Extract sighting information from aerial DAS data
Usage
airdas_sight(x, ...)
# S3 method for data.frame
airdas_sight(x, ...)
# S3 method for 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, or ObsR (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 VLI
#> 1 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 2 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 3 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 4 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 5 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 6 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 7 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 8 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 9 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 10 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 11 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 12 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 13 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 14 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 15 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 16 6 NA r FALSE FALSE TRUE 650 100 aa bb cc dd g
#> 17 6 NA n FALSE FALSE FALSE 650 100 aa bb cc dd g
#> 18 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 19 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 20 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 21 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 22 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 23 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 24 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 25 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 26 12 NA n FALSE FALSE FALSE 680 90 aa dd cc bb g
#> 27 12 NA r FALSE FALSE TRUE 680 90 aa dd cc bb g
#> 28 12 NA r FALSE FALSE TRUE 680 90 aa dd cc bb g
#> VLO VB VRI VRO EffortDot EventNum file_das line_num file_type
#> 1 g g g g TRUE 9 airdas_sample.das 9 turtle
#> 2 g g g g TRUE 10 airdas_sample.das 10 turtle
#> 3 g g g g TRUE 12 airdas_sample.das 12 turtle
#> 4 g g g g TRUE 14 airdas_sample.das 14 turtle
#> 5 g g g g TRUE 15 airdas_sample.das 15 turtle
#> 6 g g g g TRUE 16 airdas_sample.das 16 turtle
#> 7 g g g g TRUE 16 airdas_sample.das 16 turtle
#> 8 g g g g TRUE 18 airdas_sample.das 19 turtle
#> 9 g g g g TRUE 23 airdas_sample.das 24 turtle
#> 10 g g g g TRUE 26 airdas_sample.das 27 turtle
#> 11 g g g g TRUE 27 airdas_sample.das 28 turtle
#> 12 g g g g TRUE 28 airdas_sample.das 29 turtle
#> 13 g g g g TRUE 29 airdas_sample.das 30 turtle
#> 14 g g g g TRUE 31 airdas_sample.das 32 turtle
#> 15 g g g g TRUE 32 airdas_sample.das 33 turtle
#> 16 g g g g TRUE 34 airdas_sample.das 35 turtle
#> 17 g g g g TRUE 46 airdas_sample.das 47 turtle
#> 18 g g g g TRUE 65 airdas_sample.das 66 turtle
#> 19 g g g g TRUE 66 airdas_sample.das 67 turtle
#> 20 g g g g TRUE 68 airdas_sample.das 69 turtle
#> 21 g g g g TRUE 69 airdas_sample.das 70 turtle
#> 22 g g g g TRUE 70 airdas_sample.das 71 turtle
#> 23 g g g g TRUE 71 airdas_sample.das 72 turtle
#> 24 g g g g TRUE 73 airdas_sample.das 74 turtle
#> 25 g p g g TRUE 78 airdas_sample.das 79 turtle
#> 26 g p g g TRUE 80 airdas_sample.das 81 turtle
#> 27 g p g g TRUE 84 airdas_sample.das 85 turtle
#> 28 g p g g TRUE 86 airdas_sample.das 87 turtle
#> SightNo Obs Angle ObsStd SightStd Mixed SpCode GsTotal GsSp TurtleSize
#> 1 1 cc 67 TRUE TRUE FALSE mn 6 6 NA
#> 2 2 bb -60 TRUE TRUE FALSE mn 6 6 NA
#> 3 3 cc 38 TRUE TRUE FALSE mn 2 2 NA
#> 4 4 aa -50 TRUE TRUE FALSE mn 5 5 NA
#> 5 5 cc 49 TRUE TRUE FALSE bm 4 4 NA
#> 6 6 cc 42 TRUE TRUE TRUE gg 10 8 NA
#> 7 6 cc 42 TRUE TRUE TRUE er 10 2 NA
#> 8 7 aa -53 TRUE TRUE FALSE bm 5 5 NA
#> 9 8 dd 24 FALSE FALSE FALSE bm 2 2 NA
#> 10 9 aa -57 TRUE TRUE FALSE mn 4 4 NA
#> 11 10 cc 65 TRUE TRUE FALSE gg 5 5 NA
#> 12 <NA> aa -20 TRUE TRUE FALSE dc 1 1 5
#> 13 11 bb 87 TRUE TRUE FALSE pp 3 3 NA
#> 14 12 bb 82 TRUE TRUE FALSE gg 5 5 NA
#> 15 13 bb 54 TRUE TRUE FALSE pp 6 6 NA
#> 16 14 cc 62 TRUE TRUE FALSE gg 2 2 NA
#> 17 15 bb 50 TRUE TRUE FALSE mn 3 3 NA
#> 18 16 aa -31 TRUE TRUE FALSE mn 6 6 NA
#> 19 17 bb -59 FALSE FALSE FALSE bm 6 6 NA
#> 20 18 aa -62 TRUE TRUE FALSE gg 2 2 NA
#> 21 19 cc 42 TRUE TRUE FALSE bm 3 3 NA
#> 22 20 aa -48 TRUE TRUE FALSE bm 4 4 NA
#> 23 21 cc 63 TRUE TRUE FALSE pp 6 6 NA
#> 24 22 cc 43 TRUE TRUE FALSE pp 2 2 NA
#> 25 23 cc 56 TRUE TRUE FALSE mn 6 6 NA
#> 26 24 cc 37 TRUE TRUE FALSE mn 6 6 NA
#> 27 25 bb -76 FALSE FALSE FALSE pp 1 1 NA
#> 28 25 <NA> -70 NA NA NA <NA> NA NA NA
#> TurtleDirection TurtleTail
#> 1 NA <NA>
#> 2 NA <NA>
#> 3 NA <NA>
#> 4 NA <NA>
#> 5 NA <NA>
#> 6 NA <NA>
#> 7 NA <NA>
#> 8 NA <NA>
#> 9 NA <NA>
#> 10 NA <NA>
#> 11 NA <NA>
#> 12 90 n
#> 13 NA <NA>
#> 14 NA <NA>
#> 15 NA <NA>
#> 16 NA <NA>
#> 17 NA <NA>
#> 18 NA <NA>
#> 19 NA <NA>
#> 20 NA <NA>
#> 21 NA <NA>
#> 22 NA <NA>
#> 23 NA <NA>
#> 24 NA <NA>
#> 25 NA <NA>
#> 26 NA <NA>
#> 27 NA <NA>
#> 28 NA <NA>