clean_site_index | R Documentation |
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.
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
)
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 |
name_site_id |
Character. Name of the column that contains site ids.
Default |
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 |
name_coords |
Character. Column names that contain longitude and
latitude (in that order). Ignored if |
name_extra |
Character. Column names for extra data to include. If a named
vector, will rename the columns (see examples). Default |
resolve_overlaps |
Logical. Whether or not to resolve date overlaps by
shifting the start/end dates to noon (default |
quiet |
Logical. Whether to suppress progress messages and other non-essential updates. |
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.
Standardized site index data frame
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")
)
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