The goal of mort is to provide a framework to identify potentialmortalities or expelled tags in passive acoustic telemetry arrays withnon-overlapping receivers. The potential mortalities that are flagged bymort should be reviewed by the user, and considered for removal from thedataset.
Please note that this method is conservative, and therefore mayoverestimate the number of mortalities in the system. It is thereforenot advised to use the results as estimates of survival or taggingeffects. Rather, the purpose is to remove or reduce potential biasbefore conducting further analyses.
mort uses thresholds from the dataset itself, use-defined thresholds,and several customizable options, to allow application to a wide numberof species and acoustic arrays. By providing a standardized frameworkfor consideration of potential mortalities, we hope this tool will beuseful and encourage greater reproducibility in acoustic telemetryresearch.
You can install mort from CRAN with the line below.
install.packages("mort")Please see the package vignettes for more details, as well asguidelines and tips for the following functions.
residences condenses detection records into residenceevents, with a start time, end time, and duration. Residence events areused as the input for all other mort functions.
mortsplot generates plots of residence events usingggplot2. Plots are automatically formatted to maximizevisibility of the dataset, and can be further modified usingggplot2 commands. Interactive plots can also be generatedusingplotly.
morts identifies potential mortalities or expelled tags,based on the duration of single residence events or cumulative residenceevents (see vignettes for a complete explanation). Thresholds arederived from the input dataset.
infrequent identifies potential mortalities or expelledtags from infrequent or intermittent detections. Thresholds andtimeframes are defined by the user.
review examines new data to determine if an animal thatwas previously flagged as a mortality has moved, and may therefore bealive.
These are functions that may be called bymorts and/orinfrequent, depending on the options that are selected.These functions are fully documented so the user can explore their dataand the process used by mort.
stationchange identifies the most recent station orlocation 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 priorto the most recent station change for each individual.
resmaxcml generates cumulative residence events (fromthe first time an animal was detected at a given station to the lasttime an animal was detected at the same station, ignoring gaps indetection) that occurred prior to the most recent station change foreach individual.
drift creates drift events from sequential residenceevents, where detected movement between stations may be due to driftingof a dead animal or an expelled tag.
season selects residence events from user-specifiedseasons or periods of interest.
backwards shifts the start time of a flagged mortalityearlier, if the residence event that triggered the flag was not theearliest consecutive residence event at that station/location.
mort is brand new. Although it is has been tested extensively on acomplex dataset, we expect that issues will arise as mort is applied toother datasets and systems. If you run into any issues or have anysuggestions for improvements, please post an issue onGitHub, and we’llsee what we can do!