Identifying potential mortalities

Duration of residence events

After identifying the most recent station change, the longest single residence event that occurred before the station change is identified for each animal.

These long residences can be explored by the user using the resmax() function (see the Digging vignette for more information). The output will look like this:

The longest residence event (60 days in the table above) is used as the threshold.

There are two options for how to apply the threshold:

last_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="last")

any_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="any")

actel_ex<-morts(data=data,type="actel",ID="auto",station="auto",method="any")

manual_ex<-morts(data=data,type="manual",ID="ID",station="Station.Name",
                 res.start="ResidenceStart",res.end="ResidenceEnd",
                 residences="ResidenceLength.days",units="days",method="any")

Cumulative residence events

Cumulative residence events are the length of time between when an animal was first detected at a station and when it was last detected at the same station, ignoring any gaps in detection (or cutoff in residences()). The black points in the plot below indicate the start and end of the longest cumulative residence events, before a station change, for each fish.

The threshold for cumulative residence events is identified similarly to that for single residence events. The cumulative residence events can be explored by the user using the resmaxcml() function (see the Digging vignette for more information). The output will look like this:

Note that the threshold in the example above is extremely large (1139 days). In this example, the large threshold is due to the drift and can be corrected by applying drift within morts(). See the Drift vignette for more information.

The threshold is then applied to cumulative residence events that occurred after the last station change to flag potential mortalities.

cumulative_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="cumulative")

Notes on selecting a method

The methods outlined above may not all be relevant for all species and acoustic arrays. Choosing an appropriate method is the responsibility of the user. It is recommended to at least run all methods and explore the results. The thresholds for cumulative residence events are typically much longer than those for single residence events. Running method="last" will identify potential mortalities that may have occurred recently, before reaching the cumulative threshold. Conversely, method="cumulative" may identify potential mortalities from multiple short residence events, which each on their own would not be long enough to be identified by method="any". In this way, running method="all" is the most conservative method.

all_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="all")

Output

The output of morts() is a dataframe, where each row is the residence event where a flagged mortality was identified:

1. recent

For method="recent", the timeframe for assessing infrequent residence events begins with the most recent residence event, and extends back in time for the recent.period. If the sum of the duration of all residence events in this timeframe is less than the threshold, the animal is flagged as a potential mortality. In the following example, animals are flagged if they were detected for less than 72 hours within one year (52 weeks) preceding their most recent residence event.

recent_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
                      method="recent",threshold=72,threshold.units="hours",
                      recent.period=52,recent.units="weeks")

2. defined

For method="defined", the timeframe for assessing infrequent residence events is specified (defined) by the user with the start and end arguments. In the following example, an animal is flagged as potential mortality if the sum of the duration of all residence events between 15 June and 15 October 2006 is less than 12 hours.

defined_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
                       method="defined",threshold=12,threshold.units="hours",
                      start="2006-06-15",end="2006-10-15")

Note that mort will assign the UTC timezone to start and end. If you want to define the period of interest using local times, it is recommended to convert local datetimes to POSIXt and then convert the timezone to UTC:

start=as.POSIXct("2022-06-15",tz="America/Edmonton")
start
#> [1] "2022-06-15 MDT"
attributes(start)$tzone<-"UTC"
start
#> [1] "2022-06-15 06:00:00 UTC"

The output of infrequent() is in the same format as the output of morts() (see above). The output from one method can be added to the output from the other, using the morts.prev argument. See below for more information on using morts.prev.

Exclude single detections

In morts(), the argument singles specifies if single detections are included as residence events. The default setting is singles=TRUE, to include single detections.

Note there is no singles argument for infrequent(), because the duration of residence events from single detections is 0, and therefore does not contribute to meeting the threshold.

Previously identified mortalities

The morts.prev argument in both morts() and infrequent() specifies a dataframe of previously flagged mortalities. The input dataframe to morts.prev must have been previously generated by mort, or have the same column names, column types, and in the same order as data. When new mortalities are identified, animal IDs that were already included in morts.prev are skipped. This option can be useful and make processing more efficient when new detection data and residence events are added to the dataset, whether from new animals that were tagged or new detections from previously tagged animals. It can also be useful when running multiple methods of identifying mortalities, since animal IDs identified in one method are skipped when running subsequent methods.

prev_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",morts.prev=recent_ex)

Look backwards

For both morts() and infrequent(), there is the option to look backwards (i.e., earlier) in the dataset. If the most recent station change occurred before the flagged mortality (i.e., the animal was detected earlier than the flagged mortality, at the same station, and with no detections elsewhere), the start dates and times of the flagged mortalities are shifted earlier. The default is backwards=FALSE; however, it is more conservative to set backwards=TRUE.

In the plot below, the black points show the flagged mortalities with backwards=FALSE, and the blue points show the flagged mortalities with backwards=TRUE. If only a blue point is visible for a given animal ID, then the flagged mortality is not shifted earlier with backwards=TRUE.

Note, when method="cumulative" and there is no seasonality, cumulative residence events will cover all consecutive detections at a given station, and backwards is unnecessary.

Drift and season

In some systems, an expelled tag or a tag from a dead animal may seem to move, due to currents or tides, or if the tag is located within range of two overlapping receivers. Both morts() and infrequent() include an option to specify stations or locations where drift may occur and to consider drift in identifying mortalities. For more information, see the Drift vignette.

For some species or systems with seasonal patterns in movement or residency, it may be desirable to only consider specific seasons or periods of time when identifying mortalities. morts() includes an option to specify dates to calculate thresholds and flag mortalities. For more information, see the Seasonality vignette. Note there is no option to apply season to infrequent(), but the season or period of interest could be used as the defined period with method="defined", as well as start and end arguments.