Particle Learning of Gaussian Processes

Sequential Monte Carlo (SMC) inference for fully Bayesian Gaussian process (GP) regression and classification models by particle learning (PL) following Gramacy & Polson (2011) . The sequential nature of inference and the active learning (AL) hooks provided facilitate thrifty sequential design (by entropy) and optimization (by improvement) for classification and regression models, respectively. This package essentially provides a generic PL interface, and functions (arguments to the interface) which implement the GP models and AL heuristics. Functions for a special, linked, regression/classification GP model and an integrated expected conditional improvement (IECI) statistic provide for optimization in the presence of unknown constraints. Separable and isotropic Gaussian, and single-index correlation functions are supported. See the examples section of ?plgp and demo(package="plgp") for an index of demos.

Calculates the Density-Based Clustering Validation (DBCV) Index

A metric called 'Density-Based Clustering Validation index' (DBCV) index to evaluate clustering results, following the < https://github.com/pajaskowiak/clusterConfusion/blob/main/R/dbcv.R> 'R' implementation by Pablo Andretta Jaskowiak. Original 'DBCV' index article: Moulavi, D., Jaskowiak, P. A., Campello, R. J., Zimek, A., and Sander, J. (April 2014), "Density-based clustering validation", Proceedings of SDM 2014 -- the 2014 SIAM International Conference on Data Mining (pp. 839-847), .

Phenotypic Index Measures for Oak Decline Severity

Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2121) .

Diversity Index Calculation & Visualisation for Taxa and Location

Repurpose occurrence data for calculating diversity index values, creating visuals, and generating species composition matrices for a chosen taxon and location.

Transitive Index Numbers for Cross-Sections and Panel Data

Computing transitive (and non-transitive) index numbers (Coelli et al., 2005 ) for cross-sections and panel data. For the calculation of transitive indexes, the EKS (Coelli et al., 2005 ; Rao et al., 2002 ) and Minimum spanning tree (Hill, 2004 ) methods are implemented. Traditional fixed-base and chained indexes, and their growth rates, can also be derived using the Paasche, Laspeyres, Fisher and Tornqvist formulas.

Wavelet-Based Index of Storm Activity

A powerful system for estimating an improved wavelet-based index of magnetic storm activity, storm activity preindex (from individual station) and SQ variations. It also serves as a flexible visualization tool.

Urban Centrality Index

Calculates the Urban Centrality Index (UCI) as in Pereira et al., (2013) . The UCI measures the extent to which the spatial organization of a city or region varies from extreme polycentric to extreme monocentric in a continuous scale from 0 to 1. Values closer to 0 indicate more polycentric patterns and values closer to 1 indicate a more monocentric urban form.

Jaccard Index for Population Structure Identification

Uses the Jaccard similarity index to account for population structure in sequencing studies. This method was specifically designed to detect population stratification based on rare variants, hence it will be especially useful in rare variant analysis.

Wrapper for the Social Progress Index Data

In 2015, The 17 United Nations' Sustainable Development Goals were adopted. 'spiR' is a wrapper of several open datasets published by the Social Progress Imperative (< https://www.socialprogress.org/>), including the Social Progress Index (a synthetic measure of human development across the world). 'spiR''s goal is to provide data to help policymakers and researchers prioritize actions that accelerate social progress across the world in the context of the Sustainable Development Goals. Please cite: Warin, Th. (2019) "spiR: An R Package for the Social Progress Index", .

Regression for Rank-Indexed Compositional Data

Regression model where the response variable is a rank-indexed compositional vector (non-negative values that sum up to one and are ordered from the largest to the smallest). Parameters are estimated in the Bayesian framework using MCMC methods.