Seal Dive Analyser

10 August 2005

Background

I wrote the "DIVE" program while in Hobart during 1992 to analyse data on seal and penguin diving behaviour. The program handles dive records collected from TDR loggers. Supported data includes "time and depth", or "time, depth and velocity." The purpose of the original analysis was to investigate foraging behaviour. The software analyses dive records and produces a number of outputs:

It partitions the dive record into individual dives.
It identifies different phases of the dive ("descent", "active", "ascent") and computes statistics for each phase, and for the entire dive.
It identifies periods of abnormally high or low velocity ("spikes") which are believed to indicate pursuit and capture of prey.
It identifies "wiggles" (local maxima and minima) during the active phase, and calculates their statistics.
It identifies specially shaped dive profiles ("normal", "sleep", "flat bottom").

Note that some features of the analysis are only calculated when velocity data is available. This includes "spikes", horizontal distance and speed.

While I can't say how many times this software has been used, it does get an occasional mention in research on antarctic mammals. For example:

Variability in the diving activity of Antarctic fur seals, Arctocephalus gazella, at Iles Kerguelen, 2002, Mary-Anne Lea, Mark Hindell, Christophe Guinet, and Simon Goldsworthy, Polar Biology.
Dive behaviour, foraging locations, and maternalattendance patterns of Australian fur seals (Arctocephalus pusillus doriferus), John P.Y. Arnould and Mark A. Hindell, 2001, Canadian Journal of Zoology, vol. 79, no. 1, pp. 35-48.
Swimming speed and foraging strategies of northern elephant seals, 2007, Jason L. Hassrick, Daniel E. Crocker, Ramona L. Zeno, Susanna B. Blackwell, Daniel P. Costa, Burney J. Le Boeuf, Deep Sea Research Part II, vol. 54, pp 369–383.

Details of the data model and analysis are available in the Dive Version 1 User Manual. The manual describes the statistics produced by the program, and the parameters which affect the analysis. Results can be viewed on the screen, or saved as text files, or CSV ("comma-separated values") files for import into spreadsheets. Included in this document are examples of the tabular (per-dive) statistics and the summary (over all dives) statistics. Samples of other output files are available here for download (right-click the link to download files). See the user manual for explanation of the file format.

Sample CSV statistics for entire dive record. Import this into your favourite spreadsheet.
Sample summary statistics over entire dive record. View this in a text editor. See Table 2 for further explanation.
Sample tabular statistics for single dive. View this in a text editor. See Table 1 for further explanation.
Sample extracted raw data for single dive. Import this into a spreadsheet.

The dive software also includes a basic browser that allows the user to visually inspect and navigate the processed data. Some examples of the displays are included below:

Figure 1 Visualisation of dive profile.
Figure 2 Visualisation of dive partitions.
Figure 3 Sleep dive.
Figure 4 Dive with largest number of "start" events.
Figure 5 Dive with longest duration.
Figure 6 Dive with maximal depth ("flat" dive).

Table 1 Statistics for dive.
Table 2 Summary statistics over entire dive record.

Figure 1: Visualisation of dive profile.

The plots on the left hand side of the screen show velocity versus time (top) and depth versus time (bottom). Spikes identify periods of abnormally high or low velocity and are show as green ("starts") and red ("stops"). Circles on the depth plot indicate local maxima and minima ("wiggles") in the dive profile. Dashed lines in the velocity profile indicate the mean velocity (lower line) and one standard deviation above the mean velocity (upper line). The plot on the right hand side shows the distribution of time spent at different depths.

Table 1: Statistics for dive.

A summary of the important statistics for a dive may be viewed on the screen, or saved to a text file for later use. Below is a table of statistics for the dive shown above (Figure 1). The statistics include:

Start time and duration of dive.
Time at surface before and after dive.
Average velocity during ascent and descent.
For each phase of the dive:
- mean, min, max and standard deviation of speed (m/s)
- min and max of depth (m)
- horizontal and vertical depth travelled (m)
- duration (minutes)
Similar satistics are also reported for wiggles, start and stop events.
The number of times a "stop" is followed immediately by a "start" event (this is called a "stop-start" event). Similarly for "start-stop" events.

Dive:      27 of 1660
Start:     Day 307, Hour 9.833300
Duration:  16.34 minutes
Surface:   Before dive 3.33 minutes,  After dive 3.17 minutes
Asleep:    0 minutes
Descent:   0.90 m/s
Ascent:    0.89 m/s
    Phase      Speed(m/s)                    Depth(m)    Distance(m) Time(min)
               Mean  SD    Min   Max   Vert  Min   Max   Horiz Vert    
    descent    1.49  0.54  0.3   2.3   0.91  3     198   340   198   3.63 
    active     1.06  0.32  0.0   1.9   0.43  156   234   619   249   9.57 
    ascent     1.11  0.23  0.6   1.5   0.93  9     159   197   156   2.81 
    total      1.17  0.41  0.0   2.3   0.62  3     234   1155  603   16.34
Active phase: 8 wiggles, 2 starts, 1 stops
Stop-Start: 1
    up slope   1.06  0.35  0.0   1.8   0.53  156   225   294   141   4.46 
    down slope 1.06  0.28  0.3   1.9   0.36  159   234   325   108   4.95 
    all starts 1.40  0.32  0.9   1.9   0.88  156   234   139   78    1.49 
    big start  1.42  0.30  1.1   1.9   1.06  207   234   70    42    0.66 
    deep start 1.42  0.30  1.1   1.9   1.06  207   234   70    42    0.66 
    long start 1.42  0.30  1.1   1.9   1.06  207   234   70    42    0.66 
    all stops  0.68  0.49  0.0   1.4   0.30  183   192   41    15    0.83

The table below includes a summary of the critical dive parameters over 1660 dives. For each parameter, the mean and standard deviation are given. The next columns list the minimum value, and the index of the dive at which this minimum occurred, and similar for the maximum value. From this index, the browser can be used to retrieve and inspect the dive profile.

Some examples from this table are shown in the next few figures. The links in the table will take you to the example figures.

Processed dives 0 to 1659
Statistic            Mean    SD      Min     Dive  Max     Dive  Dives
Total dive time      22.20   4.59    0.22    1183  38.83   1233  1660 
Surface time         2.41    2.35    0.16    187   75.83   391   1659 
Active time          14.81   4.14    0.13    1184  27.37   708   1588 
Ascent Rate          1.36    0.33    0.00    1183  2.12    556   1660 
Descent Rate         1.27    0.46    0.20    199   2.32    1490  1660 
Vertical Distance    982.14  378.83  15.00   1183  2409.00 1374  1660 
Horizontal Distance  2006.22 642.13  12.10   1183  3555.07 1379  1660 
Vertical Speed       0.73    0.22    0.23    201   1.57    1515  1660 
Horizontal Speed     1.49    0.38    0.34    67    2.18    1176  1660 
Wiggles              10.42   4.55    0.00    1184  27.00   734   1660 
Maximum Speed        2.57    0.44    0.70    1183  4.10    817   1660 
Time Asleep          11.32   3.82    1.97    58    21.37   452   118  
Maximum Depth        327.26  175.61  12.00   1183  699.00  1439  1660 
Starts               1.44    1.25    0.00    0     9.00    1140  1660 
Start Max Speed      2.46    0.57    0.80    139   4.10    818   1245 
Start Max Vertdist   53.66   38.97   0.00    783   255.00  906   1245 
Stops                1.56    1.51    0.00    0     7.00    538   1660 
Stop-Starts          1.03    0.17    1.00    11    2.00    752   95   
Start-Stops          1.14    0.37    1.00    12    3.00    896   356  
Bottom Time          10.15   4.26    0.13    1184  18.38   940   46