Man pages for actel
Acoustic Telemetry Data Analysis

actelactel: Acoustic Telemetry Data Analysis
actel-deprecatedDeprecated functions in package 'actel'.
additional.residency.resultsExample residency results
advEfficiencyCalculate beta estimations for efficiency
appendToAppend to ...
assembleArrayCJSCombine the individual CJS's of each array into a single...
assembleGroupCJSAssembles CJS tables for all groups
assembleMatricesAssemble detection matrices
assembleOutputCreate status.df
assembleResidencyCollect summary information for the residency analysis
assembleSectionOverviewCreate section.overview
assembleSplitCJSAssembles CJS tables for all group x release site...
assembleTimetableCreate the timetable
assembleValidMovesWrapper for simplifyMovements
assembleValidSecMovesWrapper for sectionMovements
blameArraysFind which arrays to blame for a jump in movement events
blankWorkspaceCreate a Blank Workspace
breakMatricesByArrayBreak the detection matrices per array
check_argscheck.R arguments
checkArgumentsCheck argument quality
checkDeploymentStationsConfirm that the station names in the deployments table match...
checkDeploymentTimesConfirm that receivers were not re-deployed before being...
checkDetectionsBeforeReleaseCheck if there are detections for the target tags before...
checkDupDetectionsCheck if there are duplicated detection in the input data
checkDupSignalsCheck if there are duplicated signals in the detected tags.
checkFirstDetBackFromReleaseCheck for movements upstream of the release site.
checkGUICheck if the dependencies required to open a GUI are...
checkImpassablesFind out if a tag moved in an impossible direction
checkInactivenessFind if a tag is standing still in an array
checkIssue79warn users if they are about to run into an unfixed bug.
checkJumpDistanceCheck if tags are jumping over arrays
checkLinearityCheck that the tag linearly moved along the sections
checkMinimumNCheck the number of detections (total and per event) of a...
checkNoDetectionsCheck if there are detections matching the target tags.
checkReportCheck report compatibility
checkSMovesNVerify number of detections in section movements
checkSpeedscheck tag speeds against defined thresholds (in m/s)
checkTagsInUnknownReceiversCheck for target data in the unknown receivers
checkTokenVerify that the source data has been compiled using actel's...
checkUnknownReceiversFind detections from unknown receivers
circularSectionDraw a section on the outside of the circle
cjs_argsCJS.R arguments
collectStraysCollect summary information on the tags detected but that are...
combineCombine a list of vectors
combineCJSCombine multiple CJS models
compileDetectionsCombine ALS detections
completeMatrixComplete a Distances Matrix
convertCodesConvert code spaces
convertTimesConvert Times
countArrayFailuresFind and list arrays which failed during the movements of the...
countBackMovesCount backwards movements
createEventRangescollapse event indexes into ranges
createNewEventsUpon invalidating detections, recombines the remaining valid...
createStandardsStandardize serial numbers, stations and arrays in the...
createUniqueSerialsInclude the deployment in the serial number of the receive
createWorkspaceDeprecated function.
darkendarken colours
dataToListImport RData in a list format
decimalTimeConvert hh:mm:ss time to hh.hhh
deleteHelpersDelete temporary files
detectionsSingleWidgetDetections Widget (Single table version)
detectionsTabbedWidgetDetections Widget (Tabbed version)
discardFirstDiscard early detections
distancesMatrixCalculate Distances Matrix
dotListBreak the dot data frame into a list
dotMatrixCreate numerical distances between dot elements
dotPathsFind arrays valid for efficiency calculation
dualArrayCJSCalculate estimated last-array efficiency
dualMatrixCompile detection matrix for last array
efficiencyMatrixCompile inter-array detection matrix
emergencyBreakStandard procedure when aborting
emptyMatrixCreate a Template Distances Matrix
eventsSingleWidgetEvent Widget (Single table version)
eventsTabbedWidgetEvent Widget (Tabbed version)
example.biometricsExample biometric data
example.deploymentsExample deployment data
example.detectionsExample detection data
example.distancesExample distances matrix
example.resultsExample migration results
example.spatialExample spatial data
exampleWorkspaceDeploy Example Data
excludeTagsCollect summary information on the tags detected but that are...
expandEventHandler for event expansion
exploreExplorative Analysis
extractCodeSpacesExtract Code Spaces from transmitter names
extractSignalsExtract signals from transmitter names
factnearsq helper
findDirectChainsFind all arrays linked to an array in a given direction
findPeersFind efficiency peers for each array
findSecondsPerSectionCalculate number of seconds at each location per day
findShortestChainsFind the shortest paths between arrays
firstArrayFailureDetermine if the first array after release has failed
getDualMatricesPrepare intra-array matrices for selected arrays
getResidencyAssemble residency tables per tag
getSpeedsExtract speeds from the analysis results.
getTimesExtract timestamps from the analysis results.
gg_colour_hueGenerate default ggplot colours
globalRatiosCalculate number/percentage of tags at each location for each...
graphicalInvalidateOpens a new window that allows the user to determine movement...
graphicalInvalidateDetectionsOpens a new window that allows the user to determine...
groupMovementsGroup movements
includeIntraArrayEstimatesIncorporate intra-array estimates in the overall CJS object
includeMissingInclude tags that were never detected
includeUnknownReceiverTemporarily include missing receivers in the spatial object
invalidateDetectionsAllow the user to determine a given set of detections invalid
invalidateEventsAllow the user to determine a given movement event invalid
liveArrayTimesAssign live times to arrays
loadBioLoad Biometrics file
loadDeploymentsLoad deployments file and Check the structure
loadDetectionsLoad ALS detections
loadDistancesLoad distances matrix
loadSpatialLoad Spatial File
loadStudyDataLoad, structure and check the inputs
lowestSignalcleanly extract lowest signal from signals string
matchlTRUE/FALSE wrapper for match
match.POSIXtMatch POSIX values
mbGroupCJSCalculate CJS for each group for each array
mbSplitCJSCalculate CJS for each group.release combination
migrationMigration Analysis
minuteTimeConvert numeric time to HH:MM
move_argsmovements.R arguments
movementSpeedsCalculate time and speed
movementTimesCalculate movement times
myRoseDiagEdited rose diagram function NA's as FALSE
nearsqFind optimum plotting grid
oneWayMovesTrim movements table to contain only uni-directional...
overrideValidityChecksSkips all validity checks for a tag and allows the user to...
plotArrayPlot simultaneous/cumulative presences at a give array or set...
plotDetectionsPlot detections for a single tag
plotLivePlot array live times
plotMovesPlot moves for one ore more tags
plotRatiosPlot global/group residency
plotResidencyPlot residency for a single tag
plotSensorsPlot sensor data for a single tag
plotTimesPrint circular graphics for time series.
preloadLoad a dataset before running an analysis
preloadDetectionsRun quality checks on preloaded detections
printArrayOverviewprint Rmd fragment for inclusion in the report
printBiometricsPrint biometric graphics
printCircularPrint circular graphics for each array
printDotPrint DOT diagram
printDotplotsPrint dotplots
printEfficiencyPrint efficiency fragment
printExploreRmdPrint Rmd report
printGlobalRatiosprint the distribution of tags per location
printIndividualResidencyprint the individual locations per day
printIndividualsPrint individual graphics
printLastArrayPrint a simple barplot with the number of tags last seen at...
printLastSectionPrint a simple barplot with the number of tags last seen at...
printMigrationRmdPrint Rmd report
printProgressionPrint progression diagram
printResidencyRmdPrint Rmd report
printSectionTimesPrint arrival and departure times per section
printSensorDataPrint sensor data for each individual tag
printSurvivalGraphicPrint survival graphic
processStandardFileStandard detections file created for actel
processThelmaNewFileThelma new export files
processThelmaOldFileThelma old export files
processVemcoFileVemco files
readDotRead dot file or string
recoverLogRecover latest actel crash log
res_assembleOutputCreate status.df
res_efficiencyCalculate array efficiency for residency analysis
residencyResidency Analysis
resPositionsFind the location where the tag spent most time per day
resRatioscalculate residency ratios per tag
resRatiosIndOutcompile output of dailyRatios
ringsRelDraw rings at relative points
roseMeanDraw mean value in the axis margin
sectionMovementsCompress array-movements into section-movements
setSpatialStandardsCreate Standard Names for spatial elements
shapeToRasterLoad shapefile and convert to a raster object.
simpleCJSAnalytical CJS model
simplifyMovementsRemoves invalid events
speedReleaseToFirstCalculate time and speed since release.
splitDetectionsSplit detections by tag
splitNSplit a dataframe every nth row
splitSignalsSplit signals from multi-signal input
stationNameFind original station name
std.error.circularCalculate the standard error of the mean for circular data
stopAndReportstop function but paste error to the report too
storeStraysStore summary information on the stray tags detected in a...
substrRightSubset a character string counting from the right end
tableInteractionHandler for table interaction events
timesToCircularConvert a data frame with timestamps into a list of circular...
transferValidityTransfer validity updates from valid movements to all...
transformSpatialProcess spatial elements
transitionLayerCalculate Transition Layer
updateValidityupdate array-movement validity based on the section-movements
userInputWrap frequently used code to handle user input
user_interaction_argsuser_interaction.R arguments
validateDetectionsCompare original detections with the valid movements and...
vectorsIntoTablesTransform vectors into data frames with specific columns
widget_argswidget_setups.R arguments
actel documentation built on Oct. 19, 2023, 9:08 a.m.