clean_metadata: Extract and clean ARU metadata from file names

In dhope/ARUtools: Tools for management of Acoustic Recording Unit (ARU) data

Extract and clean ARU metadata from file names

Description

Using regular expressions, metadata is extracted from file names and directory structure, checked and cleaned.

Usage

clean_metadata(
  project_dir = NULL,
  project_files = NULL,
  file_type = "wav",
  subset = NULL,
  subset_type = "keep",
  pattern_site_id = create_pattern_site_id(),
  pattern_aru_id = create_pattern_aru_id(),
  pattern_date = create_pattern_date(),
  pattern_time = create_pattern_time(),
  pattern_dt_sep = create_pattern_dt_sep(),
  order_date = "ymd",
  quiet = FALSE
)

Arguments

project_dir	Character. Directory where project files are stored. File paths will be used to extract information and must actually exist.
project_files	Character. Vector of project file paths. These paths can be absolute or relative to the working directory, and don't actually need to point to existing files unless you plan to use 'clean_gps()' or other sampling steps down the line. Must be provided if 'project_dir' is 'NULL'.
file_type	Character. Type of file (extension) to summarize. Default wav.
subset	Character. Text pattern to mark a subset of files/directories to either 'keep' or 'omit' (see 'subset_type')
subset_type	Character. Either 'keep' (default) or 'omit' files/directories which match the pattern in 'subset'.
pattern_site_id	Character. Regular expression to extract site ids. See 'create_pattern_site_id()'. Can be a vector of multiple patterns to match.
pattern_aru_id	Character. Regular expression to extract ARU ids. See 'create_pattern_aru_id()'. Can be a vector of multiple patterns to match.
pattern_date	Character. Regular expression to extract dates. See 'create_pattern_date()'. Can be a vector of multiple patterns to match.
pattern_time	Character. Regular expression to extract times. See 'create_pattern_time()'. Can be a vector of multiple patterns to match.
pattern_dt_sep	Character. Regular expression to mark separators between dates and times. See 'create_pattern_dt_sep()'.
order_date	Character. Order that the date appears in. "ymd" (default), "mdy", or "dmy". Can be a vector of multiple patterns to match.
quiet	Logical. Whether to suppress progress messages and other non-essential updates.

Details

Note that times are extracted by first combining the date, date/time separator and the time patterns. This means that if there is a problem with this combination, dates might be extracted but date/times will not. This mismatch can be used to determine which part of a pattern needs to be tweaked.

See 'vignette("customizing", package = "ARUtools")' for details on customizing 'clean_metadata()' for your project.

Value

Data frame with extracted metadata

Examples

clean_metadata(project_files = example_files)
clean_metadata(project_files = example_files, subset = "P02")

dhope/ARUtools documentation built on Jan. 18, 2024, 5:47 a.m.