Package 'ARUtools' reference manual

Title:	Management and Processing of Autonomous Recording Unit (ARU) Data
Description:	Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings. Extract Metadata from your recordings, select a subset of recordings for interpretation, and prepare files for processing on the 'WildTrax' <https://wildtrax.ca/> platform. Read and process metadata from recordings collected using the SongMeter and BAR-LT types of ARUs.
Authors:	David Hope [aut, cre] , Steffi LaZerte [aut] , Government of Canada [cph, fnd]
Maintainer:	David Hope <[email protected]>
License:	MIT + file LICENSE
Version:	0.7.1.9001
Built:	2024-11-08 17:25:32 UTC
Source:	https://github.com/arutools/ARUtools

Get acoustic complexity values

Description

Wrapper for 'soundecology' package to calculate acoustic complexity, the bioacoustic index, and acoustic diversity. See Value for details about these indices.

Usage

acoustic_indices(
  path,
  min_freq = NA,
  max_freq = NA,
  units = "samples",
  quiet = FALSE
)
acoustic_indices(
  path,
  min_freq = NA,
  max_freq = NA,
  units = "samples",
  quiet = FALSE
)

Arguments

`path`	Character. Path to wave file.
`min_freq`	Numeric. Minimum frequency for acoustic complexity (see `soundecology::acoustic_complexity()`)
`max_freq`	Numeric. Maximum frequency for acoustic complexity (see `soundecology::acoustic_complexity()`)
`units`	Character. Wave file units for reading the file. Defaults to "samples" (see `tuneR::readWave()`).
`quiet`	Logical. Whether to suppress progress messages and other non-essential updates.

Value

Returns a data frame with acoustic indices. Those prefaced with

complx_ are from soundecology::acoustic_complexity()
bio_ are from soundecology::bioacoustic_index()
div_ are from soundecology::acoustic_diversity()

Examples

w <- tuneR::sine(440, duration = 300000) # > 5s
tuneR::writeWave(w, "test_wave.wav")
acoustic_indices("test_wave.wav")
acoustic_indices("test_wave.wav", quiet = TRUE)
unlink("test_wave.wav")
w <- tuneR::sine(440, duration = 300000) # > 5s
tuneR::writeWave(w, "test_wave.wav")
acoustic_indices("test_wave.wav")
acoustic_indices("test_wave.wav", quiet = TRUE)
unlink("test_wave.wav")

Add an ARU to the list of identified ARUs

Description

Add an ARU to the list of identified ARUs

Usage

add_pattern_aru_type(pattern, aru_type)
add_pattern_aru_type(pattern, aru_type)

Arguments

`pattern`	regular expression to extract from file path
`aru_type`	Name of ARUtype

Examples


org_pat <- get_pattern("pattern_aru_type")

print(org_pat)

add_pattern_aru_type("CWS\\d", "Canadian Wildlife Detector \1")

get_pattern("pattern_aru_type")

set_pattern("pattern_aru_type", org_pat)

org_pat <- get_pattern("pattern_aru_type")

print(org_pat)

add_pattern_aru_type("CWS\\d", "Canadian Wildlife Detector \1")

get_pattern("pattern_aru_type")

set_pattern("pattern_aru_type", org_pat)

Add site-level data to the metadata

Description

Uses dates to join site-level data (coordinates and site ids) to the meta data. If the site data have only single dates, then a buffer before and after is used to determine which recordings belong to that site observation. Can join by site ids alone if set by_date = NULL.

Usage

add_sites(
  meta,
  sites,
  buffer_before = 0,
  buffer_after = NULL,
  by = c("site_id", "aru_id"),
  by_date = "date_time",
  quiet = FALSE
)
add_sites(
  meta,
  sites,
  buffer_before = 0,
  buffer_after = NULL,
  by = c("site_id", "aru_id"),
  by_date = "date_time",
  quiet = FALSE
)

Arguments

`meta`	Data frame. Recording metadata. Output of `clean_metadata()`.
`sites`	Data frame. Site-level data from `clean_site_index()`.
`buffer_before`	Numeric. Number of hours before a deployment in which to include recordings. `NULL` means include the time up to the last deployment. Coupled with `buffer_after`, this creates a window around a date/time in which to join recordings to the site-level data. Ignored if `sites` has both a start and end column for date/times. Default 0.
`buffer_after`	Numeric. Number of hours after the deployment in which to include recordings. `NULL` means include the time up to the next deployment. Coupled with `buffer_before`, creates a window around a date/time in which to join recordings to the site-level data. Ignored if `sites` has both a start and end column for date/times. Default `NULL`.
`by`	Character. Columns which identify a deployment in `sites` as well as `meta`, besides date/time, which are used to join the data. Default is `site_id` and `aru_id`.
`by_date`	Character. Date/time type to join data by. `date` is faster but `date_time` is more precise. Default `date_time`. `NULL` means ignore dates and join only with `by` columns (`dplyr::left_join()`).
`quiet`	Logical. Whether to suppress progress messages and other non-essential updates.

Value

A data frame of metadata with site-level data joined in.

Examples

m <- clean_metadata(project_files = example_files)
s <- clean_site_index(example_sites_clean,
  name_date = c("date_time_start", "date_time_end")
)
m <- add_sites(m, s)

# Without dates (by site only)
m <- clean_metadata(project_files = example_files)
eg <- dplyr::select(example_sites_clean, -date_time_start, -date_time_end)
s <- clean_site_index(eg, name_date_time = NULL)
m <- add_sites(m, s, by_date = NULL)

m <- clean_metadata(project_files = example_files)
s <- clean_site_index(example_sites_clean,
  name_date = c("date_time_start", "date_time_end")
)
m <- add_sites(m, s)

# Without dates (by site only)
m <- clean_metadata(project_files = example_files)
eg <- dplyr::select(example_sites_clean, -date_time_start, -date_time_end)
s <- clean_site_index(eg, name_date_time = NULL)
m <- add_sites(m, s, by_date = NULL)

Add file name formated for Wildtrax to metadata

Description

Create and append file name appropriate for uploading data to the Wildtrax platform https://wildtrax.ca/.

Usage

add_wildtrax(meta)
add_wildtrax(meta)

Arguments

meta

Data frame. Recording metadata. Output of clean_metadata().

Value

Data frame of metadata with appended column of WildTrax appropriate file names.

Examples


m <- clean_metadata(project_files = example_files)
m <- add_wildtrax(m)
m
m <- clean_metadata(project_files = example_files)
m <- add_wildtrax(m)
m

ARUtools: Management and Processing of Autonomous Recording Unit (ARU) Data

Description

Parse Autonomous Recording Unit (ARU) data and for sub-sampling recordings. Extract Metadata from your recordings, select a subset of recordings for interpretation, and prepare files for processing on the WildTrax https://wildtrax.ca/ platform. Read and process metadata from recordings collected using the Song Meter and BAR-LT types of ARUs.

Author(s)

Maintainer: David Hope [email protected] (ORCID)

Authors:

Steffi LaZerte [email protected] (ORCID)

Other contributors:

Government of Canada [copyright holder, funder]

Calculate Selection Weights

Description

Calculate selection weights for a series of recordings based on the selection parameters defined by sim_selection_weights().

Usage

calc_selection_weights(
  meta_sun,
  params,
  col_site_id = site_id,
  col_min = t2sr,
  col_day = date
)
calc_selection_weights(
  meta_sun,
  params,
  col_site_id = site_id,
  col_min = t2sr,
  col_day = date
)

Arguments

`meta_sun`	(Spatial) Data frame. Recording meta data with time to sunrise/sunset. Output of `calc_sun()`. Must have at least `col_min`, `col_day`, and `col_site_id`.
`params`	Named list. Parameters created by `sim_selection_weights()`, containing `min_range`, `min_mean`, `min_sd`, `day_range`, `day_mean`, `day_sd`, `offset`, `return_log`, `selection_fun`.
`col_site_id`	Column. Unquoted column containing site strata IDs (defaults to `site_id`).
`col_min`	Column. Unquoted column containing minutes to sunrise (`t2sr`) or sunset (`t2ss`) output from `calc_sun()` (defaults to `t2sr`).
`col_day`	Column. Unquoted column containing dates or day-of-year (doy) to use (defaults to `date`).

Value

Returns data with appended selection weights columns:

psel_by - The minutes column used
psel_min - Probability of selection by time of day (min column)
psel_doy - Probability of selection by day of year
psel - Probability of selection overall
psel_scaled - Probability of selection scaled overall
psel_std - Probability of selection standardized within a site
psel_normalized - Probability of selection normalized within a site

Examples

s <- clean_site_index(example_sites_clean,
  name_date_time = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s) |>
  calc_sun()

params <- sim_selection_weights()
calc_selection_weights(m, params = params)
s <- clean_site_index(example_sites_clean,
  name_date_time = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s) |>
  calc_sun()

params <- sim_selection_weights()
calc_selection_weights(m, params = params)

Calculate time to sunrise/sunset

Description

Calculate the sunrise/sunset of each sound file for the day of, the day before and the day after to get the nearest sunrise to the recording. Times are calculated using the 'suncalc' package.

Usage

calc_sun(meta_sites, aru_tz = "local")
calc_sun(meta_sites, aru_tz = "local")

Arguments

`meta_sites`	(Spatial) Data frame. Recording metadata with added coordinates. Output of `clean_metadata()` and then `add_sites()` (with either `clean_gps()` or `clean_site_index()`).
`aru_tz`	Character. Must be either "local" or a timezone listed in `OlsonNames()`. See Details.

Details

Timezones. To ensure that the sunrise/sunset times are calculated correctly relative to the time of the recording, we need to know the timezone of the date/time of the recording. If ARUs were calibrated with a specific timezone before going into the field, that can be specified by using, for example, aru_tz = "America/Toronto". If on the other hand each ARU was calibrated to whichever timezone was local when it was deployed use aru_tz = "local". The specific timezone will be calculated individually based on the longitude and latitude of each recording.

Value

Data frame with metadata and added timezone of recording time (tz), and time to sunrise/sunset (t2sr, t2ss).

Examples

s <- clean_site_index(example_sites_clean,
  name_date = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s)
calc_sun(m)

s <- clean_site_index(example_sites_clean,
  name_date = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s)
calc_sun(m)

Explore a file

Description

Shows the first few lines in a text file. Useful for trying to understand problems in GPS files.

Usage

check_file(file_name, n_max = 10, ...)
check_file(file_name, n_max = 10, ...)

Arguments

`file_name`	Character. File path to check.
`n_max`	Numeric. Number of lines in the file to show. Default 10.
`...`	Arguments passed on to `readr::read_lines()`

Details

Wrapper around readr::read_lines(n_max).

Value

A character vector with one element for each line

Examples

f <- system.file("extdata", "logfile_00015141_SD1.txt", package = "ARUtools")
check_file(f)

f <- system.file("extdata", "logfile_00015141_SD1.txt", package = "ARUtools")
check_file(f)

Check output of `clean_metadata()`

Description

Cleaning metadata can take a series of tries. This function helps summarize and explore the metadata for possible patterns which may help find problems.

Usage

check_meta(meta, date = FALSE)
check_meta(meta, date = FALSE)

Arguments

`meta`	Data frame. Recording metadata. Output of `clean_metadata()`.
`date`	Logical. Whether to summarize output by date (as well as `site_id` and `aru_id`. Default `FALSE`.

Value

A data frame summarizing the metadata by site_id, aru_type, aru_id, and (optionally) by date. Presents the number of files, directories, and days worth of recordings, as well as the minimum and maximum recording times.

Examples

m <- clean_metadata(project_files = example_files)

check_meta(m)
check_meta(m, date = TRUE)

m <- clean_metadata(project_files = example_files)

check_meta(m)
check_meta(m, date = TRUE)

Check problems in output of `clean_metadata()`

Description

Cleaning metadata can take a series of tries. This function helps summarize and explore missing metadata (problems).

Usage

check_problems(
  df,
  check = c("site_id", "aru_id", "date", "date_time", "longitude", "latitude"),
  path = FALSE,
  date = FALSE
)
check_problems(
  df,
  check = c("site_id", "aru_id", "date", "date_time", "longitude", "latitude"),
  path = FALSE,
  date = FALSE
)

Arguments

`df`	Data frame. Either meta data (`clean_metadata()`) or GPS coordinates (`clean_gps()`)
`check`	Character. Character vector of columns to check for missing values. Default is `site_id`, `aru_id`, `date`, `date_time`, `longitude` and `latitude`.
`path`	Logical. Whether to return just the file paths which have missing attributes. Default `FALSE`
`date`	Logical. Whether to summarize output by date (as well as `site_id` and `aru_id`. Default `FALSE`.

Value

Examples


m <- clean_metadata(project_files = example_files, pattern_aru_id = "test")

check_problems(m)
check_problems(m, date = TRUE)
check_problems(m, path = TRUE)
m <- clean_metadata(project_files = example_files, pattern_aru_id = "test")

check_problems(m)
check_problems(m, date = TRUE)
check_problems(m, path = TRUE)

Check and clean GPS data

Description

Check and clean GPS data from ARU logs. GPS points are checked for obvious problems (expected range, distance cutoffs and timing) then attached to the meta data frame. Note that it is often safer and more reliable to create your own Site Index file including site ids, and GPS coordinates. This file can be cleaned and prepared with clean_site_index() instead.

Usage

clean_gps(
  meta = NULL,
  dist_cutoff = 100,
  dist_crs = 3161,
  dist_by = c("site_id", "aru_id"),
  quiet = FALSE,
  verbose = FALSE
)
clean_gps(
  meta = NULL,
  dist_cutoff = 100,
  dist_crs = 3161,
  dist_by = c("site_id", "aru_id"),
  quiet = FALSE,
  verbose = FALSE
)

Arguments

`meta`	Data frame. Output of `clean_metadata()`.
`dist_cutoff`	Numeric. Maximum distance (m) between GPS points within a site. Default is 100m but can be set to `Inf` to skip.
`dist_crs`	Numeric. Coordinate Reference System to use when calculating distance (should be one with m).
`dist_by`	Character. Column which identifies sites within which to compare distance among GPS points. Only valid if `dist_cutoff` is not `Inf`.
`quiet`	Logical. Whether to suppress progress messages and other non-essential updates.
`verbose`	Logical. Show extra loading information. Default `FALSE`.

Details

If checking for a maximum distance (dist_cutoff) among GPS points within a group (dist_by), the returned data frame will include a column max_dist, which represents the largest distance among points within that group.

Value

Data frame of site-level metadata.

Examples


m <- clean_metadata(project_dir = "my_project")
g <- clean_gps(meta = m)

m <- clean_metadata(project_dir = "my_project")
g <- clean_gps(meta = m)

Extract log data from BAR-LT log files

Description

Process BAR-LT log files into a data frame reflecting metadata, schedule information, and events. Events are time-stamped logs of either GPS fixes (lat and lon) or recordings (rec_file, rec_size, rec_end).

Usage

clean_logs(log_files, return = "all", progress = TRUE)
clean_logs(log_files, return = "all", progress = TRUE)

Arguments

`log_files`	Character vector of log files to process.
`return`	Character. What kind of data to return, GPS fixes (`"gps"`), recording events (`"recordings"`) or `"all"` (default).
`progress`	Logical. Whether to use `purrr::map()` progress bars (default `TRUE`).

Details

Note that log files can have glitches. If there is no start time for a recording (generally when there is a problem and no recording is made), the date_time value for that recording will be the same as the rec_end time.

Because the BAR-LT units adjust their time according to the GPS locations, all times are in "local" to that area.

Value

Data frame containing

file_names and paths of the log files
events and their date_times
lat and lon for "gps" events
rec_file, rec_size and rec_end for "recording" events (recording start is the date_time of the event)
schedule information such as schedule_date, schedule_name, schedule_lat, schedule_lon, schedule_sr (sunrise), and schedule_ss (sunset)
metadata information such as meta_serial and meta_firmware

Examples


# Replace "my_project_folder" with your directory containing your recordings and logfiles
log_files <- fs::dir_ls("my_project_folder", recurse = TRUE, glob = "*logfile*")
log_files
logs <- clean_logs(log_files)

log_files <- "../ARUtools - Extra/aru_log_files/P028/1A_BARLT10962/logfile_00010962_SD1.txt"

clean_logs(log_files)
clean_logs(log_files, return = "gps")
clean_logs(log_files, return = "recordings")

log_files <- fs::dir_ls("../ARUtools - Extra/aru_log_files/", recurse = TRUE, glob = "*logfile*")

l <- clean_logs(log_files)

# Replace "my_project_folder" with your directory containing your recordings and logfiles
log_files <- fs::dir_ls("my_project_folder", recurse = TRUE, glob = "*logfile*")
log_files
logs <- clean_logs(log_files)

log_files <- "../ARUtools - Extra/aru_log_files/P028/1A_BARLT10962/logfile_00010962_SD1.txt"

clean_logs(log_files)
clean_logs(log_files, return = "gps")
clean_logs(log_files, return = "recordings")

log_files <- fs::dir_ls("../ARUtools - Extra/aru_log_files/", recurse = TRUE, glob = "*logfile*")

l <- clean_logs(log_files)

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(),
  pattern_tz_offset = create_pattern_tz_offset(),
  order_date = "ymd",
  quiet = FALSE
)
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(),
  pattern_tz_offset = create_pattern_tz_offset(),
  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()`.
`pattern_tz_offset`	Character. Regular expression to extract time zone offsets from file names. See. `create_pattern_tz_offset()`.
`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")

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

Prepare and clean site index file

Description

A site index file contains information on when specific ARUs were deployed where. This function cleans a file (csv, xlsx) or data frame in preparation for adding these details to the output of clean_metadata(). It can be used to specify missing information according to date, such as GPS lon/lats and site ids.

Usage

clean_site_index(
  site_index,
  name_aru_id = "aru_id",
  name_site_id = "site_id",
  name_date_time = "date",
  name_coords = c("longitude", "latitude"),
  name_extra = NULL,
  resolve_overlaps = TRUE,
  quiet = FALSE
)
clean_site_index(
  site_index,
  name_aru_id = "aru_id",
  name_site_id = "site_id",
  name_date_time = "date",
  name_coords = c("longitude", "latitude"),
  name_extra = NULL,
  resolve_overlaps = TRUE,
  quiet = FALSE
)

Arguments

`site_index`	(Spatial) Data frame or file path. Site index data to clean. If file path, must be to a local csv or xlsx file.
`name_aru_id`	Character. Name of the column that contains ARU ids. Default `"aru_id"`.
`name_site_id`	Character. Name of the column that contains site ids. Default `"site_id"`.
`name_date_time`	Character. Column name that contains dates or date/times. Can be vector of two names if there are both 'start' and 'end' columns. Can be `NULL` to ignore dates. Default `"date"`.
`name_coords`	Character. Column names that contain longitude and latitude (in that order). Ignored if `site_index` is spatial. Default `c("longitude", "latitude")`
`name_extra`	Character. Column names for extra data to include. If a named vector, will rename the columns (see examples). Default `NULL`.
`resolve_overlaps`	Logical. Whether or not to resolve date overlaps by shifting the start/end dates to noon (default `TRUE`). This assumes that ARUs are generally not deployed/removed at midnight (the official start/end of a day) and so noon is used as an approximation for when an ARU was deployed or removed. If possible, use specific deployment times to avoid this issue.
`quiet`	Logical. Whether to suppress progress messages and other non-essential updates.

Details

Note that times are assumed to be in 'local' time and a timezone isn't used (and is removed if present, replaced with UTC). This allows sites from different timezones to be processed at the same time.

Value

Standardized site index data frame

Examples


s <- clean_site_index(example_sites,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = c("Date_set_out", "Date_removed"),
  name_coords = c("lon", "lat")
)

s <- clean_site_index(example_sites,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = c("Date_set_out", "Date_removed"),
  name_coords = c("lon", "lat"),
  name_extra = c("plot" = "Plots")
)

# Without dates
eg <- dplyr::select(example_sites, -Date_set_out, -Date_removed)
s <- clean_site_index(eg,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = NULL,
  name_coords = c("lon", "lat"),
  name_extra = c("plot" = "Plots")
)

s <- clean_site_index(example_sites,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = c("Date_set_out", "Date_removed"),
  name_coords = c("lon", "lat")
)

s <- clean_site_index(example_sites,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = c("Date_set_out", "Date_removed"),
  name_coords = c("lon", "lat"),
  name_extra = c("plot" = "Plots")
)

# Without dates
eg <- dplyr::select(example_sites, -Date_set_out, -Date_removed)
s <- clean_site_index(eg,
  name_aru_id = "ARU",
  name_site_id = "Sites",
  name_date_time = NULL,
  name_coords = c("lon", "lat"),
  name_extra = c("plot" = "Plots")
)

Clip multiple wave files and format names

Description

Process multiple wave files by copying them with a new filename and clipping to a given length.

Usage

clip_wave(
  waves,
  dir_out,
  dir_in = NULL,
  col_path_in = path,
  col_subdir_out = subdir_out,
  col_filename_out = filename_out,
  col_clip_length = clip_length,
  col_start_time = start_time,
  overwrite = FALSE,
  create_dir = TRUE,
  diff_limit = 30
)
clip_wave(
  waves,
  dir_out,
  dir_in = NULL,
  col_path_in = path,
  col_subdir_out = subdir_out,
  col_filename_out = filename_out,
  col_clip_length = clip_length,
  col_start_time = start_time,
  overwrite = FALSE,
  create_dir = TRUE,
  diff_limit = 30
)

Arguments

`waves`	Data frame. Details of file locations.
`dir_out`	Character. Output directory.
`dir_in`	Character. Directory wave files are read from. Default is `NULL` meaning the current working directory.
`col_path_in`	Column. Unquoted column containing the current file paths. Default `path`. Note: file paths must be either relative to `dir_in` or absolute.
`col_subdir_out`	Column. Unquoted column containing the subdirectories in which to put output files. Default `subdir_out`.
`col_filename_out`	Column. Unquoted column containing the output filenames. Default `filename_out`.
`col_clip_length`	Column. Unquoted column containing the length of the new clip. Default `length`.
`col_start_time`	Column. Unquoted column containing the start time of the new clip. Default `start_time`.
`overwrite`	Logical. Overwrite pre-existing files when clipping and moving. Default `FALSE`.
`create_dir`	Logical. Whether to create directory structure for newly formatted and clipped wave files.
`diff_limit`	Numeric. How much longer in seconds clip lengths can be compared to file lengths before triggering an error. Default `30`.

Value

TRUE if successful and clipped wave files created

Examples


w <- data.frame(
  path = temp_wavs(n = 4),
  subdir_out = c("test1/a", "test2/a", "test3/c", "test4/d"),
  subsub_dir_out = rep("zz", 4),
  filename_out = c("wave1_clean.wav", "wave2_clean.wav", "wave3_clean.wav", "wave4_clean.wav"),
  clip_length = c(1, 1, 1, 2),
  start_time = c(1.2, 0.5, 1, 0)
)

clip_wave(w, dir_out = "clean", col_subdir_out = c(subdir_out, subsub_dir_out))

unlink("clean", recursive = TRUE) # Remove this new 'clean' directory

w <- data.frame(
  path = temp_wavs(n = 4),
  subdir_out = c("test1/a", "test2/a", "test3/c", "test4/d"),
  subsub_dir_out = rep("zz", 4),
  filename_out = c("wave1_clean.wav", "wave2_clean.wav", "wave3_clean.wav", "wave4_clean.wav"),
  clip_length = c(1, 1, 1, 2),
  start_time = c(1.2, 0.5, 1, 0)
)

clip_wave(w, dir_out = "clean", col_subdir_out = c(subdir_out, subsub_dir_out))

unlink("clean", recursive = TRUE) # Remove this new 'clean' directory

Clip single wave file

Description

Clip and copy a single wave files to a given length. See clip_wave() for processing multiple files.

Usage

clip_wave_single(
  path_in,
  path_out,
  clip_length,
  start_time = 0,
  wave_length = NULL,
  overwrite = FALSE
)
clip_wave_single(
  path_in,
  path_out,
  clip_length,
  start_time = 0,
  wave_length = NULL,
  overwrite = FALSE
)

Arguments

`path_in`	Character. Path to the wave file to clip.
`path_out`	Character. Path to copy the new clipped wave file to.
`clip_length`	Numeric. Length of new clip in seconds.
`start_time`	Numeric. Time in seconds where new clip should start. Default 0.
`wave_length`	Numeric. Length of the clipped wave file in seconds (if `NULL`, default, will be the length of time from `start_time` to the end of the file).
`overwrite`	Logical. Whether to overwrite existing files when creating new clipped wave files. Default (`FALSE`) will error if the file already exists.

Value

TRUE if successful

Examples

# Create test wave file
f <- temp_wavs(1)

# Clip file and check it out
clip_wave_single(f, "new_file.wav", clip_length = 1)
tuneR::readWave("new_file.wav")
unlink("new_file.wav")
# Create test wave file
f <- temp_wavs(1)

# Clip file and check it out
clip_wave_single(f, "new_file.wav", clip_length = 1)
tuneR::readWave("new_file.wav")
unlink("new_file.wav")

Count files in a project directory

Description

Helper function to explore the number of files in a directory, recursively.

Usage

count_files(project_dir, subset = NULL, subset_type = "keep")
count_files(project_dir, subset = NULL, subset_type = "keep")

Arguments

`project_dir`	Character. Directory where project files are stored. File paths will be used to extract information and must actually exist.
`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`.

Value

A data frame with number of files in a directory

Examples


count_files("PROJECT_DIR")

count_files("PROJECT_DIR")

Create directory structure for recording folders

Description

Create a set of nested folders for storing ARU recordings by plots and sites.

Usage

create_dirs(
  plots,
  site_ids,
  base_dir = NULL,
  dir_list = FALSE,
  dry_run = TRUE,
  expect_dirs = FALSE
)
create_dirs(
  plots,
  site_ids,
  base_dir = NULL,
  dir_list = FALSE,
  dry_run = TRUE,
  expect_dirs = FALSE
)

Arguments

`plots`	Character vector. Hexagon or cluster names for folder names.
`site_ids`	Character vector. Site IDs. Should include the plot/cluster id in the name.
`base_dir`	Character. Base directory to build directory structure in.
`dir_list`	Logical. Whether to return a vector of directories (to be) created (defaults to `FALSE`).
`dry_run`	Logical. Whether to do a dry-run of the process (i.e. do not actually create directories; defaults to `TRUE`)
`expect_dirs`	Logical. Expect that directories may already exist? Default (`FALSE`) is to stop if directories to be created already exist.

Value

If dir_list = TRUE, returns a list of directories (to be) created. If not a dry run, also creates the folder structure.

Examples

# Default is to do a dry-run (don't actually create the directories)
create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings"
)

# Get a list of directories which would be created
create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings", dir_list = TRUE
)


# Create directories AND return a list of those created
d <- create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings", dir_list = TRUE, expect_dirs =TRUE,
  dry_run = FALSE
)
d

# Default is to do a dry-run (don't actually create the directories)
create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings"
)

# Get a list of directories which would be created
create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings", dir_list = TRUE
)


# Create directories AND return a list of those created
d <- create_dirs(
  plots = c("river1", "river2", "river3"),
  site_ids = c(
    "river1_sm01", "river1_sm02", "river2_sm03", "river2_sm04",
    "river3_sm05", "river3_sm06"
  ),
  base_dir = "Recordings", dir_list = TRUE, expect_dirs =TRUE,
  dry_run = FALSE
)
d

Create a look around expression and add it to an existing regular expression

Description

Lookarounds allow you to position a regular expression to more specificity.

Usage

create_lookaround(pattern, lookaround_pattern, position, negate = FALSE)
create_lookaround(pattern, lookaround_pattern, position, negate = FALSE)

Arguments

`pattern`	String. Pattern that you wish to add a look around to
`lookaround_pattern`	String. Pattern that you wish to look for.
`position`	String. One of 'before', 'after', 'ahead', or 'behind'. Capitalization doesn't matter
`negate`	Logical. allows you to exclude cases where look around is detected.

Value

Returns a string that can be used as a regular expression

Examples


# Here is a string with three patterns of digits
text <- "cars123ruin456cities789"

# To extract the first one we can use this pattern
stringr::str_extract(text, "\\d{3}")
# or
create_lookaround("\\d{3}", "cars", "before") |>
stringr::str_extract(string=text)

# To exclude the first one we can write
create_lookaround("\\d{3}", "cars", "before", negate=TRUE) |>
stringr::str_extract_all(string=text)

# To extract the second one we can write
 create_lookaround("\\d{3}", "ruin", "before") |>
stringr::str_extract(string=text)

# or

create_lookaround("\\d{3}", "cities", "after") |>
stringr::str_extract(string=text)


# Here is a string with three patterns of digits
text <- "cars123ruin456cities789"

# To extract the first one we can use this pattern
stringr::str_extract(text, "\\d{3}")
# or
create_lookaround("\\d{3}", "cars", "before") |>
stringr::str_extract(string=text)

# To exclude the first one we can write
create_lookaround("\\d{3}", "cars", "before", negate=TRUE) |>
stringr::str_extract_all(string=text)

# To extract the second one we can write
 create_lookaround("\\d{3}", "ruin", "before") |>
stringr::str_extract(string=text)

# or

create_lookaround("\\d{3}", "cities", "after") |>
stringr::str_extract(string=text)

Create a pattern to match date

Description

Helper functions to create regular expression patterns to match different metadata in file paths.

Usage

create_pattern_date(
  order = "ymd",
  sep = c("_", "-", ""),
  yr_digits = 4,
  look_ahead = "",
  look_behind = ""
)

create_pattern_time(
  sep = c("_", "-", ":", ""),
  seconds = "yes",
  look_ahead = "",
  look_behind = ""
)

create_pattern_dt_sep(
  sep = "T",
  optional = FALSE,
  look_ahead = "",
  look_behind = ""
)

create_pattern_aru_id(
  arus = c("BARLT", "S\\d(A|U)", "SM\\d", "SMM", "SMA"),
  n_digits = c(4, 8),
  sep = c("_", "-", ""),
  prefix = "",
  suffix = "",
  look_ahead = "",
  look_behind = ""
)

create_pattern_site_id(
  prefix = c("P", "Q"),
  p_digits = 2,
  sep = c("_", "-"),
  suffix = "",
  s_digits = 1,
  look_ahead = "",
  look_behind = ""
)

create_pattern_tz_offset(
  direction_from_UTC = "West",
  n_digits_hrs = 2,
  n_digits_min = 2
)

test_pattern(test, pattern)
create_pattern_date(
  order = "ymd",
  sep = c("_", "-", ""),
  yr_digits = 4,
  look_ahead = "",
  look_behind = ""
)

create_pattern_time(
  sep = c("_", "-", ":", ""),
  seconds = "yes",
  look_ahead = "",
  look_behind = ""
)

create_pattern_dt_sep(
  sep = "T",
  optional = FALSE,
  look_ahead = "",
  look_behind = ""
)

create_pattern_aru_id(
  arus = c("BARLT", "S\\d(A|U)", "SM\\d", "SMM", "SMA"),
  n_digits = c(4, 8),
  sep = c("_", "-", ""),
  prefix = "",
  suffix = "",
  look_ahead = "",
  look_behind = ""
)

create_pattern_site_id(
  prefix = c("P", "Q"),
  p_digits = 2,
  sep = c("_", "-"),
  suffix = "",
  s_digits = 1,
  look_ahead = "",
  look_behind = ""
)

create_pattern_tz_offset(
  direction_from_UTC = "West",
  n_digits_hrs = 2,
  n_digits_min = 2
)

test_pattern(test, pattern)

Arguments

`order`	Character vector. Expected orders of (y)ear, (m)onth and (d)ate. Default is "ymd" for Year-Month-Date order. Can have more than one possible order.
`sep`	Character vector. Expected separator(s) between the pattern parts. Can be "" for no separator.
`yr_digits`	Numeric vector. Number of digits in Year, either 2 or 4.
`look_ahead`	Pattern to look ahead or after string Can be a regular expression or text.
`look_behind`	Pattern to look before behind string. Can be a regular expression or text.
`seconds`	Character. Whether seconds are included. Options are "yes", "no", "maybe".
`optional`	Logical. Whether the separator should be optional or not. Allows matching on different date/time patterns.
`arus`	Character vector. Pattern(s) identifying the ARU prefix (usually model specific).
`n_digits`	Numeric vector. Number of digits expected to follow the `arus` pattern. Can be one or two (a range).
`prefix`	Character vector. Prefix(es) for site ids.
`suffix`	Character vector. Suffix(es) for site ids.
`p_digits`	Numeric vector. Number(s) of digits following the `prefix`.
`s_digits`	Numeric vector. Number(s) of digits following the `suffix`.
`direction_from_UTC`	Character. Must be on of "West", "East" or "Both"
`n_digits_hrs`	Numeric vector. Number(s) of digits for hours in offset.
`n_digits_min`	Numeric vector. Number(s) of digits for minutes in offset.
`test`	Character vector. Examples of text to test.
`pattern`	Character. Regular expression pattern to test.

Details

By default create_pattern_aru_id() matches many common ARU patterns like BARLT0000, S4A0000, SM40000, SMM0000, SMA0000.

test_pattern() is a helper function to see what a regular expression pattern will pick out of some example text. Can be used to see if your pattern grabs what you want. This is just a simple wrapper around stringr::str_extract().

Value

Either a pattern (create_pattern_xxx()) or the text extracted by a pattern (test_pattern())

Functions

create_pattern_date(): Create a pattern to match a date
create_pattern_time(): Create a pattern to match a time
create_pattern_dt_sep(): Create a pattern to match a date/time separator
create_pattern_aru_id(): Create a pattern to match an ARU id
create_pattern_site_id(): Create a pattern to match a site id
create_pattern_tz_offset(): Create a pattern to match a site id
test_pattern(): Test patterns

Examples

create_pattern_date() # Default matches 2020-01-01 or 2020_01_01 or 20200101
# ("-", "_" or "" as separators)
create_pattern_date(sep = "") # Matches only 20200101 (no separator allowed)

create_pattern_time() # Default matches 23_59_59 (_, -, :, as optional separators)
create_pattern_time(sep = "", seconds = "no") # Matches 2359 (no seconds no separators)

create_pattern_dt_sep() # Default matches 'T' as a required separator
create_pattern_dt_sep(optional = TRUE) # 'T' as an optional separator
create_pattern_dt_sep(c("T", "_", "-")) # 'T', '_', or '-' as separators

create_pattern_aru_id()
create_pattern_aru_id(prefix = "CWS")
create_pattern_aru_id(n_digits = 12)


create_pattern_site_id() # Default matches P00-0
create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
) # Matches site000a


create_pattern_site_id() # Default matches P00-0
create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
) # Matches site000a

pat <- create_pattern_aru_id(prefix = "CWS")
test_pattern("CWS_BARLT1012", pat) # No luck
pat <- create_pattern_aru_id(prefix = "CWS_")
test_pattern("CWS_BARLT1012", pat) # Ah ha!
pat <- create_pattern_site_id()

pat <- create_pattern_site_id()
test_pattern("P03", pat) # Nope
test_pattern("P03-1", pat) # Success!

pat <- create_pattern_site_id(prefix = "site", p_digits = 3, sep = "", s_digits = 0)
test_pattern("site111", pat)
pat <- create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
)
test_pattern(c("site9", "site100a"), pat)

create_pattern_date() # Default matches 2020-01-01 or 2020_01_01 or 20200101
# ("-", "_" or "" as separators)
create_pattern_date(sep = "") # Matches only 20200101 (no separator allowed)

create_pattern_time() # Default matches 23_59_59 (_, -, :, as optional separators)
create_pattern_time(sep = "", seconds = "no") # Matches 2359 (no seconds no separators)

create_pattern_dt_sep() # Default matches 'T' as a required separator
create_pattern_dt_sep(optional = TRUE) # 'T' as an optional separator
create_pattern_dt_sep(c("T", "_", "-")) # 'T', '_', or '-' as separators

create_pattern_aru_id()
create_pattern_aru_id(prefix = "CWS")
create_pattern_aru_id(n_digits = 12)


create_pattern_site_id() # Default matches P00-0
create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
) # Matches site000a


create_pattern_site_id() # Default matches P00-0
create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
) # Matches site000a

pat <- create_pattern_aru_id(prefix = "CWS")
test_pattern("CWS_BARLT1012", pat) # No luck
pat <- create_pattern_aru_id(prefix = "CWS_")
test_pattern("CWS_BARLT1012", pat) # Ah ha!
pat <- create_pattern_site_id()

pat <- create_pattern_site_id()
test_pattern("P03", pat) # Nope
test_pattern("P03-1", pat) # Success!

pat <- create_pattern_site_id(prefix = "site", p_digits = 3, sep = "", s_digits = 0)
test_pattern("site111", pat)
pat <- create_pattern_site_id(
  prefix = "site", p_digits = 3, sep = "",
  suffix = c("a", "b", "c"), s_digits = 0
)
test_pattern(c("site9", "site100a"), pat)

Example cleaned recording meta data

Description

A data frame with examples of correctly formatted metadata with added site-level information

Usage

example_clean
example_clean

Format

`example_clean`

A data frame with 42 rows and 10 columns:

file_name: Name of the file
type: File type
path: Relative file path including file name
aru_type: ARU model
aru_id: ARU ids
site_id: Site ids
date_time: Recording date/time
date: Recording date
longitude: Latitude in decimal degrees
latitude: Longitude in decimal degrees

Source

data-raw/data_test.R

Example recording files

Description

A vector of examples ARU recording files.

Usage

example_files
example_files

Format

`example_files`

A vector with 42 file paths

Source

data-raw/data_test.R

Example long-term deployment recording files

Description

A vector of examples ARU recording files. Uses the example_sites data, but deploys them for a longer deployment

Usage

example_files_long
example_files_long

Format

`example_files_long`

A vector with 614 file paths

Source

data-raw/data_long_deployment.R

Example site-level meta data

Description

A data frame with examples of incorrectly formatted site-level data.

Usage

example_sites
example_sites

Format

`example_sites`

A data frame with 10 rows and 8 columns:

Sites: Site ids
Date_set_out: Deployment start date
Date_removed: Deployment end date
ARU: ARU ids
lon: Longitude in decimal degrees
lat: Latitude in decimal degrees
Plots: Hypothetical extra plot column
Subplot: Hypothetical extra subplot column

Source

data-raw/data_test.R

Example cleaned site-level meta data

Description

A data frame with examples of correctly formatted site-level data.

Usage

example_sites_clean
example_sites_clean

Format

`example_sites_clean`

A data frame with 10 rows and 8 columns:

site_id: Site ids
aru_id: ARU ids
date_time_start: Deployment start date/time
date_time_end: Deployment end date/time
date_start: Deployment start date
date_end: Deployment end date
longitude: Latitude in decimal degrees
latitude: Longitude in decimal degrees

Source

data-raw/data_test.R

Returns the current vector of ARU types

Description

Returns the current vector of ARU types

Usage

get_pattern(pattern_name)
get_pattern(pattern_name)

Arguments

pattern_name

String of pattern variable to return. One of "pattern_aru_type", "pattern_check","pattern_data", or "pattern_date_time"

Value

named character vector

Examples


get_pattern("pattern_aru_type")
get_pattern("pattern_aru_type")

Get the length of a recording in seconds

Description

Get the length of a recording in seconds

Usage

get_wav_length(path, return_numeric = FALSE)
get_wav_length(path, return_numeric = FALSE)

Arguments

`path`	Character. Path to wave file.
`return_numeric`	Logical. Return numeric or character?

Value

Length of recording in seconds

Examples

  f <- tempfile()
  w <- tuneR::sine(440, duration = 100000)
  tuneR::writeWave(w, f)
  get_wav_length(f)
f <- tempfile()
  w <- tuneR::sine(440, duration = 100000)
  tuneR::writeWave(w, f)
  get_wav_length(f)

Try to guess the ARU type from a file path

Description

Try to guess the ARU type from a file path

Usage

guess_ARU_type(path)
guess_ARU_type(path)

Arguments

path

Character. Path to wave file

Value

Tibble with columns 'manufacturer', 'model', and 'aru_type'

Examples


get_pattern("pattern_aru_type")

guess_ARU_type("/path/to/barlt/file.wav")

guess_ARU_type("/path/to/sm/S4A2342.wav")
get_pattern("pattern_aru_type")

guess_ARU_type("/path/to/barlt/file.wav")

guess_ARU_type("/path/to/sm/S4A2342.wav")

Run `clean_logs()` on the output from `clean_metadata()`

Description

Run clean_logs() on the output from clean_metadata()

Usage

meta_clean_logs(meta)
meta_clean_logs(meta)

Arguments

meta

Data frame. meta data processed in add_sites()

Value

Data frame containing

file_names and paths of the log files
events and their date_times
lat and lon for "gps" events
rec_file, rec_size and rec_end for "recording" events (recording start is the date_time of the event)
schedule information such as schedule_date, schedule_name, schedule_lat, schedule_lon, schedule_sr (sunrise), and schedule_ss (sunset)
metadata information such as meta_serial and meta_firmware
other columns from meta provided

Examples


  file_vec <- fs::dir_ls(fs::path_package("extdata", package = "ARUtools"), recurse = TRUE,)
  m <- clean_metadata(project_files = file_vec, file_type = 'json',pattern_site_id = "000\\d+" )

  logs <- meta_clean_logs(m)
file_vec <- fs::dir_ls(fs::path_package("extdata", package = "ARUtools"), recurse = TRUE,)
  m <- clean_metadata(project_files = file_vec, file_type = 'json',pattern_site_id = "000\\d+" )

  logs <- meta_clean_logs(m)

Sample recordings

Description

Sample recordings based on selection weights from calc_selection_weights() using spsurvey::grts().

Usage

sample_recordings(
  meta_weights,
  n,
  os = NULL,
  col_site_id = site_id,
  col_sel_weights = psel_std,
  seed = NULL,
  ...
)
sample_recordings(
  meta_weights,
  n,
  os = NULL,
  col_site_id = site_id,
  col_sel_weights = psel_std,
  seed = NULL,
  ...
)

Arguments

`meta_weights`	(Spatial) Data frame. Recording meta data selection weights. Output of `calc_selection_weights()`. Must have at least the columns identified by `col_site_id` and `col_sel_weights`, as well as the probability of selection columns (those starting with `psel`) and `doy`.
`n`	Numeric, Data frame, Vector, or List. Number of base samples to choose. For stratification by site, a named vector/list of samples per site, or a data frame with columns `n` for samples, `n_os` for oversamples and the column matching that identified by `col_site_id`.
`os`	Numeric, Vector, or List. Over sample size (proportional) or named vector/list of number of samples per site Ignored if `n` is a data frame.
`col_site_id`	Column. Unquoted column containing site strata IDs (defaults to `site_id`).
`col_sel_weights`	Column. Unquoted name of column identifying selection weights (defaults to `psel_std`)
`seed`	Numeric. Random seed to use for random sampling. Seed only applies to specific sampling events (does not change seed in the environment). `NULL` does not set a seed.
`...`	Extra named arguments passed on to `spsurvey::grts()`.

Value

A sampling run from grts. Note that the included dataset is spatial, but is a dummy spatial dataset created by using dates and times to create the spatial landscape.

Examples

s <- clean_site_index(example_sites_clean,
  name_date_time = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s) |>
  calc_sun()

params <- sim_selection_weights()
w <- calc_selection_weights(m, params = params)

# No stratification by site
samples <- sample_recordings(w, n = 10, os = 0.1, col_site_id = NULL)

# Stratification by site defined by...

# lists
samples <- sample_recordings(w, n = list(P01_1 = 2, P02_1 = 5, P03_1 = 2), os = 0.2)

# vectors
samples <- sample_recordings(w, n = c(P01_1 = 2, P02_1 = 5, P03_1 = 2), os = 0.2)

# data frame
samples <- sample_recordings(
  w,
  n = data.frame(
    site_id = c("P01_1", "P02_1", "P03_1"),
    n = c(2, 5, 2),
    n_os = c(0, 0, 1)
  )
)

s <- clean_site_index(example_sites_clean,
  name_date_time = c("date_time_start", "date_time_end")
)
m <- clean_metadata(project_files = example_files) |>
  add_sites(s) |>
  calc_sun()

params <- sim_selection_weights()
w <- calc_selection_weights(m, params = params)

# No stratification by site
samples <- sample_recordings(w, n = 10, os = 0.1, col_site_id = NULL)

# Stratification by site defined by...

# lists
samples <- sample_recordings(w, n = list(P01_1 = 2, P02_1 = 5, P03_1 = 2), os = 0.2)

# vectors
samples <- sample_recordings(w, n = c(P01_1 = 2, P02_1 = 5, P03_1 = 2), os = 0.2)

# data frame
samples <- sample_recordings(
  w,
  n = data.frame(
    site_id = c("P01_1", "P02_1", "P03_1"),
    n = c(2, 5, 2),
    n_os = c(0, 0, 1)
  )
)

Set pattern into ARUtools environment

Description

Set pattern into ARUtools environment

Usage

set_pattern(pattern_name, pattern)
set_pattern(pattern_name, pattern)

Arguments

`pattern_name`	string of variable to set
`pattern`	Pattern to add into ARUtools environment

Examples


og_pat <- get_pattern("pattern_date_time")

set_pattern("pattern_date_time", create_pattern_date())

glue::glue("Default pattern: {og_pat}")
glue::glue("Updated pattern: {get_pattern('pattern_date_time')}")

set_pattern("pattern_date_time", og_pat)


og_pat <- get_pattern("pattern_date_time")

set_pattern("pattern_date_time", create_pattern_date())

glue::glue("Default pattern: {og_pat}")
glue::glue("Updated pattern: {get_pattern('pattern_date_time')}")

set_pattern("pattern_date_time", og_pat)

Create parameters and simulate selection weights

Description

This function creates and explores parameters for generating selections. These parameters define the selection distribution of minutes (min) around the sun event (sunrise/sunset), as well as of days (day).

Usage

sim_selection_weights(
  min_range = c(-70, 240),
  min_mean = 30,
  min_sd = 60,
  day_range = c(120, 201),
  day_mean = 161,
  day_sd = 20,
  offset = 0,
  return_log = TRUE,
  selection_fun = "norm",
  selection_var = "psel_normalized",
  return_params = TRUE,
  plot = TRUE
)
sim_selection_weights(
  min_range = c(-70, 240),
  min_mean = 30,
  min_sd = 60,
  day_range = c(120, 201),
  day_mean = 161,
  day_sd = 20,
  offset = 0,
  return_log = TRUE,
  selection_fun = "norm",
  selection_var = "psel_normalized",
  return_params = TRUE,
  plot = TRUE
)

Arguments

`min_range`	Numeric vector. Range of the sampling distribution of minutes around the sun event.
`min_mean`	Numeric. Mean of the sampling distribution of minutes to the sun event.
`min_sd`	Numeric. SD in minutes of the sampling distribution of minutes around the sun event.
`day_range`	Date/Datetime/Numeric vector. Range of sampling distribution of days. Can be Dates, Date-times, or DOY (day-of-year, 1-366).
`day_mean`	Date/Datetime/Numeric. Mean date of the sampling distribution of days. Can be Date, Date-time, or DOY (day-of-year, 1-366).
`day_sd`	Numeric. SD in days of the sampling distribution of days.
`offset`	Numeric. Offset to shift for time of day in minutes.
`return_log`	Logical. Log the density in the selection function?
`selection_fun`	Character. Selection function to use. Options are `lognorm`, `norm` (default), or `cauchy`.
`selection_var`	Character. Selection variable to plot (if `plot = TRUE`). Options are are `psel`, `psel_doy`, `psel_min`, `psel_std`, `psel_scaled`, or `psel_normalized` (default).
`return_params`	Logical. Return parameter list for use in calc_selection_weights()?
`plot`	Logical. Create plot of simulated selection weights? If `return_param = TRUE` and `plot = TRUE` plot is created as a side effect. Other wise, plot is returned directly.

Value

Returns either a list of selection parameters or a plot of simulated selection weights

Examples

params <- sim_selection_weights()
params <- sim_selection_weights()

Create spectrogram image from wave file

Description

Using the external program SoX (the Swiss Army knife of sound processing programs), create a spectrogram image file. Note that you must have SoX installed to use this function. Spectrograms will be silently overwritten.

Usage

sox_spectro(
  path,
  dir_out = "Spectrograms",
  prepend = "spectro_",
  width = NULL,
  height = NULL,
  start = NULL,
  end = NULL,
  rate = "20k",
  dry_run = FALSE,
  quiet = FALSE,
  sox_file_path = NULL,
  skip_check = FALSE
)
sox_spectro(
  path,
  dir_out = "Spectrograms",
  prepend = "spectro_",
  width = NULL,
  height = NULL,
  start = NULL,
  end = NULL,
  rate = "20k",
  dry_run = FALSE,
  quiet = FALSE,
  sox_file_path = NULL,
  skip_check = FALSE
)

Arguments

`path`	Character. Path to wave file.
`dir_out`	Character. Output directory.
`prepend`	Character. Text to add to the start of the output file. Defaults to "spectro_".
`width`	Numeric. Width of the spectrogram image in pixels.
`height`	Numeric. Height of the spectrogram image in pixels.
`start`	Numeric/Character. Start the spectrogram at this time (seconds or HH:MM:SS format).
`end`	Numeric/Character. End time the spectrogram at this time (seconds or HH:MM:SS format).
`rate`	Numeric. Audio sampling rate to display (used by the `rate` effect in `sox`). This effectively limits the upper frequency of the spectrogram to rate/2. The default (`"20k"`), limits the spectrogram to 10kHz. Use `rate = NULL` for no limiting.
`dry_run`	Logical. If `TRUE` show the sox command, but do not run (for debugging and understanding precise details).
`quiet`	Logical. Whether to suppress progress messages and other non-essential updates.
`sox_file_path`	Path to sox file if not installed at the system level, otherwise NULL.
`skip_check`	Logical. Should the function skip check to ensure SoX is installed. This may allow speed ups if running across large numbers of files.

Details

Most arguments are passed through to the seewave::sox() command.

width and height correspond to the -x and -y options for the spectrogram effect.
start and end are used by the trim effect
rate is passed on to the rate effect

Based on code from Sam Hache.

Value

Does not return anything, but creates a spectrogram image in dir_out.

Examples

# Prep sample file
w <- tuneR::sine(440, duration = 300000)
td <- tempdir()
temp_wave <- glue::glue("{td}/test_wave.wav")
tuneR::writeWave(w, temp_wave)

# Create spectrograms

try({sox_spectro(temp_wave)
sox_spectro(temp_wave, rate = NULL)
sox_spectro(temp_wave, start = 2, end = 3)
sox_spectro(temp_wave, start = "0:01", end = "0:04")
sox_spectro(temp_wave, prepend = "")
})

# Clean up
unlink(temp_wave)
unlink("Spectrograms", recursive = TRUE)
# Prep sample file
w <- tuneR::sine(440, duration = 300000)
td <- tempdir()
temp_wave <- glue::glue("{td}/test_wave.wav")
tuneR::writeWave(w, temp_wave)

# Create spectrograms

try({sox_spectro(temp_wave)
sox_spectro(temp_wave, rate = NULL)
sox_spectro(temp_wave, start = 2, end = 3)
sox_spectro(temp_wave, start = "0:01", end = "0:04")
sox_spectro(temp_wave, prepend = "")
})

# Clean up
unlink(temp_wave)
unlink("Spectrograms", recursive = TRUE)

Example template of tasks for WildTrax

Description

A data frame with tasks generated from example_clean using the wildRtrax::wt_make_aru_tasks() function. Allows updating of tasks on WildTrax https://wildtrax.ca/.

Usage

task_template
task_template

Format

`task_template`

A data frame with 14 rows and 13 columns:

location: Site location name
recording_date_time: Date time of the recording
method: Method of interpretation (generally '1SPT')
taskLength: Length of recording in seconds
transcriber: Transcriber ID, to be filled in with function
rain: Empty character for filling in WildTrax
wind: Empty character for filling in WildTrax
industryNoise: Empty character for filling in WildTrax
audioQuality: Empty character for filling in WildTrax
taskComments: Empty character for filling in WildTrax
internal_task_id: Empty character for filling in WildTrax

Source

data-raw/data_wt_assign_tasks.R

Helper function to create test wave files

Description

Creates a directory structure and example wave files in temp folders.

Usage

temp_wavs(n = 6)
temp_wavs(n = 6)

Arguments

`n`	Numeric. How many test files to create (up to six). D

Value

vector of paths to temporary wave files

Examples

temp_wavs(n=3)

temp_wavs(n=3)

Example template of tasks for WildTrax

Description

A data frame showing example observers and their effort

Usage

template_observers
template_observers

Format

`template_observers`

A data frame with 4 rows and 2 columns:

transcriber: Interpreter name in Wildtrax system
hrs: Number of hours to assign to interpreter

Source

data-raw/data_wt_assign_tasks.R

Pre-processing of files for Wind Detection program

Description

This function takes a vector of wave file names and returns a list of three vectors that can be provided to the wind detection software or written to files that the software can read. Details of the usable fork of the wind detection software can be found at https://github.com/dhope/WindNoiseDetection

Usage

wind_detection_pre_processing(
  wav_files,
  site_pattern,
  output_directory,
  write_to_file = FALSE,
  chunk_size = NULL
)
wind_detection_pre_processing(
  wav_files,
  site_pattern,
  output_directory,
  write_to_file = FALSE,
  chunk_size = NULL
)

Arguments

`wav_files`	Vector of path to wav files
`site_pattern`	Pattern to extract sites from file names
`output_directory`	Directory path to export files to
`write_to_file`	Logical Should the function write files to output_directory
`chunk_size`	Numeric If not NULL, sets number of files to include in each chunk

Value

List including filePath, filenames, and sites suitable for wind software.

Examples

 wind_files <-
 wind_detection_pre_processing(
 wav_files = example_clean$path,
   output_directory = td,
     site_pattern = create_pattern_site_id(
         p_digits = c(2, 3), sep = "_",
             s_digits = c(1, 2)
               ),
                 write_to_file = FALSE, chunk_size = NULL
                 )


wind_files <-
 wind_detection_pre_processing(
 wav_files = example_clean$path,
   output_directory = td,
     site_pattern = create_pattern_site_id(
         p_digits = c(2, 3), sep = "_",
             s_digits = c(1, 2)
               ),
                 write_to_file = FALSE, chunk_size = NULL
                 )

Summarize wind detection results

Description

This function takes output from the command line program and summarizes it. Details of the wind detection software can be found at https://github.com/dhope/WindNoiseDetection.

Usage

wind_detection_summarize_json(f)
wind_detection_summarize_json(f)

Arguments

`f`	filepath for json #'

Value

tibble of summarized data from json file

Examples

# example code

 example_json <- system.file("extdata",
 "P71-1__20210606T232500-0400_SS.json",
 package = "ARUtools"
 )

 wind_summary <- wind_detection_summarize_json(example_json)

# example code

 example_json <- system.file("extdata",
 "P71-1__20210606T232500-0400_SS.json",
 package = "ARUtools"
 )

 wind_summary <- wind_detection_summarize_json(example_json)

Assign tasks for interpretation on Wildtrax

Description

Assign tasks for interpretation on Wildtrax

Usage

wt_assign_tasks(
  wt_task_template_in,
  interp_hours,
  wt_task_output_file,
  interp_hours_column,
  random_seed = NULL
)
wt_assign_tasks(
  wt_task_template_in,
  interp_hours,
  wt_task_output_file,
  interp_hours_column,
  random_seed = NULL
)

Arguments

`wt_task_template_in`	Path to csv template downloaded from Wildtrax platform https://wildtrax.ca listing all tasks. Alternatively, can be a data.frame that is correctly formatted using `wildRtrax::wt_make_aru_tasks()`. See `vignette("Misc")` for details.
`interp_hours`	Path to number of hours for each interpreter or a data.table. If a file, must be csv and must include the columns "transcriber" and whatever the variable `interp_hours_column` is.
`wt_task_output_file`	Path to csv of output file for uploading to Wildtrax. If left as NULL will not write file
`interp_hours_column`	LazyEval column name with hours for interpreters
`random_seed`	Integer. Random seed to select with. If left NULL will use timestamp

Value

Returns a list with a tibble of assigned tasks and a summary tibble.

Examples

  task_output <- wt_assign_tasks(
  wt_task_template_in = task_template,
  wt_task_output_file = NULL,
  interp_hours = template_observers,
  interp_hours_column = hrs,
  random_seed = 65122
  )

task_output <- wt_assign_tasks(
  wt_task_template_in = task_template,
  wt_task_output_file = NULL,
  interp_hours = template_observers,
  interp_hours_column = hrs,
  random_seed = 65122
  )

Package 'ARUtools'

Help Index

Get acoustic complexity values

Description

Usage

Arguments

Value

Examples

Add an ARU to the list of identified ARUs

Description

Usage

Arguments

Examples

Add site-level data to the metadata

Description

Usage

Arguments

Value

Examples

Add file name formated for Wildtrax to metadata

Description

Usage

Arguments

Value

Examples

ARUtools: Management and Processing of Autonomous Recording Unit (ARU) Data

Description

Author(s)

See Also

Calculate Selection Weights

Description

Usage

Arguments

Value

Examples

Calculate time to sunrise/sunset

Description

Usage

Arguments

Details

Value

Examples

Explore a file

Description

Usage

Arguments

Details

Value

Examples

Check output of clean_metadata()

Description

Usage

Arguments

Value

Examples

Check problems in output of clean_metadata()

Description

Usage

Arguments

Value

Examples

Check and clean GPS data

Description

Usage

Arguments

Details

Value

Examples

Extract log data from BAR-LT log files

Description

Usage

Arguments

Details

Value

Examples

Extract and clean ARU metadata from file names

Description

Usage

Arguments

Details

Check output of `clean_metadata()`

Check problems in output of `clean_metadata()`

`example_clean`

`example_files`

`example_files_long`

`example_sites`