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.
explore(
tz = NULL,
datapack = NULL,
max.interval = 60,
minimum.detections = 2,
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"),
print.releases = TRUE,
plot.detections.by = c("stations", "arrays")
)The time zone of the study area. Must match one of the values
present in timezones.
A data bundle pre-compiled through the function preload.
May be used to run actel analyses based on R objects, rather than input files.
The number of minutes that must pass between detections for a new event to be created. Defaults to 60.
For tags with only one movement event, defines the minimum number of times a tag must have been recorded during the study period for it to be considered true detections and not random noise. Defaults to 2.
Detection data prior to the timestamp set in
start.time (in YYYY-MM-DD HH:MM:SS format) is not considered during
the analysis.
Detection data posterior to the timestamp set in
stop.time (in YYYY-MM-DD HH:MM:SS format) is not considered during
the analysis.
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 <U+00B4>the previous array is matched to the last detection on the target array to perform the calculations.
If a fish 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.
If a fish 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.
If a fish crosses a number of arrays equal or greater
than jump.error without being detected, a warning is issued. If left
NULL (default), no warnings are issued.
If a fish crosses a number of arrays equal or greater than
jump.error without being detected, user intervention is suggested.
If left NULL (default), user intervention is never suggested.
If a fish spends a number of days equal or greater
than inactive.error in a given array at the tail of the respective
detections, a warning is issued. If left NULL (default), no warnings are
issued.
If a fish 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.
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.
A vector of signals for which the user intends to manually define which movement events are valid and invalid.
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.
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.
Logical: Should actel automatically discard detections that do not fall within receiver deployment periods, or that were recorded before the respective fish were released?
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.
Logical: Should the processed detections be saved for future runs?
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".
Logical: Should the release sites be printed in the study area diagrams?
The type of y axis desired for the individual detection plots. One of "stations" (default) or "arrays".
A list containing:
bio: A copy of the biometrics input;
detections: A list containing all detections for each target fish;
valid.detections: A list containing the valid detections for each target fish;
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 fish;
valid.movements: A list containing the valid movement events for each target fish;
times: A data frame containing all arrival times (per fish) 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)
# NOT RUN {
# Start by moving to a temporary directory
old.wd <- getwd()
setwd(tempdir())
# Deploy the example workspace
exampleWorkspace("exampleWorkspace")
# Move your R session into the example workspace
setwd("exampleWorkspace")
# 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)
# }
# NOT RUN {
# }
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