Fit semiparametric bivariate correlated frailty models.

Fit and simulate bivariate correlated frailty models with
    proportional hazard structure. Frailty distributions, such as gamma and
    lognormal models are supported semiparametric procedures. Frailty 
    variances of the two subjects can be varied or equal. Details on the models are available in book of 
    Wienke (2011,ISBN:978-1-4200-7388-1). Bivariate gamma fit is obtained using the approach given 
    in Kifle et al (2023) <DOI: 10.4310/22-SII738> with modifications. Lognormal fit is based on the approach
    by Ripatti and Palmgren (2000) <doi:10.1111/j.0006-341X.2000.01016.x>. Frailty distributions, 
    such as gamma, inverse gaussian and power variance frailty models are supported 
    for parametric approach.

Provides bias-corrected estimates for the regression coefficients of a marginal model estimated with generalized estimating equations. Details about the bias formula used are in Lunardon, N., Scharfstein, D. (2017) <doi:10.1002/sim.7366>.

Users can estimate the treatment effect for multiple subgroups basket trials based on the Bayesian Cluster Hierarchical Model (BCHM). In this model, a Bayesian non-parametric method is applied to dynamically calculate the number of clusters by conducting the multiple cluster classification based on subgroup outcomes. Hierarchical model is used to compute the posterior probability of treatment effect with the borrowing strength determined by the Bayesian non-parametric clustering and the similarities between subgroups. To use this package, 'JAGS' software and 'rjags' package are required, and users need to pre-install them.

Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the 'Oxcal' function SUM(); currently unpublished), and reverse calibration of dates from calibrated into 14C years (also unpublished).