morts {mort}

Identify potential mortalities or expelled tags

Description

Identifies potential mortalities or expelled tags from passive acoustic telemetry data. Mortalities are identified based on thresholds derived from the dataset itself.

Usage

morts(
  data,
  type = "mort",
  ID,
  station,
  res.start = "auto",
  res.end = "auto",
  method = "all",
  units = "auto",
  residences = "auto",
  singles = TRUE,
  backwards = FALSE,
  drift = "none",
  ddd = NULL,
  from.station = NULL,
  to.station = NULL,
  drift.cutoff = NULL,
  drift.units = NULL,
  season.start = NULL,
  season.end = NULL,
  season.overlap = TRUE,
  morts.prev = NULL,
  verbose = TRUE
)

Arguments

data

a dataframe of residence events. Residence events must include tag ID, location name, start time, end time, and duration.

type

the method used to generate the residence events. Options are "mort", "actel", "glatos", "vtrack", or "manual". If "manual", then user must specify ID, station, res.start, res.end, residences, and units.

ID

a string of the name of the column in data that holds the tag or sample IDs.

station

a string of the name of the column in data that holds the station name or receiver location.

res.start

a string of the name of the column in data that holds the start date and time. Must be specified and in POSIXt or character in the format YYYY-mm-dd HH:MM:SS if type="manual".

res.end

a string of the name of the column in data that holds the end date and time. Must be specified and in POSIXt or character in the format YYYY-mm-dd HH:MM:SS if type="manual".

method

the method to be used in flagging mortalities. Options are "last", "any", "cumulative", or "all"

units

units of the duration of the residence events in data.

residences

a character string with the name of the column in data that holds the duration of the residence events.

singles

specifies if single detections (length of residence event = 0) should be retained. Default is TRUE. Note that if single detections are removed (singles=FALSE), backwards will also not include single detections.

backwards

option to examine residence events prior to the one that was flagged as a potential mortality. If prior residence events are at the same station/location as the flagged event, the time of the potential mortality is shifted earlier. Note that if backwards=TRUE, then the output of method="last" is the same as method="any".

drift

option to account for potential drifting in identifying thresholds and/or mortalities. Options are "none", "threshold", "morts", "both". Default is "none".

ddd

a dataframe of stations/locations where detected movement between stations may be due to drifting of an expelled tag or dead animal.

from.station

a string of the name of the column in ddd that contains the station/location names where drifting detections may start from. Must be identical to the station/location names in data.

to.station

a string of the name of the column in ddd that contains the station/location names where drifting detections may move to. Must be identical to the station/location names in data.

drift.cutoff

the maximum allowable time difference between detections to be considered a single residence event. Recommended to be the same as used to generate residence events in data.

drift.units

the units of the cutoff. Options are "secs", "mins", "hours", "days", and "weeks". Recommended to be the same as used to generate residence events in data.

season.start

the start date/time(s) of the period of interest. If the period of interest is the same in all study years, must be a character string in format "dd-mm". Otherwise, must be in POSIXt, or a character string in format YYYY-mm-dd HH:MM:SS.

season.end

the end date/time(s) of the period of interest. If the period of interest is the same in all study years, must be a character string in format "dd-mm". Otherwise, must be in POSIXt, or a character string in format YYYY-mm-dd HH:MM:SS.

season.overlap

option to include residence events that overlap either the beginning or the end of the period of interest. If TRUE, the full overlapping residence events will be retained. If FALSE, only the portion of the residence events that is within the period of interest will be retained, and residences will be recalculated, using specified units. Default is TRUE

morts.prev

a dataframe containing potential mortalities. The dataframe must have the same columns and in the same order as data.

verbose

option to display updates and progress bars as sub-functions are called and run. Default is TRUE.

season

a dataframe with start and end dates of the season(s) of interest

Value

a dataframe with one row for each tag ID, including the date/time of the residence start when the potential mortality or expelled tag was identified. All input data fields (e.g., any name, location, or species information that was included with the input data) will be retained.

Examples

morts_ex<-morts(data=events,type="mort",ID="ID",
station="Station.Name",method="any",verbose=FALSE)
head(morts_ex)

morts_ex_bw<-morts(data=events,type="mort",ID="ID",
station="Station.Name",method="any",backwards=TRUE,verbose=FALSE)
head(morts_ex_bw)