das_check: Check DAS file

In swfscDAS: Southwest Fisheries Science Center Shipboard DAS Data Processing

Check DAS file

Description

Check that DAS file has accepted formatting and values

Usage

das_check(
  file,
  skip = 0,
  file.out = NULL,
  sp.codes = NULL,
  print.cruise.nums = TRUE
)

Arguments

file	filename(s) of one or more DAS files
skip	integer: see read_fwf. Default is 0
file.out	filename to which to write the error log; default is NULL
sp.codes	character; filename of .dat file from which to read accepted species codes. If NULL, species codes will not be checked. Default is NULL
print.cruise.nums	logical; indicates if a table with all the cruise numbers in the x should be printed using table. Default is TRUE

Details

Precursor to a more comprehensive DASCHECK program. This function checks that the following is true:

• Event codes are one of the following: #, *, ?, 1, 2, 3, 4, 5, 6, 7, 8, A, B, C, E, F, k, K, N, P, Q, r, R, s, S, t, V, W, g, G, p, X, Y, Z

• Latitude values are between -90 and 90 (inclusive; NA values are ignored)

• Longitude values are between -180 and 180 (inclusive; NA values are ignored)

• The effort dot matches effort determined using B, R, and E events

• There are an equal number of R and E events, and they alternate occurrences

• A BR event series or R event does not occur while already on effort

• An E event does not occur while already off effort

• All Data# columns for non-C events are right-justified

• Only C events have data past the 99th column in the DAS file

• The following events have NA (blank) Data# columns: *

• All of *, B, R, E, V, W, N, P, and Q events have NA Data# columns where specified (see format pdf for more details)

• Event/column pairs meet the following requirements:

Item	Event	Column	Requirement
Cruise number	B	Data1	Can be converted to a numeric value
Mode	B	Data2	Must be one of C, P, c, p, or NA (blank)
Echo sounder	B	Data4	Must be one of Y, N, y, n, or NA (blank)
Effort type	R	Data1	Must be one of F, N, S, or NA (blank)
ESW sides	R	Data2	Effective strip width; must be one of F, H, or NA (blank)
Course	N	Data1	Can be converted to a numeric value
Speed	N	Data2	Can be converted to a numeric value
Beaufort	V	Data1	Must be a whole number between 0 and 9
Swell height	V	Data2	Can be converted to a numeric value
Wind speed	V	Data5	Can be converted to a numeric value
Rain or fog	W	Data1	Must be between 0 and 5 and either a whole number or have decimal value .5
Horizontal sun	W	Data2	Must be a whole number between 0 and 12
Vertical sun	W	Data3	Must be a whole number between 0 and 12
Visibility	W	Data5	Can be converted to a numeric value
Sighting (mammal)	S, K, M	Data3-7	Can be converted to a numeric value
Sighting (mammal)	G	Data5-7	Can be converted to a numeric value
Sighting cue (mammal)	S, K, M	Data3	Must be a whole number between 1 and 6
Sighting method (mammal)	S, K, M, G	Data4	Must be a whole number between 1 and 7
Bearing (mammal)	S, K, M, G	Data5	Must be a whole number between 0 and 360
Photos	A	Data3	Must be one of N, Y, n, y, or NA (blank)
Birds	A	Data4	Must be one of N, Y, n, y, or NA (blank)
Calibration school	S, K, M	Data10	Must be one of N, Y, n, y, or NA (blank)
Aerial photos taken	S, K, M	Data11	Must be one of N, Y, n, y, or NA (blank)
Biopsy taken	S, K, M	Data12	Must be one of N, Y, n, y, or NA (blank)
Species codes	A	Data5-8	If a species codes file is provided, must be one of the provided codes
Resight	s, k	Data2-5	Can be converted to a numeric value
Turtle species	t	Data2	If a species codes file is provided, must be one of the provided codes
Turtle sighting	t	Data3-5, 7	Can be converted to a numeric value
Turtle JFR	t	Data6	Must be one of F, J, N, R, or NA (blank)
Fishing vessel	F	Data2-4	Can be converted to a numeric value
Sighting info	1-8	Data2-8	Can be converted to a numeric value
Sighting info	1-8	Data9	The Data9 column must be NA (blank) for events 1-8

In the table above, 'between' means inclusive.

Long-term items, and checks that are not performed:

• Check that datetimes are sequential, meaning they 1) are the same as or 2) come after the previous event

• Check that A events only come immediately after a G/S/K/M event, and all G/S/K/M events have an A after them. And that each has at least one group size estimate (1:8 event)

Value

A data frame with columns: the file name, line number, cruise number, 'ID' (columns 4-39 from the DAS file), and description of the issue

If file.out is not NULL, then the error log data frame is also written to file.out using write.csv

A warning is printed if any events are r events; see das_process for details about r events

Examples

y <- system.file("das_sample.das", package = "swfscDAS")
if (interactive()) das_check(y)

swfscDAS documentation built on Aug. 10, 2023, 9:06 a.m.