Cepstrum module can now be named “BurstPulse” or “Burst Pulse” in addition to “Cepstrum” to be recognized by PAMpal
Function checker was set up poorly and would unintentially write to global env on some failed checks
calculateAverageSpectra was not passing along manual sr input properly
processPgDetections with mode='time' handles date converting better, will no longer fail with Excel rounding 12:10:00 to 12:10. Also removed some unnecessary interactive steps, will now stop and ask user to provide instead of asking user to provide during call
Fixed bug in calculateICI if large values were present rounding would lead to bad answers. Now filters results by z-score < 2 before taking ICI to get rid of outlier large values
Fixed bug in writeEventClips that was undoing buffer in the wrong direction if the buffered time was not present in any of your wav files, would previously get a false warning of “cant find wav file”
Updated how warnings work for writeEventClips, now always reported even on failure
Adding filter options to calculateAverageSpectra similar to standardClickCalcs
Fixed bug where processing with mode='time' was leaving in full binary path names instead of just file basename, messing up other stuff like getBinaryData. Fixed and temporary adjustment to getBinaryData made
getBinaryData was not doing a good job if binaries had the same name. It do better now
processPgDetections will only store file names that it actually used instead of all possible matching file names, related to other binary fix.
Added getICI, getClickData, getWhistleData, and getCepstrumData as easier accessors
Updating webpage with calculateICI and getDetectorData guides
writeEventClips now attaches clip times with _YYYYMMDDHHMMSS_mmm to the end of file nameswriteWignerData warns about bad directories instead of crashing
filter fixed for bug in species and database filtering if these keywords were present on the right hand side of the call
writeWignerData functionnewUIDs not getting used properly for some users because they were integer64
fixed bug with writeEventClips not reporting all file names if multiple databases present
addRecordings prints some failure warnings
filter for databases also removes those databasess from the files(x)$db
writeEventClips updated to use channel argument
R and package version now stored in studies when created
standardClickCalcs now uses “channelMap” from binaries to assign correct channel if it is present instead of defaulting to Channel 1 & 2
export_banter warning messagaes cleaned up
Removed extra “Peak 3dB” and “Peak 10dB” values from standardClickCalcs
filter now works with a special case for database and also works for any environmental variables added
Updating some docs for GitHub pages website
Adding calculateAverageSpectra back
Modified processPgDetections for mode='db' to work with a possible “newUID” column from PAMmisc’s updateUID function. Also does a better job of matching if there are multiple possible binary files.
addGps now asks if you want to add gps data to your database if it has none
Better warning messages for processing data
writeEventClips modified to work with events or individual detections
addRecordings function added to deal with keeping track of wav recordings in a study
Name changed to PAMpal because pamr was taken on CRAN
Lots of prep for CRAN submission
Changes to standardClickCalcs so it doesnt crash if peak frequency is 0, happens if lower filter bound is 0
Added updateFiles function to update file locations of a study object if you have changed computers or moved folders around
Added checkStudy function to do some sanity checking for possible issues after data is processed. Currently only checks for peak freq of 0 which would mean you probably want a different filter value or add a calibration function
Added test datasets to inst/extdata to go along with added testthat support
NEW FUN FUNCTION calculateAverageSpectra! Calcultes and plots average spectra from an event! Woohoo!
Fixed issue with export_banter not finding ancillary measures properly
matchEnvData compatible with update in PAMmisc package, works with custom functions now
setSpecies handles things more gracefully without provided method argument
Changed setSpecies to choose insted of stop when multiple methods provided (default)
Added filter method that works like dplyr’s filter for detections in an object. Has a special case when specifying species or Species that will filter an AcousticStudy object by the species listed in the $id spot of each species slot
Also added first version of addAnnotation function, it asks a lot of questions for now
AcousticStudy [ accessor changed to return another AcousticStudy after subsetting the events in that study
writeEventClipsFixed bug in addGps that could create duplicate rows after adding gps to your data. Would occur if two GPS entries occurred within the same second, now adds milliseconds before matching so that this is avoided.
Added support for SoundTrap files for writeEventClips with format='soundtrap'
Added better progress bar for mode='db' that is based on binary files not databases
Added writeEventClips function for creating wav clips of events. Currently needs some adjustments but should work for Pamguard data if your selection of wav files definitely covers all of your events
Fixed bug where click detectors were being improperly named if a matched classifier was present in the binary file
matchEnvData extends a function of the same name in the “PAMmisc” package (as of PAMmisc v1.4.1). This lets you download environmental data and match it to your AcousticStudy and AcousticEvent objectsexport_banter if an event had exactly 1 detection fixedexport_banter for list of AcousticStudy objects not propagated event names properlyexport_banter can take list of AcousticStudy objects now, and fixed a bug where NA values were being introducedSkip over binaries with no UIDs in mode='db'
mode='db' was not properly passing along an ID if you supply it
export_banter now lists which measures were NA in the $na dataframe output
egClicksError message in processPgDetections for mode='db' now reports db and binary file failed on better
Changed folder choosing funciton for addBinaries, previous version was windows-only and would not properly start in current working directory
addDatabase now prints added databases for reference
setSpecies now has method = 'reassign' that can reassign species id to new ones provided in a dataframeprocessPgDetctions bug fixed when encountering a binary with 0 detectionsprocessPgDetections shouldnt crash on empty binary file that also didnt finish writing the header and footer for mode='time'processPgDetections handles binary files that never finished writing without a mysterious crash now. Should only affect mode='time'.standardClickCalcs changed to have a filterfrom_khz and filterto_khz option so that a bandpass filter can be applied. If only a highpass filter is desired simply leave filterto_khz as the default NULLaddCalibration reworked slightly again, created calibration function now takes frequency in Hz as input and outputs dB correction to add instead of taking in result of seewave::spec and outputting corrected spec. This makes it more flexible and means we aren’t calculating spectrum twice for no reason
standardClickCalcs adjusted to use new calibration, and temporarily has a new parameter calculated - dBPP - which is the peak to peak value as traditionally defined in acoustics. This is mostly for testing comparability to other Matlab based code of new calibration stuff. Also the spectrum is never rescaled to a max of 0 like it was previously, hopefully should represent accurate SPL levels with new calibration code
addCalibration now asks for units of your calibration, and should properly add or subtract this value from calculated spectrum depending on units selectedexport_banter now has an option to split your data into training and test sets by specifying a proportion for the training argument, and now puts out a pretty table showing a summary of your events and speciesprocessPgDetections has some minor updates to improve clarity when binary files or databases aren’t found using mode='time'getPgDetections has now been re-named to processPgDetections to more accurately reflect what it is doing. Functions starting with get___ will be used just for accessing data
showWaveform and related functions have been renamed to plotWaveform
General naming consistency overhaul - sr and db should now be used in place of sampleRate and database wherever these were previously used, and this should be the naming convention going forward. This means included functions will need to be re-added (they previously relied on it being named sampleRate), and any custom functions should expect data to contain the item sr and not sampleRate
AcousticStudy class has been added. This will now be the class of object returned by processPgDetections, it stores your list of AcousticEvent objects with other important data.
Any data processed in previous versions will need to be re-run, and all functions in older PAMrSettings files will need to be removed and re-added
New Function: calculateICI calculates the inter-click interval of click data, and stores it in the ancillary slot of an AcousticEvent.
New Function: plotDataExplorer creates an interactive plot to allow users to explore the data in an AcousticStudy, AcousticEvent, or data.frame. Plot can be colored or facetted by any columns that are characters or factors, and any numeric columns can be plotted with ggplot’s geom_density
New Function: getDetectorData gathers all detector data into single data frames for each detector type ('click', 'whistle', and 'cepstrum') for easier manipulation
Detector dataframes in AcousticEvents now have a 'calltype' associated with them, currently one of ’whistle', 'click', or 'cepstrum'. This allows for future fun stuff to happen
getBinaryData will now attempt to get the appropriate sample rate for each data point, either from the settings or matching by time using the database file if more than one sample rate was in your data.
Many speed improvements - click calculations should take about half the time, and processPgDetections with mode='time' will now skip over binaries that are outside of the time range of specified events
getPgDetections no longer has an option mode='all', and it is no longer necessary to supply a sample rate for mode='time'. It will now attempt to match events to a correct database used on time stamps, the match the appropriate sample rate the same way that mode='db' does. If a manual sample rate needs to be applied it should now be entered into the grouping table
Functions addBinaries and addDatabase can now add files from another PAMrSettings object, and will report how many files have been added when finishing
export_banter will now attempt to find event level measures in the 'measures' item in the ancillary slot of each AcousticEvent.
export_banter no longer has a reportNA option, any NA values that are removed are now always saved to a separate 'na' item in the list output. The function also reports how many detections were processed.
addGps now also stores all of the gps data loaded into the gps slot of the AcousticStudy instead of only adding coordinates to detections
getPgDetections will name events with database appended for method = 'db' instead of just event ID number to ensure uniqueness across multiple databasessetSpecies can now use a dataframe for method = 'manual', and has a top secret option for SRexport_banter with options to exclude certain species and to export data without species codes to use for prediction only instead of training a banter modelBetter error tracking when functions cause getPgDetections to crash
Now reads in angles and angleErrors from click data
export_banter allows you to specify certain columns to not export
'time' mode for getPgDetections will now report a sample event time so you can see if times are being converted properly from your csv before proceeding with calculations
Fixed an issue where getPgDetections would not work if both Detection Group Localizer and Offline Click events were present in a database.
Renamed eventType and Text_Annotation columns from event databases to eventLabel within detection dataframes so there is consistency between the two
Removed some unnecessary columns from detection dataframes, including detectorName, sampleRate, Id, parentUID, and comment
Fixed a bug in how getBinaryData was checking for multiple matches on the same UID
'db'Added an id slot to AcousticEvent objects. Note that this will cause existing AcousticEvent objects to behave poorly until they have their id slot created / updated using the new setIdSlot function.
Added setIdSlot function to update older AcousticEvent objects to the new format
Changed event naming for mode='time' in getPgDetections. Will now only append numbers if event is not unique, and will also insert an underscore before the number
export_banter now properly checks for cases when there are no detectors in an event instead of crashing confusingly
export_banter no longer using list names to index and create unique event namesexport_banter now removes NA rows, and has reportNA option to see which ones are NA
Detector names have spaces replaced with _ to avoid weird issues later
Dealing with zero detection events better for export_banter
Temporary fix for click calculations with lots of zeroes in wave form - no more NA
standardClickCalcs now supports manual input of sample rate. Default argument is 'auto', which will read from the database. User can supply a numeric value for sample rate in hertz instead.Added a check in addDatabase to see if all files are actually .sqlite3 databases
Added a tryCatch in getPgDetections for mode db so that it shouldn’t stop completely when encountering an error and lose all previously analysed DBs
seewave::spec, it can produce NA values for the frequency if the input wave is long. Adjusted parts standardClickCalcs and addCalibration to work around this.getPgDetections changed to work by specifying a mode as an argument instead of calling separate functions. Can now create events using a csv or dataframe with start and end times specified.
Changed export_banter to export a list with named item detectors instead of detections, no other functional change.
Added setSpecies functions for assigning species classifications to AcousticEvents.
Changed getDbData to default to looking for both OfflineEvents tables and DetectionGroupLocaliser tables, will still only load one if a specific type is provided for grouping.
Added addCalibration, applyCalibration, and findCalibration functions, as well as a plot method that will show the calibration function used. See the Calibration section above for more details.
Fixed a bug in removeFunction that would cause the incorrect number of functions to show in certain cases, and that would cause all functions to be removed when only one was selected.
standardClickCalcs has been adjusted to work with the new calibration methods. See Calibration section above for more details.
Added addGps function for adding matching GPS data to your detections. This allows you to supply a dataframe of Lat/Long locations with timestamps to match to your detections.
Added showWaveform, showSpectrogram, and showWigner functions that allow you to easily plot the waveform, spectrogram, or wigner plot of a detection in an AcousticEvent object by selecting the UID(s) you want to investigate further. getBinaryData is also added as a helper function for these, lets you easily get the binary file data for a single detection.
standardClickCalcs now supports supplying a Wave class object as input
Rocca (roccaWhistleCalcs) and cepstrum (standardCepstrumCalcs) functions added. These are also added by default to a new PRS.
changed AcousticEvent class slot name from specClass to species