This package implements a joint cointegration testing approach that combines Engle-Granger, Johansen maximum eigenvalue, Boswijk, and Banerjee tests into a unified test-statistic for the null of non-cointegration. Also see Bayer and Hanck (2013) <doi:10.1111/j.1467-9892.2012.00814.x>.

This package provides estimators and utilities for large panel-data models with cross-sectional dependence, including mean group (MG), common correlated effects (CCE) and dynamic CCE (DCCE) estimators, and cross-sectionally augmented ARDL (CS-ARDL) specifications, plus related inference and diagnostics.

This package provides a series of wrapper functions to implement the 10 maximum likelihood models of animal orientation described by Schnute and Groot (1992) <DOI:10.1016/S0003-3472(05)80068-5>. The functions also include the ability to use different optimizer methods and calculate various model selection metrics (i.e., AIC, AICc, BIC). The ability to perform variants of the Hermans-Rasson test and Pycke test is also included as described in Landler et al. (2019) <DOI:10.1186/s12898-019-0246-8>. The latest version also includes a new method to calculate circular-circular and circular-linear distance correlations.

This package provides a tool that imports, subsets, visualizes, and exports the Correlates of State Policy Project dataset assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy>. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States. Users with only a basic understanding of R can subset this data across multiple dimensions, export their search results, create map visualizations, export the citations associated with their searches, and more.

This package contains functions to estimate the Correlation-Adjusted Regression Survival (CARS) Scores. The method is described in Welchowski, T. and Zuber, V. and Schmid, M., (2018), Correlation-Adjusted Regression Survival Scores for High-Dimensional Variable Selection, <arXiv:1802.08178>.

As different antipsychotic medications have different potencies, the doses of different medications cannot be directly compared. Various strategies are used to convert doses into a common reference so that comparison is meaningful. Chlorpromazine (CPZ) has historically been used as a reference medication into which other antipsychotic doses can be converted, as "chlorpromazine-equivalent doses". Using conversion keys generated from widely-cited scientific papers, e.g. Gardner et. al 2010 <doi:10.1176/appi.ajp.2009.09060802> and Leucht et al. 2016 <doi:10.1093/schbul/sbv167>, antipsychotic doses are converted to CPZ (or any specified antipsychotic) equivalents. The use of the package is described in the included vignette. Not for clinical use.

This package provides functions for implementing the novel algorithm CASCORE, which is designed to detect latent community structure in graphs with node covariates. This algorithm can handle models such as the covariate-assisted degree corrected stochastic block model (CADCSBM). CASCORE specifically addresses the disagreement between the community structure inferred from the adjacency information and the community structure inferred from the covariate information. For more detailed information, please refer to the reference paper: Yaofang Hu and Wanjie Wang (2022) <arXiv:2306.15616>. In addition to CASCORE, this package includes several classical community detection algorithms that are compared to CASCORE in our paper. These algorithms are: Spectral Clustering On Ratios-of Eigenvectors (SCORE), normalized PCA, ordinary PCA, network-based clustering, covariates-based clustering and covariate-assisted spectral clustering (CASC). By providing these additional algorithms, the package enables users to compare their performance with CASCORE in community detection tasks.

Using polygenic scores (PGS, or PRS/GRS for binary outcomes), this package allows to investigate shared predisposition between different conditions, and do fast association analysis, export plots and views of the PGS distribution using ggplot2 object.

This package provides a companion package to cmstatr <https://cran.r-project.org/package=cmstatr>. cmstatr contains statistical methods that are published in the Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4), while cmstatrExt contains statistical methods that are not included in that handbook.

Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <doi:10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns cross-sectional correlation, autocorrelation, and volatility clustering without power loss.

Calculates centrality indices additional to the igraph package centrality functions.

Estimate, assess, test, and study linear, nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures, including estimation techniques such as partial least squares path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc), generalized structured component analysis (GSCA), generalized structured component analysis with uniqueness terms (GSCAm), generalized canonical correlation analysis (GCCA), principal component analysis (PCA), factor score regression (FSR) using sum score, regression or Bartlett scores (including bias correction using Croonâ s approach), as well as several tests and typical postestimation procedures (e.g., verify admissibility of the estimates, assess the model fit, test the model fit etc.).

Run computer experiments using the adaptive composite grid algorithm with a Gaussian process model. The algorithm works best when running an experiment that can evaluate thousands of points from a deterministic computer simulation. This package is an implementation of a forthcoming paper by Plumlee, Erickson, Ankenman, et al. For a preprint of the paper, contact the maintainer of this package.

This package provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis. Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.

Computes effect sizes, standard errors, and confidence intervals for total, direct, and indirect effects in continuous-time mediation models as described in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.

This package provides a simple set of classes and methods for mapping between scalar intensity values and colors. There is also support for layering maps on top of one another using alpha composition.

This package provides tools for modeling time-to-event data with a cure fraction under correlated destructive negative binomial cure rate models. The models assume multiple latent competing causes with possible dependence and allow for elimination (inactivation) of some initial causes. Estimation is performed via an Expectation-Maximization algorithm, and diagnostic tools based on Cox-Snell residuals are provided.

Computes maximum response from Cardiac Magnetic Resonance Images using spatial and voxel wise spline based Bayesian model. This is an implementation of the methods described in Schmid (2011) <doi:10.1109/TMI.2011.2109733> "Voxel-Based Adaptive Spatio-Temporal Modelling of Perfusion Cardiovascular MRI". IEEE TMI 30(7) p. 1305 - 1313.

Cluster Evolution Analytics allows us to use exploratory what if questions in the sense that the present information of an object is plugged-in a dataset in a previous time frame so that we can explore its evolution (and of its neighbors) to the present. See the URL for the papers associated with this package, as for instance, Morales-Oñate and Morales-Oñate (2024) <doi:10.1016/j.softx.2024.101921>.

This package provides functions to assess complex heterogeneity in the strength of a surrogate marker with respect to multiple baseline covariates, in either a randomized treatment setting or observational setting. For a randomized treatment setting, the functions assess and test for heterogeneity using both a parametric model and a semiparametric two-step model. More details for the randomized setting are available in: Knowlton, R., Tian, L., & Parast, L. (2025). "A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker," Statistics in Medicine, 44(5), e70001 <doi:10.1002/sim.70001>. For an observational setting, functions in this package assess complex heterogeneity in the strength of a surrogate marker using meta-learners, with options for different base learners. More details for the observational setting will be available in the future in: Knowlton, R., Parast, L. (2025) "Assessing Surrogate Heterogeneity in Real World Data Using Meta-Learners." A tutorial for this package can be found at <https://www.laylaparast.com/cohetsurr>.

This package provides a tiny package to generate CRediT author statements (<https://credit.niso.org/>). It provides three functions: create a template, read it back and generate the CRediT author statement in a text file.

Reads Word documents containing incomplete bibliographic references and produces an updated file with standardized and complete references. The package provides functions to retrieve missing authors, titles, journal details, volume, issue, and page numbers. Digital object identifiers (DOIs) are retrieved using the CrossRef application programming interface (API) <https://api.crossref.org>, and references are formatted following DOI-based citation standards as described by Paskin (2010) <doi:10.1000/182> and the citation.doi.org service <https://citation.doi.org>. The package is intended to simplify reference preparation for scientific journal submissions.

The congeneric normal-ogive model is a popular model for psychometric data (McDonald, R. P. (1997) <doi:10.1007/978-1-4757-2691-6_15>). This model estimates the model, calculates theoretical and concrete reliability coefficients, and predicts the latent variable of the model. This is the companion package to Moss (2020) <doi:10.31234/osf.io/nvg5d>.

This package provides automated small-cell suppression for one- and two-way frequency tables. Cells falling below a user-defined frequency threshold are masked, with suppression propagated to secondary cells to prevent indirect disclosure. Designed for clinical and health administrative data, the package supports a range of tabular structures and fits into reproducible reporting pipelines, reducing manual review while applying consistent suppression rules across data sharing workflows.