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Help find_dives
Find the start and end of dives in a depth
Syntax
Matlab & Octave
T = find_dives(p,fs,mindepth) or T = find_dives(p,fs,mindepth,surface) or T = find_dives(p,fs,mindepth,surface,findall)
R
T = find_dives(p,fs,mindepth) or T = find_dives(p,fs,mindepth,surface) or T = find_dives(p,fs,mindepth,surface,findall)
Description
Find time cues for the start and end of either dives in a depth record or flights in an altitude record.
Inputs
| Input var | Description | Units | Default value |
|---|---|---|---|
| p | is a depth or altitude time series (vector) | meters | N/A |
| fs | is the sampling rate of the sensor data | Hz (samples per second) | N/A |
| mindepth | is the threshold at which to recognize a dive or flight. | meters | N/A |
| surface | is the threshold at which the animal is presumed to have reached the surface. | meters | 1 |
| findall | when 1 forces the algorithm to include incomplete dives at the start and end of the record. | N/A | 0 (only recognize complete dives) |
Outputs
| Output var | Description | Units |
|---|---|---|
| T | is a structure array with size equal to the number of dives/flights found. The fields of T are:start: time in seconds of the start of each dive/flight,end: time in seconds of the start of each dive/flight, max: maximum depth/altitude reached in each dive/flight,tmaxtime in seconds at which the animal reaches the max depth/altitude | N/A |
Notes & assumptions
- Dives shallow or flights lower than mindepth will be ignored.
- A smaller value for surface can be used if the dive/altitude data are very accurate and you need to detect shallow dives/flights.
- If there are n dives/flights beyond mindepth in p, then T will be a structure containing n-element vectors, e.g., to access the start time of the kth dive/flight use T.start(k).
Example
Matlab & Octave
The example below uses data from the file testset1.nc. You can download it from the animaltags website's example data sets. If the file is saved in your current working directory, load it via:
testset1 = load_nc(‘testset1.nc’)
T = find_dives(testset1.P.data, testset1.P.sampling_rate, 5)
R
The example below uses data from the file testset1.nc. You can download it from the animaltags website's example data sets. If the file is saved in your current working directory, load it via:
testset1 <- load_nc(‘testset1.nc’)
T <- find_dives(p = testset1$P$data, fs = testset1$P$sampling_rate, mindepth = 5, surface = 2, findall = NULL)
About
bugs@animaltags.org Last modified: 10 May 2017