A collection of miscellaneous functions for passive acoustics. 
    Much of the content here is adapted to R from code written by other people.
    If you have any ideas of functions to add, please contact Taiki Sakai.

The Piece-wise exponential (Additive Mixed) Model
    (PAMM; Bender and others (2018) <doi: 10.1177/1471082X17748083>) is a
    powerful model class for the analysis of survival (or time-to-event) data,
    based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2019)), as well as support for left-truncated, competing risks and recurrent events data.
    pammtools provides tidy workflow for survival analysis with PAMMs,
    including data simulation, transformation and other functions for data
    preprocessing and model post-processing as well as visualization.

Tools for loading and processing passive acoustic data. Read in data
    that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
    processing functions, and export data for reports or external modeling tools. Parameter 
    calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
    Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
    <doi:10.1121/1.3479549>.

Implements the Panel Data Approach Method for program evaluation as developed in Hsiao, Ching and Ki Wan (2012). pampe estimates the effect of an intervention by comparing the evolution of the outcome for a unit affected by an intervention or treatment to the evolution of the unit had it not been affected by the intervention.

Some functions for sample classification in microarrays.

A variety of tools relevant to the analysis
    of marine soundscape data. There are tools for downloading AIS (automatic identification system)
    data from Marine Cadastre <https://marinecadastre.gov/ais/>,
    connecting AIS data to GPS coordinates, plotting summaries of various soundscape
    measurements, and downloading relevant environmental variables (wind, swell height) from the
    National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>.
    Most tools were developed to work well with output from 'Triton' software, but can be adapted
    to work with any similar measurements.