actel: preload – R documentation

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preload

Load a dataset before running an analysis

Description

This function allows the user to prepare a set of R objects to be run through an explore, migration or residency analysis.

Usage

preload(
  biometrics,
  spatial,
  deployments,
  detections,
  dot,
  distances,
  tz,
  start.time = NULL,
  stop.time = NULL,
  section.order = NULL,
  exclude.tags = NULL,
  disregard.parallels = FALSE,
  discard.orphans = FALSE
)

Arguments

`biometrics`	A data frame containing biometric information.
`spatial`	A data frame containing spatial information.
`deployments`	A data frame containing deployment information.
`detections`	A data frame containing the detections.
`dot`	A DOT string of the array configuration.
`distances`	A distances matrix between arrays. See `distancesMatrix`.
`tz`	The time zone of the study area. Must match one of the values present in `timezones`.
`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.
`section.order`	A vector containing the order by which sections should be aligned in the results.
`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.
`disregard.parallels`	Logical: Should the presence of parallel arrays invalidate potential efficiency peers? See the vignettes for more details.
`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?

Value

A dataset that can be used as an input for actel's main analyses. This dataset contains:

bio: The biometric data
sections: The sections of the study area, if set using the argument sections (required to run residency and migration analyses)
deployments: The deployment data
spatial: The spatial data, split in stations and release sites.
dot: A table of array connections.
arrays: A list with the details of each array
dotmat: A matrix of distances between arrays (in number of arrays).
dist.mat: The distances matrix.
detections.list: A processed list of detections for each tag.
paths: A list of the possible paths between each pair of arrays.
disregard.parallels: Logical: Should parallel arrays invalidate efficiency peers? (required to run residency and migration analyses)
tz: The time zone of the study area

Examples

# This function requires a series of pre-created R objects.
# We can create them by loading the example files from actel:
aux <- system.file(package = "actel")[1]

bio <- read.csv(paste0(aux, "/example_biometrics.csv"))
deployments <- read.csv(paste0(aux, "/example_deployments.csv"))
spatial <- read.csv(paste0(aux, "/example_spatial.csv"))
detections <- read.csv(paste0(aux, "/example_detections.csv"))

dot <- "A0--A1--A2--A3--A4--A5--A6--A7--A8--A9"

# Now that we have the R objects created, we can run preload:

x <- preload(biometrics = bio, deployments = deployments, spatial = spatial,
 detections = detections, dot = dot, tz = "Europe/Copenhagen")

actel

Acoustic Telemetry Data Analysis

v1.2.1

GPL-3

Authors

Hugo Flávio [aut, cre] (<https://orcid.org/0000-0002-5174-1197>)

Initial release