Flexible framework for coalescent analyses in R. It includes a main function running the  MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

A covariate-augmented overdispersed Poisson factor model is proposed to jointly perform a high-dimensional Poisson factor analysis and estimate a large coefficient matrix for overdispersed count data.
    More details can be referred to Liu et al. (2024) <doi:10.1093/biomtc/ujae031>.

Functions to analyze coarse data.
    Specifically, it contains functions to (1) fit parametric accelerated
    failure time models to interval-censored survival time data, and (2)
    estimate the case-fatality ratio in scenarios with under-reporting.
    This package's development was motivated by applications to infectious
    disease: in particular, problems with estimating the incubation period and
    the case fatality ratio of a given disease.  Sample data files are included
    in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, 
    Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and 
    Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.

Calculating the fractal dimension of a coastline using the boxes and dividers methods.

Agreement of continuously scaled measurements made by two techniques, devices or methods is usually
             evaluated by the well-established Bland-Altman analysis or plot. Conditional method agreement trees (COAT),
             proposed by Karapetyan, Zeileis, Henriksen, and Hapfelmeier (2025) <doi:10.1093/jrsssc/qlae077>,
             embed the Bland-Altman analysis in the framework of recursive partitioning to explore heterogeneous method
             agreement in dependence of covariates. COAT can also be used to perform a Bland-Altman test for differences
             in method agreement.