-axis to be unscaled or to set the upper limit for the scaled version(from 0 to 3).

  • By AgeClass: This tab visualizes the changes through time of the variables by age. In this function the user is able to:

    • Visualize any combination of variables, by activating and deactivating variables from the visualization (this provides increased flexibility to explore the changes in the variables and compare between them).

    • Scaled, this option allows for visualization of the values normalised by the value in the initial conditions (this option is very helpful for checking the main changes in variables during the calibration process).

    • Limit-axis which allows the user to set the visualization to either total or scaled values (this option allows the y-axis to be unscaled or to set the limit from 0 to 3 for the normalized version.

Author(s)

Javier Porobic


Atlantis-Ecosystem-Model/ReactiveAtlantis documentation built on Feb. 10, 2023, 2 a.m.