mort

The goal of mort is to provide a framework to identify potential mortalities or expelled tags in passive acoustic telemetry arrays with non-overlapping receivers. The potential mortalities that are flagged by mort should be reviewed by the user, and considered for removal from the dataset.

Please note that this method is conservative, and therefore may overestimate the number of mortalities in the system. It is therefore not advised to use the results as estimates of survival or tagging effects. Rather, the purpose is to remove or reduce potential bias before conducting further analyses.

mort uses thresholds from the dataset itself, use-defined thresholds, and several customizable options, to allow application to a wide number of species and acoustic arrays. By providing a standardized framework for consideration of potential mortalities, we hope this tool will be useful and encourage greater reproducibility in acoustic telemetry research.

Installation

You can install mort from CRAN with the line below.

install.packages("mort")

To install mort directly from GitHub, including any updates that might not be released on CRAN yet, use the line below. Note that you must have the package devtools installed.

devtools::install_github("rosieluain/mort")

Package contents

Please see the package vignettes for more details, as well as guidelines and tips for the following functions.

Data preparation and visualization

residences condenses detection records into residence events, with a start time, end time, and duration. Residence events are used as the input for all other mort functions.

mortsplot generates plots of residence events using ggplot2. Plots are automatically formatted to maximize visibility of the dataset, and can be further modified using ggplot2 commands. Interactive plots can also be generated using plotly.

Identifying potential mortalities or expelled tags

morts identifies potential mortalities or expelled tags, based on the duration of single residence events or cumulative residence events (see vignettes for a complete explanation). Thresholds are derived from the input dataset.

infrequent identifies potential mortalities or expelled tags from infrequent or intermittent detections. Thresholds and timeframes are defined by the user.

review examines new data to determine if an animal that was previously flagged as a mortality has moved, and may therefore be alive.

Data and process exploration

These are functions that may be called by morts and/or infrequent, depending on the options that are selected. These functions are fully documented so the user can explore their data and the process used by mort.

stationchange identifies the most recent station or location change for each animal (i.e., the last time each animal moved, and therefore was assumed to be alive).

resmax extracts the residence events that occurred prior to the most recent station change for each individual.

resmaxcml generates cumulative residence events (from the first time an animal was detected at a given station to the last time an animal was detected at the same station, ignoring gaps in detection) that occurred prior to the most recent station change for each individual.

drift creates drift events from sequential residence events, where detected movement between stations may be due to drifting of a dead animal or an expelled tag.

season selects residence events from user-specified seasons or periods of interest.

backwards shifts the start time of a flagged mortality earlier, if the residence event that triggered the flag was not the earliest consecutive residence event at that station/location.

Disclaimer

mort is pretty new. Although it is has been tested extensively on a complex dataset, we expect that issues will arise as mort is applied to other datasets and systems. If you run into any issues or have any suggestions for improvements, please post an issue on GitHub, and we’ll see what we can do!