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.
You can install mort from CRAN with the line below.
install.packages("mort")Please see the package vignettes for more details, as well as guidelines and tips for the following functions.
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.
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.
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.
mort is brand 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!