explore: Explorative Analysis

In actel: Acoustic Telemetry Data Analysis

Explorative Analysis

Description

explore allows you to quickly get a summary of your data. You can use explore to get a general feel for the study results, and check if the input files are behaving as expected. It is also a good candidate if you just want to validate your detections for later use in other analyses.

Usage

explore(
  tz = NULL,
  datapack = 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,
  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.
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.
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?
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:

• bio: A copy of the biometrics input;

• 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;

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

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

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

See Also

migration, residency

Examples

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

# Deploy the example workspace
exampleWorkspace("explore_example")

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

# run the explore analysis. Ensure the tz argument
# matches the time zone of the study area. For the
# example dataset, tz = "Europe/Copenhagen"
results <- explore(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)

actel documentation built on Oct. 19, 2023, 9:08 a.m.