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Create a Zonation command file

Source: R/command_file.R
command_file.Rd

This function generates a command file for running Zonation and specifies the analysis options and related parameters. The file is saved with a .cmd (Windows) or .sh (Linux) suffix.

Usage

command_file(
  os = "os_detection",
  zonation_path,
  flags = "",
  marginal_loss_mode = "CAZ2",
  gui_activated = FALSE,
  settings_file = "settings_file.z5",
  output_dir = "output"
)

Arguments

os

Operating system. By default, the system is detected automatically. Alternatively, users can explicitly specify "Windows" or "Linux".

zonation_path

The specification for the path where Zonation 5 is installed.

flags

Flags that control which analysis options are used. Used to include single letter codes that switch analysis options on. Available options are: a, w, g, h, x, X, t.

marginal_loss_mode

Character string specifying the marginal loss rule. Available options are "CAZ1", "CAZ2", "ABF", "CAZMAX", "LOAD", and "RAND". Default is "CAZ2".

gui_activated

This parameter controls whether the Zonation Graphical User Interface (GUI) is launched when running the command file. Default is FALSE.

settings_file

Character string specifying the settings file. Default is "settings_file.z5".

output_dir

A character string specifying the name of the output directory where the analysis results will be saved. Default is "output".

Value

A Zonation command file containing the specified analysis options.

See also

Other preprocessing: feature_list(), settings_file()

Examples

if (FALSE) { # \dontrun{
command_file(
  zonation_path = "C:/Program Files (x86)/Zonation5"
)

command_file(
  zonation_path = "C:/Program Files (x86)/Zonation5",
  marginal_loss_mode = "ABF",
  gui_activated = TRUE
)
} # }