NEWS.md

In TaikiSan21/PAMr: Load and Process Passive Acoustic Data

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

TaikiSan21/PAMr documentation built on Nov. 15, 2020, 9:46 p.m.