The fossil record is a joint expression of ecological, taphonomic, 
    evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
    This package allowing to simulate biological processes in the time domain
    (e.g., trait evolution, fossil abundance), and examine how their expression
    in the rock record (stratigraphic domain) is influenced based on 
    age-depth models, ecological niche models, and taphonomic effects.
    Functions simulating common processes used in modeling trait evolution or 
    event type data such as first/last occurrences are provided and can be used 
    standalone or as part of a pipeline. The package comes with example 
    data sets and tutorials in several vignettes, which can be used as a 
    template to set up one's own simulation.

Provides functions to estimate a strategic selection estimator. A strategic selection estimator is an agent error model in which the two random components are not assumed to be orthogonal. In addition this package provides generic functions to print and plot objects of its class as well as the necessary functions to create tables for LaTeX. There is also a function to create dyadic data sets.

For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.

An Optimization Algorithm Applied to
    Stratification Problem.This function aims
    at constructing optimal strata with an optimization algorithm
    based on a global optimisation technique called vns.

The main function is icweib(), which fits a stratified Weibull
    proportional hazards model for left censored, right censored, interval censored,
    and non-censored survival data. We parameterize the Weibull regression model
    so that it allows a stratum-specific baseline hazard function, but where the
    effects of other covariates are assumed to be constant across strata. 
    Please refer to Xiangdong Gu, David Shapiro, Michael D. Hughes and
    Raji Balasubramanian (2014) <doi:10.32614/RJ-2014-003> for more details.