divebomb 0.1.0

divebomb dive classification algorithm

Divebomb is a python package that uses pandas to divide a timeseries of depths into individual dives.

Each dive is then profiled with the following attributes:

• max_depth - the max depth in the dive

• dive_start - the timestamp of the first point in the dive

• dive_end - the timestamp of the last point in the dive

• bottom_start - the timestamp of the first point in the dive when the animal is at depth

• td_bottom_duration - a timedelta object containing the duration of the time the animal is at depth in seconds

• td_descent_duration - a timedelta object containing the duration of the time the animal is descending in seconds

• td_ascent_duration - a timedelta object containing the duration of the time the animal is ascending in seconds

• td_surface_duration - a timedelta object containing the duration of the time the animal is at the surface in seconds

• bottom_variance - the variance of the depth while the animal is at the bottom of the dive

• dive_variance - the variance of the depth for the entire dive.

• descent_velocity - the average velocity of the descent

• ascent_velocity - the average velocity of the descent

• peaks - the number of peaks found in the dive profile

• left_skew - a boolean of 1 or 0 indicating if the dive is left skewed

• right_skew - a boolean of 1 or 0 indicating if the dive is right skewed

• no_skew - a boolean of 1 or 0 indicating if the dive is not skewed

The dive profiles are reduced to 8 dimensions using Principal Component Analsysis. Guassian Mixed Models are generated using theses variables and the minimal Bayesian Information Criterion is used to determine the optimal number of clusters. The dives are split into the clutsers using Agglomerative Hierarchical Clustering (from sklearn). The dives are then display through iPython notebooks or saved to netCDF files organized by cluster.