Provides a comprehensive library for date-time manipulations
    using a new family of orthogonal date-time classes (durations, time
    points, zoned-times, and calendars) that partition responsibilities so
    that the complexities of time zones are only considered when they are
    really needed. Capabilities include: date-time parsing, formatting,
    arithmetic, extraction and updating of components, and rounding.

A wrapper for the Clockify API <https://docs.clockify.me/>, making it possible to query, insert and update time keeping data.

A set of functions to fit a boosting conditional logit model.

Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.

Quickly estimate the net growth rate of a
    population or clone whose growth can be approximated by a birth-death
    branching process.  Input should be phylogenetic tree(s) of clone(s) with
    edge lengths corresponding to either time or mutations. Based on
    coalescent results in Johnson et al. (2023) <doi:10.1093/bioinformatics/btad561>. Simulation
    techniques as well as growth rate methods build on prior work from
    Lambert A. (2018) <doi:10.1016/j.tpb.2018.04.005> and Stadler T. (2009)
    <doi:10.1016/j.jtbi.2009.07.018>.

Defines the classes and functions used to simulate and
  to analyze data sets describing copy number variants and,
  optionally, sequencing mutations in order to detect clonal subsets.
  See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.

Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) <doi:10.1126/scitranslmed.aac9511>.