Extract sighting information from aerial DAS data
Usage
airdas_sight(x, ...)
# S3 method for class 'data.frame'
airdas_sight(x, ...)
# S3 method for class 'airdas_df'
airdas_sight(x, angle.min = 12, ...)Arguments
- x
airdas_dfobject; output fromairdas_process, or a data frame that can be coerced to aairdas_dfobject- ...
ignored
- angle.min
numeric; the minimum (absolute value) angle for which to consider a sighting a standard sighting. Default is 12
Value
Data frame with 1) the columns from x, excluding the 'Data#' columns,
and 2) columns with sighting information extracted from 'Data#' columns as described below.
The data frame has one row for each sighting, or one row for each
species of each sighting if it is a multi-species (mixed) sighting.
Added sighting information columns:
| Sighting information | Column name | Notes |
| Sighting number | SightNo | Observer that made the sighting |
| Obs | Angle of declination | Angle |
| Left is negative | Sighting by standard observer | ObsStd |
| Logical; described in Details | Standard sighting | SightStd |
| Logical; described in Details | Mixed species sighting | Mixed |
| Logical | Species code | SpCode |
| All characters converted to lower case | Group size of school | GsTotal |
| Only different from GsSp for mixed species sightings | Group size of species | GsSp |
| Turtle length (feet if numeric) | TurtleSize | NA for non-"t" events; may be character or numeric |
| Turtle travel direction (degrees) | TurtleDirection | NA for non-"t" events |
| Turtle tail visible? | TurtleTail | NA for non-"t" events |
The TurtleSize will be of class character is there is any
CARETTA data in x, and of class numeric otherwise.
Details
AirDAS events contain specific information in the 'Data#' columns,
with the information depending on the event code and file type for that row.
This function extracts relevant data for sighting events, and returns a
data frame with dedicated columns for each piece of sighting information.
It can handle multiple file types in x; for instance,
x could be processed PHOCOENA and TURTLE data
combined using rbind.
See airdas_format_pdf for more information about the expected
events and event formats, depending on the file type.
All species codes are converted to lower case using tolower.
Abbreviations used in column names include: Gs = group size, Sp = species,
Mixed = mixed species (multi-species) sighting.
In addition, note that multi-species group sizes are rounded to
the nearest whole number using round(, 0)
A 'sighting by a standard observer' ('ObsStd') is a sighting
made by ObsL, ObsB, ObsR, ObsLR, or ObsRR (not the data recorder or pilot).
A 'standard sighting' ('SightStd') is a sighting
that was made while on effort, by a standard observer,
and with the absolute value of the angle of declination
being greater than or equal to angle.min.
Resights (Events 's') are not considered standard events,
and thus both 'ObsStd' and 'SightStd' will be NA for 's' events.
Examples
y <- system.file("airdas_sample.das", package = "swfscAirDAS")
y.proc <- airdas_process(y)
airdas_sight(y.proc)
#> Event DateTime Lat Lon OnEffort Trans Bft CCover Jelly
#> 1 S 2015-04-09 12:31:35 39.23367 -123.1783 TRUE T1 1 10 0
#> 2 S 2015-04-09 12:31:47 39.23350 -123.1857 TRUE T1 1 10 0
#> 3 S 2015-04-09 12:31:56 39.23333 -123.1917 TRUE T1 1 10 0
#> 4 S 2015-04-09 12:32:20 39.23233 -123.2053 TRUE T1 1 10 0
#> 5 S 2015-04-09 12:32:30 39.23233 -123.2108 TRUE T1 1 10 0
#> 6 S 2015-04-09 12:32:42 39.23233 -123.2195 TRUE T1 1 10 0
#> 7 S 2015-04-09 12:32:42 39.23233 -123.2195 TRUE T1 1 10 0
#> 8 S 2015-04-09 12:33:43 39.23333 -123.2550 TRUE T1 1 10 0
#> 9 S 2015-04-09 12:35:13 39.23317 -123.3073 TRUE T1 1 10 2
#> 10 S 2015-04-09 12:36:13 39.23333 -123.3418 TRUE T1 1 10 2
#> 11 S 2015-04-09 12:36:26 39.23350 -123.3500 TRUE T1 1 10 2
#> 12 t 2015-04-09 12:36:26 39.23350 -123.3500 TRUE T1 1 10 2
#> 13 S 2015-04-09 12:36:43 39.23350 -123.3592 TRUE T1 1 10 2
#> 14 S 2015-04-09 12:37:01 39.23400 -123.3697 TRUE T1 1 10 2
#> 15 S 2015-04-09 12:37:16 39.23433 -123.3790 TRUE T1 1 10 2
#> 16 S 2015-04-09 12:37:37 39.23417 -123.3910 TRUE T1 1 10 2
#> 17 S 2015-04-09 12:42:13 39.23250 -123.5515 TRUE T1 1 20 0
#> 18 S 2015-04-09 12:51:40 39.21750 -123.4410 TRUE T2 1 20 0
#> 19 S 2015-04-09 12:51:55 39.21750 -123.4317 TRUE T2 1 20 0
#> 20 S 2015-04-09 12:52:03 39.21733 -123.4270 TRUE T2 1 20 0
#> 21 S 2015-04-09 12:52:04 39.21733 -123.4270 TRUE T2 1 20 0
#> 22 S 2015-04-09 12:52:07 39.21733 -123.4258 TRUE T2 1 20 0
#> 23 S 2015-04-09 12:52:17 39.21700 -123.4185 TRUE T2 1 20 0
#> 24 S 2015-04-09 12:52:54 39.21700 -123.3982 TRUE T2 1 20 0
#> 25 S 2015-04-09 12:54:34 39.21667 -123.3422 TRUE T2 2 20 0
#> 26 S 2015-04-09 12:55:20 39.21700 -123.3172 TRUE T2 2 20 0
#> 27 S 2015-04-09 12:56:49 39.21717 -123.2685 TRUE T2 2 20 0
#> 28 s 2015-04-09 12:57:00 39.21700 -123.2617 TRUE T2 2 20 0
#> HorizSun VertSun HKR Haze Kelp RedTide AltFt SpKnot ObsL ObsB ObsR Rec
#> 1 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 2 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 3 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 4 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 5 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 6 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 7 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 8 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 9 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 10 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 11 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 12 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 13 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 14 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 15 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 16 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd
#> 17 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd
#> 18 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 19 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 20 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 21 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 22 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 23 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 24 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 25 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 26 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb
#> 27 12 NA r FALSE FALSE TRUE 680 90 aa dd cc bb
#> 28 12 NA r FALSE FALSE TRUE 680 90 aa dd cc bb
#> ObsLR ObsRR VLI VLO VB VRI VRO EffortDot EventNum file_das line_num
#> 1 <NA> <NA> g g g g g TRUE 9 airdas_sample.das 9
#> 2 <NA> <NA> g g g g g TRUE 10 airdas_sample.das 10
#> 3 <NA> <NA> g g g g g TRUE 12 airdas_sample.das 12
#> 4 <NA> <NA> g g g g g TRUE 14 airdas_sample.das 14
#> 5 <NA> <NA> g g g g g TRUE 15 airdas_sample.das 15
#> 6 <NA> <NA> g g g g g TRUE 16 airdas_sample.das 16
#> 7 <NA> <NA> g g g g g TRUE 16 airdas_sample.das 16
#> 8 <NA> <NA> g g g g g TRUE 18 airdas_sample.das 19
#> 9 <NA> <NA> g g g g g TRUE 23 airdas_sample.das 24
#> 10 <NA> <NA> g g g g g TRUE 26 airdas_sample.das 27
#> 11 <NA> <NA> g g g g g TRUE 27 airdas_sample.das 28
#> 12 <NA> <NA> g g g g g TRUE 28 airdas_sample.das 29
#> 13 <NA> <NA> g g g g g TRUE 29 airdas_sample.das 30
#> 14 <NA> <NA> g g g g g TRUE 31 airdas_sample.das 32
#> 15 <NA> <NA> g g g g g TRUE 32 airdas_sample.das 33
#> 16 <NA> <NA> g g g g g TRUE 34 airdas_sample.das 35
#> 17 <NA> <NA> g g g g g TRUE 46 airdas_sample.das 47
#> 18 <NA> <NA> g g g g g TRUE 65 airdas_sample.das 66
#> 19 <NA> <NA> g g g g g TRUE 66 airdas_sample.das 67
#> 20 <NA> <NA> g g g g g TRUE 68 airdas_sample.das 69
#> 21 <NA> <NA> g g g g g TRUE 69 airdas_sample.das 70
#> 22 <NA> <NA> g g g g g TRUE 70 airdas_sample.das 71
#> 23 <NA> <NA> g g g g g TRUE 71 airdas_sample.das 72
#> 24 <NA> <NA> g g g g g TRUE 73 airdas_sample.das 74
#> 25 <NA> <NA> g g p g g TRUE 78 airdas_sample.das 79
#> 26 <NA> <NA> g g p g g TRUE 80 airdas_sample.das 81
#> 27 <NA> <NA> g g p g g TRUE 84 airdas_sample.das 85
#> 28 <NA> <NA> g g p g g TRUE 86 airdas_sample.das 87
#> file_type SightNo Obs Angle ObsStd SightStd Mixed SpCode GsTotal GsSp
#> 1 turtle 1 cc 67 TRUE TRUE FALSE mn 6 6
#> 2 turtle 2 bb -60 TRUE TRUE FALSE mn 6 6
#> 3 turtle 3 cc 38 TRUE TRUE FALSE mn 2 2
#> 4 turtle 4 aa -50 TRUE TRUE FALSE mn 5 5
#> 5 turtle 5 cc 49 TRUE TRUE FALSE bm 4 4
#> 6 turtle 6 cc 42 TRUE TRUE TRUE gg 10 8
#> 7 turtle 6 cc 42 TRUE TRUE TRUE er 10 2
#> 8 turtle 7 aa -53 TRUE TRUE FALSE bm 5 5
#> 9 turtle 8 dd 24 FALSE FALSE FALSE bm 2 2
#> 10 turtle 9 aa -57 TRUE TRUE FALSE mn 4 4
#> 11 turtle 10 cc 65 TRUE TRUE FALSE gg 5 5
#> 12 turtle <NA> aa -20 TRUE TRUE FALSE dc 1 1
#> 13 turtle 11 bb 87 TRUE TRUE FALSE pp 3 3
#> 14 turtle 12 bb 82 TRUE TRUE FALSE gg 5 5
#> 15 turtle 13 bb 54 TRUE TRUE FALSE pp 6 6
#> 16 turtle 14 cc 62 TRUE TRUE FALSE gg 2 2
#> 17 turtle 15 bb 50 TRUE TRUE FALSE mn 3 3
#> 18 turtle 16 aa -31 TRUE TRUE FALSE mn 6 6
#> 19 turtle 17 bb -59 FALSE FALSE FALSE bm 6 6
#> 20 turtle 18 aa -62 TRUE TRUE FALSE gg 2 2
#> 21 turtle 19 cc 42 TRUE TRUE FALSE bm 3 3
#> 22 turtle 20 aa -48 TRUE TRUE FALSE bm 4 4
#> 23 turtle 21 cc 63 TRUE TRUE FALSE pp 6 6
#> 24 turtle 22 cc 43 TRUE TRUE FALSE pp 2 2
#> 25 turtle 23 cc 56 TRUE TRUE FALSE mn 6 6
#> 26 turtle 24 cc 37 TRUE TRUE FALSE mn 6 6
#> 27 turtle 25 bb -76 FALSE FALSE FALSE pp 1 1
#> 28 turtle 25 <NA> -70 NA NA NA <NA> NA NA
#> TurtleSize TurtleDirection TurtleTail
#> 1 NA NA <NA>
#> 2 NA NA <NA>
#> 3 NA NA <NA>
#> 4 NA NA <NA>
#> 5 NA NA <NA>
#> 6 NA NA <NA>
#> 7 NA NA <NA>
#> 8 NA NA <NA>
#> 9 NA NA <NA>
#> 10 NA NA <NA>
#> 11 NA NA <NA>
#> 12 5 90 n
#> 13 NA NA <NA>
#> 14 NA NA <NA>
#> 15 NA NA <NA>
#> 16 NA NA <NA>
#> 17 NA NA <NA>
#> 18 NA NA <NA>
#> 19 NA NA <NA>
#> 20 NA NA <NA>
#> 21 NA NA <NA>
#> 22 NA NA <NA>
#> 23 NA NA <NA>
#> 24 NA NA <NA>
#> 25 NA NA <NA>
#> 26 NA NA <NA>
#> 27 NA NA <NA>
#> 28 NA NA <NA>