High-Performance Open-Source Archive
Update to allow fastReadWave to read extensible wav
without crashing
Update to read large files in chunks for
fastReadWave to avoid unexplained crashes on certain
computing platforms
fastReadWave on incomplete wav files
to no longer crash just return what it gotaddPgEvent not creating millisecond
characters properly (character(0) text bug)pwelch accidentally using too many windows, now
correctly stops at the last window that extends past the length of
inputfastReadWave with header=TRUE was not
properly closing file connections
matchEnvData and ncToData were not
returning failed files properly when raw=TRUE
Adding window option to pwelch
Allowing downloadEnv, matchEnvData,
erddapToEdinfo, and ncToData to work with
certain stationary Tabledap datasets (previously only griddap)
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
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