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Summarize number of sightings and animals for selected species by segment

Usage

airdas_effort_sight(x.list, sp.codes, sp.events = c("S", "t"))

Arguments

x.list

list; output of airdas_effort

sp.codes

character; species code(s) to include in segdata. These code(s) will be converted to lower case to match airdas_sight

sp.events

character; event code(s) to include in the sightinfo output. This argument supersedes the 'included' value when determining whether a sighting is included in the segment summaries. Must be one or more of: "S", "t" (case-sensitive). The default is that all of these event codes are kept

Value

A list, identical to x.list except for 1) the nSI and ANI columns added to x.list$segdata, one each for each element of sp.codes, and 2) the included column of x.list$sightinfo, which has been set as FALSE for sightings of species not listed in sp.codes

Details

This function takes the output of airdas_effort and adds columns for the number of sightings (nSI) and number of animals (ANI) for selected species (selected via sp.codes) for each segment to the segdata element of x.list. However, only sightings with an included value of TRUE (included is a column in sightinfo) are included in the summaries. Having this step separate from airdas_effort allows users to personalize the included values as desired for their analysis.

Examples

y <- system.file("airdas_sample.das", package = "swfscAirDAS")
y.proc <- airdas_process(y)
y.cond <- airdas_effort(
  y.proc, method = "condition", conditions = "Bft", seg.min.km = 0.05, 
  num.cores = 1
)

airdas_effort_sight(y.cond, sp.codes = c("mn", "bm"))
#> $segdata
#>   segnum section_id section_sub_id event transect              file stlin
#> 1      1          1              1     T       T1 airdas_sample.das     3
#> 2      2          1              2     T       T1 airdas_sample.das    36
#> 3      3          2              1     R       T1 airdas_sample.das    40
#> 4      4          2              2     R       T1 airdas_sample.das    44
#> 5      5          3              1     T       T2 airdas_sample.das    53
#> 6      6          3              2     T       T2 airdas_sample.das    78
#>   endlin     lat1      lon1           DateTime1     lat2      lon2
#> 1     36 39.23550 -123.1563 2015-04-09 12:30:59 39.23400 -123.4033
#> 2     37 39.23400 -123.4033 2015-04-09 12:37:57 39.23400 -123.4047
#> 3     44 39.23400 -123.4742 2015-04-09 12:40:00 39.23317 -123.5143
#> 4     49 39.23317 -123.5143 2015-04-09 12:41:08 39.23283 -123.6032
#> 5     78 39.22000 -123.6078 2015-04-09 12:46:51 39.21683 -123.3605
#> 6     88 39.21683 -123.3605 2015-04-09 12:54:04 39.21700 -123.2418
#>             DateTime2     mlat      mlon           mDateTime    dist year month
#> 1 2015-04-09 12:37:57 39.23309 -123.2797 2015-04-09 12:34:28 21.2882 2015     4
#> 2 2015-04-09 12:38:00 39.23400 -123.4040 2015-04-09 12:37:58  0.1148 2015     4
#> 3 2015-04-09 12:41:08 39.23323 -123.4942 2015-04-09 12:40:34  3.4595 2015     4
#> 4 2015-04-09 12:43:43 39.23245 -123.5588 2015-04-09 12:42:25  7.6620 2015     4
#> 5 2015-04-09 12:54:04 39.21667 -123.4842 2015-04-09 12:50:27 21.3146 2015     4
#> 6 2015-04-09 12:57:30 39.21700 -123.3011 2015-04-09 12:55:47 10.2336 2015     4
#>   day    mtime maxdistBft nSI_bm ANI_bm nSI_mn ANI_mn
#> 1   9 12:34:28          1      2      9      5     23
#> 2   9 12:37:58          2      0      0      0      0
#> 3   9 12:40:34          2      0      0      0      0
#> 4   9 12:42:25          1      0      0      1      3
#> 5   9 12:50:27          1      2      7      1      6
#> 6   9 12:55:47          2      0      0      2     12
#> 
#> $sightinfo
#>    segnum     mlat      mlon Event            DateTime      Lat       Lon
#> 1       1 39.23309 -123.2797     S 2015-04-09 12:31:35 39.23367 -123.1783
#> 2       1 39.23309 -123.2797     S 2015-04-09 12:31:47 39.23350 -123.1857
#> 3       1 39.23309 -123.2797     S 2015-04-09 12:31:56 39.23333 -123.1917
#> 4       1 39.23309 -123.2797     S 2015-04-09 12:32:20 39.23233 -123.2053
#> 5       1 39.23309 -123.2797     S 2015-04-09 12:32:30 39.23233 -123.2108
#> 6       1 39.23309 -123.2797     S 2015-04-09 12:32:42 39.23233 -123.2195
#> 7       1 39.23309 -123.2797     S 2015-04-09 12:32:42 39.23233 -123.2195
#> 8       1 39.23309 -123.2797     S 2015-04-09 12:33:43 39.23333 -123.2550
#> 9       1 39.23309 -123.2797     S 2015-04-09 12:35:13 39.23317 -123.3073
#> 10      1 39.23309 -123.2797     S 2015-04-09 12:36:13 39.23333 -123.3418
#> 11      1 39.23309 -123.2797     S 2015-04-09 12:36:26 39.23350 -123.3500
#> 12      1 39.23309 -123.2797     t 2015-04-09 12:36:26 39.23350 -123.3500
#> 13      1 39.23309 -123.2797     S 2015-04-09 12:36:43 39.23350 -123.3592
#> 14      1 39.23309 -123.2797     S 2015-04-09 12:37:01 39.23400 -123.3697
#> 15      1 39.23309 -123.2797     S 2015-04-09 12:37:16 39.23433 -123.3790
#> 16      1 39.23309 -123.2797     S 2015-04-09 12:37:37 39.23417 -123.3910
#> 17      4 39.23245 -123.5588     S 2015-04-09 12:42:13 39.23250 -123.5515
#> 18      5 39.21667 -123.4842     S 2015-04-09 12:51:40 39.21750 -123.4410
#> 19      5 39.21667 -123.4842     S 2015-04-09 12:51:55 39.21750 -123.4317
#> 20      5 39.21667 -123.4842     S 2015-04-09 12:52:03 39.21733 -123.4270
#> 21      5 39.21667 -123.4842     S 2015-04-09 12:52:04 39.21733 -123.4270
#> 22      5 39.21667 -123.4842     S 2015-04-09 12:52:07 39.21733 -123.4258
#> 23      5 39.21667 -123.4842     S 2015-04-09 12:52:17 39.21700 -123.4185
#> 24      5 39.21667 -123.4842     S 2015-04-09 12:52:54 39.21700 -123.3982
#> 25      6 39.21700 -123.3011     S 2015-04-09 12:54:34 39.21667 -123.3422
#> 26      6 39.21700 -123.3011     S 2015-04-09 12:55:20 39.21700 -123.3172
#> 27      6 39.21700 -123.3011     S 2015-04-09 12:56:49 39.21717 -123.2685
#>    OnEffort Trans Bft CCover Jelly HorizSun VertSun HKR  Haze  Kelp RedTide
#> 1      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 2      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 3      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 4      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 5      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 6      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 7      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 8      TRUE    T1   1     10     0        6      NA   n FALSE FALSE   FALSE
#> 9      TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 10     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 11     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 12     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 13     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 14     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 15     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 16     TRUE    T1   1     10     2        6      NA   r FALSE FALSE    TRUE
#> 17     TRUE    T1   1     20     0        6      NA   n FALSE FALSE   FALSE
#> 18     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 19     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 20     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 21     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 22     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 23     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 24     TRUE    T2   1     20     0       12      NA   n FALSE FALSE   FALSE
#> 25     TRUE    T2   2     20     0       12      NA   n FALSE FALSE   FALSE
#> 26     TRUE    T2   2     20     0       12      NA   n FALSE FALSE   FALSE
#> 27     TRUE    T2   2     20     0       12      NA   r FALSE FALSE    TRUE
#>    AltFt SpKnot ObsL ObsB ObsR Rec VLI VLO VB VRI VRO EffortDot EventNum
#> 1    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE        9
#> 2    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       10
#> 3    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       12
#> 4    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       14
#> 5    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       15
#> 6    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       16
#> 7    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       16
#> 8    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       18
#> 9    650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       23
#> 10   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       26
#> 11   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       27
#> 12   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       28
#> 13   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       29
#> 14   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       31
#> 15   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       32
#> 16   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       34
#> 17   650    100   aa   bb   cc  dd   g   g  g   g   g      TRUE       46
#> 18   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       65
#> 19   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       66
#> 20   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       68
#> 21   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       69
#> 22   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       70
#> 23   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       71
#> 24   680     90   aa   dd   cc  bb   g   g  g   g   g      TRUE       73
#> 25   680     90   aa   dd   cc  bb   g   g  p   g   g      TRUE       78
#> 26   680     90   aa   dd   cc  bb   g   g  p   g   g      TRUE       80
#> 27   680     90   aa   dd   cc  bb   g   g  p   g   g      TRUE       84
#>             file_das line_num file_type SightNo Obs Angle ObsStd SightStd Mixed
#> 1  airdas_sample.das        9    turtle       1  cc    67   TRUE     TRUE FALSE
#> 2  airdas_sample.das       10    turtle       2  bb   -60   TRUE     TRUE FALSE
#> 3  airdas_sample.das       12    turtle       3  cc    38   TRUE     TRUE FALSE
#> 4  airdas_sample.das       14    turtle       4  aa   -50   TRUE     TRUE FALSE
#> 5  airdas_sample.das       15    turtle       5  cc    49   TRUE     TRUE FALSE
#> 6  airdas_sample.das       16    turtle       6  cc    42   TRUE     TRUE  TRUE
#> 7  airdas_sample.das       16    turtle       6  cc    42   TRUE     TRUE  TRUE
#> 8  airdas_sample.das       19    turtle       7  aa   -53   TRUE     TRUE FALSE
#> 9  airdas_sample.das       24    turtle       8  dd    24  FALSE    FALSE FALSE
#> 10 airdas_sample.das       27    turtle       9  aa   -57   TRUE     TRUE FALSE
#> 11 airdas_sample.das       28    turtle      10  cc    65   TRUE     TRUE FALSE
#> 12 airdas_sample.das       29    turtle    <NA>  aa   -20   TRUE     TRUE FALSE
#> 13 airdas_sample.das       30    turtle      11  bb    87   TRUE     TRUE FALSE
#> 14 airdas_sample.das       32    turtle      12  bb    82   TRUE     TRUE FALSE
#> 15 airdas_sample.das       33    turtle      13  bb    54   TRUE     TRUE FALSE
#> 16 airdas_sample.das       35    turtle      14  cc    62   TRUE     TRUE FALSE
#> 17 airdas_sample.das       47    turtle      15  bb    50   TRUE     TRUE FALSE
#> 18 airdas_sample.das       66    turtle      16  aa   -31   TRUE     TRUE FALSE
#> 19 airdas_sample.das       67    turtle      17  bb   -59  FALSE    FALSE FALSE
#> 20 airdas_sample.das       69    turtle      18  aa   -62   TRUE     TRUE FALSE
#> 21 airdas_sample.das       70    turtle      19  cc    42   TRUE     TRUE FALSE
#> 22 airdas_sample.das       71    turtle      20  aa   -48   TRUE     TRUE FALSE
#> 23 airdas_sample.das       72    turtle      21  cc    63   TRUE     TRUE FALSE
#> 24 airdas_sample.das       74    turtle      22  cc    43   TRUE     TRUE FALSE
#> 25 airdas_sample.das       79    turtle      23  cc    56   TRUE     TRUE FALSE
#> 26 airdas_sample.das       81    turtle      24  cc    37   TRUE     TRUE FALSE
#> 27 airdas_sample.das       85    turtle      25  bb   -76  FALSE    FALSE FALSE
#>    SpCode GsTotal GsSp TurtleSize TurtleDirection TurtleTail included
#> 1      mn       6    6         NA              NA       <NA>     TRUE
#> 2      mn       6    6         NA              NA       <NA>     TRUE
#> 3      mn       2    2         NA              NA       <NA>     TRUE
#> 4      mn       5    5         NA              NA       <NA>     TRUE
#> 5      bm       4    4         NA              NA       <NA>     TRUE
#> 6      gg      10    8         NA              NA       <NA>    FALSE
#> 7      er      10    2         NA              NA       <NA>    FALSE
#> 8      bm       5    5         NA              NA       <NA>     TRUE
#> 9      bm       2    2         NA              NA       <NA>    FALSE
#> 10     mn       4    4         NA              NA       <NA>     TRUE
#> 11     gg       5    5         NA              NA       <NA>    FALSE
#> 12     dc       1    1          5              90          n    FALSE
#> 13     pp       3    3         NA              NA       <NA>    FALSE
#> 14     gg       5    5         NA              NA       <NA>    FALSE
#> 15     pp       6    6         NA              NA       <NA>    FALSE
#> 16     gg       2    2         NA              NA       <NA>    FALSE
#> 17     mn       3    3         NA              NA       <NA>     TRUE
#> 18     mn       6    6         NA              NA       <NA>     TRUE
#> 19     bm       6    6         NA              NA       <NA>    FALSE
#> 20     gg       2    2         NA              NA       <NA>    FALSE
#> 21     bm       3    3         NA              NA       <NA>     TRUE
#> 22     bm       4    4         NA              NA       <NA>     TRUE
#> 23     pp       6    6         NA              NA       <NA>    FALSE
#> 24     pp       2    2         NA              NA       <NA>    FALSE
#> 25     mn       6    6         NA              NA       <NA>     TRUE
#> 26     mn       6    6         NA              NA       <NA>     TRUE
#> 27     pp       1    1         NA              NA       <NA>    FALSE
#> 
#> $randpicks
#> NULL
#>