load_nc_annage: Load Atlantis annual age outputfiles (netcdf)
In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

load_nc_annage

R Documentation

Load Atlantis annual age outputfiles (netcdf)

Description

This function loads Atlantis ANNAGEBIO and ANNAGECATCH outputfiles (netcdf) and converts them to a data.frame.

Usage

load_nc_annage(
  dir = getwd(),
  file_nc,
  file_fish,
  bps,
  fgs,
  biolprm,
  select_groups,
  select_variable = c("Nums", "Weight", "Catch", "Discard"),
  check_acronyms = TRUE,
  bboxes = c(0),
  verbose = FALSE
)

Arguments

`dir`	The directory of the atlantis model output, where the default is `getwd()`.
`file_nc`	A character value giving the file name of the netcdf file you are trying to read in. The file should be located in your current working directory or the folder you specify in `dir`. The argument can also be specified as the full path name, just as long as argument `dir` is specified as `NULL`.
`bps`	A character vector of biomass pools as read in from `load_bps`. The biomass pools are not true biomass pools but all epibenthic groups from the functional groups file.
`fgs`	A data frame created by `load_fgs` that reads in the csv file containing functional group names, usually `"functionalGroups.csv"`.
`biolprm`	A list of biological parameters available from the `[...]_Biol.prm` file, as read in by `load_biolprm`.
`select_groups`	Character vector of funtional groups to select. Names have to match the ones used in the ncdf file, and therefore must be in the column `"Name"` in the `fgs`.
`select_variable`	A character value spefifying which variable to return. loaded. Only one variable of the options available (i.e., `c( "Nums", "Weight")`) can be loaded at a time.
`check_acronyms`	A logical, specifying if selected groups are active in the model run. This is used in automated runs. All groups are passed when plotting is called via batch-file, (which cannot be changed easily) this will result in errors if some groups are not active in the model run. By default this argument is `TRUE`.
`bboxes`	A vector of boundary boxes. The default value is `c(0)` because all Atlantis models must specify box zero as a boundary box. The boundary boxes can automatically be determined using `get_boundary(load_box())`.
`verbose`	A logical value specifying if output should be written to the screen or not. The default value is `FALSE`.

Value

A data.frame in long format with the following coumn names: Species, timestep, polygon, agecl, and atoutput (i.e., variable).

Author(s)

Alexander Keth, modified by Sarah Gaichas

Other load functions: load_agebioind(), load_bioind(), load_biolprm(), load_boxarea(), load_box(), load_bps(), load_catch(), load_detailed_diet_comp(), load_diet_comp(), load_fgs(), load_fisheries(), load_meta(), load_nc_catchtons(), load_nc(), load_runprm(), load_yoy()