checkArguments: Check argument quality

Description

Check argument quality

Usage

checkArguments(
  dp,
  tz,
  min.total.detections,
  min.per.event,
  max.interval,
  speed.method = c("last to first", "last to last"),
  speed.warning,
  speed.error,
  start.time,
  stop.time,
  report,
  auto.open,
  save.detections,
  jump.warning,
  jump.error,
  inactive.warning,
  inactive.error,
  exclude.tags,
  override,
  print.releases,
  detections.y.axis = c("auto", "stations", "arrays"),
  if.last.skip.section = NULL,
  replicates = NULL,
  section.warning,
  section.error,
  section.order = NULL,
  timestep = c("days", "hours")
)

Value

updated parameters

Arguments

dp: A preloaded datapack (or NULL if no data was preloaded).
tz: The time zone of the study area. Must match one of the values present in timezones.
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.
max.interval: The number of minutes that must pass between detections for a new event to be created. Defaults to 60.
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.
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.
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.
save.detections: Logical: Should the processed detections be saved for future runs?
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.
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".
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.
section.warning: If a tag has section movement events with less or equal to section.warning detections, a warning is issued. Defaults to 1. To disable section warnings, set to 0. Must be equal to or greater than section.error.
section.error: If a tag has section movement events with less or equal to section.error detections, user intervention is suggested. Defaults to 1. To disable user intervention suggestions, set to 0.
section.order: A vector containing the order by which sections should be aligned in the results.
timestep: The resolution desired for the residency calculations. One of "days" (default) or "hours".