Gene-Based Association Tests using the Actual Impurity Reduction (AIR) Variable Importance

Gene-based association tests using the actual impurity reduction (AIR) variable importance. The function aggregates AIR importance measures from a group of SNPs or probes and outputs a p-value for each gene. The procedures builds upon the method described in and will be published soon.

Research Assessment Tools

Includes algorithms to assess research productivity and patterns, such as the h-index and i-index. Cardoso et al. (2022) Cardoso, P., Fukushima, C.S. & Mammola, S. (2022) Quantifying the internationalization and representativeness in research. Trends in Ecology and Evolution, 37: 725-728.

Linear Dynamical System Reconstruction

Streamflow (and climate) reconstruction using Linear Dynamical Systems. The advantage of this method is the additional state trajectory which can reveal more information about the catchment or climate system. For details of the method please refer to Nguyen and Galelli (2018) .

Extra Functionality for 'leaflet' Package

The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.

Self Organising Maps for the Analysis of Molecular Dynamics Data

Processes data from Molecular Dynamics simulations using Self Organising Maps. Features include the ability to read different input formats. Trajectories can be analysed to identify groups of important frames. Output visualisation can be generated for maps and pathways. Methodological details can be found in Motta S et al (2022) . I/O functions for xtc format files were implemented using the 'xdrfile' library available under open source license. The relevant information can be found in inst/COPYRIGHT.

Develop a 'Telegram Bot' with R

Provides a pure interface for the 'Telegram Bot API' < http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.

Create Interactive Web Maps Using 'The National Map' Services

Creates interactive web maps using the 'JavaScript' 'Leaflet' library with base layers of 'The National Map' ('TNM'). 'TNM' services provide access to base geospatial information that describes the landscape of the United States and its territories. This package is dependent on, and intended to be used with, the 'leaflet' package.

Lagged Weighted Quantile Sum Regression

Wrapper functions for the implementation of lagged weighted quantile sum regression, as per 'Gennings et al' (2020) .

Tools for Analysis, Design, and Operation of Water Supply Storages

Measure single-storage water supply system performance using resilience, reliability, and vulnerability metrics; assess storage-yield-reliability relationships; determine no-fail storage with sequent peak analysis; optimize release decisions for water supply, hydropower, and multi-objective reservoirs using deterministic and stochastic dynamic programming; generate inflow replicates using parametric and non-parametric models; evaluate inflow persistence using the Hurst coefficient.

A Modification of Fleiss' Kappa in Case of Nominal and Ordinal Variables

The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.