Provides a function for fitting Poisson and negative binomial regression models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.

Provides tools for penalized estimation of flexible hidden Markov models for time series of counts w/o the need to specify a (parametric) family of distributions. These include functions for model fitting, model checking, and state decoding. For details, see Adam, T., Langrock, R., and Weiß, C.H. (2019): Penalized Estimation of Flexible Hidden Markov Models for Time Series of Counts. <arXiv:1901.03275>.

A set of functions for applying a 
    restricted linear algebra to the analysis of 
    count-based data. See the accompanying preprint
    manuscript: "Normalizing need not be the norm:
    count-based math for analyzing single-cell data"
    Church et al (2022) <doi:10.1101/2022.06.01.494334>
    This tool is specifically designed to analyze 
    count matrices from single cell RNA sequencing 
    assays. The tools implement several count-based
    approaches for standard steps in single-cell 
    RNA-seq analysis, including scoring genes and cells, 
    comparing cells and clustering, calculating differential 
    gene expression, and several methods for rank 
    reduction. There are many opportunities for further
    optimization that may prove useful in the analysis of
    other data. We provide the source code freely
    available at <https://github.com/shchurch/countland>
    and encourage users and developers to fork the code for 
    their own purposes.

Calculates metrics of proportionality using the logit-normal multinomial model.  It can also provide empirical and plugin estimates of these metrics.

Flexible univariate count models based on renewal processes. The
    models may include covariates and can be specified with familiar formula
    syntax as in glm() and package 'flexsurv'.  The methodology is described by
    Kharrat et all (2019) <doi:10.18637/jss.v090.i13> (included as vignette
    'Countr_guide' in the package).
    If the suggested package 'pscl' is not available from CRAN, it can be
    installed with 'remotes::install_github("cran/pscl")'. It is no longer used
    by the functions in this package but is needed for some of the extended
    examples.