Fits multiple variable mixtures of various parametric proportional hazard models using the EM-Algorithm. Proportionality restrictions can be imposed on the latent groups and/or on the variables. Several survival distributions can be specified. Missing values and censored values are allowed. Independence is assumed over the single variables.

Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.

The estimation of the parameters in mixed Poisson models.

Supports the generation of parallelogram, equilateral triangle, regular hexagon, isosceles trapezoid, Koch snowflake, hexaflake', Sierpinski triangle, Sierpinski carpet and Sierpinski trapezoid mazes via TurtleGraphics'. Mazes are generated by the recursive method: the domain is divided into sub-domains in which mazes are generated, then dividing lines with holes are drawn between them, see J. Buck, Recursive Division, <http://weblog.jamisbuck.org/2011/1/12/maze-generation-recursive-division-algorithm>.

This package implements methods to normalize multiplexed imaging data, including statistical metrics and visualizations to quantify technical variation in this data type. Reference for methods listed here: Harris, C., Wrobel, J., & Vandekar, S. (2022). mxnorm: An R Package to Normalize Multiplexed Imaging Data. Journal of Open Source Software, 7(71), 4180, <doi:10.21105/joss.04180>.

Calculates exact hypothesis tests to compare a treatment and a reference group with respect to multiple binary endpoints. The tested null hypothesis is an identical multidimensional distribution of successes and failures in both groups. The alternative hypothesis is a larger success proportion in the treatment group in at least one endpoint. The tests are based on the multivariate permutation distribution of subjects between the two groups. For this permutation distribution, rejection regions are calculated that satisfy one of different possible optimization criteria. In particular, regions with maximal exhaustion of the nominal significance level, maximal power under a specified alternative or maximal number of elements can be found. Optimization is achieved by a branch-and-bound algorithm. By application of the closed testing principle, the global hypothesis tests are extended to multiple testing procedures.

Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously. It is an implementation of the work proposed by Mai, Q., Yang, Y., and Zou, H. (2019) <doi:10.5705/ss.202016.0117>.

This package provides tools to conduct Monte Carlo simulations under different conditions (e.g., varying sample size, data normality) for structural equation models (SEMs). Data can be simulated based on user-defined factor loadings and correlations, with optional non-normality added via Fleishman's power method (1978) <doi:10.1007/BF02293811>. Once generated, models can be estimated using lavaan'. This package facilitates testing model performance across multiple simulation scenarios. When data generation is completed (or when generated data sets are given) model tests can also be run. Please cite as "Orçan, F. (2021). MonteCarloSEM An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713.".

Perform the model confidence set procedure of Hansen et al (2011) <doi:10.3982/ECTA5771>.

This package contains a set of tools for constructing and coercing into and from the "mdate" class. This date class implements ISO 8601-2:2019(E) and allows regular dates to be annotated to express unspecified date components, approximate or uncertain date components, date ranges, and sets of dates. This is useful for describing and analysing temporal information, whether historical or recent, where date precision may vary.

Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data".

This package provides a tidy workflow for landscape-scale analysis. multilandr offers tools to generate landscapes at multiple spatial scales and compute landscape metrics, primarily using the landscapemetrics package. It also features utility functions for plotting and analyzing multi-scale landscapes, exploring correlations between metrics, filtering landscapes based on specific conditions, generating landscape gradients for a given metric, and preparing datasets for further statistical analysis. Documentation about multilandr is provided in an introductory vignette included in this package and in the paper by Huais (2024) <doi:10.1007/s10980-024-01930-z>; see citation("multilandr") for details.

Get map data frames for the Indian subcontinent with different region levels (e.g., district, state). The package also offers convenience functions for plotting choropleths, visualizing spatial data, and handling state/district codes.

Nonparametric estimation and inference for natural direct and indirect effects by Chan, Imai, Yam and Zhang (2016) <arXiv:1601.03501>.

This package provides a framework to perform soft clustering using simplex-structured matrix factorisation (SSMF). The package contains a set of functions for determining the optimal number of prototypes, the optimal algorithmic parameters, the estimation confidence intervals and the diversity of clusters. Abdolali, Maryam & Gillis, Nicolas (2020) <doi:10.1137/20M1354982>.

The Cauchy distribution is a special case of the t distribution when the degrees of freedom are equal to 1. The functions are related to the multivariate Cauchy distribution and include simulation, computation of the density, maximum likelihood estimation, contour plot of the bivariate Cauchy distribution, and discriminant analysis. References include: Nadarajah S. and Kotz S. (2008). "Estimation methods for the multivariate t distribution". Acta Applicandae Mathematicae, 102(1): 99--118. <doi:10.1007/s10440-008-9212-8>, and Kanti V. Mardia, John T. Kent and John M. Bibby (1979). "Multivariate analysis", ISBN:978-0124712522. Academic Press, London.

This package provides methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.

Mapping Averaged Pairwise Information (MAPI) is an exploratory method providing graphical representations summarizing the spatial variation of pairwise metrics (eg. distance, similarity coefficient, ...) computed between georeferenced samples.

Analyze multilevel networks as described in Lazega et al (2008) <doi:10.1016/j.socnet.2008.02.001> and in Lazega and Snijders (2016, ISBN:978-3-319-24520-1). The package was developed essentially as an extension to igraph'.

The Washington Metropolitan Area Transit Authority is a government agency operating light rail and passenger buses in the Washington D.C. area. With a free developer account, access their Metro Transparent Data Sets API <https://developer.wmata.com/> to return data frames of transit data for easy analysis.

To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. MACER accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The MACER package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.

This package performs multivariate meta-analysis for high-dimensional data to integrate and collectively analyse individual-level data from multiple studies, as well as to combine summary estimates. This approach accounts for correlation between outcomes, incorporates withinâ and betweenâ study variability, handles missing values, and uses shrinkage estimation to accommodate high dimensionality. The MetaHD R package provides access to our multivariate meta-analysis approach, along with a comprehensive suite of existing meta-analysis methods, including fixed-effects and random-effects models, Fisherâ s method, Stoufferâ s method, the weighted Z method, Lancasterâ s method, the weighted Fisherâ s method, and vote-counting approach. A detailed vignette with example datasets and code for data preparation and analysis is available at <https://alyshadelivera.github.io/MetaHD_vignette/>.

Computing the Mann-Whitney effect based on copula models. Estimation of the association parameter in survival copula models. A description of the underlying methods is described in Nakazono et al. (2024) <doi:10.3390/math12101453> and Nakazono et al. (accepted for publication in Statistical Papers).

Optimization algorithms implemented in R, including conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the limited memory BFGS (L-BFGS) methods. Most internal parameters can be set through the call interface. The solvers hold up quite well for higher-dimensional problems.