Analysis flags in ZonationR

ZonationR provides a set of single-letter flags that control analysis options through command_file(). Certain flags require specific columns in the feature list (e.g., weight or group), while others need additional raster inputs supplied via settings_file(). As additional material to the function documentation, this vignette provides a guide to the available analysis flags and their relationships to feature and settings inputs, helping users better understand how to configure ZonationR workflows.

Feature list

The feature_list() function produces a file specifying biodiversity features (e.g., species or habitat distributions). Users can assign weights, groups, and thresholds to control prioritization. Columns in the feature list, such as weight, group, and threshold, are used by the prioritization algorithm according to the flags set in command_file().

Table 1. Arguments accepted by feature_list() and their parameter flags

Argument	ParameterFlags	DataType	Explanation
filename	-	string	Feature distribution file name
weight	w	floating-point	Feature weight
group	g	integer	Output group number
threshold	t	floating-point	Numeric threshold below which values are cut to zero

Settings file

The settings_file() function generates a configuration file that defines the inputs for a Zonation analysis. Some spatial inputs, such as analysis area masks or hierarchic masks, are optional but require activation via the corresponding flags in command_file(). File inputs include the feature list (i.e., the output from the feature_list() function), optional external solutions (external solution), analysis area masks (analysis area mask layer), hierarchic masks (hierarchic mask layer), and cost layers (cost layer).

Table 2. Arguments accepted by settings_file()

FileParameter	CommandFlag	RequiredFileType
feature list file	always required	plain text file
external solution	–mode=LOAD	floating-point raster
analysis area mask layer	a	integer raster
hierarchic mask layer	h	integer raster
cost layer	x, X	floating-point raster

Command file

Analysis options in ZonationR are controlled via single-letter flags specified in command_file(). Some flags require corresponding columns in the feature list (e.g., weight, group, threshold), while others require additional raster inputs supplied through settings_file(). The table below summarizes the available flags, the required feature list columns, and any additional raster inputs needed.

Table 3. Analysis flags available in ZonationR and their requirements

Flag	Explanation	FeatureListColumn	AdditionalRaster
a	Use analysis area mask	-	1 integer raster (analysis area)
w	Apply feature weights	weight	-
g	Use output groups	group	-
h	Hierarchic analysis	-	1 integer raster (hierarchic mask)
x	Include cost in outputs only	-	1 floating-point raster
X	Include cost in prioritization	-	1 floating-point raster
t	Apply thresholding	threshold	-