RootscanR (version 0.0.1)

getOverviewInput: Get an overview of the given root scans

Description

getOverviewInput - This function filters a set of root scan directories by checking if they comply with the given naming convention and then returns overview data about these directories.

Usage

getOverviewInput(data_dir, data_dirs = NULL, naming_conv = "standard")

Value

getOverviewInput A data frame containing the information about the various root scan directories (see also getDepthLvlInfo() for further explanations).

Arguments

data_dir

(Optional, default = NULL) String specifying the name (full path) of the directory containing all root scan directories of interest.

data_dirs

(Optional, default = NULL) Character vector specifying all of the individual root scan directories of interest. This is only used if data_dir is set to NULL.

naming_conv

A string specifying the naming convention, i.e., what information is provided within the names of the root scans. The file format can be png, tiff, jpg, or jpeg (upper or lowercase). Available are:

• "standard" (default): This is a commonly used naming convention and has the following structure:
  project_tube_depth_date_ID_session_operator
  Example:
  Testproject_T007_L004_12.12.2025_123394_016_Testoperator.jpg
  Explanation of the abbreviations:
  -- project: Project name ('unlimited' letters or digits)
  -- tube: ID of the minirhizotron ("T"+3 digits)
  -- depth: ID of the depth-level/window ("L"+3 digits)
  -- date: Date of the scanning (format day.month.year, 2 digits +"."+ 2 digits +"."+ 2 or 4 digits)
  -- ID: ID of the scan (6 digits) or timecode 14:23:10 -> 142310
  -- session: ID of the scan session (3 digits).
  -- operator: ID of the person that scanned the root ('unlimited' letters or digits)

Examples

getOverviewInput(data_dir = NULL, naming_conv = "standard")