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.