sh.init: Shiny application for viewing Atlantis initialisation data
In shanearichards/shinyrAtlantis: Make Atlantis Shiny

sh.init

R Documentation

Shiny application for viewing Atlantis initialisation data

Description

Takes data from a .bgm box geometry file and a netCDF Atlantis input parameter file and provides a visualisation of the data in the form of a shiny application. The two data files must first be pre-processed by make.sh.init.object, which generates a list object that is the parameter to sh.init (see Examples).

The Habitat tab displays the number of water layers and the habitat cover for each box. Use this tab to check that reef + flat + soft cover sum to 1 for the interior boxes.

The Abiotic (2D) and Abiotic (3D) tabs display benthic and pelagic abiotic variables.

The Biotic (2D) and Biotic (3D) tabs display benthic and pelagic biotic variables.

The Nitrogen tab displays the initial nitrogen content of biotic groups that are modelled using cohorts.

Usage

sh.init(input.object)

Arguments

input.object

R list object generated from make.sh.init.object.

Value

Object of class 'shiny.appobj' see shinyApp.

Examples

## Not run: 
bgm.file <- "VMPA_setas.bgm"
nc.file  <- "INIT_VMPA_Jan2015.nc"
input.object <- make.sh.init.object(bgm.file, nc.file)
sh.init(input.object)

## End(Not run)

shanearichards/shinyrAtlantis documentation built on April 10, 2024, 7:19 a.m.