Assists in analyzing the lying behavior of cows from raw data 
    recorded with a triaxial accelerometer attached to the hind leg of a cow. Allows 
    the determination of common measures for lying behavior including total lying duration, the 
    number of lying bouts, and the mean duration of lying bouts. Further capabilities are the 
    description of lying laterality and the calculation of proxies for the level of physical 
    activity of the cow. Reference: Simmler M., Brouwers S. P. (2023) <https://gitlab.com/AgroSimi/triact_manuscript>.

Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.

Implements target trial emulation methods to apply randomized
    clinical trial design and analysis in an observational setting. Using
    marginal structural models, it can estimate intention-to-treat and
    per-protocol effects in emulated trials using electronic health
    records. A description and application of the method can be found in
    Danaei et al (2013) <doi:10.1177/0962280211403603>.

A collection of clinical trial designs and methods, implemented in 
    'rstan' and R, including: the Continual Reassessment Method by O'Quigley et 
    al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) 
    <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of
    Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the 
    Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and
    more. We provide functions to aid model-fitting and analysis. 
    The 'rstan' implementations may also serve as a cookbook to anyone looking 
    to extend or embellish these models. We hope that this package encourages 
    the use of Bayesian methods in clinical trials. There is a preponderance of 
    early phase trial designs because this is where Bayesian methods are used 
    most. If there is a method you would like implemented, please get in touch.