R/README_Rscripts.md

In EmmaLiTsai/recoverKBTDR: Recovering Records From Kooyman-Billups Time Depth Recorders (KBTDRs)

Series of .R scripts that fixes various issues with the KBTDR traces:

1. read_trace.R -- contains two functions to read and tidy the sample trace data (time dots and dive trace) into the global environment.

2. centering_functions.R -- contains methods for centering records and another function, centered_psi_calibration, that extracts the psi calibration curve after centering. It creates a data frame and was intended to make future depth calculations more accurate after centering.

3. zoc_functions.R -- contains functions for zero offset correction (zoc) of the trace before arc removal. This file is modeled after code that can be found in the diveMove package. The sample trace in this repo doesn't require zoc before arc removal, but some of the other records have extreme level shifts and/or drift in depth = 0 within a bout, so I thought this file may be useful to include. This file also includes an extra function (zoc_big_drift) to help zoc records that have extreme drift in depth = 0 such that zoc was usually difficult.

4. dive_tidy_functions.R -- contains organized production code that can be broken up into five main steps: (1-2) Transform coordinates: this aims to remove the arc in these data and also transform the x axis into time using the timing dots; (3) Creating a regular time series using linear interpolation. This helps with records that are discontinuous which makes future dive analysis challenging; (4) Transform y axis to depth: this step will transform interpolated y values to psi using the psi calibration at the end of the trace, and transform these psi values to depth; (5) Smoothing: this step smooths these data to simplify the trace. This is needed to help remove noise and extract the main trace from the thickness of the line, and for future dive analysis.

5. fast_recovery.R -- contains a non-essentail wrapper function that uses an argument file to pass trace-specific arguments to all functions in this repository. Intended to make recovery faster instead of having to run each function individually, but it is up to the user. This is likely more helpful if you have many KBTDR records to recover.

6. helper_functions.R -- non-essential functions intended to help with finding the best spar smoothing penalty and the height of the transducer arm for arc removal.

All other files within this folder are for documentation purposes.

EmmaLiTsai/recoverKBTDR documentation built on Aug. 29, 2024, 10:38 a.m.