fastReadWave with header=TRUE was not properly closing file connections
matchEnvData and ncToData were not returning failed files properly
when raw=TRUE
nc='HYCOM' option to make it easier to specify that you want
to (try) to get to HYCOM data from matchEnvDatamatchEnvData and ncToData were really slow in some cases, up
to 30x faster now in some cases
Merging in fastReadWave C-based wav file reading function. Must faster
than current alternatives, based on the not-always-working audio::load.wave
but with improvements
Added pwelch apparently
wignerTransform bug introduced in 1.12.0findEchoTimes function and tests for DCLDE workshophoardr dependency because defaults go against CRAN
wishes on MacOSerddapToEdInfo was crashing instead of working through
the server listmatchEnvData functinosalpha wasn't working for plotPresGrid single color plotspeakTroughAllowing for smaller HYCOM download with modification to formatURL
Adding another NetCDF time format check
Fixing readSpecAnno if no rows in anno table
plotPresBar and plotPresGrid added plotTz option to control timezone
of output
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
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
Added getFigshareInfo function
Dropped stringr dependency (was only using str_trim before)
matchEnvData can now set timeout length with timeout arg
createSSP has new args progress and ... to pass to matchEnvData
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
downloadEnv timeout time to 120s. Not sure why it was set to 1200
previously, either type or misunderstanding of units?addPgEvent to work with events that have 0 detections, and also
allow for manual setting of start/end times (useful for creating validation
events)plotPresBar and plotPresGrid functionstrainSplitPermute functionplotPresBar and plotPresGrid plotting functionssoundtrapQAQC to have option for internal/external battery voltagesoundtrapQAQCPull 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)
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
soundtrapQAQC functionAdded 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
readSpecAnno adjusted to allow for different table names
Added option unique to squishList to try and simplify results to only unique values
readSpecAnno function to read Spectrogram_Annotation tables
from PAMGuard databasesUpdated 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)
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
addPgGpsAdded 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
wignerTransform plotting now uses option useRaster = TRUEaddPgEvent fixed issue with repeated Lookup codes and added coloursaddPgEvent fixed potential issue with reading empty binariessquishList no longer breaks on data.table objectspeakTrough 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
wignerTransform fixed output size to actually be n x t
updateUID progress bar minor bug fix
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
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
updateUID function to try and realign UID mismatches in Pamguard databases
between event detections and their corresponding binary filesChanged 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
Checks in database adding function to make sure file exists
writeAMWave example resets par() settings to original
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
Whoa, environmental data functions might work fine for crossing the dateline now.
getFittedMap also removed because ggmap package has been orphaned.
*Added addPgGps to add GPS data to a Pamguard database
matchEnvData a generic method so can write methods
for non-dataframe sources easierAdded 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.
straightPath was not properly averaging angles. Changed to
polar coordinate style averaging, will now handle angles near the 0-360 border properlyformatURL functions for making ERDDAP downloading URLs automaticallyminor change in error handling for peakTrough
writeClickWave can handle vectors for CPS and frequency
writeAMWave function added to create synthetic amplitude modulated wavesaddPgEvent function added to add new events to an existing Pamguard database by
providing a vector of UIDswignerTransformwignerTransform, resizes back to length of
original signaldecimateWavFiles when trying to write a folder of fileswignerTransform added