NEWS.md

PAMscapes 0.17.2

• General improvements for effort formatting to speed up any effort-based plots and data processing

• Adding matchEffort and detectedValue options to all detection plotting functions to be able to more accurately handle effort

• loadDetectionData now loads DETECTED and NOT_DETECTED by default for Makara data and also reports the number and type loaded when verbose=TRUE

PAMscapes 0.17.1

• Adjustment to how binDetectionData handles binning

• Adding frequency slider and stop page to runDailyLTSAReview

• createOctaveLevel allows for multiple band specifications with type='bb'

PAMscapes 0.17.0

• Adding new addDataQuality function for updating data quality matrices in soundscape NetCDF files

• Adding more fail catches for matchGFS

PAMscapse 0.16.0

• Adding options linetype, lwd, borderLwd, showNObs, alpha to plotPSD

• Allowing color and linetype options of plotPSD to be named vectors for easier assigning of specific values to specific levels

PAMscapes 0.15.5

• Adding opendap option to matchGFS to try and use OPeNDAP protocol for data access to see if that is any more reliable

PAMscapes 0.15.4

• matchGFS broken again, changing to netcdf3 output format

PAMscapes 0.15.3

• Adding quantileBorder optiont to plotPSD

PAMscapes 0.15.2

• Adding UTC offset capability to loadSoundscapeData nc reading

PAMscapes 0.15.1

• Updating loadDetectionData for better Makara interaction

PAMscapes 0.15.0

• Removing tdigest dependency before pending archival of that package

• prepPSDData functionality removed, and plotPSD now only accepts single dataframe inputs rather than lists of dataframes like previously. This was previously developed and necessary for full-scale 1Hz PSD files, so should no longer be needed with the move to HMD resolution data.

PAMscapes 0.14.6

• Updating matchGFS to hopefully work more consistently and use new gdex URL

PAMscapes 0.14.5

• Adding netcdf calibration option to evaluateDeployment & evaluateRecordings

• Adjusting source='makara' names for loadDetectionData to most recent

PAMscapes 0.14.4

• PMAR and WISPR wav file formats added for evaluateDeployment

PAMscapes 0.14.3

• binSoundscapeData with method='mean' was not linearizing properly befre calculation.

• evaluateDeployment small bug with timeRange

PAMscapes 0.14.2

• evaluateDeployment was not working correctly for separate log and wav directories

PAMscapes 0.14.1

• Fixing facet in plotPSD to work for year,month,hour

• Updating runSoundscapeExplorer to show proper dataframe names in code sample

PAMScapes 0.14.0

• Adding matchDetectionData function for integrating detections wiht other types of data

• Added default Makara effort columns to loadDetectionData

• Added effortStart/effortEnd to runDetLoadHelper column map

• plotDetectionBoxplot and plotAcousticScene can automatically account for effort if "effortStart" and "effortEnd" columns are present (no separate effort dataframe required)

• runDetectionExplorer Shiny app created as a replacement and upgrade of the previous runDetLoadHelper app. Combines the data loading functionality with plot previews similar to runSoundscapeExplorer

• Added plotPolarDetections plotting function

PAMscapes 0.13.1

• Adding time range slider to runDailyLTSAReview

• Fixing loadDetectionData and runDetLoadHelper to work with dataframe input

PAMscapes 0.13.0

• Added runDailyLTSAReview function to review and annotate NetCDF soundscape files with both data quality values and comments

PAMscapes 0.12.0

• Added runDetLoadHelper function to assist users with loadDetectionData parameter setup for arbitrary detection data

PAMscapes 0.11.4

• Occasional problem with edge bands with createOctaveLevel, partial bands were not correctly identified and removed

• matchGFS URL changed seemingly yesterday so was borked

PAMscapes 0.11.3

• Adding ability for 1day style presence for loading detections

• Small rework of naming pattern for column maps in loadDetectionData

PAMscapes 0.11.2

• Addressing minor QAQC workflow potential bugs

• Fixing issue with dropNonHmd option of loadSoundscapeData and added warning when it appears to be fully non-standard HMD

• Adding error catch to createOctaveLevel for non-standard HMD levels since these can't accurately be summed

PAMscapes 0.11.1

• Adding a better error message when users attempt to load MANTA Metadata NetCDF files with loadSoundscapeData

• Adding broadband option to type for createOctaveLevel to allow users to create arbitrary broadband measures

PAMscapes 0.11.0

• Adding QAQC functions evaluateRecordings, evaluateDeployment and runQAQCReview

• Oh and the plotting functions

PAMscapes 0.10.1

• Added keepQuals argument to loadSoundscapeData and loadMultiscapeData

• Some bug fixes for loading SanctSound data

PAMscapes 0.10.0

• Adding formatEffort and related internal helper functions

• Adding effort to plotAcousticScene to plot off-effort times

• Adding some tests for detection data processing

• Adding plotDetectionBoxplot plotting function

• Deprecating cpal argument in plotScaledTimeseries in favor of color for better naming consistency

PAMscapes 0.9.1

• Bug fix for bad Lat/Long WKT in some nc files

• Reducing columns of PSD example file to 3kHz instead of 24kHz because it was causing UBSAN errors (I think)

PAMscapes 0.9.0

• Adding binDetectionData function for converting detection data to presence data (e.g. hourly/daily presence)

• Adding by option to plotAcousticScene to allow for faceting the plot

• Adding ability for plotAcousticScene to work without frequency ranges, just plotting equal size bars for each detection type present

PAMscapes 0.8.2

• Adding binCount to loadSoundscapeData, binSoundscapeData, and loadMultiscapeData to return number of times in each bin

• Adding keepEffort to loadSoundscapeData and loadMultiscapeData to return effort column. Can also be used to set a threshold for an amount of effort to keep in results

PAMscapes 0.8.1

• plotLTSA with facet changed labeling scheme

PAMscapes 0.8.0

• HMD type input standardized to always use same rounded column names (why was this such a headache). Also new option for all data loaders dropNonHmd to auto-remove any columns in HMD data that are not standard HMD levels - most commonly exactly Nyquist in some datasets

• Deprecating checkSoundscapeInput in favor of loadSoundscapeData because the old name was stupid

• Adding new function loadMultiscapeData to load multiple folders of soundscape data to better allow for large scale comparisons

• Adding parallelization ability to loadSoundscapeData using future.apply package

• Adding facet options to plotLTSA and plotPSD to create faceted plots by a column in the data. Also added to runSoundscapeExplorer for plotPSD

• createOctaveLevel updated to accurately handle HMD data at lower frequencies by summing partial bands. Also dropped the method argument because we are always summing (normalize argument handles what people might want from a mean/median solution??)

• binSoundscapeData changed to use character function argument instead of actual function (to better incorporate na.rm=TRUE)

• Adding referenceLevel option to plotPSD that plots different values of by column as difference between the selected reference column instead of absolutes

PAMscapes 0.7.3

• Bug in plotPSD for log scale frequency axis if frequency of 0 was present

PAMscapes 0.7.2

• Updating createOctaveLevel to work properly for hybrid-millidecade data. Was previously not correcting for binwidth correction. Also added a normalized option to allow for bin width-normalized outputs

• createOctaveLevel also now properly keeps track of any added columns in addition to the standard soundscape metric data (e.g. GPS)

• Updating matchGFS with new progress and keepMatch options, and adding windMag to the standard output

• Updating tutorial with PyPam examples and data and to keep up with more recent developments

• Fixed problem in plotScaledTimeseries if second plotted column was all the same value

• Added "Copy to create this plot" text output to all runSoundscapeExplorer plots

• Updated loadMantaNc (and thus checkSoundscapeInput) to use a more standard naming scheme for HMD data from netCDF files - will now always be rounded to a single decimal point

PAMscapes 0.7.1

• loadMantaNc (and thus checkSoundscapeInput) now knows to look for coordinates and platform from NC files to create Latitude Longitude and platform columns in the loaded data

PAMscapes 0.7.0

• Adding new runSoundscapeExplorer function that launches a shiny app to explore the various visualization options for soundscape data

PAMscapes 0.6.3

• Adding tz option for checkSoundscapeInput if data are not already in UTC timezone

• checkSoundscapeInput combines multiple files by default

PAMscapes 0.6.2

• Adding by option for plotPSD

• Improving performance for large datasets in plotPSD when they are provided as a single dataframe

• Adding binSoundscapeData function to summarise data by a smaller unit of time

• Added binning options directly to checkSoundscapeInput

• Adding returnData option for most plotting functions to return the plotted data instead of a plot

PAMscapes 0.6.1

• Adding matchSeascape function

PAMscapes 0.6.0

• Fixing CRAN checking issue with matchGFS example

• Added plotLTSA function

• Speed improvements for many functions

PAMscapes 0.5.8

• dropping hoardr and trying to fix cache path on MacOS for CRAN

PAMscapes 0.5.7

• ggplot 3.5.0 broke some auto date scaling so I ahve to add it back

PAMscapes 0.5.6

• Adding by option for markNA

PAMscapes 0.5.5

• Adding by option for plotPSD

• Adding keepQuals option for loadMantaNc to honor data quality flags

PAMscapes 0.5.4

• Updates for readLocalAIS to work better with stationary deployments

PAMscapes 0.5.3

• Added examples for all functions and a small AIS file for use in examples

PAMscapes 0.5.2

• Exporting prepPSDData so people can use to make summarised data separate from the plotting portion

PAMscapes 0.5.1

• Bug fix for addAIS for interptype='all' and interpType='close' where it was accidentally creating extra duplicate NA valued rows

PAMscapes 0.5.0

• Adding plotPSD function
• Exporting checkSoundscapeInput so that others can use it to load data
• Adding both of these updates to the tutorial doc

PAMscapes 0.4.1

• Added loadMantaNc function to support MANTA NetCDF file input

PAMscapes 0.4.0

• Added createOctaveLevel function and updated tutorial doc to include it
• Added tests

PAMscapes 0.3.2

• Added alpha param to plotAcousticScene

PAMscapes 0.3.1

• Some bugfixes from creating tutorial
• Uploading PAMscapesTutorial RMarkdown doc

PAMscapes 0.3.0

• Adding plotScaledTimeseries function
• Adding addAISSumamry function

PAMscapes 0.2.0

• Adding plotting functions
• Adding GHActions

PAMscapes 0.1.1

• Removing slide# from exports

PAMscapes 0.1.0

• First commit! AIS functions, GFS download functions