Man pages for actel
Acoustic Telemetry Data Analysis
| actel | actel: Acoustic Telemetry Data Analysis |
| actel-deprecated | Deprecated functions in package 'actel'. |
| additional.residency.results | Example residency results |
| advEfficiency | Calculate beta estimations for efficiency |
| appendTo | Append to ... |
| assembleArrayCJS | Combine the individual CJS's of each array into a single... |
| assembleGroupCJS | Assembles CJS tables for all groups |
| assembleMatrices | Assemble detection matrices |
| assembleOutput | Create status.df |
| assembleResidency | Collect summary information for the residency analysis |
| assembleSectionOverview | Create section.overview |
| assembleSplitCJS | Assembles CJS tables for all group x release site... |
| assembleTimetable | Create the timetable |
| assembleValidMoves | Wrapper for simplifyMovements |
| assembleValidSecMoves | Wrapper for sectionMovements |
| blameArrays | Find which arrays to blame for a jump in movement events |
| blankWorkspace | Create a Blank Workspace |
| breakMatricesByArray | Break the detection matrices per array |
| check_args | check.R arguments |
| checkArguments | Check argument quality |
| checkDeploymentStations | Confirm that the station names in the deployments table match... |
| checkDeploymentTimes | Confirm that receivers were not re-deployed before being... |
| checkDetectionsBeforeRelease | Check if there are detections for the target tags before... |
| checkDupDetections | Check if there are duplicated detection in the input data |
| checkDupSignals | Check if there are duplicated signals in the detected tags. |
| checkFirstDetBackFromRelease | Check for movements upstream of the release site. |
| checkGUI | Check if the dependencies required to open a GUI are... |
| checkImpassables | Find out if a tag moved in an impossible direction |
| checkInactiveness | Find if a tag is standing still in an array |
| checkIssue79 | warn users if they are about to run into an unfixed bug. |
| checkJumpDistance | Check if tags are jumping over arrays |
| checkLinearity | Check that the tag linearly moved along the sections |
| checkMinimumN | Check the number of detections (total and per event) of a... |
| checkNoDetections | Check if there are detections matching the target tags. |
| checkReport | Check report compatibility |
| checkSMovesN | Verify number of detections in section movements |
| checkSpeeds | check tag speeds against defined thresholds (in m/s) |
| checkTagsInUnknownReceivers | Check for target data in the unknown receivers |
| checkToken | Verify that the source data has been compiled using actel's... |
| checkUnknownReceivers | Find detections from unknown receivers |
| circularSection | Draw a section on the outside of the circle |
| cjs_args | CJS.R arguments |
| collectStrays | Collect summary information on the tags detected but that are... |
| combine | Combine a list of vectors |
| combineCJS | Combine multiple CJS models |
| compileDetections | Combine ALS detections |
| completeMatrix | Complete a Distances Matrix |
| convertCodes | Convert code spaces |
| convertTimes | Convert Times |
| copyOfCirclePlotRad | circular:::circlePlotRad |
| copyOfRosediagRad | circular:::RosediagRad |
| countArrayFailures | Find and list arrays which failed during the movements of the... |
| countBackMoves | Count backwards movements |
| createEventRanges | collapse event indexes into ranges |
| createNewEvents | Upon invalidating detections, recombines the remaining valid... |
| createStandards | Standardize serial numbers, stations and arrays in the... |
| createUniqueSerials | Include the deployment in the serial number of the receive |
| createWorkspace | Deprecated function. |
| darken | darken colours |
| dataToList | Import RData in a list format |
| decimalTime | Convert hh:mm:ss time to hh.hhh |
| deleteHelpers | Delete temporary files |
| detectionsSingleWidget | Detections Widget (Single table version) |
| detectionsTabbedWidget | Detections Widget (Tabbed version) |
| discardFirst | Discard early detections |
| distancesMatrix | Calculate Distances Matrix |
| dotList | Break the dot data frame into a list |
| dotMatrix | Create numerical distances between dot elements |
| dotPaths | Find arrays valid for efficiency calculation |
| dualArrayCJS | Calculate estimated last-array efficiency |
| dualMatrix | Compile detection matrix for last array |
| efficiencyMatrix | Compile inter-array detection matrix |
| emergencyBreak | Standard procedure when aborting |
| emptyMatrix | Create a Template Distances Matrix |
| eventsSingleWidget | Event Widget (Single table version) |
| eventsTabbedWidget | Event Widget (Tabbed version) |
| example.biometrics | Example biometric data |
| example.deployments | Example deployment data |
| example.detections | Example detection data |
| example.distances | Example distances matrix |
| example.results | Example migration results |
| example.spatial | Example spatial data |
| exampleWorkspace | Deploy Example Data |
| excludeTags | Collect summary information on the tags detected but that are... |
| expandEvent | Handler for event expansion |
| explore | Explorative Analysis |
| extractCodeSpaces | Extract Code Spaces from transmitter names |
| extractSignals | Extract signals from transmitter names |
| fact | nearsq helper |
| findDirectChains | Find all arrays linked to an array in a given direction |
| findPeers | Find efficiency peers for each array |
| findSecondsPerSection | Calculate number of seconds at each location per day |
| findShortestChains | Find the shortest paths between arrays |
| firstArrayFailure | Determine if the first array after release has failed |
| getDualMatrices | Prepare intra-array matrices for selected arrays |
| getResidency | Assemble residency tables per tag |
| getSpeeds | Extract speeds from the analysis results. |
| getTimes | Extract timestamps from the analysis results. |
| gg_colour_hue | Generate default ggplot colours |
| globalRatios | Calculate number/percentage of tags at each location for each... |
| graphicalInvalidate | Opens a new window that allows the user to determine movement... |
| graphicalInvalidateDetections | Opens a new window that allows the user to determine... |
| groupMovements | Group movements |
| includeIntraArrayEstimates | Incorporate intra-array estimates in the overall CJS object |
| includeMissing | Include tags that were never detected |
| includeUnknownReceiver | Temporarily include missing receivers in the spatial object |
| invalidateDetections | Allow the user to determine a given set of detections invalid |
| invalidateEvents | Allow the user to determine a given movement event invalid |
| liveArrayTimes | Assign live times to arrays |
| loadBio | Load Biometrics file |
| loadDeployments | Load deployments file and Check the structure |
| loadDetections | Load ALS detections |
| loadDistances | Load distances matrix |
| loadDot | Load spatial.dot |
| loadShape | DEPRECATED |
| loadSpatial | Load Spatial File |
| loadStudyData | Load, structure and check the inputs |
| lowestSignal | cleanly extract lowest signal from signals string |
| matchl | TRUE/FALSE wrapper for match |
| match.POSIXt | Match POSIX values |
| mbGroupCJS | Calculate CJS for each group for each array |
| mbSplitCJS | Calculate CJS for each group.release combination |
| migration | Migration Analysis |
| minuteTime | Convert numeric time to HH:MM |
| move_args | movements.R arguments |
| movementSpeeds | Calculate time and speed |
| movementTimes | Calculate movement times |
| myRoseDiag | Edited rose diagram function |
| na.as.false | Consider NA's as FALSE |
| nearsq | Find optimum plotting grid |
| oneWayMoves | Trim movements table to contain only uni-directional... |
| overrideValidityChecks | Skips all validity checks for a tag and allows the user to... |
| plotArray | Plot simultaneous/cumulative presences at a give array or set... |
| plotDetections | Plot detections for a single tag |
| plotLive | Plot array live times |
| plotMoves | Plot moves for one ore more tags |
| plotRatios | Plot global/group residency |
| plotResidency | Plot residency for a single tag |
| plotSensors | Plot sensor data for a single tag |
| plotTimes | Print circular graphics for time series. |
| preload | Load a dataset before running an analysis |
| preloadDetections | Run quality checks on preloaded detections |
| printArrayOverview | print Rmd fragment for inclusion in the report |
| printBiometrics | Print biometric graphics |
| printCircular | Print circular graphics for each array |
| printDot | Print DOT diagram |
| printDotplots | Print dotplots |
| printEfficiency | Print efficiency fragment |
| printExploreRmd | Print Rmd report |
| printGlobalRatios | print the distribution of tags per location |
| printIndividualResidency | print the individual locations per day |
| printIndividuals | Print individual graphics |
| printLastArray | Print a simple barplot with the number of tags last seen at... |
| printLastSection | Print a simple barplot with the number of tags last seen at... |
| printMigrationRmd | Print Rmd report |
| printProgression | Print progression diagram |
| printResidencyRmd | Print Rmd report |
| printSectionTimes | Print arrival and departure times per section |
| printSensorData | Print sensor data for each individual tag |
| printSurvivalGraphic | Print survival graphic |
| processStandardFile | Standard detections file created for actel |
| processThelmaNewFile | Thelma new export files |
| processThelmaOldFile | Thelma old export files |
| processVemcoFile | Vemco files |
| readDot | Read dot file or string |
| recoverLog | Recover latest actel crash log |
| res_assembleOutput | Create status.df |
| res_efficiency | Calculate array efficiency for residency analysis |
| residency | Residency Analysis |
| resPositions | Find the location where the tag spent most time per day |
| resRatios | calculate residency ratios per tag |
| resRatiosIndOut | compile output of dailyRatios |
| ringsRel | Draw rings at relative points |
| roseMean | Draw mean value in the axis margin |
| sectionMovements | Compress array-movements into section-movements |
| setSpatialStandards | Create Standard Names for spatial elements |
| shapeToRaster | Load shapefile and convert to a raster object. |
| simpleCJS | Analytical CJS model |
| simplifyMovements | Removes invalid events |
| speedReleaseToFirst | Calculate time and speed since release. |
| splitDetections | Split detections by tag |
| splitN | Split a dataframe every nth row |
| splitSignals | Split signals from multi-signal input |
| stationName | Find original station name |
| std.error.circular | Calculate the standard error of the mean for circular data |
| stopAndReport | stop function but paste error to the report too |
| storeStrays | Store summary information on the stray tags detected in a... |
| substrRight | Subset a character string counting from the right end |
| tableInteraction | Handler for table interaction events |
| timesToCircular | Convert a data frame with timestamps into a list of circular... |
| transferValidity | Transfer validity updates from valid movements to all... |
| transformSpatial | Process spatial elements |
| transitionLayer | Calculate Transition Layer |
| updateValidity | update array-movement validity based on the section-movements |
| userInput | Wrap frequently used code to handle user input |
| user_interaction_args | user_interaction.R arguments |
| validateDetections | Compare original detections with the valid movements and... |
| vectorsIntoTables | Transform vectors into data frames with specific columns |
| widget_args | widget_setups.R arguments |
