Allows for multiple group item response theory alignment a la Mplus to be applied to lists of single-group models estimated in lavaan or mirt'. Allows item sets that are overlapping but not identical, facilitating alignment in secondary data analysis where not all items may be shared across assessments.

Combines the magick and imager packages to streamline image analysis, focusing on feature extraction and quantification from biological images, especially microparticles. By providing high throughput pipelines and clustering capabilities, biopixR facilitates efficient insight generation for researchers (Schneider J. et al. (2019) <doi:10.21037/jlpm.2019.04.05>).

This package provides a computational tool to describe patterns in black and white images from natural structures. bwimage implemented functions for exceptionally broad subject. For instance, bwimage provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.

Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, etc. following Cannon (2012) <doi:10.1016/j.cageo.2011.08.023>.

The primary motivation of this package is to take the things that are great about the R packages flextable <https://davidgohel.github.io/flextable/> and officer <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.

Gives access to data visualisation methods that are relevant from the statistician's point of view. Using D3''s existing data visualisation tools to empower R language and environment. The throw chart method is a line chart used to illustrate paired data sets (such as before-after, male-female).

Functionalities for analyzing high-dimensional and longitudinal biomarker data to facilitate precision medicine, using a joint model of Bayesian sparse factor analysis and dependent Gaussian processes. This paper illustrates the method in detail: J Cai, RJB Goudie, C Starr, BDM Tom (2023) <doi:10.48550/arXiv.2307.02781>.

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

Implementation of the fast univariate inference approach (Cui et al. (2022) <doi:10.1080/10618600.2021.1950006>, Loewinger et al. (2024) <doi:10.7554/eLife.95802.2>) for fitting functional mixed models. User guides and Python package information can be found at <https://github.com/gloewing/photometry_FLMM>.

This package provides a unified algorithm, blockwise-majorization-descent (BMD), for efficiently computing the solution paths of the group-lasso penalized least squares, logistic regression, Huberized SVM and squared SVM. The package is an implementation of Yang, Y. and Zou, H. (2015) <doi:10.1007/s11222-014-9498-5>.

Read all commit messages of your local git repository and sort them according to tags or specific text pattern into chapters of a HTML book using bookdown'. The git history book presentation helps organisms required to testify for every changes in their source code, in relation to features requests.

Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for semi and fully parametric models (parametric only for accelerated failure time models) and Bayesian parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.

For a single variable, the IVY Plot stacks tied values in the form of leaflets. Five leaflets join to form a leaf. Leaves are stacked vertically. At most twenty leaves are shown; For high frequency, each leaflet may represent more than one observation with multiplicity declared in the subtitle.

An instrumental variable estimator under structural cumulative additive intensity model is fitted, that leverages initial randomization as the IV. The estimator can be used to fit an additive hazards model under time to event data which handles treatment switching (treatment crossover) correctly. We also provide a consistent variance estimate.

The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Performs active and passive transforms and has the ability to use units in which the speed of light is not unity. Includes some experimental functionality for celerity and rapidity. For general relativity, see the schwarzschild package.

Create custom labels, badges, certificates and other documents. Automate the production of potentially large numbers of herbarium and collection labels, accreditation badges, attendance and participation certificates, etc, and deliver them automatically. Documents are generated in PDF format, which requires a working installation of LaTeX', such as TinyTeX'.

Computing metabolite set enrichment analysis (MSEA) (Yamamoto, H. et al. (2014) <doi:10.1186/1471-2105-15-51>), single sample enrichment analysis (SSEA) (Yamamoto, H. (2023) <doi:10.51094/jxiv.262>) and over-representation analysis (ORA) that accounts for undetected metabolites (Yamamoto, H. (2024) <doi:10.51094/jxiv.954>).

This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) <doi:10.1186/1471-2105-8-278> "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.".

Estimation of models with dependent variable left-censored at zero. Null values may be caused by a selection process Cragg (1971) <doi:10.2307/1909582>, insufficient resources Tobin (1958) <doi:10.2307/1907382>, or infrequency of purchase Deaton and Irish (1984) <doi:10.1016/0047-2727(84)90067-7>.

This package implements the out-of-treatment testing from Kuelpmann and Kuzmics (2020) <doi:10.2139/ssrn.3441675> based on the Vuong Test introduced in Vuong (1989) <doi:10.2307/1912557>. Out-of treatment testing allows for a direct, pairwise likelihood comparison of theories, calibrated with pre-existing data.

Simulates the cultural evolution of quantitative traits of bird song. SongEvo is an individual- (agent-) based model. SongEvo is spatially-explicit and can be parameterized with, and tested against, measured song data. Functions are available for model implementation, sensitivity analyses, parameter optimization, model validation, and hypothesis testing.

An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) <doi:10.1016/j.isci.2020.100882> for more details.

Collection (syllogi in greek) of real and fictitious data sets for teaching purposes. The datasets were manually entered by the author from the respective references as listed in the individual dataset documentation. The fictions datasets are the creation of the author, that he has found useful for teaching statistics.

An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.