Ordination Methods for the Analysis of Beta-Diversity Indices

The analysis of different aspects of biodiversity requires specific algorithms. For example, in regionalisation analyses, the high frequency of ties and zero values in dissimilarity matrices produced by Beta-diversity turnover produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, visualisation of biogeographical regionalisation can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to visualise and analyse pattern of biodiversity and to improve occurrence data for cryptic taxa. Other functions related to recluster (e.g. the biodecrypt family) are currently available in GitHub at < https://github.com/leondap/recluster>.

Large Amplitude Oscillatory Shear (LAOS)

The Sequence of Physical Processes (SPP) framework is a way of interpreting the transient data derived from oscillatory rheological tests. It is designed to allow both the linear and non-linear deformation regimes to be understood within a single unified framework. This code provides a convenient way to determine the SPP framework metrics for a given sample of oscillatory data. It will produce a text file containing the SPP metrics, which the user can then plot using their software of choice. It can also produce a second text file with additional derived data (components of tangent, normal, and binormal vectors), as well as pre-plotted figures if so desired. It is the R version of the Package SPP by Simon Rogers Group for Soft Matter (Simon A. Rogers, Brian M. Erwin, Dimitris Vlassopoulos, Michel Cloitre (2011) ).

Koeppen-Geiger Climatic Zones

Aids in identifying the Koeppen-Geiger (KG) climatic zone for a given location. The Koeppen-Geiger climate zones were first published in 1884, as a system to classify regions of the earth by their relative heat and humidity through the year, for the benefit of human health, plant and agriculture and other human activity [1]. This climate zone classification system, applicable to all of the earths surface, has continued to be developed by scientists up to the present day. Recently one of use (FZ) has published updated, higher accuracy KG climate zone definitions [2]. In this package we use these updated high-resolution maps as the data source [3]. We provide functions that return the KG climate zone for a given longitude and lattitude, or for a given United States zip code. In addition the CZUncertainty() function will check climate zones nearby to check if the given location is near a climate zone boundary. In addition an interactive shiny app is provided to define the KG climate zone for a given longitude and lattitude, or United States zip code. Digital data, as well as animated maps, showing the shift of the climate zones are provided on the following website < http://koeppen-geiger.vu-wien.ac.at>. This work was supported by the DOE-EERE SunShot award DE-EE-0007140. [1] W. Koeppen, (2011) . [2] F. Rubel and M. Kottek, (2010) . [3] F. Rubel, K. Brugger, K. Haslinger, and I. Auer, (2016) .

Reference-Based Imputation for Longitudinal Clinical Trials with Protocol Deviation

Imputation of missing numerical outcomes for a longitudinal trial with protocol deviations. The package uses distinct treatment arm-based assumptions for the unobserved data, following the general algorithm of Carpenter, Roger, and Kenward (2013) , and the causal model of White, Royes and Best (2020) . Sensitivity analyses to departures from these assumptions can be done by the Delta method of Roger. The program uses the same algorithm as the 'mimix' 'Stata' package written by Suzie Cro, with additional coding for the causal model and delta method. The reference-based methods are jump to reference (J2R), copy increments in reference (CIR), copy reference (CR), and the causal model, all of which must specify the reference treatment arm. Other methods are missing at random (MAR) and the last mean carried forward (LMCF). Individual-specific imputation methods (and their reference groups) can be specified.

Ontology Tools with Data FAIRification in Development

Translates several CSV files with ontological terms and corresponding data into RDF triples. These RDF triples are stored in OWL and JSON-LD files, facilitating data accessibility, interoperability, and knowledge unification. The triples are also visualized in a graph saved as an SVG. The input CSVs must be formatted with a template from a public Google Sheet; see README or vignette for more information. This is a tool is used by the SDLE Research Center at Case Western Reserve University to create and visualize material science ontologies, and it includes example ontologies to demonstrate its capabilities. This work was supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under Solar Energy Technologies Office (SETO) Agreement Numbers E-EE0009353 and DE-EE0009347, Department of Energy (National Nuclear Security Administration) under Award Number DE-NA0004104 and Contract number B647887, and U.S. National Science Foundation Award under Award Number 2133576.

Import and Export Data

Import and export data from the most common statistical formats by using R functions that guarantee the least loss of the data information, giving special attention to the date variables and the labelled ones.

Read-Write Support for 'NumPy' Files via 'Rcpp'

The 'cnpy' library written by Carl Rogers provides read and write facilities for files created with (or for) the 'NumPy' extension for 'Python'. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with as C++11 which should be the default on all platforms since the release of R 3.3.0.

Fault Trees for Risk and Reliability Analysis

Construction, calculation and display of fault trees. Methods derived from Clifton A. Ericson II (2005, ISBN: 9780471739425) , Antoine Rauzy (1993) , Tim Bedford and Roger Cooke (2012, ISBN: 9780511813597) , Nikolaos Limnios, (2007, ISBN: 9780470612484) .

Optimization Frameworks for Tie-Oriented and Actor-Oriented Relational Event Models

A comprehensive set of tools designed for optimizing likelihood within a tie-oriented (Butts, C., 2008, ) or an actor-oriented modelling framework (Stadtfeld, C., & Block, P., 2017, ) in relational event networks. The package accommodates both frequentist and Bayesian approaches. The frequentist approaches that the package incorporates are the Maximum Likelihood Optimization (MLE) and the Gradient-based Optimization (GDADAMAX). The Bayesian methodologies included in the package are the Bayesian Sampling Importance Resampling (BSIR) and the Hamiltonian Monte Carlo (HMC). The flexibility of choosing between frequentist and Bayesian optimization approaches allows researchers to select the estimation approach which aligns the most with their analytical preferences.

Turing Geovisualization Engine R package

Turing Geovisualization Engine R package for geospatial visualization and analysis.