actel

actel: Acoustic Telemetry Data Analysis

Deprecated functions in package actel.

Example residency results

Calculate beta estimations for efficiency

Append to ...

Combine the individual CJS's of each array into a single table

Assembles CJS tables for all groups

Assemble detection matrices

Create status.df

Collect summary information for the residency analysis

Create section.overview

Assembles CJS tables for all group x release site combinations

Create the timetable

Wrapper for simplifyMovements

Wrapper for sectionMovements

Find which arrays to blame for a jump in movement events

Break the detection matrices per array

Check argument quality

Confirm that the station names in the deployments table match those listed in the spatial file

Confirm that receivers were not re-deployed before being retrieved

Check if there are detections for the target tags before release.

Check if there are duplicated detection in the input data

Check if there are duplicated signals in the detected tags.

Check if the dependencies required to open a GUI are installed, and if opening a GUI does not throw an error. Some code adapted from RGtk2's .onLoad function.

Find out if a tag moved in an impossible direction

Find if a tag is standing still in an array

Check if tags are jumping over arrays

Check that the tag linearly moved along the sections

Check that the tag have enough detections to be valid

Check if there are detections matching the target tags.

Check report compatibility

Verify number of detections in section movements

check tag speeds against defined thresholds (in m/s)

Check for target data in the unknown receivers

Verify that the source data has been compiled using actel's preload function

Find detections from unknown receivers

Check for movements upstream of the release site.

check.R arguments

Draw a section on the outside of the circle

CJS.R arguments

Collect summary information on the tags detected but that are not part of the study.

Combine a list of vectors

Combine multiple CJS models

Combine ALS detections

Complete a Distances Matrix

Convert code spaces

Convert Times

circular:::circlePlotRad

circular:::RosediagRad

Find and list arrays which failed during the movements of the tags

Count backwards movements

collapse event indexes into ranges

Upon invalidating detections, recombines the remaining valid detections into new events, and merges them with the remaining events.

Standardize serial numbers, stations and arrays in the detections

Include the deployment in the serial number of the receive

Create a Default Workspace

darken colours

Import RData in a list format

Convert hh:mm:ss time to hh.hhh

Delete temporary files

Detections Widget (Single table version)

Detections Widget (Tabbed version)

Discard early detections

Calculate Distances Matrix

Break the dot data frame into a list

Create numerical distances between dot elements

Find arrays valid for efficiency calculation

Calculate estimated last-array efficiency

Compile detection matrix for last array

Compile inter-array detection matrix

Standard procedure when aborting

Create a Template Distances Matrix

Event Widget (Single table version)

Event Widget (Tabbed version)

Example biometric data

Example deployment data

Example detection data

Example distances matrix

Example migration results

Example spatial data

Deploy Example Data

Collect summary information on the tags detected but that are not part of the study.

Handler for event expansion

Explorative Analysis

Extract Code Spaces from transmitter names

Extract signals from transmitter names

nearsq helper

Find all arrays linked to an array in a given direction

Find efficiency peers for each array

Calculate number of seconds at each location per day

Find the shortest paths between arrays

Determine if the first array after release has failed

Prepare intra-array matrices for selected arrays

Assemble residency tables per tag

Extract speeds from the analysis results.

Extract timestamps from the analysis results.

Generate default ggplot colours

Calculate number/percentage of tags at each location for each day

Opens a new window that allows the user to determine movement event invalidity

Opens a new window that allows the user to determine detection invalidity

Group movements

Incorporate intra-array estimates in the overall CJS object

Include tags that were never detected

Temporarily include missing receivers in the spatial object

Allow the user to determine a given set of detections invalid

Allow the user to determine a given movement event invalid

Assign live times to arrays

Load Biometrics file

Load deployments file and Check the structure

Load ALS detections

Load distances matrix

Load spatial.dot

Load shapefile and convert to a raster object.

Load Spatial File

Load, structure and check the inputs

Match POSIX values

TRUE/FALSE wrapper for match

Calculate CJS for each group for each array

Calculate CJS for each group.release combination

Migration Analysis

Convert numeric time to HH:MM

movements.R arguments

Calculate time and speed

Calculate movement times

Edited rose diagram function

Consider NA's as FALSE

Find optimum plotting grid

Trim movements table to contain only uni-directional movements

Skips all validity checks for a tag and allows the user to freely invalidate events

Plot simultaneous/cumulative presences at a give array or set of arrays

Plot detections for a single tag

Plot array live times

Plot moves for one ore more tags

Plot global/group residency

Plot residency for a single tag

Plot sensor data for a single tag

Print circular graphics for time series.

Load a dataset before running an analysis

Run quality checks on preloaded detections

print Rmd fragment for inclusion in the report

Print biometric graphics

Print circular graphics for each array

Print DOT diagram

Print dotplots

Print efficiency fragment

Print Rmd report

print the distribution of tags per location

print the individual locations per day

Print individual graphics

Print a simple barplot with the number of tags last seen at each section

Print a simple barplot with the number of tags last seen at each section

Print Rmd report

Print progression diagram

Print Rmd report

Print arrival and departure times per section

Print sensor data for each individual tag

Print survival graphic

Standard detections file created for actel

Thelma new export files

Thelma old export files

Vemco files

Read dot file or string

Recover latest actel crash log

Find the location where the tag spent most time per day

calculate residency ratios per tag

compile output of dailyRatios

Create status.df

Calculate array efficiency for residency analysis

Residency Analysis

Draw rings at relative points

Draw mean value in the axis margin

Forcefully round a number down

Forcefully round a number up

Compress array-movements into section-movements

Create Standard Names for spatial elements

Analytical CJS model

Removes invalid events

Calculate time and speed since release.

Split detections by tag

Split a dataframe every nth row

Find original station name

Calculate the standard error of the mean for circular data

stop function but paste error to the report too

Store summary information on the stray tags detected in a permanent file.

Subset a character string counting from the right end

Handler for table interaction events

Convert a data frame with timestamps into a list of circular objects

Transfer validity updates from valid movements to all movements

Process spatial elements

Calculate Transition Layer

update array-movement validity based on the section-movements

Wrap frequently used code to handle user input

user_interaction.R arguments

Compare original detections with the valid movements and exclude invalid detections

Transform vectors into data frames with specific columns

widget_setups.R arguments