clean_site_index: Prepare and clean site index file

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

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,
  col_aru_id = "aru_id",
  col_site_id = "site_id",
  col_date_time = "date",
  col_coords = c("longitude", "latitude"),
  col_extra = NULL,
  resolve_overlaps = TRUE,
  quiet = FALSE
)

Arguments

site_index	Data frame (can be spatial) or file path. Site index data to clean. If file path, must be to a local csv or xlsx file.
col_aru_id	Character. Column name that contains ARU ids. Default 'aru_id'.
col_site_id	Character. Column name that contains site ids.
col_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.
col_coords	Character. Column names that contain longitude and latitude (in that order). Ignored if 'site_index' is spatial.
col_extra	Character. Column names for extra data to include. If a named vector, will rename the columns (see examples).
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,
                      col_aru_id = "ARU",
                      col_site_id = "Sites",
                      col_date_time = c("Date_set_out", "Date_removed"),
                      col_coords = c("lon", "lat"))

s <- clean_site_index(example_sites,
                      col_aru_id = "ARU",
                      col_site_id = "Sites",
                      col_date_time = c("Date_set_out", "Date_removed"),
                      col_coords = c("lon", "lat"),
                      col_extra = c("plot" = "Plots"))

# Without dates
eg <- dplyr::select(example_sites, -Date_set_out, -Date_removed)
s <- clean_site_index(eg,
                      col_aru_id = "ARU",
                      col_site_id = "Sites",
                      col_date_time = NULL,
                      col_coords = c("lon", "lat"),
                      col_extra = c("plot" = "Plots"))

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