| das_check {swfscDAS} | R Documentation |
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 |
file.out |
filename to which to write the error log;
default is |
sp.codes |
character; filename of .dat file from which to read
accepted species codes. If |
print.cruise.nums |
logical; indicates if a table with all the
cruise numbers in the |
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)