Python interface to R package diveMove
Project description
scikit-diveMove is a Python interface to R package diveMove for scientific data analysis, with a focus on diving behaviour analysis. It has utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided. scikit-diveMove communicates with a single R instance for access to low-level tools of package diveMove.
The table below shows which features of diveMove are accessible from scikit-diveMove:
diveMove |
scikit-diveMove |
Notes |
|
---|---|---|---|
Functionality |
Functions/Methods |
||
Movement |
austFilter rmsDistFilter grpSpeedFilter distSpeed readLocs |
Under consideration. |
|
Bout analysis |
boutfreqs boutinit bouts2.nlsFUN bouts2.nls bouts3.nlsFUN bouts3.nls bouts2.mleFUN bouts2.ll bouts2.LL bouts.mle labelBouts plotBouts plotBouts2.cdf bec2 bec3 |
BoutsNLS BoutsMLE |
Fully implemented in Python. |
Dive analysis |
readTDR createTDR |
TDR.__init__ TDRSource.__init__ |
Fully implemented. Single TDR class for data with or without speed measurements. |
calibrateDepth |
TDR.calibrate TDR.zoc TDR.detect_wet TDR.detect_dives TDR.detect_dive_phases |
Fully implemented |
|
calibrateSpeed rqPlot |
TDR.calibrate_speed |
New implementation of the algorithm entirely in Python. The procedure generates the plot concurrently. |
|
diveStats stampDive timeBudget |
TDR.dive_stats TDR.time_budget TDR.stamp_dives |
Fully implemented |
|
plotTDR plotDiveModel plotZOC |
TDR.plot TDR.plot_zoc_filters TDR.plot_phases TDR.plot_dive_model |
Fully implemented. Interactivity is the default, as standard matplotlib. |
|
getTDR getDepth getSpeed getTime getCCData getDtime getFileName |
TDR.tdr TDR.get_depth TDR.get_speed TDR.tdr.index TDR.src_file TDR.dtime |
Fully implemented. getCCData deemed redundant, as the columns can be accessed directly from the TDR.tdr attribute. |
|
getDAct getDPhaseLab getDiveDeriv getDiveModel getGAct |
TDR.get_wet_activity TDR.get_dives_details TDR.get_dive_deriv |
Fully implemented |
|
extractDive |
Fully implemented |
Installation
Type the following at a terminal command line:
pip install scikit-kinematics
Or install from source tree by typing the following at the command line:
python setup.py install
The documentation can also be installed as described in Documentation.
Once installed, skdiveMove can be easily imported as:
import skdiveMove as skdive
Dependencies
skdiveMove depends primarily on R package diveMove, which must be installed and available to the user running Python. If needed, install diveMove at the R prompt:
install.packages("diveMove")
Required Python packages are listed in the requirements file.
Documentation
Available at: https://spluque.github.io/scikit-diveMove
Alternatively, installing the package as follows:
pip install -e .["docs"]
allows the documentation to be built locally (choosing the desired target {“html”, “pdf”, etc.}):
make -C docs/ html
The html tree is at docs/build/html.
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