PAMmisc is a collection of random utility functions that might be useful for anyone working in passive acoustics. If you have any useful tools you’d like to add, please contact Taiki Sakai: taiki.sakai@noaa.gov.
Install the latest version from GitHub:
# make sure you have Rtools installed
if(!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('TaikiSan21/PAMmisc')writeClickWave - Create synthetic delphinid click
wav files
writeAMWave - Create synthetic amplitude modulated
wav files
decimateWavFiles - Decimate .wav files to a new
sample rate and write them to a new folder. Works on either a single
.wav file or an entire folder. Currently only works with single channel
data, if multi-channel wav files are fed in it will only process and
output the first channel.
squishList - A utility for compressing a list that
has elements with the same name. See examples.
peakTrough - Find multiple peaks and the troughs /
valleys between those peaks in the spectrum of a click. Also has a
plotting feature so that you can easily see the values being chosen as
peaks / troughs in the spectrum and adjust the search parameters. See
help file for algorithm details.
wignerTransform - Compute the Wigner-Ville transform
of a signal, and optionally plot the result. This will zero-pad the
input signal to the next power of two, and the result is an NxN matrix
where N is the zero-padded length. Returns a list with the NxN matrix,
as well as the values for the time and frequency axes.
addPgEvent - Add a new Event to a Pamguard database.
Provide the database to add the event to, the UIDs of the individual
detections for this event, the binary files that these detections are
found in, and an “eventType” name for the event. Existing events cannot
be added to, so all detections for an event must be added at the same
time. This function should only add to an existing database, it will not
modify or remove existing entries in the database.
addPgGps - Add a gpsData table to a Pamguard
database. Gps source can either be a dataframe, SPOT csv file, or SPOT
gpx file, or csv file with UTC, Longitude, and Latitude
Environmental data fetching functions to be described later
Rework decimateWavFiles to work with multi-channel
data.