DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data

Perform differential analysis for methylation array data. Detect differentially methylated regions (DMRs) from array M-values. The core is a Non-homogeneous Hidden Markov Model for estimating spatial correlation and a novel Constrained Gaussian Mixture Model for modeling the M-value pairs of each individual locus.

Interior Point Conic Optimization Solver

A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (< https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.

'NOAA' Weather Data from R

Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at < https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.

Improves the Interpretation of the Standardized Precipitation Index Under Changing Climate Conditions

Improves the interpretation of the Standardized Precipitation Index under changing climate conditions. The package uses the nonstationary approach proposed in Blain et al. (2022) to detect trends in rainfall quantities and to quantify the effect of such trends on the probability of a drought event occurring.

NUtrient Cycling and COMpetition Model Undisturbed Open Bog Ecosystems in a Temperate to Sub-Boreal Climate

Modelling the vegetation, carbon, nitrogen and water dynamics of undisturbed open bog ecosystems in a temperate to sub-boreal climate. The executable of the model can downloaded from < https://github.com/jeroenpullens/NUCOMBog>.

A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

Applies the CREST climate reconstruction method. It can be used using the calibration data that can be obtained through the package or by importing private data. An ensemble of graphical outputs were designed to facilitate the use of the package and the interpretation of the results. More information can be obtained from Chevalier (2022) .

Interface to the 'Daymet' Web Services

Programmatic interface to the 'Daymet' web services (< http://daymet.ornl.gov>). Allows for easy downloads of 'Daymet' climate data directly to your R workspace or your computer. Routines for both single pixel data downloads and gridded (netCDF) data are provided.

Ecological Inference by Linear Programming under Homogeneity

Provides a bunch of algorithms based on linear programming for estimating, under the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices) using mainly aggregate data (from voting units). References: Pavía and Romero (2024) . Pavía and Romero (2024) . Pavía (2023) . Pavía (2024) . Pavía (2024) . Pavía and Penadés (2024). A bottom-up approach for ecological inference. Romero, Pavía, Martín and Romero (2020) . Acknowledgements: The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grants AICO/2021/257, CIAICO/2023/031) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.

Improved q-Values for Discrete Uniform and Homogeneous Tests

We consider a multiple testing procedure used in many modern applications which is the q-value method proposed by Storey and Tibshirani (2003), . The q-value method is based on the false discovery rate (FDR), hence versions of the q-value method can be defined depending on which estimator of the proportion of true null hypotheses, p0, is plugged in the FDR estimator. We implement the q-value method based on two classical pi0 estimators, and furthermore, we propose and implement three versions of the q-value method for homogeneous discrete uniform P-values based on pi0 estimators which take into account the discrete distribution of the P-values.

Tools for CM SAF NetCDF Data

The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (< https://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafops' R-package provides a collection of R-operators for the analysis and manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time, longitude and latitude dimension should be applicable, but there is no guarantee for an error-free application. CM SAF climate data records are provided for free via (< https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (< http://www.cmsaf.eu/R_toolbox>).