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.

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.

API for fast data extraction for .hic files that provides programmatic access to the matrices. It doesn't store the pointer data for all the matrices, only the one queried, and currently we are only supporting matrices (not vectors).

This is a modification of 'HDoutliers' package. The 'HDoutliers' algorithm is a powerful 
    unsupervised algorithm for detecting anomalies in high-dimensional data, with a 
    strong theoretical foundation. However, it suffers from some limitations that 
    significantly hinder its performance level, under certain circumstances. This package 
    implements the algorithm proposed in Talagala, Hyndman and Smith-Miles (2019) 
    <arXiv:1908.04000>  for detecting anomalies in high-dimensional data
    that addresses these limitations of 'HDoutliers' algorithm. We define an anomaly as an observation that deviates markedly from the majority
    with a large distance gap. An approach based on extreme value theory is used 
    for the anomalous threshold calculation.