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Estimation of Transmissibility in the Early Stages of a Disease Outbreak
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013)
ICS via a Shiny Application
Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009)
Dynamic Model of Ammonia Emission from Field-Applied Manure
An implementation of the ALFAM2 dynamic emission model for ammonia volatilization from field-applied animal slurry (manure with dry matter below about 15%). The model can be used to predict cumulative emission and emission rate of ammonia following field application of slurry. Predictions may be useful for emission inventory calculations, fertilizer management, assessment of mitigation strategies, or research aimed at understanding ammonia emission. Default parameter sets include effects of application method, slurry composition, and weather. The model structure is based on a simplified representation of the physical-chemical slurry-soil-atmosphere system. See Hafner et al. (2018)
Tandem Clustering with Invariant Coordinate Selection
Implementation of tandem clustering with invariant coordinate
selection with different scatter matrices and several choices for the
selection of components as described in Alfons, A., Archimbaud, A., Nordhausen, K.and Ruiz-Gazen, A. (2022)
Tools for Modeling Rate-Dependent Hysteretic Processes and Ellipses
Fit, summarize and plot sinusoidal hysteretic processes using:
two-step simple harmonic least squares, ellipse-specific non-linear least
squares, the direct method, geometric least squares or linear least squares. See
Yang, F and A. Parkhurst, "Efficient Estimation of Elliptical Hysteresis with
Application to the Characterization of Heat Stress"
Tools for Tidy Vowel Normalization
An implementation of tidy speaker vowel normalization.
This includes generic functions for defining new normalization methods for
points, formant tracks, and Discrete Cosine Transform coefficients, as well
as convenience functions implementing established normalization methods.
References for the implemented methods are:
Johnson, Keith (2020)
Bayesian Time-Stratified Population Analysis
Provides advanced Bayesian methods to estimate
abundance and run-timing from temporally-stratified
Petersen mark-recapture experiments. Methods include
hierarchical modelling of the capture probabilities
and spline smoothing of the daily run size. Theory
described in Bonner and Schwarz (2011)
Estimation of Caribou Abundance Based on Radio Telemetry Data
Estimation of population size of migratory caribou herds based on large scale aggregations monitored by radio telemetry. It implements the methodology found in the article by Rivest et al. (1998) about caribou abundance estimation. It also includes a function based on the Lincoln-Petersen Index as applied to radio telemetry data by White and Garrott (1990).
Wrangle, Analyze, and Visualize Animal Movement Data
Tools to import, clean, and visualize movement data, particularly from motion capture systems such as Optitrack's 'Motive', the Straw Lab's 'Flydra', or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli.
Hybrid ARIMA-GARCH and Two Specially Designed ML-Based Models
Describes a series first. After that does time series analysis using one hybrid model and two specially structured Machine Learning (ML) (Artificial Neural Network or ANN and Support Vector Regression or SVR) models. More information can be obtained from Paul and Garai (2022)