docs/PAMrSettings.md

In TaikiSan21/PAMr: Load and Process Passive Acoustic Data

The PAMrSettings object

The first step in using PAMr is to create a PAMrSettings object. This is an S4 class created for this package, and will store all settings related to a particular anaylsis. The goal of this object is to make it easy to share and replicate results between users. All you need to do is send someone your PAMrSettings object and they can see exactly how you analysed your data, or even point the PRS at their own data and process it in the exact same way.

A PAMrSettings object has four slots:

• db - This stores the full path to any SQLite databases that will be analysed
• binaries - This stores the folder names of any binaries, as well as the full path to all individual Pamguard binary (.pgdf) files within those folders
• functions - This stores a set of functions that will be applied to the data when read in from the database/binary files. Stores functions for the 'ClickDetector', 'WhistlesMoans', and 'Cepstrum' modules separately. When adding a new function, users are asked to supply values for any arguments of the function. These values are saved with the function and cannot be changed without removing the function entirely.
• calibration - Stores a calibration function to correct for different hydrophone characteristics. Optional, currently only affects certain 'ClickDetector' functions

Note that none of these slots should ever be manually edited, use the functions described below if you want to add or remove anything.

A PAMrSettings object can be created without supplying any arguments (as described in the quick start guide), or it can be created by directly supplying the database and binary file paths, although the user will still be asked to input parameters for the standardClickCalcs function.

myDb <- './Data/TestDB.sqlite3'
myBinaryFolder <- './Data/Binaries'
myPrs <- PAMrSettings(db = myDb, binaries = myBinaryFolder)

Adding to Your PRS

After the initial set-up of your PRS, you may want to add to it. There are four functions that accomplish this: addDatabase, addBinaries, addFunction, and addCalibration. The first two are simple, and can be called interactively just like the initial PRS setup or by providing the paths.

myPrs <- addDatabase(myPrs)
myPrs <- addBinaries(myPrs)
newDb <- './Data/NewDB.sqlite3'
newBinaries <- './Data/NewBinaries/'
myPrs <- addDatabase(myPrs, newDb)
myPrs <- addBinaries(myPrs, newBinaries)

Adding a function is slightly more involved. First make sure the function (or the package the function is in) is already sourced. Then add the function by name, also specifying the module as either 'ClickDetector' or 'WhistlesMoans'. If you do not specify, you will be asked to choose. addFunction will also ask the use to set the value for any parameters that are arguments to the function you provide, except for parameters named "data" or "calibration". In this example, the user would be ask to set values for "a", then "b", and would be told that the default for "a" is 1, and that there is not a default value for "b".

Adding from another PRS

Removing Things From Your PRS

There are three functions that remove items from your PRS, and it is recommended that you use this instead of trying to alter the PRS manually. All of them can be called interactively and provide menus for the user to select the item to remove. See the help pages for more info.

myPrs <- removeDatabase(myPrs)
myPrs <- removeBinaries(myPrs)
myPrs <- removeFunction(myPrs)

TaikiSan21/PAMr documentation built on Nov. 15, 2020, 9:46 p.m.