atlantis_dietextract: Extract availability matrix from biological parameters file

In rgirardi/atlantisfmsy: Estimation of a functional group's Fmsy in Atlantis ecosystem model

Extract availability matrix from biological parameters file

Description

Extract diet from Biological parameters file and save it if wanted into a readable csv file.

Usage

atlantis_dietextract(path, exe_name, save.out = F, output_path = NULL)

Arguments

path	The directory of the batch or shell file.
exe_name	The name of the atlantis executable you used (ex: atlantismain, atlantisNew).
save.out	Flag that indicate if you want to save the output or not. If TRUE, output_path need to be provided. (Default value is FALSE).
output_path	The directory were you want to save the csv file (Default value is NULL).

Value

availability Dataframe containing input availability matrix from the biological parameters file.

See Also

atlantis_paraselect for parameters file selection, atlantis_openfile to open a parameters file and select a parameter, str_split_fixed to split a chain of characters, read.table to open table stored in text files (.txt, .csv ...).

Examples

  atlantis_dietextract("C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantismain")
  atlantis_dietextract("/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantisNew")
  atlantis_dietextract("C:/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantismain", save.out = T, output_path =
                    "C:/Atlantis/AtlantisEEC/AtlantisMSY/COD/output")
  atlantis_dietextract("/home/Atlantis/AtlantisEEC/AtlantisMSY/COD",
                    "atlantisNew", save.out = T, output_path =
                    "/home/Atlantis/AtlantisEEC/AtlantisMSY/COD/output")

rgirardi/atlantisfmsy documentation built on Aug. 30, 2022, 9:11 a.m.