add_sites: Add site-level data to the metadata

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

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
)

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,
                      col_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, col_date_time = NULL)
m <- add_sites(m, s, by_date = NULL)

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