Tool for exploring DNA and amino acid variation and inferring the presence of target lineages from microbial high-throughput genomic DNA samples that potentially contain mixtures of variants/lineages. MixviR was originally created to help analyze environmental SARS-CoV-2/Covid-19 samples from environmental sources such as wastewater or dust, but can be applied to any microbial group. Inputs include reference genome information in commonly-used file formats (fasta, bed) and one or more variant call format (VCF) files, which can be generated with programs such as Illumina's DRAGEN, the Genome Analysis Toolkit, or bcftools. See DePristo et al (2011) <doi:10.1038/ng.806> and Danecek et al (2021) <doi:10.1093/gigascience/giab008> for these tools, respectively. Available outputs include a table of mutations observed in the sample(s), estimates of proportions of target lineages in the sample(s), and an R Shiny dashboard to interactively explore the data.

Estimates Variable Length Markov Chains (VLMC) models and VLMC with
    covariates models from discrete sequences. Supports model selection via
    information criteria and simulation of new sequences from an estimated
    model. See Bühlmann, P. and Wyner, A. J. (1999) <doi:10.1214/aos/1018031204>
    for VLMC and Zanin Zambom, A., Kim, S. and Lopes Garcia, N. (2022)
    <doi:10.1111/jtsa.12615> for VLMC with covariates.

Optimization algorithms implemented in R, including
    conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the
    limited memory BFGS (L-BFGS) methods. Most internal parameters can be set 
    through the call interface. The solvers hold up quite well for 
    higher-dimensional problems.

A set of classes and methods to set up and run multi-species, trait
    based and community size spectrum ecological models, focused on the marine
    environment.

Multivariate joint models of longitudinal and time-to-event data based on functional principal components implemented with 'bamlss'. Implementation for Volkmann, Umlauf, Greven (2023) <arXiv:2311.06409>.