Fit Probabilistic Index Models

Fit a probabilistic index model as described in Thas et al, 2012: . The interface to the modeling function has changed in this new version. The old version is still available at R-Forge.

The tRNA Adaptation Index

Functions and example files to calculate the tRNA adaptation index, a measure of the level of co-adaptation between the set of tRNA genes and the codon usage bias of protein-coding genes in a given genome. The methodology is described in dos Reis, Wernisch and Savva (2003) , and dos Reis, Savva and Wernisch (2004) .

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) .

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.

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.

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", .

Geospatial Grid Indexing with the British National Grid

Offers a streamlined programmatic interface to Ordnance Survey's British National Grid (BNG) index system, enabling efficient spatial indexing and analysis based on grid references. It supports a range of geospatial applications, including statistical aggregation, data visualisation, and interoperability across datasets. Designed for developers and analysts working with geospatial data in Great Britain, 'osbng' simplifies integration with geospatial workflows and provides intuitive tools for exploring the structure and logic of the BNG system.