NEWS.md

In PAMmisc: Miscellaneous Functions for Passive Acoustic Analysis

PAMmisc 1.11.6

• Safer fail case in peakTrough

PAMmisc 1.11.5

• Allowing for smaller HYCOM download with modification to formatURL

• Adding another NetCDF time format check

PAMmisc 1.11.4

• Dealing with NA coordinate values for enviro functions

PAMmisc 1.11.3

• Fixing readSpecAnno if no rows in anno table

• plotPresBar and plotPresGrid added plotTz option to control timezone of output

PAMmisc 1.11.2

• Added by argument to plotPresGrid that will either overlay colors with an alpha value or split graphs with facet_wrap

• Removed data.table dependency and changed viridisLite to scales

PAMmisc 1.11.1

• Changed plotPresGrid and plotPresBar arguments to be more intuitive. Both now just use bin for the binning, and plotPresBar can be specified as hours/day instead of having to remember which was which.

• Updates to ncToData to allow more flexible time specification. Should work with a larger variety of netcdf files with more arbitrary time specs

PAMmisc 1.11.0

• Added getFigshareInfo function

• Dropped stringr dependency (was only using str_trim before)

PAMmisc 1.10.6

• matchEnvData can now set timeout length with timeout arg

• createSSP has new args progress and ... to pass to matchEnvData

PAMmisc 1.10.5

• Bug fix so that environmental data functions work properly with NA values (they are just not matched, previously would error)

• Change to varSelect, ncToData, and matchEnvData to be able to use variable names in var argument to select without interaction

PAMmisc 1.10.4

• Changing downloadEnv timeout time to 120s. Not sure why it was set to 1200 previously, either type or misunderstanding of units?

PAMmisc 1.10.3

• Updating addPgEvent to work with events that have 0 detections, and also allow for manual setting of start/end times (useful for creating validation events)

PAMmisc 1.10.2

• Adding some type checks for plotPresBar and plotPresGrid functions

PAMmisc 1.10.1

• Adding trainSplitPermute function

PAMmisc 1.10.0

• Adding plotPresBar and plotPresGrid plotting functions

PAMmisc 1.9.6

• Updating soundtrapQAQC to have option for internal/external battery voltage

PAMmisc 1.9.5

• Fixing as.character(POSIX) errors for r-devel update

PAMmisc 1.9.4

• Bug fix for bad XML files in soundtrapQAQC

PAMmisc 1.9.3

• Pull request adding a new time format for ncToData

• Adding logic to drop variables with no dimensions in ncToData and also deal with variables that have non-standard dimensions (default behavior is to read all - if you need to do something in particular with it use the raw option)

PAMmisc 1.9.2

• Fixed a bug where error message in matchEnvData could cause R to crash (oh the irony)

• ncToData was not behaving well if columns were not Latitude and Longitude

• ncToData also bug if some vars had depth and others did not

• LEV is lev is Depth

PAMmisc 1.9.1

• Adding soundtrapQAQC function

PAMmisc 1.9.0

• Added addPgAnno function to add spectrogram annotations to Pamguard databases

• addPgEvent now has a type argument to specify adding Click Detector events vs Detection Grouper events

PAMmisc 1.8.3

• readSpecAnno adjusted to allow for different table names

• Added option unique to squishList to try and simplify results to only unique values

PAMmisc 1.8.2

• Added readSpecAnno function to read Spectrogram_Annotation tables from PAMGuard databases

PAMmisc 1.8.1

• Updated decimateWavFiles to work with wav files with bit rates different than 16 (bugs in seewave functions do not pass along bit rate properly)

• Bug fix in matchEnvData for datasets that had no UTC axis

• Changed defaults in matchEnvData and ncToData to only calculate mean, not median and sd

• matchEnvData and ncToData have a depth parameter you can use to specify matching depth values to use. This makes it possibly to specify a range of depths to summarise over for a single coordinate (previously only single depth or all)

PAMmisc 1.8.0

• Reworking of enviro functions to make HYCOM datasets easier to use. Will now automatically figure out which ones you need based on dates and partition your data for you

• Enviro functions reworked for temporary download to be much faster - no longer does a separate download for every row, will check to estimate download size first and break in to ~20MB chunks at once

• Added createSSP function to create soundspeed profiles

PAMmisc 1.7.1

• Minor changes to smooth out usability of addPgGps

PAMmisc 1.7.0

• Added raytrace function based on MATLAB code by Val Schmidt

• Updating matchEnvData and associated functions to work with provided Depth values instead of only being able to return all Depth values if a Z dimension is present

• squishList works with matrices

• Added readGPXTrack to remove dependency on plotKML::readGPX

PAMmisc 1.6.12

• wignerTransform plotting now uses option useRaster = TRUE

PAMmisc 1.6.11

• addPgEvent fixed issue with repeated Lookup codes and added colours

PAMmisc 1.6.10

• addPgEvent fixed potential issue with reading empty binaries

PAMmisc 1.6.9

• squishList no longer breaks on data.table objects

PAMmisc 1.6.8

• peakTrough ignores first and last frequencies for possible peaks

• addPgEvent and addPgGps added na.rm=TRUE to Id checking logic to avoid issues with NULL id values in current database

• Improvements for addPgEvent check for duplicate data

PAMmisc 1.6.7

• wignerTransform fixed output size to actually be n x t

• updateUID progress bar minor bug fix

PAMmisc 1.6.6

• wignerTransform works with Wave class input

• wignerTransform scaled output by length

• updateUID bug checking for SR, should crash less with missing data

• tests for UID adding plus test data for bad UIDs added

PAMmisc 1.6.5

• Bug fixes for updateUID. Will check for "ClickNo" column first if that is more accurate, and will not update a UID if it is matching based on time and there is more than one match

• Changed database testing to work on copied file in tmpdir for CRAN checks

PAMmisc 1.6.4

• Added updateUID function to try and realign UID mismatches in Pamguard databases between event detections and their corresponding binary files

PAMmisc 1.6.3

• Changed addPgGps to use parse_date_time for date conversions to allow for truncated date formats to be properly parsed because thanks Excel for rounding those dates didn't need to know there were 0 seconds anyway

• matchEnvData not propagating progress argument properly

PAMmisc 1.6.2

• Checks in database adding function to make sure file exists

• writeAMWave example resets par() settings to original

PAMmisc 1.6.1

• Added a NEWS.md file to track changes to the package.

• Fixing addPgGps for spot CSVs

• Tons of documentation in prep of CRAN

• Added files in inst/extdata for testing

• Adding lots of unit testing

PAMmisc 1.6.0

• Whoa, environmental data functions might work fine for crossing the dateline now.

• getFittedMap also removed because ggmap package has been orphaned.

PAMmisc 1.5.0

*Added addPgGps to add GPS data to a Pamguard database

PAMmisc 1.4.1

• Internal changes to make matchEnvData a generic method so can write methods for non-dataframe sources easier

PAMmisc 1.4.0

• Added functions for downloading environmental data and matching it to your data. Replaced older verison of formatURL from v 1.3.0

• New exported functions are edinfoToURL, downloadEnv, erddapToEdinfo, varSelect, getEdinfo, ncToData, matchEnvData, browseEdinfo. Updated tutorial to follow later.

PAMmisc 1.3.1

• bug fix where straightPath was not properly averaging angles. Changed to polar coordinate style averaging, will now handle angles near the 0-360 border properly

PAMmisc 1.3.0

• added formatURL functions for making ERDDAP downloading URLs automatically

PAMmisc 1.2.1

• minor change in error handling for peakTrough

• writeClickWave can handle vectors for CPS and frequency

PAMmisc 1.2.0

• writeAMWave function added to create synthetic amplitude modulated waves

PAMmisc 1.1.0

• addPgEvent function added to add new events to an existing Pamguard database by providing a vector of UIDs

PAMmisc 1.0.4

• fixed typo that broke wignerTransform

PAMmisc 1.0.3

• minor change to output of wignerTransform, resizes back to length of original signal

PAMmisc 1.0.2

• bug fixed in decimateWavFiles when trying to write a folder of files

PAMmisc 1.0.1

• wignerTransform added

PAMmisc documentation built on Aug. 17, 2023, 1:06 a.m.