The residency analysis runs the same initial checks as
explore, but, similarly to migration, explores
particular points of the fish behaviour. If you want to know where your fish
were in each day of the study, how many fish were in each section each day,
and other residency-focused variables, this is the analysis you are looking
for!
residency(
tz = NULL,
sections,
section.order = 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,
section.minimum = 2,
replicates = NULL,
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.
DEPRECATED - list the sections in the spatial input instead.
A vector containing the order by which sections should be aligned in the results.
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?
If a fish has less than section.minimum
consecutive detections in a section, a warning is issued. Defaults to 2.
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.
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:
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;
section.movements: A list containing the valid section shifts for each target fish;
status.df: A data frame containing summary information for each fish, including the
following columns:
Times.entered.[section]: Total number of times the fish entered a given section
Average.entry.[section]: Average entry time at a given section
Average.time.[section]: Average time the fish spent in a given section during each visit
Average.departure.[section]: Average departure time from a given section
Total.time.[section]: Total time spent in a given section
Very.last.array: Last array where the fish was detected
Very.last.time: Time of the last valid detection
Status: Fate assigned to the fish
Valid.detections: Number of valid detections
Invalid.detections: Number of invalid detections
Valid.events: Number of valid events
Invalid.events: Number of invalid events
P.type: Type of processing:
'Skipped' if no data was found for the fish,
'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 fish in the
override argument.
Comments: Comments left by the user during the analysis
last.seen: A data frame containing the number of fish last seen in
each study area section;
array.times: A data frame containing ALL the entry times of each fish
in each array;
section.times: A data frame containing all the entry times of each
fish in each section;
residency.list: A list containing the places of residency between first and last
valid detection for each fish;
daily.ratios: A list containing the daily location per section (both in seconds spent
and in percentage of day) for each fish;
daily.positions: A data frame showing the location where each
fish spent the most time per day;
global.ratios: A list containing summary tables showing the number of active fish
(and respective percentages) present at each location per day;
efficiency: A list containing the results of the inter-array Multi-way efficiency
calculations (see vignettes for more details);
intra.array.CJS: A list containing the results of the intra-array CJS calculations;
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)
# 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 residency 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 <- residency(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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