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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")

To install mort directly from GitHub, including any updates that mightnot be released on CRAN yet, use the line below. Note that you must havethe packagedevtools installed.

devtools::install_github("rosieluain/mort")

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

residences condenses detection records into residence events, with astart time, end time, and duration. Residence events are used as theinput for all other mort functions.

mortsplot generates plots of residence events usingggplot2. Plotsare automatically formatted to maximize visibility of the dataset, andcan be further modified usingggplot2 commands. Interactive plots canalso be generated usingplotly.

morts identifies potential mortalities or expelled tags, based on theduration of single residence events or cumulative residence events (seevignettes for a complete explanation). Thresholds are derived from theinput dataset.

infrequent identifies potential mortalities or expelled tags frominfrequent or intermittent detections. Thresholds and timeframes aredefined by the user.

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

These are functions that may be called bymorts and/orinfrequent,depending on the options that are selected. These functions are fullydocumented so the user can explore their data and the process used bymort.

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

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

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

drift creates drift events from sequential residence events, wheredetected movement between stations may be due to drifting of a deadanimal or an expelled tag.

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

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

mort is pretty 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’ll see whatwe can do!