migration {actel}

Migration Analysis

Description

The migration analysis runs the same initial checks as explore, but on top of it, it analyses the animal behaviour. By selecting the arrays that lead to success, you can define whether or not your animals survived the migration. Additional plots help you find out if some animal/tag has been acting odd. Multiple options allow you to tweak the analysis to fit your study perfectly.

Usage

migration(
  tz = NULL,
  section.order = NULL,
  datapack = NULL,
  success.arrays = NULL,
  max.interval = 60,
  minimum.detections,
  min.total.detections = 2,
  min.per.event = 1,
  start.time = NULL,
  stop.time = NULL,
  speed.method = c("last to first", "last to last"),
  speed.warning = NULL,
  speed.error = NULL,
  jump.warning = 2,
  jump.error = 3,
  inactive.warning = NULL,
  inactive.error = NULL,
  exclude.tags = NULL,
  override = NULL,
  report = FALSE,
  auto.open = TRUE,
  discard.orphans = FALSE,
  discard.first = NULL,
  save.detections = FALSE,
  if.last.skip.section = TRUE,
  replicates = NULL,
  disregard.parallels = TRUE,
  GUI = c("needed", "always", "never"),
  save.tables.locally = FALSE,
  print.releases = TRUE,
  detections.y.axis = c("auto", "stations", "arrays")
)

Arguments

tz

The time zone of the study area. Must match one of the values present in timezones.

section.order

A vector containing the order by which sections should be aligned in the results.

datapack

A data bundle pre-compiled through the function preload. May be used to run actel analyses based on R objects, rather than input files.

success.arrays

The arrays that mark the end of the study area. If a tag crosses one of these arrays, the respective animal is considered to have successfully migrated through the study area.

max.interval

The number of minutes that must pass between detections for a new event to be created. Defaults to 60.

minimum.detections

DEPRECATED. Please use the arguments min.total.detections and min.per.event instead.

min.total.detections

Minimum number of times a tag must have been detected during the study period for the detections to be considered true and not just random noise. Defaults to 2.

min.per.event

Minimum number of detections an event must have to be deemed valid. For analyses with both array and section events, a vector of two values can be provided. If only one value is provided, the same threshold applies for both types of events. Defaults to 1.

start.time

Detection data prior to the timestamp set in start.time (in YYYY-MM-DD HH:MM:SS format) is not considered during the analysis.

stop.time

Detection data posterior to the timestamp set in stop.time (in YYYY-MM-DD HH:MM:SS format) is not considered during the analysis.

speed.method

Can take two forms: 'last to first' or 'last to last'. If 'last to first' (default), the last detection on the previous array is matched to the first detection on the target array to perform the calculations. If 'last to last', the last detection on ´the previous array is matched to the last detection on the target array to perform the calculations.

speed.warning

If a tag moves at a speed equal or greater than speed.warning (in metres per second), a warning is issued. If left NULL (default), no warnings are issued. Must be equal to or lower than speed.error

speed.error

If a tag moves at a speed equal or greater than speed.error (in metres per second), user intervention is suggested. If left NULL (default), user intervention is never suggested.

jump.warning

If a tag crosses a number of arrays equal or greater than jump.warning without being detected, a warning is issued. Defaults to 2. To disable jump warnings, set to Inf. Must be equal to or lower than jump.error.

jump.error

If a tag crosses a number of arrays equal or greater than jump.error without being detected, user intervention is suggested. Defaults to 3. To disable user intervention suggestions, set to Inf.

inactive.warning

If a tag spends a number of days equal or greater than inactive.warning in a given array at the tail of the respective detections, a warning is issued. If left NULL (default), no warnings are issued. Must be equal to or lower than innactive.error.

inactive.error

If a tag spends a number of days equal or greater than inactive.error in a given array at the tail of the respective detections, user intervention is suggested. If left NULL (default), user intervention is never suggested.

exclude.tags

A vector of tags that should be excluded from the detection data before any analyses are performed. Intended to be used if stray tags from a different code space but with the same signal as a target tag are detected in the study area.

override

A vector of signals for which the user intends to manually define which movement events are valid and invalid.

report

Logical. Should an HTML report be created at the end of the analysis? NOTE: Setting report to TRUE will generate an HTML file in the current directory. Additionally, if auto.open = TRUE (default), the web browser will automatically be launched to open the report once the function terminates.

auto.open

Logical: Should the report be automatically opened once the analysis is over? Defaults to TRUE. NOTE: If report = TRUE and auto.open = TRUE, the web browser will automatically be launched to open the report once the function terminates.

discard.orphans

Logical: Should actel automatically discard detections that do not fall within receiver deployment periods, or that were recorded before the respective animals were released?

discard.first

A threshold amount of time (in hours) that must pass after release for the respective detections to be valid. Set to 0 to discard only the release-to-first-detection calculations.

save.detections

Logical: Should the processed detections be saved for future runs?

if.last.skip.section

Logical: Should a tag detected at the last array of a given section be considered to have disappeared in the next section?

replicates

A list containing, for each array to which intra-array efficiency is to be calculated: The standard names of the stations to be used as a replicate. See the vignettes for more details.

disregard.parallels

Logical: Should the presence of parallel arrays invalidate potential efficiency peers? See the vignettes for more details.

GUI

One of "needed", "always" or "never". If "needed", a new window is opened to inspect the movements only when the movements table is too big to be displayed in R's console. If "always", a graphical interface is always created when the possibility to invalidate events emerges. If "never", a graphical interface is never invoked. In this case, if the table to be displayed does not fit in R's console, a temporary file will be saved and the user will be prompted to open that file and examine it. Defaults to "needed".

save.tables.locally

Logical: If a table must be temporarily stored into a file for user inspection, should it be saved in the current working directory, or in R's temporary folder?

print.releases

Logical: Should the release sites be printed in the study area diagrams?

detections.y.axis

The type of y axis desired for the individual detection plots. While the argument defaults to "auto", it can be hard-set to one of "stations" or "arrays".

Value

A list containing:

• detections: A list containing all detections for each target tag;

• valid.detections: A list containing the valid detections for each target tag;

• spatial: A list containing the spatial information used during the analysis;

• deployments: A data frame containing the deployments of each receiver;

• arrays: A list containing the array details used during the analysis;

• movements: A list containing all movement events for each target tag;

• valid.movements: A list containing the valid movement events for each target tag;

• section.movements: A list containing the valid section shifts for each target tag;

• status.df: A data.frame containing summary information for each tag, including the following columns:

  • Times.entered.[section]: Number of times the tag was recorded entering a given section.

  • Average.time.until.[section]: Time spent between release or leaving another section and reaching at the given section.

  • Average.speed.to.[section]: Average speed from release or leaving one section and reaching the given section (if speed.method = "last to first"), or from release/leaving one section and leaving the given section (if speed.method = "last to last").

  • First.array.[section]: Array in which the tag was first detected in a given section

  • First.station.[section]: Standard name of the first station where the tag was detected in a given section

  • First.arrived.[section]: Very first arrival time at a given section

  • Average.time.in.[section]: Average time spent within a given section at each stay.

  • Average.speed.in.[section]: Average speed within a given section at each stay (only displayed if speed.method = "last to first").

  • Last.array.[section]: Array in which the tag was last detected in a given section

  • Last.station.[section]: Standard name of the last station where the tag was detected in a given section

  • Last.left.[section]: Very last departure time from a given section

  • Total.time.in[section]: Total time spent in a given section

  • Very.last.array: Last array where the tag was detected

  • Status: Fate assigned to the tag

  • Valid.detections: Number of valid detections

  • Invalid.detections: Number of invalid detections

  • Backwards.movements: Number of backward movement events

  • Max.cons.back.moves: Longest successive backwards movements

  • P.type: Type of processing:

    • 'Skipped' if no data was found for the tag,

    • 'Auto' if no user interaction was required,

    • 'Manual' if user interaction was suggested and the user made changes to the validity of the events,

    • 'Overridden' if the user listed the tag in the override argument.

  • Comments: Comments left by the user during the analysis

• section.overview: A data frame containing the number of tags that disappeared in each section;

• group.overview: A list containing the number of known and estimated tags to have passed through each array, divided by group;

• release.overview: A list containing the number of known and estimated tags to have passed through each array, divided by group and release sites;

• matrices: A list of CJS matrices used for the efficiency calculations;

• overall.CJS: A list of CJS results of the inter-array CJS calculations;

• intra.array.CJS: A list of CJS results of the intra-array CJS calculations;

• times: A data frame containing all arrival times (per tag) at each array;

• rsp.info: A list containing appendix information for the RSP package;

• dist.mat: The distance matrix used in the analysis (if a valid distance matrix was supplied)

See Also

explore, residency

Examples

# Start by moving to a temporary directory
old.wd <- getwd()
setwd(tempdir())

# Deploy the example workspace
exampleWorkspace("migration_example")

# Move your R session into the example workspace
setwd("migration_example")

# run the migration analysis. Ensure the tz argument
# matches the time zone of the study area and that the
# sections match your array names. The line below works
# for the example data.
results <- migration(tz = "Europe/Copenhagen")

# to obtain an HTML report, run the analysis with report = TRUE

# return to original working directory
setwd(old.wd)
rm(old.wd)