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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)
Sourcing Archaeological Materials by Chemical Composition
Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
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)
Create Sankey and Alluvial Diagrams Using 'ggplot2'
Sankey and alluvial diagrams visualise flows of quantities across stages in stacked bars. This package makes it easy to create such diagrams using 'ggplot2'.
Two Event Mark-Recapture Experiment
Tools are provided for estimating, testing, and simulating
abundance in a two-event (Petersen) mark-recapture experiment. Functions are
given to calculate the Petersen, Chapman, and Bailey estimators and associated
variances. However, the principal utility is a set of functions to simulate
random draws from these estimators, and use these to conduct hypothesis
tests and power calculations. Additionally, a set of functions are provided
for generating confidence intervals via bootstrapping. Functions are also
provided to test abundance estimator consistency under complete or partial
stratification, and to calculate stratified or partially stratified estimators.
Functions are also provided to calculate recommended sample sizes.
Referenced methods can be found in Arnason et al. (1996)
Analysis of Chronological Patterns from Archaeological Count Data
A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.
Bayesian Model for Genotyping using RNA-Seq
The method models RNA-seq reads using a mixture of 3 beta-binomial distributions to generate posterior probabilities for genotyping bi-allelic single nucleotide polymorphisms. Elena Vigorito, Anne Barton, Costantino Pitzalis, Myles J. Lewis and Chris Wallace (2023)