load_raw_all | R Documentation |
This is a wrapper function which loads and combines raw data files. If
r_dir
is specified, these include all files in series of nested
folders, if r_list
is specified it includes only the list of files
specified.
load_raw_all( r_dir, r_list, pattern = "DATA", tz = Sys.timezone(), tz_disp = NULL, dst = FALSE, details = 1, logger_pattern = NA, time_format = "mdy HMS", extra_pattern = NULL, extra_name = NULL, sep = "", skip = 0, verbose = TRUE, feeder_pattern )
r_dir |
Character. The director that holds all your raw data files (can be in subdirectories). |
r_list |
Character. A list of files to import. |
pattern |
Character. A regular expression pattern that matches the files you wish to include. Defaults to "DATA" to include only DATA files and not NOTE files. |
tz |
Character. The time zone the date/times are in (should match one of
the zones produced by |
tz_disp |
Character. The time zone the date/times should be displayed in
(if not the same as |
dst |
Logical. Whether or not to use Daylight Savings. When set to FALSE timezones are converted to the Etc/GMT+X timezones which do not include DST. (Note this overrides the timezone specification such that a timezone of America/Vancouver, which would normally include DST in the summer, will be transformed to a timezone with the same GMT offset, but not including DST). |
details |
Numeric. Where to find logger details, either 0 (file name), 1 (first line) or 2 (first two lines). See 'details'. |
logger_pattern |
Character. A regular expression matching the logger id
in the file name. NA (default) matches file name (extension omitted) or
first line of the file (See the |
time_format |
Character. The date/time format of the 'date' and 'time'
columns combined. Defaults to "mdy HMS". Should be in formats usable by the
|
extra_pattern |
Character vector. A vector of regular expressions matching any extra information in the file or directory names. |
extra_name |
Character vector. A vector of column names matching the
order of |
sep |
Character. An override for the separator in the
|
skip |
Character. Extra lines to skip in addition to the lines specified by details. |
verbose |
Logical. Whether to include progress messages or not. |
feeder_pattern |
Deprecated. Use logger_pattern instead. |
Note that if both r_dir
and r_list
are specified, the directory
overrides the file list.
Each data file is assumed to contain three columns (without column names)
corresponding to animal_id
, date
and time
(without
date). By default they are expected to be separated by white space, but the
sep
argument can be modified to reflect other separators, such as
comma- or tab-separated data.
The columns date
and time
will be combined to extract the
date/time of each event. Thus, the time_format
argument specifies the
order of the combined date and time columns and should be in formats usable
by the lubridate::parse_date_time()
function from the
lubridate package (e.g., "ymd HMS", "mdy HMS", "dmy HMS", etc.). For
example, the default "mdy HMS" expects a date column in the format of
month/day/year and a time column in the format of H:M:S (note that separators
and leading zeros are ignored, thus month-day-year is equivalent to
month/day/year, see the order
argument of the
parse_date_time function for more information. More complex
formats can also be specified: For example, 09/30/16 2:00 pm can be
specified by time_format = "mdy HM p".
Logger details are the logger_id and the lat/lon for the logger. A value of 0 reflects that the logger_id is in the file name, defined by the pattern logger_pattern. A value of 1 reflects that the logger_id is in the first line of the file, also defined by the pattern logger_pattern. A value of 2 reflects that in addition to the logger_id being in the first line ofthe file, the lat/lon information is on the second line, in the format of "latitude, longitude" both in decimal format (spacing doesn't matter, but the comma does).
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