This package implements several string comparison algorithms, including calACS (count all common subsequences), lenACS (calculate the lengths of all common subsequences), and lenLCS (calculate the length of the longest common subsequence). Some algorithms differentiate between the more strict definition of subsequence, where a common subsequence cannot be separated by any other items, from its looser counterpart, where a common subsequence can be interrupted by other items. This difference is shown in the suffix of the algorithm (-Strict vs -Loose). For example, q-w is a common subsequence of q-w-e-r and q-e-w-r on the looser definition, but not on the more strict definition. calACSLoose Algorithm from Wang, H. All common subsequences (2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.

This package provides a database of Chinese surnames and given names (1930-2008). This database contains nationwide frequency statistics of 1,806 Chinese surnames and 2,614 Chinese characters used in given names, covering about 1.2 billion Han Chinese population (96.8 percent of the Han Chinese household-registered population born from 1930 to 2008 and still alive in 2008). This package also contains a function for computing multiple indices of Chinese surnames and given names for social science research (e.g., name uniqueness, name gender, name valence, and name warmth/competence). Details are provided at <https://psychbruce.github.io/ChineseNames/>.

Fits mixtures of multivariate contaminated normal distributions (with eigen-decomposed scale matrices) via the expectation conditional- maximization algorithm under a clustering or classification paradigm Methods are described in Antonio Punzo, Angelo Mazza, and Paul D McNicholas (2018) <doi:10.18637/jss.v085.i10>.

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.

We propose a consistent monitoring procedure to detect a structural change from a cointegrating relationship to a spurious relationship. The procedure is based on residuals from modified least squares estimation, using either Fully Modified, Dynamic or Integrated Modified OLS. It is inspired by Chu et al. (1996) <DOI:10.2307/2171955> in that it is based on parameter estimation on a pre-break "calibration" period only, rather than being based on sequential estimation over the full sample. See the discussion paper <DOI:10.2139/ssrn.2624657> for further information. This package provides the monitoring procedures for both the cointegration and the stationarity case (while the latter is just a special case of the former one) as well as printing and plotting methods for a clear presentation of the results.

Incorporates colour gradients from the cpt-city web archive available at <http://seaviewsensing.com/pub/cpt-city/>.

Covariance is of universal prevalence across various disciplines within statistics. We provide a rich collection of geometric and inferential tools for convenient analysis of covariance structures, topics including distance measures, mean covariance estimator, covariance hypothesis test for one-sample and two-sample cases, and covariance estimation. For an introduction to covariance in multivariate statistical analysis, see Schervish (1987) <doi:10.1214/ss/1177013111>.

Color and visualize wildlife distributions in space-time using raster data. In addition to enabling display of sequential change in distributions through the use of small multiples, colorist provides functions for extracting several features of interest from a sequence of distributions and for visualizing those features using HCL (hue-chroma-luminance) color palettes. Resulting maps allow for "fair" visual comparison of intensity values (e.g., occurrence, abundance, or density) across space and time and can be used to address questions about where, when, and how consistently a species, group, or individual is likely to be found.

Connect and pull data from the CJA API, which powers CJA Workspace <https://github.com/AdobeDocs/cja-apis>. The package was developed with the analyst in mind and will continue to be developed with the guiding principles of iterative, repeatable, timely analysis. New features are actively being developed and we value your feedback and contribution to the process.

This package provides a standard test is observed on all specimens. We treat the second test (or sampled test) as being conducted on only a stratified sample of specimens. Verification Bias is this situation when the specimens for doing the second (sampled) test is not under investigator control. We treat the total sample as stratified two-phase sampling and use inverse probability weighting. We estimate diagnostic accuracy (category-specific classification probabilities; for binary tests reduces to specificity and sensitivity, and also predictive values) and agreement statistics (percent agreement, percent agreement by category, Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating the agreement and diagnostic accuracy of two diagnostic tests when one test is conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5) <doi:10.1002/sim.4422>.

In clinical practice and research settings in medicine and the behavioral sciences, it is often of interest to quantify the correlation of a continuous endpoint that was repeatedly measured (e.g., test-retest correlations, ICC, etc.). This package allows for estimating these correlations based on mixed-effects models. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.

This package provides methods for interpreting CoDa (Compositional Data) regression models along the lines of "Pairwise share ratio interpretations of compositional regression models" (Dargel and Thomas-Agnan 2024) <doi:10.1016/j.csda.2024.107945>. The new methods include variation scenarios, elasticities, elasticity differences and share ratio elasticities. These tools are independent of log-ratio transformations and allow an interpretation in the original space of shares. CoDaImpact is designed to be used with the compositions package and its ecosystem.

Implementation of Hurst exponent estimators based on complex-valued lifting wavelet energy from Knight, M. I and Nunes, M. A. (2018) <doi:10.1007/s11222-018-9820-8>.

Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) <DOI: 10.1890/10-2037.1>.

This package provides a system containing easy-to-use tools to compute the bioequivalence assessment in the univariate framework using the methods proposed in Boulaguiem et al. (2023) <doi:10.1101/2023.03.11.532179>.

This package provides routines for fitting Cox models by likelihood based boosting for single event survival data with right censoring or in the presence of competing risks. The methodology is described in Binder and Schumacher (2008) <doi:10.1186/1471-2105-9-14> and Binder et al. (2009) <doi:10.1093/bioinformatics/btp088>.

Collective matrix factorization (a.k.a. multi-view or multi-way factorization, Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a (potentially very sparse or having many missing values) matrix X as the product of two low-dimensional matrices, optionally aided with secondary information matrices about rows and/or columns of X', which are also factorized using the same latent components. The intended usage is for recommender systems, dimensionality reduction, and missing value imputation. Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce different factorizations such as the weighted implicit-feedback model (Hu, Koren, Volinsky, (2008) <doi:10.1109/ICDM.2008.22>), the weighted-lambda-regularization model, (Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>), or the enhanced model with implicit features (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009) <doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver (Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>), providing efficient methods for sparse and dense data, and mixtures thereof. Supports L1 and L2 regularization in the main models, offers alternative most-popular and content-based models, and implements functionality for cold-start recommendations and imputation of 2D data.

This package provides some simple functions for printing text in color in markdown or Quarto documents, to be rendered as HTML or LaTeX. This is useful when writing about the use of colors in graphs or tables, where you want to print their names in their actual color to give a direct impression of the color, like â redâ shown in red, or â blueâ shown in blue.

This package provides a tool to estimate IRT item parameters (2 PL) using CTT-based item statistics from small samples via artificial neural networks and regression trees.

This package provides a local haplotyping visualization toolbox to capture major patterns of co-inheritance between clusters of linked variants, whilst connecting findings to phenotypic and demographic traits across individuals. crosshap enables users to explore and understand genomic variation across a trait-associated region. For an example of successful local haplotype analysis, see Marsh et al. (2022) <doi:10.1007/s00122-022-04045-8>.

This package provides functions to prepare and filter an origin-destination matrix for thematic flow mapping purposes. This comes after Bahoken, Francoise (2016), Mapping flow matrix a contribution, PhD in Geography - Territorial sciences. See Bahoken (2017) <doi:10.4000/netcom.2565>.

This package provides a collection of helper functions and htmlwidgets to help publishers curate content collections on Posit Connect'. The components, Card, Grid, Table, Search, and Filter can be used to produce a showcase page or gallery contained within a static or interactive R Markdown page.

This package implements a wide range of dose escalation designs. The focus is on model-based designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy to setup a new design with custom JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules. Further details are presented in Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.

Utilizes spatial association marginal contributions derived from spatial stratified heterogeneity to capture the degree of correlation between spatial patterns.