Archive Meta Data

Author(s)

Frederik Hindborg Jensen

Title

Detecting narwhal foraging behaviour

Description

Code and data for paper "Detecting narwhal foraging behaviour from accelerometer and depth data using mixed-effects logistic regression" by F.H. Jensen, O.M. Tervo, M.P. Heide-Jørgensen and S. Ditlevsen.

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buzz_data.txt contains data from used in the paper. To make the code more user friendly, we provide data with acceleration features already calculated as extracting these features are a long but trivial process (for instance: extracting the mean and SD of the 100 observations per second). We assume the reader is able to extract these from their own data set, using the descriptions in Section 2.3 of the paper. Results differ slightly from the published paper because of minor adjustments to the code. 

Buzz_detection_code.pdf contains an overview of the results and implementations reported in the paper

Buzz_detection_code.rmd is the R markdown version of the "Buzz_detection_code.pdf" with code and comments included.

Buzz_detection_code_chronological.R and Buzz_detection_code_leave_one_out.R contains the R code of "Buzz_detection_code.rmd" in separate files.

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Included data is measured at 1Hz and includes the following columns:
- Posixct: Date and time.
- Ind: Identification number of observed narwhal. 2017M3 and 2018M3 is the same narwhal tagged at different years.
- corrected_depth: Depth of the narwhal corrected for drifting as described in the paper.
- Buzz: Binary variable indicating whether a buzz startup was registered in the given second or not (1=yes 0=n).
- SD_X, SD_Y, SD_Z: Standard deviation of acceleration over 100 observations per second in dimension x, y, z.
- Mean_X, Mean_Y, Mean_Z: Mean acceleration over 100 observations per second in dimension x, y, z.
- RMS_X, RMS_Y, RMS_Z: Root mean square over 100 observations per second in dimension x, y, z.
- MinMax_X, MinMax_Y, MinMax_Z: Distance between minimum and maximum acceleration over 100 observations per second in dimension x, y, z.
- Corr_XY, Corr_YZ, Corr_ZX: Correlation between the respective acceleration dimensions over 100 observations per second.
- SD_Am, RMS_Am, MinMax_Am: Standard deviation, root mean square and min-max distance of magnitude of acceleration (defined by sqrt(A_x^2+A_y^2+A_z^2)).
- Mean_RMSjerk, SD_RMSjerk, RMS_RMSjerk and MinMax_RMSjerk: Mean, Standard deviation, root mean square, min-max distance of RMS jerk (described in section 2.2 of the paper).

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To reproduce results:

- Download dataset buzz_data.txt to working directory.

- Install relevant packages from the R file.

- Run R or rmd file to reproduce results from the paper and pdf.