This package provides tools for calculating I-Scores, a simple way to measure how successful minor political parties are at influencing the major parties in their environment. I-Scores are designed to be a more comprehensive measurement of minor party success than vote share and legislative seats won, the current standard measurements, which do not reflect the strategies that most minor parties employ. The procedure leverages the Manifesto Project's NLP model to identify the issue areas that sentences discuss, see Burst et al. (2024) <doi:10.25522/manifesto.manifestoberta.56topics.context.2024.1.1>, and the Wordfish algorithm to estimate the relative positions that platforms take on those issue areas, see Slapin and Proksch (2008) <doi:10.1111/j.1540-5907.2008.00338.x>.

This package implements a computational framework to predict microbial community-based metabolic profiles with O2PLS model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.

Run flexible mediation analyses using natural effect models as described in Lange, Vansteelandt and Bekaert (2012) <DOI:10.1093/aje/kwr525>, Vansteelandt, Bekaert and Lange (2012) <DOI:10.1515/2161-962X.1014> and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013) <DOI:10.1080/00273171.2013.832132>.

Generate a monochrome palette from a starting colour for a specified number of colours. The package can also be used to display colour palettes in the plot window, with or without hex codes and colour labels.

Efficient finite difference method for valuing European and American multi-asset options.

Quickly make tables of descriptive statistics (i.e., counts, means, confidence intervals) for continuous variables. This package is designed to work in a Tidyverse pipeline, and consideration has been given to get results from R to Microsoft Word ® with minimal pain.

Computation of various Markovian models for categorical data including homogeneous Markov chains of any order, MTD models, Hidden Markov models, and Double Chain Markov Models.

Implementation of the Monothetic Clustering algorithm (Chavent, 1998 <doi:10.1016/S0167-8655(98)00087-7>) on continuous data sets. A lot of extensions are included in the package, including applying Monothetic clustering on data sets with circular variables, visualizations with the results, and permutation and cross-validation based tests to support the decision on the number of clusters.

This package implements multivariate Fay-Herriot models for small area estimation. It uses empirical best linear unbiased prediction (EBLUP) estimator. Multivariate models consider the correlation of several target variables and borrow strength from auxiliary variables to improve the effectiveness of a domain sample size. Models which accommodated by this package are univariate model with several target variables (model 0), multivariate model (model 1), autoregressive multivariate model (model 2), and heteroscedastic autoregressive multivariate model (model 3). Functions provide EBLUP estimators and mean squared error (MSE) estimator for each model. These models were developed by Roberto Benavent and Domingo Morales (2015) <doi:10.1016/j.csda.2015.07.013>.

Identifying comorbidities, frailty, and multimorbidity in claims and administrative data is often a duplicative process. The functions contained in this package are meant to first prepare the data to a format acceptable by all other packages, then provide a uniform and simple approach to generate comorbidity and multimorbidity metrics based on these claims data. The package is ever evolving to include new metrics, and is always looking for new measures to include. The citations used in this package include the following publications: Anne Elixhauser, Claudia Steiner, D. Robert Harris, Rosanna M. Coffey (1998) <doi:10.1097/00005650-199801000-00004>, Brian J Moore, Susan White, Raynard Washington, et al. (2017) <doi:10.1097/MLR.0000000000000735>, Mary E. Charlson, Peter Pompei, Kathy L. Ales, C. Ronald MacKenzie (1987) <doi:10.1016/0021-9681(87)90171-8>, Richard A. Deyo, Daniel C. Cherkin, Marcia A. Ciol (1992) <doi:10.1016/0895-4356(92)90133-8>, Hude Quan, Vijaya Sundararajan, Patricia Halfon, et al. (2005) <doi:10.1097/01.mlr.0000182534.19832.83>, Dae Hyun Kim, Sebastian Schneeweiss, Robert J Glynn, et al. (2018) <doi:10.1093/gerona/glx229>, Melissa Y Wei, David Ratz, Kenneth J Mukamal (2020) <doi:10.1111/jgs.16310>, Kathryn Nicholson, Amanda L. Terry, Martin Fortin, et al. (2015) <doi:10.15256/joc.2015.5.61>, Martin Fortin, José Almirall, and Kathryn Nicholson (2017)<doi:10.15256/joc.2017.7.122>.

This package provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to R.matlab', which creates a MATLAB server.

Multiscale Graph Correlation (MGC) is a framework developed by Vogelstein et al. (2019) <DOI:10.7554/eLife.41690> that extends global correlation procedures to be multiscale; consequently, MGC tests typically require far fewer samples than existing methods for a wide variety of dependence structures and dimensionalities, while maintaining computational efficiency. Moreover, MGC provides a simple and elegant multiscale characterization of the potentially complex latent geometry underlying the relationship.

Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.

Analysis and visualisation of synchrony, interaction, and joint movements from audio and video movement data of a group of music performers. The demo is data described in Clayton, Leante, and Tarsitani (2021) <doi:10.17605/OSF.IO/KS325>, while example analyses can be found in Clayton, Jakubowski, and Eerola (2019) <doi:10.1177/1029864919844809>. Additionally, wavelet analysis techniques have been applied to examine movement-related musical interactions, as shown in Eerola et al. (2018) <doi:10.1098/rsos.171520>.

Estimation of multivariate normal (MVN) and student-t data of arbitrary dimension where the pattern of missing data is monotone. See Pantaleo and Gramacy (2010) <doi:10.48550/arXiv.0907.2135>. Through the use of parsimonious/shrinkage regressions (plsr, pcr, lasso, ridge, etc.), where standard regressions fail, the package can handle a nearly arbitrary amount of missing data. The current version supports maximum likelihood inference and a full Bayesian approach employing scale-mixtures for Gibbs sampling. Monotone data augmentation extends this Bayesian approach to arbitrary missingness patterns. A fully functional standalone interface to the Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown), Horseshoe (from Carvalho, Polson, & Scott), and ridge regression with model selection via Reversible Jump, and student-t errors (from Geweke) is also provided.

The Markov Decision Processes (MDP) toolbox proposes functions related to the resolution of discrete-time Markov Decision Processes: finite horizon, value iteration, policy iteration, linear programming algorithms with some variants and also proposes some functions related to Reinforcement Learning.

Electronic health records (EHR) linked with biorepositories are a powerful platform for translational studies. A major bottleneck exists in the ability to phenotype patients accurately and efficiently. Towards that end, we developed an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language processing (NLP). Specifically, our proposed method, called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. (2019) <doi:10.1093/jamia/ocz066>.).

An S4 implementation of the unbiased extension of the model- assisted synthetic-regression estimator proposed by Mandallaz (2013) <DOI:10.1139/cjfr-2012-0381>, Mandallaz et al. (2013) <DOI:10.1139/cjfr-2013-0181> and Mandallaz (2014) <DOI:10.1139/cjfr-2013-0449>. It yields smaller variances than the standard bias correction, the generalised regression estimator.

Maps and other related data of Finland.

Bending non-positive-definite (symmetric) matrices to positive-definite, using weighted and unweighted methods. Jorjani, H., et al. (2003) <doi:10.3168/jds.S0022-0302(03)73646-7>. Schaeffer, L. R. (2014) <http://animalbiosciences.uoguelph.ca/~lrs/ELARES/PDforce.pdf>.

Density, distribution function, quantile function, and random generation function based on Salem, H. M. (2019)<doi:10.5539/mas.v13n2p54>. In addition, a numerical method for maximum likelihood estimation is provided.

The chi-squared test for goodness of fit and independence test.

This package contains functions for performing Mokken scale analysis on test and questionnaire data. It includes an automated item selection algorithm, and various checks of model assumptions.

Developed for the following tasks. 1- simulating realizations from the canonical, restricted, and unrestricted finite mixture models. 2- Monte Carlo approximation for density function of the finite mixture models. 3- Monte Carlo approximation for the observed Fisher information matrix, asymptotic standard error, and the corresponding confidence intervals for parameters of the mixture models sing the method proposed by Basford et al. (1997) <https://espace.library.uq.edu.au/view/UQ:57525>.