Four-Step Biodiversity Analysis Based on 'iNEXT'

Expands 'iNEXT' to include the estimation of sample completeness and evenness. The package provides simple functions to perform the following four-step biodiversity analysis: STEP 1: Assessment of sample completeness profiles. STEP 2a: Analysis of size-based rarefaction and extrapolation sampling curves to determine whether the asymptotic diversity can be accurately estimated. STEP 2b: Comparison of the observed and the estimated asymptotic diversity profiles. STEP 3: Analysis of non-asymptotic coverage-based rarefaction and extrapolation sampling curves. STEP 4: Assessment of evenness profiles. The analyses in STEPs 2a, 2b and STEP 3 are mainly based on the previous 'iNEXT' package. Refer to the 'iNEXT' package for details. This package is mainly focusing on the computation for STEPs 1 and 4. See Chao et al. (2020) for statistical background.

Wavelet ANN Model

The wavelet and ANN technique have been combined to reduce the effect of data noise. This wavelet-ANN conjunction model is able to forecast time series data with better accuracy than the traditional time series model. This package fits hybrid Wavelet ANN model for time series forecasting using algorithm by Anjoy and Paul (2017) .

Data Sets for 'ArchaeoPhases' Vignettes

Provides the data sets used to build the 'ArchaeoPhases' vignettes. The data sets were formerly distributed with 'ArchaeoPhases', however they exceed current CRAN policy for package size.

Collection and Analysis of Otolith Shape Data

Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise described in Haines and Crampton (2000) , choose from conducting either a Fourier or wavelet see Gençay et al (2001) transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.

Measuring Ecosystem Multi-Functionality and Its Decomposition

Provide simple functions to (i) compute a class of multi-functionality measures for a single ecosystem for given function weights, (ii) decompose gamma multi-functionality for pairs of ecosystems and K ecosystems (K can be greater than 2) into a within-ecosystem component (alpha multi-functionality) and an among-ecosystem component (beta multi-functionality). In each case, the correlation between functions can be corrected for. Based on biodiversity and ecosystem function data, this software also facilitates graphics for assessing biodiversity-ecosystem functioning relationships across scales.

Tools for Exploring Multivariate Data via ICS/ICA

Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009, ) and Oja, Sirkia and Eriksson's (AJS, 2006, < https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different scatter matrices to obtain an invariant coordinate system or independent components, depending on the underlying assumptions.

MARS Based ANN Hybrid Model

Multivariate Adaptive Regression Spline (MARS) based Artificial Neural Network (ANN) hybrid model is combined Machine learning hybrid approach which selects important variables using MARS and then fits ANN on the extracted important variables.

Comparison of Variance - Covariance Patterns

Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) . Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) .

Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' < https://chronomodel.com/>, 'Oxcal' < https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' < https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) .

'REPPlab' via a Shiny Application

Performs exploratory projection pursuit via 'REPPlab' (Daniel Fischer, Alain Berro, Klaus Nordhausen & Anne Ruiz-Gazen (2019) ) using a Shiny app.