NEWS.md

In PAMpal: Load and Process Passive Acoustic Data

PAMpal 1.0.0

• Probably about time this was 1.0.0, just in time for a paper!

• Updating front page readme

PAMpal 0.20.3

• Fixed an issue where some rare clicks would cause processing to result in only NA values

PAMpal 0.20.2

• Adding addMeasures and getMeasures functions

PAMpal 0.20.1

• Exporting timeJoin from matchTimeData so other packages can use

PAMpal 0.20.0

• Adding support for Click Train Detector with grouping='clickTrain' when processing with mode='db'. Events have prefix CT instead of OE or DGL. By default mode='db' will process all three of grouping=c('event', 'detGroup', 'clickTrain')

PAMpal 0.19.5

• Adding sampleDetector function to subsample by detector

PAMpal 0.19.4

• Adding addFPOD and getFPODData functions to deal with adding/getting FPOD data from AcousticStudies

PAMpal 0.19.3

• Updating getClipData and writeEventClips to have a fixLength option that allows users to create clips of a fixed length using just the buffer argument

• Allowing processPgDetections to take multiple label arguments to specify different table columns if using both DG and OE events in same db

PAMpal 0.19.2

• Updating markAnnotated to give warnings on NA values instead of failing

• Updating roccaWhistleCalcs to avoid divide by zero NA/Inf values

PAMpal 0.19.1

• Adding markAnnotated function to flag whether or not detections are within annotation boxes

PAMpal 0.19.0

• Adding matchTimeData function to add arbitrary data to AcousticStudies

• Bug fixes for some random stuff

PAMpal 0.18.1

• Updated to warnings in addGps to now be less overwhelming

• Fixed bug for displaying some notes after combining with bindStudies

• addGps now adds gpsUncertainty which says how many meters since to the closest GPS point. Useful to catch points where we have interpolated a lot.

PAMpal 0.18.0

• Adding addAnnotation and related functions for annomate exporting

• Explicitly marking joins that are expected to have multiple matches re: dplyr::join's new behavior

PAMpal 0.17.2

• Smol change to not grab unnecessary columns in addGps

• Big speed improvements for processing with mode='time' and mode='recording'

PAMpal 0.17.1

• Converting all paths to use '/' instead of '\'

• Found out updateFiles was unuseably slow, so I fixed it. I dunno, maybe 1000x faster depending on how many files you have?

PAMpal 0.17.0

• Removing the $source item in the settings slot for each AcousticEvent. These were not used for anything, and when the source was wav files it would end up with a huge repetitive list for every event. Ended up taking up a huge amount of memory, removing this results in AcousticStudys that are half the size.

• Updated filter function for a 2x speed increase. Turns out quos(...) is expensive when you need to do it thousands of times, so now passing along the character version of dots when we can instead of recomputing it.

• JK pdate again filter is actually 10x faster. Way better to pull out all the data into a single df and then just reassign everything to the proper event

• Updated localizations slot to use more standardized names for imported PGTargetMotion locs. Currently using latitude, longitude, perpDist, perpDistErr, depth, depthErr. These seem like good standard localization columns going forward. Changed the ppVars()$tarMoCols to pull in only columns corresponding to these, and added new ppVars()$locCols to reflect new standard column names

• Added addNote, getNotes, removeNote functions for adding and viewing notes. Can be added to study or event, and will print when they are printed.

PAMpal 0.16.8

• addDatabase not working properly for directory of dbs

PAMpal 0.16.7

• Bug fixes for addGps when using a dataframe as the source, thresh argument was not doing anything

PAMpal 0.16.6

• Changing myGram function used for power spectrum calculations to normalize by average window energy instead of average window amplitude because we are almost always using power spectra

PAMpal 0.16.5

• Updating addHydrophoneDepth to be able to take numeric input for constant depth

PAMpal 0.16.4

• Changing added column fro depth to hpDepth in addHydrophoneDepth

• writeEventClips now has a filter option to apply low/high/bandpass filters

• getSr and matchSR functions were not working properly in some edge cases

• changed getDetectorData to return db for more usefulness

• getBinaryData returns UIDs in the order given

PAMpal 0.16.3

• Minor adjustment to mode='db' to not repeat UIDs within a single event

PAMpal 0.16.2

• Missed a bug in new addRecordings

• addBinaries now works with vector of folders

PAMpal 0.16.1

• Changing addRecordings to return NA values when reads are not possible instead of omitting

• Some fixes to plotGram - previously whistle contours could plot at wrong frequnecy and time scale could be thrown off

PAMpal 0.16.0

• addDatabase can now accept a folder containing databases

• cepstrum calculations handled better internally

• Detection Group Localiser had changed in PAMGuard - reworked code to work with new naming scheme and fail less often if some tables are missing

• filter has more regular behavior - no longer returns NULL if no detections are present, was previously causing odd behavior in loops

• Event order is now preserved when doing mode='time'

• Added functions nDetections, nClicks, nWhistles, nCepstrum, nGPL that get total number of detections in an event or study

• getICI for type='data' returns one big dataframe instead of lists of lists of dataframes

• Added showBreaks option to calculateAverageSpectra to toggle showing line breaks for multiple events in concatenated spectrogram

• Added bindStudies function to combine multiple AcousticStudy objects

PAMpal 0.15.3

• Trying to stabilize processing against minor errors - should no longer crash entire processing if one piece of binary data fails, will try again instead

• Trying to fix some crashes with missing Sound Acquisition data

PAMpal 0.15.2

• Bug with mode='time' where sample rate could be read in as a character, causing crashes

• calculateAverageSpectra would have problems when doing multiple events that had detections with repeated UIDs

• matchEnvData now has a depth parameter to specify depth or range of depths to match

• Store and print total processing time for processPgDetections

PAMpal 0.15.1

• Added ability to add functions during PAMpalSettings call

PAMpal 0.15.0

• Added support for GPL Detector data!

• Added processDate to ancillary info of each study

• Removing some unnecessary package dependencies

PAMpal 0.14.6

• Changed included testClick from 192kHz to 500kHz to avoid unnecessary errors when trying to add filters > 96kHz

PAMpal 0.14.5

• Some bug fixes for weird SoundTrap click detector stuff

PAMpal 0.14.4

• Added brightness and contrast parameters to calculateAverageSpectra. These only affect the concatenated spectra plot. Also added a ylim parameter for the mean spectra plot.

PAMpal 0.14.3

• Bug fixed in calculateAverageSpectra, previously was not working with event names as an argument for evNum

PAMpal 0.14.2

• calculateAverageSpectra was always computing noise spectrum cuz I'm bad at stuff

• Bug fix for addRecordings with certain SoundAcquisition table setups

• getBinaryData was improperly complaining about multiple matches

PAMpal 0.14.1

• checkStudy complains about too many things, shush already

PAMpal 0.14.0

• Normalizing some paths internally

• checkStudy checks for NA values and reports

• Small bug in addRecordings that wasn't assigning startSample properly for separate wav files

• Trying to re-work how we can consistently access SR after processing. Functions should now be able to automatically tell if a decimated sample rate is appropriate (calculateAverageSpectra and writeEventClips mainly) for clicks in binaries as long as XML settings have been added with addSettings before processing.

• PAMpalSettings has new parameter settings to add XML settings without an additional call to addSettings

• filter works better with detector names

• Grouping in mode='recording' wasn't working well when recordings were processed with "Merge contiguous files" checked, fixed now

• writeEventClips works with decimated data now with useSample = TRUE

PAMpal 0.13.0

• Added more info to loadPamguardXML. Now loads in click sweep classifier type data as well as pre-filter and trigger filter data

• standardClickCalcs no longer fails if upper end of filter >= to Nyquist

• processPgDetections with mode='time' can run successfully if no Sound_Acquisition table is present by providing columns db and sr the grouping file (db not needed if processing a single database)

• processPgDetections with mode='db' can run successfully if no Sound_Acquisition table is present, will ask for sample rate during processing

• Missed some function warnings with new warning system

PAMpal 0.12.8

• calculateAverageSpectra now draws lines breaking up events in concatenated spectrogram if plotting multiple events at once

• plotGram now uses start and end times based on the start of the event, not the recording

PAMpal 0.12.7

• standardClickCalcs incorrectly had outputs labelled centerHz_3dB and centerHz_10dB when units were actually in kilohertz. Names have been changed to centerkHz_3dB and centerkHz_10dB

• calculateAverageSpectra has a few new features. plot can be a vector of lenght two specifying which of the two plots to create, useful when only one is desired. New parameters mode and decimate added. mode allows users to specify 'spec'(default) or 'ceps' to calculate either spectrum or cepstrum of signal. decimate reduces the samplerate of the signal by an integer factor before calculations, this can be especially useful for cepstrum data.

• Fixed bug in processPgDetetions for detection group localiser data crashing with an error related to tarMoCols, and also updated code to automatically check for event labels. Will look for (in order) Text_Annotation column, column with species in the name, column with label in the name, or column with id in the name. If none of these exist, defaults to the first non-standard column present in the database.

PAMpal 0.12.6

• filter has new special case to filter by detector names

• processPgDetections rare bug fix with processing bad event grouping files for mode='time' and mode='recording'

PAMpal 0.12.5

• getBinaryData can now select for detection type, other functions updated to use this

• filter works better with species, in particular can do is.na(species) now

PAMpal 0.12.4

• addHydrophoneDepth function added that will try to read depth data from a database

• processPgDetections for mode='db' now adds target motion localizations if they are present and stores in the localizations slot of events

PAMpal 0.12.3

• addRecordings stores some sample number and samplerate data

• writeEventClips has new option useSample to try and use the startSample values stored in binary files instead of just UTC times

PAMpal 0.12.2

• addRecordings tries to use to get start sample data from database

• Fixed bug where processPgDetections would crash if no comment field was present

PAMpal 0.12.1

• calculateICI error fixed when exactly two detections were present for a detector

• export_banter reports names of event level measures it finds

• Switching from using eventUID to event ID for all labeling and id() purposes

PAMpal 0.12.0

• Added ability to work with Pamguard's XML settings files with functions addSettings, removeSettings, and loadPamguardXML. Currently this lets PAMpal tell if a decimator was in use and adjust the sample rate accordingly, no longer need to manually set the sr_hz parameter for standardClickCalcs if XML settings have been added to the pps.

• PAMpalSettings objects now have a @settings slot to accommodate this addition, older objects will need to have this slot manually added or they will give warnings of Not a validObject(), no slot of name "settings" for this object of class "PAMpalsettings"

• Added updatePamObject function to deal with updating S4 classes created in older versions of PAMpal

• Added message on load to warn about updating objects

• Added new warning system that captures warnings during processing and function calls and stores them in the ancillary slot of the AcousticStudy object. These can be accessed with the new getWarnings function

PAMpal 0.11.2

• calculateICI keeps UID info with the data

PAMpal 0.11.1

• calculateAverageSpectra has a sort option to sort clicks by peak frequency in the concatenated spectrogram

• processPgDetections with mode='time' does a better job of parsing sample rates from database

PAMpal 0.11.0

• Added mode='recording' to processPgDetections that will group events by the start and end times of wav files used

• processPgDetections will try to auotmatically determine an appropriate mode if none specified

PAMpal 0.10.6

• processPgDetections with mode='db' now reads in the comment column of the database and stores in the ancillary() slot of each event

• addRecordings reads in an extra format of dates [0-9]{14}_[0-9]{3}

• Channels for clicks are read in separately from standardClickCalcs, now these will be saved even if no calc functions are present along with UID and UTC

• checkStudy behaves better if run on a study with no events

PAMpal 0.10.5

• calculateAverageSpectra doesn't fail on high SNR values anymore

• plotWaveform and friends have a length argument and will now attempt to get sample rate values from the AcousticStudy object if possible

• getBinaryData tries to get sample rate better

• plotGram added in preliminary form. Plots spectrograms and cepstrograms of events, can also overlay WMD detections onto plot.

PAMpal 0.10.4

• calculateAverageSpectra - more improvements. Noise shouldnt fail anymore, added SNR threshold argument, returns all noise data and UIDs. Output names changed from all and average to allSpec and avgSpec.

PAMpal 0.10.3

• calculateAverageSpectra has a channel argument, better color scaling for concatenated spectrogram, and a beta version of average noise floor

• processPgDetections will now automatically use mode='time' if a grouping argument is provided and is either a dataframe or a valid filepath

• processPgDetections now properly updates progress bar for mode='time' when some binary files have no data or are not within any events, previously would not get to 100% or would jump

PAMpal 0.10.2

• calculateAverageSpectra now averages in exponential space rather than in dB space, and plots are created in separate plotting windows. The norm option now just scales to a maximum dB value of 0

PAMpal 0.10.1

• Multiple functions that tried to match files against a list would fail if filepaths contained "\" as file separators, these have been changed to use fixed=TRUE so that this no longer happens

• Can now set function parameters for functions being adding during the initial call to PAMpalSettings and addFunction instead of being forced to go through interactive menus

PAMpal 0.9.14

• 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

PAMpal 0.9.13

• 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

PAMpal 0.9.12

• 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

PAMpal 0.9.11

• writeEventClips now attaches clip times with _YYYYMMDDHHMMSS_mmm to the end of file names

PAMpal 0.9.10

• writeWignerData 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

PAMpal 0.9.9

• Added writeWignerData function

PAMpal 0.9.8

• newUIDs not getting used properly for some users because they were integer64

• fixed bug with writeEventClips not reporting all file names if multiple databases present

PAMpal 0.9.7

• addRecordings prints some failure warnings

• filter for databases also removes those databasess from the files(x)$db

PAMpal 0.9.6

• 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

PAMpal 0.9.5

• 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

PAMpal 0.9.4

• Big update to documentation and testing for CRAN prep

PAMpal 0.9.3

• addRecordings function added to deal with keeping track of wav recordings in a study

• Name changed to PAMpal because pamr was taken on CRAN

PAMr 0.9.2

• 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

PAMr 0.9.1

• 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)

PAMr 0.9.0

• 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

PAMr 0.8.3

• Minor bug fix for writeEventClips

PAMr 0.8.2

• Fixed 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'

PAMr 0.8.1

• 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

PAMr 0.8.0

• Finally not just a bug fix! New function 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 objects

PAMr 0.7.18

• Bug in export_banter if an event had exactly 1 detection fixed

PAMr 0.7.17

• Fixed bug in export_banter for list of AcousticStudy objects not propagated event names properly

PAMr 0.7.16

• export_banter can take list of AcousticStudy objects now, and fixed a bug where NA values were being introduced

PAMr 0.7.15

• Skip 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

PAMr 0.7.14

• First pass fixing egClicks

PAMr 0.7.13

• Error 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

PAMr 0.7.12

• Fixed calibration loading file if first column is just row names

PAMr 0.7.11

• setSpecies now has method = 'reassign' that can reassign species id to new ones provided in a dataframe

PAMr 0.7.10

• processPgDetctions bug fixed when encountering a binary with 0 detections

PAMr 0.7.9

• processPgDetections shouldnt crash on empty binary file that also didnt finish writing the header and footer for mode='time'

PAMr 0.7.8

• processPgDetections handles binary files that never finished writing without a mysterious crash now. Should only affect mode='time'.

PAMr 0.7.6 and 0.7.7 because oops

• Just adde a debugger for JKs problem

PAMr 0.7.5

• 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 NULL

PAMr 0.7.4

• addCalibration 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

PAMr 0.7.3

• addCalibration now asks for units of your calibration, and should properly add or subtract this value from calculated spectrum depending on units selected

PAMr 0.7.2

• export_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 species

PAMr 0.7.1

• processPgDetections has some minor updates to improve clarity when binary files or databases aren't found using mode='time'

PAMr 0.7.0

Functions Renamed

• 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

Major Changes

• 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

Minor Changes

• 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

PAMr 0.6.8

• getPgDetections will name events with database appended for method = 'db' instead of just event ID number to ensure uniqueness across multiple databases

PAMr 0.6.7

• I don't remember what happened here. I bet it was important

PAMr 0.6.6

• setSpecies can now use a dataframe for method = 'manual', and has a top secret option for SR

PAMr 0.6.5

• Updated export_banter with options to exclude certain species and to export data without species codes to use for prediction only instead of training a banter model

PAMr 0.6.4

• Better 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

PAMr 0.6.3

• 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

PAMr 0.6.2

• Fixed an issue with repeated entries in click detections for modes other than 'db'

PAMr 0.6.1

• Sometimes whistles would not get proper decimated sample rate, fixed

PAMr 0.6.0

• 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

PAMr 0.5.9

• Fixed bug in SR / FFT parameter calculation in whistles if there was a gap in the whistle contour

PAMr 0.5.8

• 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

PAMr 0.5.7

• Rocca whistle calcs minor change - boundary settings for sweeps set to "flat", should reduce number of inflection points

PAMr 0.5.6

• minor change to export_banter no longer using list names to index and create unique event names

PAMr 0.5.5

• export_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

PAMr 0.5.4

• Dealing with zero detection events better for export_banter

• Temporary fix for click calculations with lots of zeroes in wave form - no more NA

PAMr 0.5.3

• 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.

PAMr 0.5.2

• 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

PAMr 0.5.1

• Minor bug fix when using 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.

PAMr 0.5.0

• 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.

PAMr 0.4.0

• 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.

PAMr 0.3.0

• 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.

PAMr 0.2.2

• 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

PAMr 0.2.0

• 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

PAMpal documentation built on Aug. 12, 2023, 1:06 a.m.