Provides an R interface to the Copernicus Marine Service for downloading and accessing marine data. Integrates with the official 'copernicusmarine' Python library through 'reticulate'. Requires Python 3.7+ and a free Copernicus Marine account. See <https://marine.copernicus.eu/> and <https://pypi.org/project/copernicusmarine/> for more information.

A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see   
     Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.

Performs Bayesian nonparametric density estimation using Martingale
 posterior distributions including the Copula Resampling (CopRe) algorithm. 
 Also included are a Gibbs sampler for the marginal Gibbs-type mixture model and
 an extension to include full uncertainty quantification via a predictive 
 sequence resampling (SeqRe) algorithm. The CopRe and SeqRe samplers generate 
 random nonparametric distributions as output, leading to complete nonparametric 
 inference on posterior summaries. Routines for calculating arbitrary 
 functionals from the sampled distributions are included as well as an important 
 algorithm for finding the number and location of modes, which can then be used 
 to estimate the clusters in the data using, for example, k-means.
 Implements work developed in Moya B., Walker S. G. (2022).
 <doi:10.48550/arxiv.2206.08418>, Fong, E., Holmes, C., Walker, S. G. (2021) 
 <doi:10.48550/arxiv.2103.15671>, and Escobar M. D., West, M. (1995) 
 <doi:10.1080/01621459.1995.10476550>.

Multidimensional scaling (MDS) methods that aim at pronouncing the clustered appearance of the configuration (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>). They achieve this by transforming proximities/distances with explicit power functions and penalizing the fitting criterion with a clusteredness index, the OPTICS Cordillera (Rusch, Hornik & Mair, 2018, <doi:10.1080/10618600.2017.1349664>). There are two variants: One for finding the configuration directly (COPS-C) with given explicit power transformations and implicit ratio, interval and non-metric optimal scaling transformations (Borg & Groenen, 2005, ISBN:978-0-387-28981-6), and one for using the augmented fitting criterion to find optimal hyperparameters for the explicit transformations (P-COPS). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different MDS models (most of the functionality in smacofx) in the COPS framework. The package further contains a function for pattern search optimization, the ``Adaptive Luus-Jaakola Algorithm'' (Rusch, Mair & Hornik, 2021,<doi:10.1080/10618600.2020.1869027>) and a functions to calculate the phi-distances for count data or histograms.