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Read Atlantis inputs and outputs files

Source: R/read.R
read_atlantis_files.Rd

Functions to read Atlantis inputs and outputs.

Usage

read_atlantis_files(files, filenames = basename(files))

read_bgm(path)

read_nc(path)

read_group_file(path)

read_prm_files(path)

read_txt_files(path, filename)

read_xml(path)

Arguments

files

vector of paths that point to file(s) to read.

filenames

file basenames. This is important for the Shiny app as files uploaded are renamed but the basename remains available.

path

path that points to the file to read.

filename

File basename.

Value

Returns an object of class atlantis_file, which is a list of 3 elements:

  • path: the path to the file;

  • type: the type of input or output;

  • object: the R object used by the Shiny App.

Details

The read_atlantis_files() function implements a file processing pipeline for handling diverse Atlantis ecosystem model file formats. One or several files can be processed at once. Internally, the way files are processed is determined by file extension using a switch statement:

  • .bgm: Box geometry files → [read_bgm()]

  • .nc: NetCDF files → [read_nc()]

  • .prm: Parameter files → [read_prm_files()]

  • .csv: Group definition files → [read_group_file()]

  • .txt: Various output formats → [read_txt_files()] Basic examination of the content is done to determine the type of file and exhaustive validation is carried out if available. Note that unknown file types are marked as "unknown" rather than causing crashes, and unreadable files are marked as "cannot read".

Functions

  • read_bgm(): Read BGM (box geometry) files

  • read_nc(): Read NetCDF files and classify as init or main output

  • read_group_file(): Read CSV group definition files

  • read_prm_files(): Read and classify PRM parameter files

  • read_txt_files(): Read and classify TXT output files. The name of the file is used as a clue to determine the type of files.

  • read_xml(): Read XML files and convert them to lists

Examples

hh <- system.file("examples", "inputs", "tiny_biol.prm", package = "atlantio") |>
  read_atlantis_files()